http://2009.igem.org/wiki/index.php?title=Special:Contributions/Christophe.R&feed=atom&limit=50&target=Christophe.R&year=&month=2009.igem.org - User contributions [en]2024-03-29T09:02:40ZFrom 2009.igem.orgMediaWiki 1.16.5http://2009.igem.org/Team:ParisTeam:Paris2009-10-22T03:46:27Z<p>Christophe.R: /* Collaborations and Visitors */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris#top | Home]] > [[Team:Paris#bottom | Synopsis]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
==Message in a Bubble==<br />
<br />
<html><br />
<style type="text/css"><br />
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display:block; <br />
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document.getElementById('image5').style.visibility='hidden';<br />
"<br />
></div><br />
<img id="image2" style="visibility: visible;" src="https://static.igem.org/mediawiki/2009/b/ba/Paris01.png" height=379px width=800px/><br />
<img id="image3" style="visibility: hidden;" src="https://static.igem.org/mediawiki/2009/f/fc/Paris02.png" height=379px width=800px/><br />
<img id="image4" style="visibility: hidden;" src="https://static.igem.org/mediawiki/2009/d/d4/Paris03.png" height=379px width=800px/><br />
<img id="image5" style="visibility: hidden;" src="https://static.igem.org/mediawiki/2009/9/9c/Paris04.png" height=379px width=800px/><br />
<br />
<div id="image_prod" onmouseover="<br />
document.getElementById('image2').style.visibility='hidden';<br />
document.getElementById('image4').style.visibility='hidden';<br />
document.getElementById('image5').style.visibility='hidden';<br />
document.getElementById('image3').style.visibility='visible';<br />
"<br />
><a class="bloc" href="https://2009.igem.org/Team:Paris/Addressing_overview#top"></a></div><br />
<br />
<div id="image_addre" onmouseover="<br />
document.getElementById('image2').style.visibility='hidden';<br />
document.getElementById('image3').style.visibility='hidden';<br />
document.getElementById('image5').style.visibility='hidden';<br />
document.getElementById('image4').style.visibility='visible';<br />
"<br />
><a class="bloc" href="https://2009.igem.org/Team:Paris/Production_overview#top"></a></div><br />
<br />
<div id="image_recep" onmouseover="<br />
document.getElementById('image2').style.visibility='hidden';<br />
document.getElementById('image3').style.visibility='hidden';<br />
document.getElementById('image4').style.visibility='hidden';<br />
document.getElementById('image5').style.visibility='visible';<br />
"<br />
><a class="bloc" href="https://2009.igem.org/Team:Paris/Transduction_overview#top"></a></div><br />
</html><br />
<br />
<br />
<center style="color:#b0310e; font-weight: bold; font-size: 2em;"> Interactive schema </center><br />
===Abstract===<br />
'''Message in a Bubble: a robust inter-cellular communication system based on outer membrane vesicles.'''<br />
Sending a message across the ocean… Outer membrane vesicles (OMV), naturally produced by gram negative bacteria such as ''E. Coli'', are strong candidates for long-distance messaging. Our engineered communication platform consists in controlling OMV production by destabilizing membrane integrity through over-expression of specific periplasmic proteins (''e.g.'' TolR). In order to control and modulate message content, we used fusions with OmpA signal sequence and the ClyA hemolysin as delivery tags. A targeting system was developed, based on the outer-membrane expression of Jun/Fos leucine zippers to control the vesicle flux between donor and recipient cells. Once received, the signal from incoming vesicles is transduced through a modified Fec pathway, whereby the receptor is provided by the OMV. Computational models provided insight to all of the above steps. Such reliable communications systems have wide biotechnological implications, ranging from targeted drugs delivery and detoxification to advanced division of labor or even cell-based computing.<br />
<br />
===Strategy===<br />
<br />
We aimed developing a long distance communication system between gram-negative bacteria that is based on the ability of these organisms to produce Outer-Membrane Vesicles (OMVs). We designed a framework which can be easily expanded to a lot of different inputs/ouputs. We hope this standardized approach will increase our capacity to manipulate information and/or exchange it between bacteria. This can be used in any engineered biological process requiring transformation or a system of information transfer, including medical applications and bio-remediation.<br />
<br />
<br />
We did our best to standardize: <br />
# the increase of vesicle production; <br />
# the system to address proteins to these vesicles;<br />
# their fusion with target bacteria. <br />
<br />
You can find detailed information in our [[Team:Paris/Project#top | OMV Project]] description or in our different parts.<br />
<br />
<br />
By analogy to the Internet Protocol, we called our process a Bacterial Protocol. We found that the title <i>Message in a bubble </i>described it quite nicely. In a simple way, the comprehension of vesicles process sounds like a build of a bacteria language.<br />
<br />
<br />
For more information on how we came up with this idea, please have a look at our [[Team:Paris/Brainstorm#top | brainstorming area]].<br />
<br />
===Navigation===<br />
Here we are ! You have some problems to navigate in our wiki ?? Just look at [[Team:Paris/navigation#top | this page]], and we hope it will help you. <br />
<br />
And, if your are interested in a guided visit of the iGEM Paris 2009 wiki,..., just open the book...<br />
<br />
{{Template:Paris2009_guided2|#top|/Project#top}}<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
== Extended Team ==<br />
<br />
=== iGEM Paris Team ===<br />
'''Hello everyone and welcome on our wiki webpage !'''<br />
<br />
<br />
We are a team of 13 highly motivated students ready to give our best in the iGEM competition. We decided to involve our different backgrounds (6 biologists, 2 mathematicians, a computer scientist, a sociologist, an infectiologist, a geneticist, and a chemist) and our enthusiasm in this scientific and human adventure.<br />
Regarding the team's supervisors, we have the honnor to have been adviced by some great scientists/professors like Ariel Lindner, Guillaume Cambray and Samuel Bottani among others, almost always at the [http://www.cri-paris.org CRI].<br><br />
<br />
<br />
More details on our team [[Team:Paris/Team#top | here]].<br><br />
More details on the CRI at the bottom of our [[Team:Paris/Acknowledgements#top | Acknowledgement page]].<br><br />
Additional information about all iGEM Paris teams since 2007 here : [http://www.igem-paris.org http://www.igem-paris.org]<br><br />
<br />
<br />
<br />
=== Our Sponsors ===<br />
<html><br />
<center> <br />
<table class="sponsor"><br />
<tr><br />
<td rowspan="3"><br />
<a href="http://www.fondationbs.org/"><br />
<img src="https://static.igem.org/mediawiki/2009/b/b5/Paris_FBS.jpg" height=150px><br />
</a><br />
</td><br />
<td><br />
<a href="http://www.ambafrance-us.org/spip.php?rubrique=2"><br />
<img src="https://static.igem.org/mediawiki/2009/5/5c/Paris_Embassy.jpg" height=50px><br />
</a><br />
</td><br />
<td><br />
<a href="http://www.ensmp.fr/"><br />
<img src="https://static.igem.org/mediawiki/2009/f/f7/Paris_Mines.jpg" height=100px><br />
</a><br />
</td><br />
</tr><br />
<tr><br />
<td rowspan="2"><br />
<a href="http://www.inria.fr/"><br />
<img src="https://static.igem.org/mediawiki/2009/b/bd/Paris_Inria.jpg" height=90px ><br />
</a><br />
</td><br />
<td><center><br />
<a href="http://www.echosens.com/"><br />
<img src="http://i82.servimg.com/u/f82/14/22/39/68/echose10.jpg" height=60px ><br />
</a></center><br />
</td><br />
<tr><br />
<td><center><br />
<a href="http://www.neb.com/nebecomm/default.asp"><br />
<img src="http://i82.servimg.com/u/f82/14/22/39/68/biolab10.jpg" height=60px><br />
</a></center><br />
</td><br />
</tr><br />
</table><br />
</center><br />
</html><br />
<br />
=== Collaborations and Visitors ===<br />
<br />
With the [https://2009.igem.org/Team:BCCS-Bristol team BCCS-Bristol] , we shared our modeling part concerning the production of vesicles which is supposed to be complementary of their and we hope that we will be able to combine both approaches to make one big model of the production, adressing, and fusion of the vesicles. For more details, see our [[Team:Paris/Collaborations#top | Collaborations]] web page.<br />
<br />
<br />
We have also created a poll concerning the Iphone Software and we sent it to the other iGEM teams, among which four replied. Find the results and more details on our [[Team:Paris/Collaborations#top | Collaborations]] page.<br />
<br />
<br />
All members of our team answered to the Valencia ethics poll that is why you can see this gorgeous gold medal with our name on it. More seriously it was very interesting to see what the members answered to each question. Looking for more details ? see our [[Team:Paris/Collaborations#top | Collaborations]] web page.<br />
<br />
<br />
And we thank all our visitors, without them we would not have such an eclectic cluster map !<br />
<br />
<br />
<html><br />
<center><br />
<a href="http://www3.clustrmaps.com/counter/maps.php?url=https://2009.igem.org/Team:Paris" id="clustrMapsLink"><img src="http://www3.clustrmaps.com/counter/index2.php?url=https://2009.igem.org/Team:Paris" style="border:0px;" alt="Locations of visitors to this page" title="Locations of visitors to this page" id="clustrMapsImg" onerror="this.onerror=null; this.src='http://www2.clustrmaps.com/images/clustrmaps-back-soon.jpg'; document.getElementById('clustrMapsLink').href='http://www2.clustrmaps.com';" /><br />
</a><br />
<a href="https://2009.igem.org/Team:Valencia/Human" target="_blank"> <img src="https://static.igem.org/mediawiki/2009/5/50/V_Paris.JPG" width="110" height="110"></a> Thank you <a href="https://2009.igem.org/Team:Valencia"><a3>Valencia</a3></a> !<br />
<br />
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</html></div>Christophe.Rhttp://2009.igem.org/Team:ParisTeam:Paris2009-10-22T03:45:56Z<p>Christophe.R: /* Collaborations and Visitors */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris#top | Home]] > [[Team:Paris#bottom | Synopsis]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
==Message in a Bubble==<br />
<br />
<html><br />
<style type="text/css"><br />
a.bloc {<br />
display:block; <br />
height:100%<br />
}<br />
<br />
<br />
#image1 {<br />
position: relative;<br />
height:379px;<br />
width:800px;<br />
background:transparent;<br />
z-index:10;<br />
}<br />
<br />
<br />
#image2 {<br />
position: absolute;<br />
top: 80px;<br />
left: -70px;<br />
}<br />
<br />
#image3 {<br />
position: absolute;<br />
top: 80px;<br />
left: -70px;<br />
}<br />
<br />
#image4 {<br />
position: absolute;<br />
top: 80px;<br />
left: -70px;<br />
}<br />
<br />
#image5 {<br />
position: absolute;<br />
top: 80px;<br />
left: -70px;<br />
}<br />
<br />
#image_prod {<br />
width: 150px;<br />
height: 90px;<br />
position: absolute;<br />
top: 85px;<br />
left: -25px;<br />
background: transparent;<br />
z-index:11;<br />
}<br />
<br />
#image_addre {<br />
width: 180px;<br />
height: 90px;<br />
position: absolute;<br />
top: 106px;<br />
left: 110px;<br />
background: transparent;<br />
z-index:12;<br />
}<br />
<br />
<br />
#image_recep {<br />
width: 220px;<br />
height: 160px;<br />
position: absolute;<br />
top: 86px;<br />
left: 405px;<br />
background: transparent;<br />
z-index:13;<br />
}<br />
</style><br />
<div id="image1" onmouseover="<br />
document.getElementById('image2').style.visibility='visible';<br />
document.getElementById('image3').style.visibility='hidden';<br />
document.getElementById('image4').style.visibility='hidden';<br />
document.getElementById('image5').style.visibility='hidden';<br />
"<br />
></div><br />
<img id="image2" style="visibility: visible;" src="https://static.igem.org/mediawiki/2009/b/ba/Paris01.png" height=379px width=800px/><br />
<img id="image3" style="visibility: hidden;" src="https://static.igem.org/mediawiki/2009/f/fc/Paris02.png" height=379px width=800px/><br />
<img id="image4" style="visibility: hidden;" src="https://static.igem.org/mediawiki/2009/d/d4/Paris03.png" height=379px width=800px/><br />
<img id="image5" style="visibility: hidden;" src="https://static.igem.org/mediawiki/2009/9/9c/Paris04.png" height=379px width=800px/><br />
<br />
<div id="image_prod" onmouseover="<br />
document.getElementById('image2').style.visibility='hidden';<br />
document.getElementById('image4').style.visibility='hidden';<br />
document.getElementById('image5').style.visibility='hidden';<br />
document.getElementById('image3').style.visibility='visible';<br />
"<br />
><a class="bloc" href="https://2009.igem.org/Team:Paris/Addressing_overview#top"></a></div><br />
<br />
<div id="image_addre" onmouseover="<br />
document.getElementById('image2').style.visibility='hidden';<br />
document.getElementById('image3').style.visibility='hidden';<br />
document.getElementById('image5').style.visibility='hidden';<br />
document.getElementById('image4').style.visibility='visible';<br />
"<br />
><a class="bloc" href="https://2009.igem.org/Team:Paris/Production_overview#top"></a></div><br />
<br />
<div id="image_recep" onmouseover="<br />
document.getElementById('image2').style.visibility='hidden';<br />
document.getElementById('image3').style.visibility='hidden';<br />
document.getElementById('image4').style.visibility='hidden';<br />
document.getElementById('image5').style.visibility='visible';<br />
"<br />
><a class="bloc" href="https://2009.igem.org/Team:Paris/Transduction_overview#top"></a></div><br />
</html><br />
<br />
<br />
<center style="color:#b0310e; font-weight: bold; font-size: 2em;"> Interactive schema </center><br />
===Abstract===<br />
'''Message in a Bubble: a robust inter-cellular communication system based on outer membrane vesicles.'''<br />
Sending a message across the ocean… Outer membrane vesicles (OMV), naturally produced by gram negative bacteria such as ''E. Coli'', are strong candidates for long-distance messaging. Our engineered communication platform consists in controlling OMV production by destabilizing membrane integrity through over-expression of specific periplasmic proteins (''e.g.'' TolR). In order to control and modulate message content, we used fusions with OmpA signal sequence and the ClyA hemolysin as delivery tags. A targeting system was developed, based on the outer-membrane expression of Jun/Fos leucine zippers to control the vesicle flux between donor and recipient cells. Once received, the signal from incoming vesicles is transduced through a modified Fec pathway, whereby the receptor is provided by the OMV. Computational models provided insight to all of the above steps. Such reliable communications systems have wide biotechnological implications, ranging from targeted drugs delivery and detoxification to advanced division of labor or even cell-based computing.<br />
<br />
===Strategy===<br />
<br />
We aimed developing a long distance communication system between gram-negative bacteria that is based on the ability of these organisms to produce Outer-Membrane Vesicles (OMVs). We designed a framework which can be easily expanded to a lot of different inputs/ouputs. We hope this standardized approach will increase our capacity to manipulate information and/or exchange it between bacteria. This can be used in any engineered biological process requiring transformation or a system of information transfer, including medical applications and bio-remediation.<br />
<br />
<br />
We did our best to standardize: <br />
# the increase of vesicle production; <br />
# the system to address proteins to these vesicles;<br />
# their fusion with target bacteria. <br />
<br />
You can find detailed information in our [[Team:Paris/Project#top | OMV Project]] description or in our different parts.<br />
<br />
<br />
By analogy to the Internet Protocol, we called our process a Bacterial Protocol. We found that the title <i>Message in a bubble </i>described it quite nicely. In a simple way, the comprehension of vesicles process sounds like a build of a bacteria language.<br />
<br />
<br />
For more information on how we came up with this idea, please have a look at our [[Team:Paris/Brainstorm#top | brainstorming area]].<br />
<br />
===Navigation===<br />
Here we are ! You have some problems to navigate in our wiki ?? Just look at [[Team:Paris/navigation#top | this page]], and we hope it will help you. <br />
<br />
And, if your are interested in a guided visit of the iGEM Paris 2009 wiki,..., just open the book...<br />
<br />
{{Template:Paris2009_guided2|#top|/Project#top}}<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
== Extended Team ==<br />
<br />
=== iGEM Paris Team ===<br />
'''Hello everyone and welcome on our wiki webpage !'''<br />
<br />
<br />
We are a team of 13 highly motivated students ready to give our best in the iGEM competition. We decided to involve our different backgrounds (6 biologists, 2 mathematicians, a computer scientist, a sociologist, an infectiologist, a geneticist, and a chemist) and our enthusiasm in this scientific and human adventure.<br />
Regarding the team's supervisors, we have the honnor to have been adviced by some great scientists/professors like Ariel Lindner, Guillaume Cambray and Samuel Bottani among others, almost always at the [http://www.cri-paris.org CRI].<br><br />
<br />
<br />
More details on our team [[Team:Paris/Team#top | here]].<br><br />
More details on the CRI at the bottom of our [[Team:Paris/Acknowledgements#top | Acknowledgement page]].<br><br />
Additional information about all iGEM Paris teams since 2007 here : [http://www.igem-paris.org http://www.igem-paris.org]<br><br />
<br />
<br />
<br />
=== Our Sponsors ===<br />
<html><br />
<center> <br />
<table class="sponsor"><br />
<tr><br />
<td rowspan="3"><br />
<a href="http://www.fondationbs.org/"><br />
<img src="https://static.igem.org/mediawiki/2009/b/b5/Paris_FBS.jpg" height=150px><br />
</a><br />
</td><br />
<td><br />
<a href="http://www.ambafrance-us.org/spip.php?rubrique=2"><br />
<img src="https://static.igem.org/mediawiki/2009/5/5c/Paris_Embassy.jpg" height=50px><br />
</a><br />
</td><br />
<td><br />
<a href="http://www.ensmp.fr/"><br />
<img src="https://static.igem.org/mediawiki/2009/f/f7/Paris_Mines.jpg" height=100px><br />
</a><br />
</td><br />
</tr><br />
<tr><br />
<td rowspan="2"><br />
<a href="http://www.inria.fr/"><br />
<img src="https://static.igem.org/mediawiki/2009/b/bd/Paris_Inria.jpg" height=90px ><br />
</a><br />
</td><br />
<td><center><br />
<a href="http://www.echosens.com/"><br />
<img src="http://i82.servimg.com/u/f82/14/22/39/68/echose10.jpg" height=60px ><br />
</a></center><br />
</td><br />
<tr><br />
<td><center><br />
<a href="http://www.neb.com/nebecomm/default.asp"><br />
<img src="http://i82.servimg.com/u/f82/14/22/39/68/biolab10.jpg" height=60px><br />
</a></center><br />
</td><br />
</tr><br />
</table><br />
</center><br />
</html><br />
<br />
=== Collaborations and Visitors ===<br />
<br />
With the [https://2009.igem.org/Team:BCCS-Bristol team BCCS-Bristol] , we shared our modeling part concerning the production of vesicles which is supposed to be complementary of their and we hope that we will be able to combine both approaches to make one big model of the production, adressing, and fusion of the vesicles. For more details, see our [[Team:Paris/Collaborations#top | Collaborations]] web page.<br />
<br />
<br />
We have also created a poll concerning the Iphone Software and we sent it to the other iGEM teams, among which four replied. Find the results and more details on our [[Team:Paris/Collaborations#top | Collaborations]] page.<br />
<br />
<br />
All members of our team answered to the Valencia ethics poll that is why you can see this gorgeous gold medal with our name on it. More seriously it was very interesting to see what the members answered to each question. Looking for more details ? see our [[Team:Paris/Collaborations#top | Collaborations]] web page.<br />
<br />
<br />
And we thank all our visitors, without them we would not have such an eclectic cluster map !<br />
<br />
<br />
<html><br />
<center><br />
<div class="leftcolumn"><br />
<a href="http://www3.clustrmaps.com/counter/maps.php?url=https://2009.igem.org/Team:Paris" id="clustrMapsLink"><img src="http://www3.clustrmaps.com/counter/index2.php?url=https://2009.igem.org/Team:Paris" style="border:0px;" alt="Locations of visitors to this page" title="Locations of visitors to this page" id="clustrMapsImg" onerror="this.onerror=null; this.src='http://www2.clustrmaps.com/images/clustrmaps-back-soon.jpg'; document.getElementById('clustrMapsLink').href='http://www2.clustrmaps.com';" /><br />
</a><br />
</div><br />
<div class="rightcolumn"><br />
<a href="https://2009.igem.org/Team:Valencia/Human" target="_blank"> <img src="https://static.igem.org/mediawiki/2009/5/50/V_Paris.JPG" width="110" height="110"></a> Thank you <a href="https://2009.igem.org/Team:Valencia"><a3>Valencia</a3></a> !<br />
</div><br />
<br />
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} catch(err) {}</script><br />
</center><br />
<br />
</html></div>Christophe.Rhttp://2009.igem.org/Team:Paris/CollaborationsTeam:Paris/Collaborations2009-10-22T03:45:04Z<p>Christophe.R: /* Modeling collaborations */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris#top | Home]] > [[Team:Paris/Collaborations#bottom | Collaborations]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
==Modeling collaborations==<br />
<br />
As it happened that we share with the [https://2009.igem.org/Team:BCCS-Bristol BCCS-Bristol] projet some similarities and especially on the modeling part we have decided to contact them in order to either find synergies or just to be sure not to make a redondant modeling work. Obviously it seems that we were not working on the same domain.<br />
<br />
So in order to make a complete modelisation of the "project" we provided them unconditionally with the Mathlab source code of the production of vesicles. <br />
<br />
<br />
Here you can find the Matlab code, with respect to the iGEM Open Source concept :<br />
<br><br />
<I>'''function Delay_Device_Simple'''</I><br />
<br />
close all<br />
for k = 1:6<br />
H = k;<br />
t0 = 0 ;<br />
tf = 10 ;<br />
x0 = [0 ; 0 ; 4000 ; 0];<br />
[t, x] = ode23(@delaydevice, [t0:0.1:tf],x0,[],H);<br />
subplot(3,2,k)<br />
plot (t,x)<br />
end <br />
legend({'prot','lacI','TetR','TolRII'});<br />
function solver(k)<br />
end<br />
function xd = delaydevice(t, x, H)<br />
%Resolution of a differential system<br />
% Dilution of proteins<br />
gamma = 1;<br />
gammaLVA = 3;<br />
% pBad Activation<br />
Ara = 10000;<br />
beta1 = 4000;<br />
beta2 = 4000;<br />
K1 = 40;<br />
K2 = 40;<br />
% pLac Repression<br />
beta3 = 2000;<br />
K3 = 40;<br />
% pTet Repression<br />
beta4 = 2000;<br />
K4 = 40;<br />
xd = zeros(size(x));<br />
xd(1) = -gamma*x(1)+ beta1*(Ara/K1)/(1+(Ara/K1)); %Protein creation<br />
xd(2) = -gammaLVA*x(2)+ beta2*(Ara/K2)/(1+(Ara/K2)); % lacI creation<br />
xd(3) = -gamma*x(3)+ beta3*(K3/(K3+(x(2))^2)); % TetR creation<br />
xd(4) = -gamma*x(4)+ beta4*(K4/(K4+x(3))); % TolRII creation<br />
end<br />
end<br />
<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
==Ethic collaborations==<br />
<br />
We wanted to support the debates around ethics in science, in fact we also developped several points with our specialist in epistemology.<br />
<br />
<br />
Therefore answering the Valencia poll was the opportunity to widen our range of questions about biosciences, to share knowledge, and to prove that we feel concerned by the problem that ethics tackles.<br />
<br />
<br />
All the team answered the poll and we are grateful to Valencia for rewarding us with a gold medal ^^<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
== Software tool collaborations==<br />
<br />
In order to develop a fully operational tool we created a poll that we send to other igem team to ask if it could be a great help for them or not and if they have also advices and expectations concerning this software.<br />
<br />
<br />
2 Teams answered : <br />
*[https://2009.igem.org/Team:TUDelft TUDelf] Specially to Sriram and Tim <br />
*[https://2009.igem.org/Team:Valencia Valencia] Specially to Juny<br />
<br />
<br />
We had some interactions with the [https://2009.igem.org/Team:Freiburg_software Freiburg_software team], specially with Paul Staab. They have developed a synthetic biological software suite, based on Google's collaboration and communication tool Wave : '''SynBiowave'''. The actual version is 0.2 but it is a project with a great potential! <br />
<br />
<br />
<br />
{{Template:Paris2009_guided|Team#top|Contact#top}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/CollaborationsTeam:Paris/Collaborations2009-10-22T03:44:51Z<p>Christophe.R: /* Modeling collaborations */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris#top | Home]] > [[Team:Paris/Collaborations#bottom | Collaborations]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
==Modeling collaborations==<br />
<br />
As it happened that we share with the [https://2009.igem.org/Team:BCCS-Bristol BCCS-Bristol] projet some similarities and especially on the modeling part we have decided to contact them in order to either find synergies or just to be sure not to make a redondant modeling work. Obviously it seems that we were not working on the same domain.<br />
<br />
So in order to make a complete modelisation of the "project" we provided them unconditionally with the Mathlab source code of the production of vesicles. <br />
<br />
<br />
Here you can find the Matlab code, with respect to the iGEM Open Source concept :<br />
<br><br />
<I>'''function Delay_Device_Simple'''</I><br />
<br />
close all<br />
for k = 1:6<br />
H = k;<br />
t0 = 0 ;<br />
tf = 10 ;<br />
x0 = [0 ; 0 ; 4000 ; 0];<br />
[t, x] = ode23(@delaydevice, [t0:0.1:tf],x0,[],H);<br />
subplot(3,2,k)<br />
plot (t,x)<br />
end <br />
legend({'prot','lacI','TetR','TolRII'});<br />
function solver(k)<br />
end<br />
function xd = delaydevice(t, x, H)<br />
%Resolution of a differential system<br />
% Dilution of proteins<br />
gamma = 1;<br />
gammaLVA = 3;<br />
<br />
% pBad Activation<br />
Ara = 10000;<br />
beta1 = 4000;<br />
beta2 = 4000;<br />
K1 = 40;<br />
K2 = 40;<br />
% pLac Repression<br />
beta3 = 2000;<br />
K3 = 40;<br />
% pTet Repression<br />
beta4 = 2000;<br />
K4 = 40;<br />
xd = zeros(size(x));<br />
xd(1) = -gamma*x(1)+ beta1*(Ara/K1)/(1+(Ara/K1)); %Protein creation<br />
xd(2) = -gammaLVA*x(2)+ beta2*(Ara/K2)/(1+(Ara/K2)); % lacI creation<br />
xd(3) = -gamma*x(3)+ beta3*(K3/(K3+(x(2))^2)); % TetR creation<br />
xd(4) = -gamma*x(4)+ beta4*(K4/(K4+x(3))); % TolRII creation<br />
end<br />
end<br />
<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
==Ethic collaborations==<br />
<br />
We wanted to support the debates around ethics in science, in fact we also developped several points with our specialist in epistemology.<br />
<br />
<br />
Therefore answering the Valencia poll was the opportunity to widen our range of questions about biosciences, to share knowledge, and to prove that we feel concerned by the problem that ethics tackles.<br />
<br />
<br />
All the team answered the poll and we are grateful to Valencia for rewarding us with a gold medal ^^<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
== Software tool collaborations==<br />
<br />
In order to develop a fully operational tool we created a poll that we send to other igem team to ask if it could be a great help for them or not and if they have also advices and expectations concerning this software.<br />
<br />
<br />
2 Teams answered : <br />
*[https://2009.igem.org/Team:TUDelft TUDelf] Specially to Sriram and Tim <br />
*[https://2009.igem.org/Team:Valencia Valencia] Specially to Juny<br />
<br />
<br />
We had some interactions with the [https://2009.igem.org/Team:Freiburg_software Freiburg_software team], specially with Paul Staab. They have developed a synthetic biological software suite, based on Google's collaboration and communication tool Wave : '''SynBiowave'''. The actual version is 0.2 but it is a project with a great potential! <br />
<br />
<br />
<br />
{{Template:Paris2009_guided|Team#top|Contact#top}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/CollaborationsTeam:Paris/Collaborations2009-10-22T03:42:41Z<p>Christophe.R: /* Modeling collaborations */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris#top | Home]] > [[Team:Paris/Collaborations#bottom | Collaborations]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
==Modeling collaborations==<br />
<br />
As it happened that we share with the [https://2009.igem.org/Team:BCCS-Bristol BCCS-Bristol] projet some similarities and especially on the modeling part we have decided to contact them in order to either find synergies or just to be sure not to make a redondant modeling work. Obviously it seems that we were not working on the same domain.<br />
<br />
So in order to make a complete modelisation of the "project" we provided them unconditionally with the Mathlab source code of the production of vesicles. <br />
<br />
<br />
Here you can find the Matlab code, with respect to the iGEM Open Source concept :<br />
<br><br />
<I>'''function Delay_Device_Simple'''</I><br />
<br />
close all<br />
for k = 1:6<br />
<br />
H = k;<br />
<br />
t0 = 0 ;<br />
<br />
tf = 10 ;<br />
<br />
x0 = [0 ; 0 ; 4000 ; 0];<br />
<br />
[t, x] = ode23(@delaydevice, [t0:0.1:tf],x0,[],H);<br />
<br />
subplot(3,2,k)<br />
<br />
plot (t,x)<br />
<br />
end <br />
<br />
legend({'prot','lacI','TetR','TolRII'});<br />
<br />
function solver(k)<br />
<br />
end<br />
<br />
<br />
function xd = delaydevice(t, x, H)<br />
<br />
%Resolution of a differential system<br />
<br />
<br />
% Dilution of proteins<br />
<br />
gamma = 1;<br />
<br />
gammaLVA = 3;<br />
<br />
<br />
<br />
% pBad Activation<br />
<br />
Ara = 10000;<br />
<br />
beta1 = 4000;<br />
<br />
beta2 = 4000;<br />
<br />
K1 = 40;<br />
<br />
K2 = 40;<br />
<br />
<br />
<br />
% pLac Repression<br />
<br />
beta3 = 2000;<br />
<br />
K3 = 40;<br />
<br />
% pTet Repression<br />
<br />
beta4 = 2000;<br />
<br />
K4 = 40;<br />
<br />
<br />
<br />
<br />
xd = zeros(size(x));<br />
<br />
<br />
xd(1) = -gamma*x(1)+ beta1*(Ara/K1)/(1+(Ara/K1)); %Protein creation<br />
<br />
xd(2) = -gammaLVA*x(2)+ beta2*(Ara/K2)/(1+(Ara/K2)); % lacI creation<br />
<br />
xd(3) = -gamma*x(3)+ beta3*(K3/(K3+(x(2))^2)); % TetR creation<br />
<br />
xd(4) = -gamma*x(4)+ beta4*(K4/(K4+x(3))); % TolRII creation<br />
<br />
end<br />
<br />
<br />
end<br />
<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
==Ethic collaborations==<br />
<br />
We wanted to support the debates around ethics in science, in fact we also developped several points with our specialist in epistemology.<br />
<br />
<br />
Therefore answering the Valencia poll was the opportunity to widen our range of questions about biosciences, to share knowledge, and to prove that we feel concerned by the problem that ethics tackles.<br />
<br />
<br />
All the team answered the poll and we are grateful to Valencia for rewarding us with a gold medal ^^<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
== Software tool collaborations==<br />
<br />
In order to develop a fully operational tool we created a poll that we send to other igem team to ask if it could be a great help for them or not and if they have also advices and expectations concerning this software.<br />
<br />
<br />
2 Teams answered : <br />
*[https://2009.igem.org/Team:TUDelft TUDelf] Specially to Sriram and Tim <br />
*[https://2009.igem.org/Team:Valencia Valencia] Specially to Juny<br />
<br />
<br />
We had some interactions with the [https://2009.igem.org/Team:Freiburg_software Freiburg_software team], specially with Paul Staab. They have developed a synthetic biological software suite, based on Google's collaboration and communication tool Wave : '''SynBiowave'''. The actual version is 0.2 but it is a project with a great potential! <br />
<br />
<br />
<br />
{{Template:Paris2009_guided|Team#top|Contact#top}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/CollaborationsTeam:Paris/Collaborations2009-10-22T03:42:27Z<p>Christophe.R: /* Modeling collaborations */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris#top | Home]] > [[Team:Paris/Collaborations#bottom | Collaborations]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
==Modeling collaborations==<br />
<br />
As it happened that we share with the [https://2009.igem.org/Team:BCCS-Bristol BCCS-Bristol] projet some similarities and especially on the modeling part we have decided to contact them in order to either find synergies or just to be sure not to make a redondant modeling work. Obviously it seems that we were not working on the same domain.<br />
<br />
So in order to make a complete modelisation of the "project" we provided them unconditionally with the Mathlab source code of the production of vesicles. <br />
<br />
<br />
Here you can find the Matlab code, with respect to the iGEM Open Source concept :<br />
<br><br />
<I>'''function Delay_Device_Simple'''</I><br />
<br />
close all<br />
for k = 1:6<br />
<br />
H = k;<br />
<br />
t0 = 0 ;<br />
<br />
tf = 10 ;<br />
<br />
x0 = [0 ; 0 ; 4000 ; 0];<br />
<br />
[t, x] = ode23(@delaydevice, [t0:0.1:tf],x0,[],H);<br />
<br />
subplot(3,2,k)<br />
<br />
plot (t,x)<br />
<br />
end <br />
<br />
legend({'prot','lacI','TetR','TolRII'});<br />
<br />
function solver(k)<br />
<br />
end<br />
<br />
<br />
function xd = delaydevice(t, x, H)<br />
<br />
%Resolution of a differential system<br />
<br />
<br />
% Dilution of proteins<br />
<br />
gamma = 1;<br />
<br />
gammaLVA = 3;<br />
<br />
<br />
<br />
% pBad Activation<br />
<br />
Ara = 10000;<br />
<br />
beta1 = 4000;<br />
<br />
beta2 = 4000;<br />
<br />
K1 = 40;<br />
<br />
K2 = 40;<br />
<br />
<br />
<br />
% pLac Repression<br />
<br />
beta3 = 2000;<br />
<br />
K3 = 40;<br />
<br />
% pTet Repression<br />
<br />
beta4 = 2000;<br />
<br />
K4 = 40;<br />
<br />
<br />
<br />
<br />
xd = zeros(size(x));<br />
<br />
<br />
xd(1) = -gamma*x(1)+ beta1*(Ara/K1)/(1+(Ara/K1)); %Protein creation<br />
<br />
xd(2) = -gammaLVA*x(2)+ beta2*(Ara/K2)/(1+(Ara/K2)); % lacI creation<br />
<br />
xd(3) = -gamma*x(3)+ beta3*(K3/(K3+(x(2))^2)); % TetR creation<br />
<br />
xd(4) = -gamma*x(4)+ beta4*(K4/(K4+x(3))); % TolRII creation<br />
<br />
end<br />
<br />
<br />
end<br />
<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
==Ethic collaborations==<br />
<br />
We wanted to support the debates around ethics in science, in fact we also developped several points with our specialist in epistemology.<br />
<br />
<br />
Therefore answering the Valencia poll was the opportunity to widen our range of questions about biosciences, to share knowledge, and to prove that we feel concerned by the problem that ethics tackles.<br />
<br />
<br />
All the team answered the poll and we are grateful to Valencia for rewarding us with a gold medal ^^<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
== Software tool collaborations==<br />
<br />
In order to develop a fully operational tool we created a poll that we send to other igem team to ask if it could be a great help for them or not and if they have also advices and expectations concerning this software.<br />
<br />
<br />
2 Teams answered : <br />
*[https://2009.igem.org/Team:TUDelft TUDelf] Specially to Sriram and Tim <br />
*[https://2009.igem.org/Team:Valencia Valencia] Specially to Juny<br />
<br />
<br />
We had some interactions with the [https://2009.igem.org/Team:Freiburg_software Freiburg_software team], specially with Paul Staab. They have developed a synthetic biological software suite, based on Google's collaboration and communication tool Wave : '''SynBiowave'''. The actual version is 0.2 but it is a project with a great potential! <br />
<br />
<br />
<br />
{{Template:Paris2009_guided|Team#top|Contact#top}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/CollaborationsTeam:Paris/Collaborations2009-10-22T03:42:11Z<p>Christophe.R: /* Modeling collaborations */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris#top | Home]] > [[Team:Paris/Collaborations#bottom | Collaborations]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
==Modeling collaborations==<br />
<br />
As it happened that we share with the [https://2009.igem.org/Team:BCCS-Bristol BCCS-Bristol] projet some similarities and especially on the modeling part we have decided to contact them in order to either find synergies or just to be sure not to make a redondant modeling work. Obviously it seems that we were not working on the same domain.<br />
<br />
So in order to make a complete modelisation of the "project" we provided them unconditionally with the Mathlab source code of the production of vesicles. <br />
<br />
<br />
Here you can find the Matlab code, with respect to the iGEM Open Source concept :<br />
<br><br />
<I>'''function Delay_Device_Simple'''</I><br />
<br />
close all<br />
<br />
for k = 1:6<br />
<br />
H = k;<br />
<br />
t0 = 0 ;<br />
<br />
tf = 10 ;<br />
<br />
x0 = [0 ; 0 ; 4000 ; 0];<br />
<br />
[t, x] = ode23(@delaydevice, [t0:0.1:tf],x0,[],H);<br />
<br />
subplot(3,2,k)<br />
<br />
plot (t,x)<br />
<br />
end <br />
<br />
legend({'prot','lacI','TetR','TolRII'});<br />
<br />
function solver(k)<br />
<br />
end<br />
<br />
<br />
function xd = delaydevice(t, x, H)<br />
<br />
%Resolution of a differential system<br />
<br />
<br />
% Dilution of proteins<br />
<br />
gamma = 1;<br />
<br />
gammaLVA = 3;<br />
<br />
<br />
<br />
% pBad Activation<br />
<br />
Ara = 10000;<br />
<br />
beta1 = 4000;<br />
<br />
beta2 = 4000;<br />
<br />
K1 = 40;<br />
<br />
K2 = 40;<br />
<br />
<br />
<br />
% pLac Repression<br />
<br />
beta3 = 2000;<br />
<br />
K3 = 40;<br />
<br />
% pTet Repression<br />
<br />
beta4 = 2000;<br />
<br />
K4 = 40;<br />
<br />
<br />
<br />
<br />
xd = zeros(size(x));<br />
<br />
<br />
xd(1) = -gamma*x(1)+ beta1*(Ara/K1)/(1+(Ara/K1)); %Protein creation<br />
<br />
xd(2) = -gammaLVA*x(2)+ beta2*(Ara/K2)/(1+(Ara/K2)); % lacI creation<br />
<br />
xd(3) = -gamma*x(3)+ beta3*(K3/(K3+(x(2))^2)); % TetR creation<br />
<br />
xd(4) = -gamma*x(4)+ beta4*(K4/(K4+x(3))); % TolRII creation<br />
<br />
end<br />
<br />
<br />
end<br />
<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
==Ethic collaborations==<br />
<br />
We wanted to support the debates around ethics in science, in fact we also developped several points with our specialist in epistemology.<br />
<br />
<br />
Therefore answering the Valencia poll was the opportunity to widen our range of questions about biosciences, to share knowledge, and to prove that we feel concerned by the problem that ethics tackles.<br />
<br />
<br />
All the team answered the poll and we are grateful to Valencia for rewarding us with a gold medal ^^<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
== Software tool collaborations==<br />
<br />
In order to develop a fully operational tool we created a poll that we send to other igem team to ask if it could be a great help for them or not and if they have also advices and expectations concerning this software.<br />
<br />
<br />
2 Teams answered : <br />
*[https://2009.igem.org/Team:TUDelft TUDelf] Specially to Sriram and Tim <br />
*[https://2009.igem.org/Team:Valencia Valencia] Specially to Juny<br />
<br />
<br />
We had some interactions with the [https://2009.igem.org/Team:Freiburg_software Freiburg_software team], specially with Paul Staab. They have developed a synthetic biological software suite, based on Google's collaboration and communication tool Wave : '''SynBiowave'''. The actual version is 0.2 but it is a project with a great potential! <br />
<br />
<br />
<br />
{{Template:Paris2009_guided|Team#top|Contact#top}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/CollaborationsTeam:Paris/Collaborations2009-10-22T03:41:53Z<p>Christophe.R: /* Modeling collaborations */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris#top | Home]] > [[Team:Paris/Collaborations#bottom | Collaborations]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
==Modeling collaborations==<br />
<br />
As it happened that we share with the [https://2009.igem.org/Team:BCCS-Bristol BCCS-Bristol] projet some similarities and especially on the modeling part we have decided to contact them in order to either find synergies or just to be sure not to make a redondant modeling work. Obviously it seems that we were not working on the same domain.<br />
<br />
So in order to make a complete modelisation of the "project" we provided them unconditionally with the Mathlab source code of the production of vesicles. <br />
<br />
<br />
Here you can find the Matlab code, with respect to the iGEM Open Source concept :<br />
<br><br />
<I>'''function Delay_Device_Simple'''</I><br />
<br />
close all<br />
<br />
for k = 1:6<br />
<br />
H = k;<br />
<br />
t0 = 0 ;<br />
<br />
tf = 10 ;<br />
<br />
x0 = [0 ; 0 ; 4000 ; 0];<br />
<br />
[t, x] = ode23(@delaydevice, [t0:0.1:tf],x0,[],H);<br />
<br />
subplot(3,2,k)<br />
<br />
plot (t,x)<br />
<br />
end <br />
<br />
legend({'prot','lacI','TetR','TolRII'});<br />
<br />
function solver(k)<br />
<br />
end<br />
<br />
<br />
function xd = delaydevice(t, x, H)<br />
<br />
%Resolution of a differential system<br />
<br />
<br />
% Dilution of proteins<br />
<br />
gamma = 1;<br />
<br />
gammaLVA = 3;<br />
<br />
<br />
<br />
% pBad Activation<br />
<br />
Ara = 10000;<br />
<br />
beta1 = 4000;<br />
<br />
beta2 = 4000;<br />
<br />
K1 = 40;<br />
<br />
K2 = 40;<br />
<br />
<br />
<br />
% pLac Repression<br />
<br />
beta3 = 2000;<br />
<br />
K3 = 40;<br />
<br />
% pTet Repression<br />
<br />
beta4 = 2000;<br />
<br />
K4 = 40;<br />
<br />
<br />
<br />
<br />
xd = zeros(size(x));<br />
<br />
<br />
xd(1) = -gamma*x(1)+ beta1*(Ara/K1)/(1+(Ara/K1)); %Protein creation<br />
<br />
xd(2) = -gammaLVA*x(2)+ beta2*(Ara/K2)/(1+(Ara/K2)); % lacI creation<br />
<br />
xd(3) = -gamma*x(3)+ beta3*(K3/(K3+(x(2))^2)); % TetR creation<br />
<br />
xd(4) = -gamma*x(4)+ beta4*(K4/(K4+x(3))); % TolRII creation<br />
<br />
end<br />
<br />
<br />
end<br />
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==Ethic collaborations==<br />
<br />
We wanted to support the debates around ethics in science, in fact we also developped several points with our specialist in epistemology.<br />
<br />
<br />
Therefore answering the Valencia poll was the opportunity to widen our range of questions about biosciences, to share knowledge, and to prove that we feel concerned by the problem that ethics tackles.<br />
<br />
<br />
All the team answered the poll and we are grateful to Valencia for rewarding us with a gold medal ^^<br />
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== Software tool collaborations==<br />
<br />
In order to develop a fully operational tool we created a poll that we send to other igem team to ask if it could be a great help for them or not and if they have also advices and expectations concerning this software.<br />
<br />
<br />
2 Teams answered : <br />
*[https://2009.igem.org/Team:TUDelft TUDelf] Specially to Sriram and Tim <br />
*[https://2009.igem.org/Team:Valencia Valencia] Specially to Juny<br />
<br />
<br />
We had some interactions with the [https://2009.igem.org/Team:Freiburg_software Freiburg_software team], specially with Paul Staab. They have developed a synthetic biological software suite, based on Google's collaboration and communication tool Wave : '''SynBiowave'''. The actual version is 0.2 but it is a project with a great potential! <br />
<br />
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<br />
{{Template:Paris2009_guided|Team#top|Contact#top}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/ProjectTeam:Paris/Project2009-10-22T03:40:12Z<p>Christophe.R: /* A.2. The reception system */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris#top | Home]] > [[Team:Paris/Project#bottom | OMV Project]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
== '''Overall project:''' '''''Message in a bubble'''''==<br />
<br />
<center>'''Message in a Bubble: cell-cell communication using vesicles. '''</center><br />
<br />
<br />
<center>''Communication is a "two way" process. When you communicate you perceive the other persons responses and react with your own thoughts and feelings. It is only by paying attention to the other person that you have any idea about what to say or do next.''</center><br />
<br />
<br />
*''Bacterial communication:''<br />
<br />
Bacteria communicate with another one using chemical signal molecules. As in higher organisms, the information supplied by these molecules is critical for synchronizing the activities of large groups of cells. In bacteria, chemical communication involves producing, releasing, detecting, and responding to small hormone-like molecules<br />
(called acylhomoserine lactones, AHL). This process, also known as quorum sensing, allows bacteria to monitor the environment for other bacteria and to alter behavior on a population-wide scale in response to changes in the number and/or species present in a community. Nevertheless, AHL molecules are broken down by other bacteria, and some AHL signals are poorly soluble in water, so '''they cannot travel far in an aqueous environment (this factor limits their potential as a long communication signals)'''. <br />
<br />
<br />
*''Outer membrane vesicules in bacteria''<br />
Growing '''gram-negative bacteria (like ''E.Coli'' ) release vesicles from their outer membranes as a means of delivering toxins to host cells and other bacteria'''. This mecanism is conserved among Gram-negative bacteria. The vesicles consist of a lipid bilayer surrounding an aqueous core and they can therefore transport lipid-soluble toxins (lipopolysaccharide endotoxin) on their surface and protein toxins in their core. They release their content by fusing with the lipid bilayer of target cells. <br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<center>'''''The project :'''''</center><br />
<br />
We decided to''' improve bacterial communication''' thanks to the vesicles formation process. In this direction our engineered communication platform consists in '''controlling OMV production''' by destabilizing membrane integrity through over-expression of specific periplasmic proteins of the Tol/Pal system. The over-production of TolR (a major protein of the Tol/Pal system which ensure the membrane integrity) has to be controled to avoid the bacteria death. <br />
Another important key point of our project is to obtain a delay between the production of protein of interest and the vesicle formation, to be sure that the produced vesicles carried the different protein required for the recognition of the target bacteria and thus the one essential for the signal transduction.<br />
<br />
<br />
<font color=red>Producing the messenger :</font> <br />
<br />
In order to control and modulate message content, we used fusions with our protein of interest and OmpA signal sequence or the ClyA hemolysin as delivery tags. OmpA is a major protein of the external membrane of ''E.Coli'' and is also localize on OMVs. In this direction OmpA seems to be appropriate to deliver a specific protein to the outer membrane and, by consequence into vesicles. As OmpA, ClyA is an interesting way to explore to send protein to the external membrane.<br />
<br />
<br />
<font color=red>Addressing the message :</font> <br />
<br />
To own the communication between the donnor and the receiver a targeting system was developed. This system is based on the outer-membrane expression of Jun/Fos leucine zippers to control the vesicle flux between donor and recipient cells. Jun was mutated into its leucine zipper-motif to abolished the homodimer formation but to allow the development of heterodimer with Fos. To express these protein to the outer membrane of bacteria, they were merged with AIDA autotransporter. In this direction, the direction and the specificity of communication is controled.<br />
<br />
<br />
<font color=red>Receiving the message :</font><br />
<br />
Once received, the signal from incoming vesicles is transduced through a modified Fec pathway, whereby the receptor is provided by the OMV. Few ABC transporter such as FecABCD (iron transporter) are able to induce a response regardless of the tranlocation, due to the activity of FecA. Moreover some mutant can also have a constitutive expression of FecABCD .So, we would like to use FecA- mutant receiver and FecA+ mutant donor to transfert the constitutive FecA protein to the receiver to transmit to the target cell the message (which comes from vesicles (bubbles)). <br />
<br />
<br />
Computational models provided insight to all of the above steps and suggested directions for system improvement. '''Such reliable communications systems have wide biotechnological implications, ranging from targeted drugs delivery and detoxification to advanced division of labor or even cell-based computing.'''<br />
<br />
<br />
<br />
<br />
All of our constructions are just [[Team:Paris/constructions | here]]<br />
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==='''A. Plasmid construction'''===<br />
<br />
The plasmid construction is divided into 2 functional modules :<br />
*'''The emission system''', which aims at producing vesicules.<br />
*'''The reception system''' of the signal sent via the vesicules.<br />
<br />
====A.1. The emission system ====<br />
<br />
To implement our vesicles emission project, we had to take several constrains into account. To put into place all the functionalities we needed, we designed 2 different plasmids as shown on the image below.<br />
<br />
<br />
<font color=red>Writing the message: production of signaling proteins </font><br><br />
First of all, before sending vesicles into the surrounding medium, we have to make sure that every molecule and protein that has to be inside the vesicles is already into place before the bacteria starts the creation of vesicles. In other words, the "emitting" bacteria must produce the proteins of interest, the export systems, the FecA proteins as well as the fusion mechanism before creating vesicles.<br />
<br />
To create this delay between the creation of proteins and the production of vesicles, we designed a regulatory cascade consisting of the LacI and TetR repressors. The LacI biobrick is placed in the first plasmid, downstream the pBad promoter and once synthesized acts as a repressor on the pLac promoter. The pLac promoter in the second plasmid then stops expressing TetR. The ptet promoter is then no longer repressed and the creation of non functional TolR can start leading to the emission of vesicles.<br />
<br />
<br />
<font color=red>Preparing the messenger: creation of the vesicles </font><br><br />
As the creation of vesicles via the over-expression of TolR disturbs the membrane integrity and can create an important cell lysis, it appeared very important to find a way to avoid a long lasting expression of our TolR biobrick once the input signal is on (presence of arabinose in the medium). <br />
<br />
To solve this problem, we decided to place a tag on the LacI protein to speed up its degradation. As a consequence, once the arabinose in the medium is depleted, LacI production stops and the remaining LacI is rapidly degraded. The production of TetR can resume and inhibit vesicle production.<br />
<br />
<br />
* In '''presence of Arabinose''', proteins of interest are created as well as vesicles :<br />
[[Image:Global_On.jpg|800px|center| Plasmid construction of the emitting bacteria]]<br />
<br />
<br />
<br />
<br />
*In the '''absence of Arabinose''', the pBad promoter is repressed and there is no production of proteins nor vesicles :<br />
[[Image:Global_Off.jpg|800px|center| Plasmid construction of the emitting bacteria]]<br />
<br />
<br />
A more accurate description of the parts used at each step of the creation process (including links to the parts registry and references) can be found in the different subdivision of the project.<br />
<br />
====A.2. The reception system====<br />
<br />
To implement our vesicles reception project, we had to take several constrains into account. To put into place all the functionalities we needed, we designed 2 different types of experiments.<br />
<br />
<br />
<font color=red>Giving the message: fusion of the vesicles with the receiver.</font><br><br />
To merge the OMVs with the targeted bacteria. We have explored two different methods : Jun/Fos dimere and G3P. <br>With Jun/Fos, after mutations into the leucine zipper motif of Jun, we fused it to AIDA to send them to the extern membrane of bacteria. <br>With G3P, we fuse it to the OmpA- Linker protein to target it at the surface of the vesicles.<br />
<br />
<br />
<br />
<font color=red>Transduction: decryption of the message.</font><br />
<br><br />
We plan to use FecA- mutant receiver and FecA+ mutant donor to transfert the constitutive FecA protein to the receiver. In this case the receiver will express the FecABCD operon without being induce by ferric citrate in the medium , and so we could place under the control of the Fec ABCD promoter, which is called pfec, the gene sequence encoding for the response. For the moment a response that would be easy to detect is the fluorescence of the RFP and the biobrick BBa-J61002 is the perfect candidate to test the system. <br />
<br><br />
We also discovered that some fecR and fecI mutants can be use to amplify the signal because they have a constitutive activity. So we put under the control of pfec a FecR and FecI mutated. When they will be expressed, they will be activators of pfec and consequently of RFP. Normaly we would be able to obtain a increasing fluorescence. <br />
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{{Template:Paris2009_guided2|#top|/DryLab}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/PapersTeam:Paris/Papers2009-10-22T03:34:41Z<p>Christophe.R: /* Bibliography */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Papers#bottom | Papers]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
==Bibliography==<br />
<br />
In order to class our reading, you can see here a part of it. Some sith the [X] symbol doe not figure in the wiki as support for the main parts. Every paper can be numeroted several time in different parts. Some reading does not figure here, but are link with all the information in its respective part. <br />
<br />
<br />
For the references of the Ethical part go to the [https://2009.igem.org/Team:Paris/Ethics_Materials#top Material] or [https://2009.igem.org/Team:Paris/EthicalReportReferences#bottom References].<br />
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<br />
==OMV Overview==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white; font-weight:bold; "<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px| [X]<br />
|1999<br />
|Terry J. Beveridge<br />
|Structures of gram-negative cell walls and their derived membrane vesicles.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93954 10438737]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Miller SI & Guina T.<br />
|Bacterial vesicle formation as a mechanism of protein transfer to animals.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14531993?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 14531993]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2005<br />
|Kuehn MJ & Kesty NC.<br />
|Bacterial outer membrane vesicles and the host-pathogen interaction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16291643?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16291643]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|McBroom AJ & Kuehn MJ.<br />
|Outer membrane vesicle production by Escherichia coli is independent of membrane instability.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16855227?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16855227]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 1]]<br />
|2007<br />
|McBroom AJ & Kuehn MJ.<br />
|Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17163978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17163978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 2]]<br />
|2009<br />
|Deatherage BL & Cookson BT.<br />
|Biogenesis of bacterial membrane vesicles<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19432795?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 19432795]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2009<br />
|Purnick PE & Weiss R.<br />
|The second wave of synthetic biology: from modules to systems.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19461664?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 19461664]<br />
|}<br />
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==OMV Production==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Mashburn-Warren L & Whiteley M.<br />
|Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18630345?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 18630345]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Addressing_overview4#top|[2]]]<br />
|2001<br />
|Arora A. & Tamm LK.<br />
|Structure of outer membrane protein A transmembrane domain by NMR spectroscopy.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11276254?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 11276254]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|2007<br />
|Brown EA & Hardwidge PR.<br />
|Biochemical characterization of the enterotoxigenic Escherichia coli LeoA protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17975086?ordinalpos=16&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17975086]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2008<br />
|Burgess NK & Fleming KG.<br />
|Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18641391?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 18641391]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Tol/Pal<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|1986<br />
|Robert CHEN & Ulf HENNING.<br />
|Nucleotide sequence of the gene for the peptidoglycan-associated lipoprotein of Escherichia coli K12<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=210680 210680]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[3]]]<br />
|1995<br />
|Lazzaroni & Geli -<br />
|Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179564 179564]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|1999<br />
|Derouiche & Loret<br />
|Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10380085 10380085]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[4]]]<br />
|2001<br />
|Lloubès & RJournet L.<br />
|The Tol-Pal proteins of the Escherichia coli cell envelope: an energized system required for outer membrane integrity?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11501670 11501670]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|2002<br />
|Dubuisson JF & Lazzaroni JC.<br />
|Mutational analysis of the TolA C-terminal domain of Escherichia coli and genetic evidence for an interaction between TolA and TolB.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12142433 12142433]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2003<br />
|Llamas M & ARamos JL.<br />
|Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12896989 12896989]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[5]]]<br />
|2004<br />
|Henry T & Lloubès R.<br />
|Improved methods for producing outer membrane vesicles in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15249060 15249060]<br />
|}<br />
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==OMV Adressing==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1997<br />
|Kadurugamuwa JL & Beveridge TJ.<br />
|Natural release of virulence factors in membrane vesicles by Pseudomonas aeruginosa and the effect of aminoglycoside antibiotics on their release.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9421308 9421308]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|1998<br />
|Santini CL & Wu LF.<br />
|A novel sec-independent periplasmic protein translocation pathway in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9427745 9427745]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Berks BC & Palmer T.<br />
|The Tat protein export pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10652088 10652088]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2001<br />
|Mishima Y & Murata K.<br />
|Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11731126 11731126]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2001<br />
|Sargent F & Berks BC.<br />
|Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11422364 11422364]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2001<br />
|Yahr TL & Wickner WT.<br />
|Functional reconstitution of bacterial Tat translocation in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11350936 11350936]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2004<br />
|Robinson C & Bolhuis A.<br />
|Tat-dependent protein targeting in prokaryotes and chloroplasts.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15546663 15546663]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Sargent F & Palmer T.<br />
|Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16445746 16445746]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Lee PA & Georgiou G.<br />
|The bacterial twin-arginine translocation pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16756481 16756481]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Maillard J & Sargent F.<br />
|Structural diversity in twin-arginine signal peptide-binding proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17901208 17901208]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Sargent F.<br />
|The twin-arginine transport system: moving folded proteins across membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17956229 17956229]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Ferrandez Y & Condemine G.<br />
|Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2009<br />
|Pradel N & Bonnet R<br />
|Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2009<br />
|de Marco A.<br />
|Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19442264 19442264]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | ClyA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 5]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 1]]<br />
|2008<br />
|Kim JY & DeLisa MP.<br />
|Engineered bacterial outer membrane vesicles with enhanced functionality.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 1]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 2]]<br />
|2009<br />
|Mueller M & Ban N.<br />
|The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[Team:Paris/Addressing_overview4#top|[1]]]<br />
|2002<br />
|Wang Y.<br />
|The function of OmpA in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Dramsi S & Arthur M.<br />
|Covalent attachment of proteins to peptidoglycan.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18266854 18266854]<br />
|}<br />
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<br />
==OMV Reception==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Adhesin<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1989<br />
|Smeal T & Karin M.<br />
|Different requirements for formation of Jun:Jun and Jun:Fos complexes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|1994<br />
|Heffernan EJ & Guiney DG.<br />
|Specificity of the complement resistance and cell association phenotypes encoded by the outer membrane protein genes rck from Salmonella typhimurium and ail from Yersinia enterocolitica.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7927803 7927803]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Veiga E & Fernández LA.<br />
|Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12949111 12949111]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 6]]<br />
|2004<br />
|Kesty NC & Kuehn MJ.<br />
|Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14578354 14578354]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | G3P<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1982<br />
|JEF D. BOEKE & PETER MODEL<br />
|A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 8]]<br />
|1999<br />
|Chatellier J & Riechmann L.<br />
|Interdomain interactions within the gene 3 protein of filamentous phage.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 9]]<br />
|1999<br />
|Lubkowski J & Wlodawer A.<br />
|Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 10]]<br />
|2002<br />
|Baek H & Cha S.<br />
|An improved helper phage system for efficient isolation of specific antibody molecules in phage display.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 11]]<br />
|2003<br />
|Karlsson F & Malmborg-Hager AC.<br />
|The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Snare<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 17]]<br />
|2000<br />
|Waters MG & Hughson FM.<br />
|Membrane tethering and fusion in the secretory and endocytic pathways.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Woodbury DJ & Rognlien K.<br />
|The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11067766 11067766]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2002<br />
|Bowen ME,Brunger AT.<br />
|Mutational analysis of synaptobrevin transmembrane domain oligomerization.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12501216 12501216]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Hu C & Rothman JE.<br />
|Fusion of cells by flipped SNAREs.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Weninger K & Brunger AT.<br />
|Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14657376 14657376]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006 <br />
|Giraudo CG & Rothman JE.<br />
|A clamping mechanism involved in SNARE-dependent exocytosis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16794037 16794037]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Low HH & Löwe J.<br />
|A bacterial dynamin-like protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17122778 17122778]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Weninger K & Brunger AT.<br />
|Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18275821 18275821]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Delevoye C & Subtil A.<br />
|SNARE protein mimicry by an intracellular bacterium.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18369472 18369472]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 18]]<br />
|2009<br />
|Giraudo CG & Rothman JE.<br />
|Alternative zippering as an on-off switch for SNARE-mediated fusion.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19164750 19164750]<br />
<br />
|}<br />
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<br />
==OMV Signal transduction==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|1984<br />
|Lopilato JE & Beckwith JR.<br />
|D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6327616 6327616]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1995<br />
|Härle C & Braun V.<br />
|Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7729419 7729419]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[1]]]<br />
|1998<br />
|Tomii K & Kanehisa M.<br />
|A comparative analysis of ABC transporters in complete microbial genomes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1999<br />
|De Wulf P & Lin EC.<br />
|The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10542180 10542180]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[6]]]<br />
|2000<br />
|Stock AM & Goudreau PN.<br />
|Two-component signal transduction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Yaron S & Matthews KR.<br />
|Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11010892 11010892]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2004<br />
|Dwyer MA & Hellinga HW.<br />
|Periplasmic binding proteins: a versatile superfamily for protein engineering.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15313245 15313245]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Braun V & Sauter A.<br />
|Gene regulation by transmembrane signaling.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16718597 16718597]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Baker MD & Stock JB<br />
|Signal transduction: networks and integrated circuits in bacterial cognition.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18054766 18054766]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Baker MD & Stock JB.<br />
|Systems biology of bacterial chemotaxis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16529985 16529985]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Ibrahim M & Monnet V.<br />
|Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17921293 17921293]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[9]]]<br />
|2009<br />
|Kyriakidis DA & Tiligada E.<br />
|Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2009<br />
|Tomii & Kanehisa<br />
|comparative analysis of ABC transporter<br />
|[http://genome.cshlp.org/content/8/10/1048.full.html#ref-list-1 pdf-link]<br />
|}<br />
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<br />
==Modelling==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Genetic Regulatory Network<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 1]]<br />
|1977<br />
|Gillespie Daniel T.<br />
|Exact Stochastic Simlation of Coupled Chemical Equations<br />
|[http://www.dna.caltech.edu/courses/cs191/paperscs191/gillespie2.pdf Gillespie1]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 3]]<br />
|1997<br />
|J.B. Andersen & S.Molin<br />
|New Stable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria<br />
|[http://aem.asm.org/cgi/reprint/64/6/2240.pdf LVA tag]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 6]]<br />
|1999<br />
|M.Ellowitz & S.Leibler<br />
|A Synthetic oscillatory network of transcriptionnal regulators <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10659856 10659856]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 2]]<br />
|1997<br />
|D.T.Gillespie<br />
|The Chemical Langevin Equation<br />
|[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000113000001000297000001&idtype=cvips&gifs=yes Gillespie2]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 5]]<br />
|2002<br />
|N.Rosenfold & U.Alon<br />
|Negative Autoregulation Speeds The Response TImes of Transcription Network <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12417193 2417193]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2002<br />
|M.B.Ellowitz & P.S.Swain<br />
|Stochastic Gene Expression In A Single Cell<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12183631 12183631]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 7]]<br />
|2003<br />
|S.Mangan & U.Alon<br />
|Structure and function ot the feed-forward Loop Network Motif<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14530388 14530388]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 4]]<br />
|2003<br />
|S.Basu & R.Weiss<br />
|Spatiotemporal control of gene expression with pulse-generating networks<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15096621 15096621]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 1]]<br />
|2005<br />
|S.Hooshangi & R.Weiss<br />
|Ultrasensitivity and noise propagation in a synthetic transcriptional cascade<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15738412 15738412]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 3]]<br />
|2006<br />
|H.Li & L.Petzold<br />
|Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems<br />
|[http://www.cs.ucsb.edu/~cse/Files/ldm0513.pdf Sto.Sim]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 2]]<br />
|2007<br />
|U.Alon<br />
|Network motifs : theory and experimental approaches<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17510665 117510665]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|J.Stricker & J.Hasty<br />
|A Fast Robust and Tunable synthetic gene oscillator<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18971928 18971928]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Vesicle biophysics model<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 6]]<br />
|1977<br />
|Harbich et al<br />
|Optical observation of rotationally symmetric lecithin vesicle shapes<br />
|J. Physique, 38:727–729<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 4]]<br />
|1987<br />
|Ou-Yang & Helfrich<br />
|Instability and deformation of a spherical vesicle by pressure<br />
|Phys. Rev. Lett., 59:2486-2488 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 1]]<br />
|1991<br />
|Lipowsky<br />
|The conformation of membranes<br />
|Nature, 349(6309):475-481<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 5]]<br />
|1995 <br />
|Fattal et al <br />
|The vesicle-micelle transition in mixed lipid-surfactant<br />
|Langmuir, 11:1154-1161 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 3]]<br />
|1998<br />
|Zhou et al<br />
|On the origin of membrane vesicles in gram-negative bacteria<br />
|FEMS microbiology letters, 163(2):223-228 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 8]]<br />
|2005 <br />
|Kuehn & Kesty<br />
|Bacterial outer membrane vesicles and the host pathogen interaction<br />
|Genes & Dev, 19:2645-2655 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 2]]<br />
|2008<br />
|Park & Uehara<br />
|How bacteria consume their own exoskeletons<br />
|Microbiol Mol Biol Rev, 72(2):211-227 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 7]]<br />
|2009<br />
|Deatherage et al <br />
|Biogenesis of bacterial membrane vesicles,<br />
|Mol Microbiol, 72(6):1395-1407<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 9]]<br />
|2009<br />
|Kumaran & Losick<br />
|Negative membrane curvature as a cue for subcellular localization of a bacterial protein.<br />
|PNAS USA, 106(32):13541-13545 <br />
|}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/PapersTeam:Paris/Papers2009-10-22T03:34:27Z<p>Christophe.R: /* Bibliography */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Papers#bottom | Papers]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
==Bibliography==<br />
<br />
In order to class our reading, you can see here a part of it. Some sith the [X] symbol doe not figure in the wiki as support for the main parts. Every paper can be numeroted several time in different parts. Some reading does not figure here, but are link with all the information in its respective part. <br />
<br />
<br />
For the references of the Ethical part fo to the [https://2009.igem.org/Team:Paris/Ethics_Materials#top Material] or [https://2009.igem.org/Team:Paris/EthicalReportReferences#bottom References].<br />
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==OMV Overview==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white; font-weight:bold; "<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px| [X]<br />
|1999<br />
|Terry J. Beveridge<br />
|Structures of gram-negative cell walls and their derived membrane vesicles.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93954 10438737]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Miller SI & Guina T.<br />
|Bacterial vesicle formation as a mechanism of protein transfer to animals.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14531993?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 14531993]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2005<br />
|Kuehn MJ & Kesty NC.<br />
|Bacterial outer membrane vesicles and the host-pathogen interaction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16291643?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16291643]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|McBroom AJ & Kuehn MJ.<br />
|Outer membrane vesicle production by Escherichia coli is independent of membrane instability.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16855227?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16855227]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 1]]<br />
|2007<br />
|McBroom AJ & Kuehn MJ.<br />
|Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17163978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17163978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 2]]<br />
|2009<br />
|Deatherage BL & Cookson BT.<br />
|Biogenesis of bacterial membrane vesicles<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19432795?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 19432795]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2009<br />
|Purnick PE & Weiss R.<br />
|The second wave of synthetic biology: from modules to systems.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19461664?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 19461664]<br />
|}<br />
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<br />
==OMV Production==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Mashburn-Warren L & Whiteley M.<br />
|Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18630345?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 18630345]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Addressing_overview4#top|[2]]]<br />
|2001<br />
|Arora A. & Tamm LK.<br />
|Structure of outer membrane protein A transmembrane domain by NMR spectroscopy.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11276254?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 11276254]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|2007<br />
|Brown EA & Hardwidge PR.<br />
|Biochemical characterization of the enterotoxigenic Escherichia coli LeoA protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17975086?ordinalpos=16&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17975086]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2008<br />
|Burgess NK & Fleming KG.<br />
|Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18641391?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 18641391]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Tol/Pal<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|1986<br />
|Robert CHEN & Ulf HENNING.<br />
|Nucleotide sequence of the gene for the peptidoglycan-associated lipoprotein of Escherichia coli K12<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=210680 210680]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[3]]]<br />
|1995<br />
|Lazzaroni & Geli -<br />
|Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179564 179564]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|1999<br />
|Derouiche & Loret<br />
|Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10380085 10380085]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[4]]]<br />
|2001<br />
|Lloubès & RJournet L.<br />
|The Tol-Pal proteins of the Escherichia coli cell envelope: an energized system required for outer membrane integrity?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11501670 11501670]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|2002<br />
|Dubuisson JF & Lazzaroni JC.<br />
|Mutational analysis of the TolA C-terminal domain of Escherichia coli and genetic evidence for an interaction between TolA and TolB.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12142433 12142433]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2003<br />
|Llamas M & ARamos JL.<br />
|Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12896989 12896989]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[5]]]<br />
|2004<br />
|Henry T & Lloubès R.<br />
|Improved methods for producing outer membrane vesicles in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15249060 15249060]<br />
|}<br />
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<br />
==OMV Adressing==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1997<br />
|Kadurugamuwa JL & Beveridge TJ.<br />
|Natural release of virulence factors in membrane vesicles by Pseudomonas aeruginosa and the effect of aminoglycoside antibiotics on their release.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9421308 9421308]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|1998<br />
|Santini CL & Wu LF.<br />
|A novel sec-independent periplasmic protein translocation pathway in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9427745 9427745]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Berks BC & Palmer T.<br />
|The Tat protein export pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10652088 10652088]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2001<br />
|Mishima Y & Murata K.<br />
|Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11731126 11731126]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2001<br />
|Sargent F & Berks BC.<br />
|Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11422364 11422364]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2001<br />
|Yahr TL & Wickner WT.<br />
|Functional reconstitution of bacterial Tat translocation in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11350936 11350936]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2004<br />
|Robinson C & Bolhuis A.<br />
|Tat-dependent protein targeting in prokaryotes and chloroplasts.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15546663 15546663]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Sargent F & Palmer T.<br />
|Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16445746 16445746]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Lee PA & Georgiou G.<br />
|The bacterial twin-arginine translocation pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16756481 16756481]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Maillard J & Sargent F.<br />
|Structural diversity in twin-arginine signal peptide-binding proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17901208 17901208]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Sargent F.<br />
|The twin-arginine transport system: moving folded proteins across membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17956229 17956229]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Ferrandez Y & Condemine G.<br />
|Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2009<br />
|Pradel N & Bonnet R<br />
|Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2009<br />
|de Marco A.<br />
|Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19442264 19442264]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | ClyA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 5]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 1]]<br />
|2008<br />
|Kim JY & DeLisa MP.<br />
|Engineered bacterial outer membrane vesicles with enhanced functionality.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 1]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 2]]<br />
|2009<br />
|Mueller M & Ban N.<br />
|The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[Team:Paris/Addressing_overview4#top|[1]]]<br />
|2002<br />
|Wang Y.<br />
|The function of OmpA in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Dramsi S & Arthur M.<br />
|Covalent attachment of proteins to peptidoglycan.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18266854 18266854]<br />
|}<br />
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<br />
==OMV Reception==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Adhesin<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1989<br />
|Smeal T & Karin M.<br />
|Different requirements for formation of Jun:Jun and Jun:Fos complexes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|1994<br />
|Heffernan EJ & Guiney DG.<br />
|Specificity of the complement resistance and cell association phenotypes encoded by the outer membrane protein genes rck from Salmonella typhimurium and ail from Yersinia enterocolitica.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7927803 7927803]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Veiga E & Fernández LA.<br />
|Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12949111 12949111]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 6]]<br />
|2004<br />
|Kesty NC & Kuehn MJ.<br />
|Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14578354 14578354]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | G3P<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1982<br />
|JEF D. BOEKE & PETER MODEL<br />
|A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 8]]<br />
|1999<br />
|Chatellier J & Riechmann L.<br />
|Interdomain interactions within the gene 3 protein of filamentous phage.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 9]]<br />
|1999<br />
|Lubkowski J & Wlodawer A.<br />
|Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 10]]<br />
|2002<br />
|Baek H & Cha S.<br />
|An improved helper phage system for efficient isolation of specific antibody molecules in phage display.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 11]]<br />
|2003<br />
|Karlsson F & Malmborg-Hager AC.<br />
|The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Snare<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 17]]<br />
|2000<br />
|Waters MG & Hughson FM.<br />
|Membrane tethering and fusion in the secretory and endocytic pathways.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Woodbury DJ & Rognlien K.<br />
|The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11067766 11067766]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2002<br />
|Bowen ME,Brunger AT.<br />
|Mutational analysis of synaptobrevin transmembrane domain oligomerization.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12501216 12501216]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Hu C & Rothman JE.<br />
|Fusion of cells by flipped SNAREs.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Weninger K & Brunger AT.<br />
|Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14657376 14657376]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006 <br />
|Giraudo CG & Rothman JE.<br />
|A clamping mechanism involved in SNARE-dependent exocytosis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16794037 16794037]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Low HH & Löwe J.<br />
|A bacterial dynamin-like protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17122778 17122778]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Weninger K & Brunger AT.<br />
|Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18275821 18275821]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Delevoye C & Subtil A.<br />
|SNARE protein mimicry by an intracellular bacterium.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18369472 18369472]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 18]]<br />
|2009<br />
|Giraudo CG & Rothman JE.<br />
|Alternative zippering as an on-off switch for SNARE-mediated fusion.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19164750 19164750]<br />
<br />
|}<br />
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<br />
==OMV Signal transduction==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|1984<br />
|Lopilato JE & Beckwith JR.<br />
|D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6327616 6327616]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1995<br />
|Härle C & Braun V.<br />
|Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7729419 7729419]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[1]]]<br />
|1998<br />
|Tomii K & Kanehisa M.<br />
|A comparative analysis of ABC transporters in complete microbial genomes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1999<br />
|De Wulf P & Lin EC.<br />
|The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10542180 10542180]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[6]]]<br />
|2000<br />
|Stock AM & Goudreau PN.<br />
|Two-component signal transduction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Yaron S & Matthews KR.<br />
|Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11010892 11010892]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2004<br />
|Dwyer MA & Hellinga HW.<br />
|Periplasmic binding proteins: a versatile superfamily for protein engineering.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15313245 15313245]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Braun V & Sauter A.<br />
|Gene regulation by transmembrane signaling.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16718597 16718597]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Baker MD & Stock JB<br />
|Signal transduction: networks and integrated circuits in bacterial cognition.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18054766 18054766]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Baker MD & Stock JB.<br />
|Systems biology of bacterial chemotaxis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16529985 16529985]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Ibrahim M & Monnet V.<br />
|Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17921293 17921293]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[9]]]<br />
|2009<br />
|Kyriakidis DA & Tiligada E.<br />
|Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2009<br />
|Tomii & Kanehisa<br />
|comparative analysis of ABC transporter<br />
|[http://genome.cshlp.org/content/8/10/1048.full.html#ref-list-1 pdf-link]<br />
|}<br />
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<br />
==Modelling==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Genetic Regulatory Network<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 1]]<br />
|1977<br />
|Gillespie Daniel T.<br />
|Exact Stochastic Simlation of Coupled Chemical Equations<br />
|[http://www.dna.caltech.edu/courses/cs191/paperscs191/gillespie2.pdf Gillespie1]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 3]]<br />
|1997<br />
|J.B. Andersen & S.Molin<br />
|New Stable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria<br />
|[http://aem.asm.org/cgi/reprint/64/6/2240.pdf LVA tag]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 6]]<br />
|1999<br />
|M.Ellowitz & S.Leibler<br />
|A Synthetic oscillatory network of transcriptionnal regulators <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10659856 10659856]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 2]]<br />
|1997<br />
|D.T.Gillespie<br />
|The Chemical Langevin Equation<br />
|[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000113000001000297000001&idtype=cvips&gifs=yes Gillespie2]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 5]]<br />
|2002<br />
|N.Rosenfold & U.Alon<br />
|Negative Autoregulation Speeds The Response TImes of Transcription Network <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12417193 2417193]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2002<br />
|M.B.Ellowitz & P.S.Swain<br />
|Stochastic Gene Expression In A Single Cell<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12183631 12183631]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 7]]<br />
|2003<br />
|S.Mangan & U.Alon<br />
|Structure and function ot the feed-forward Loop Network Motif<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14530388 14530388]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 4]]<br />
|2003<br />
|S.Basu & R.Weiss<br />
|Spatiotemporal control of gene expression with pulse-generating networks<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15096621 15096621]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 1]]<br />
|2005<br />
|S.Hooshangi & R.Weiss<br />
|Ultrasensitivity and noise propagation in a synthetic transcriptional cascade<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15738412 15738412]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 3]]<br />
|2006<br />
|H.Li & L.Petzold<br />
|Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems<br />
|[http://www.cs.ucsb.edu/~cse/Files/ldm0513.pdf Sto.Sim]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 2]]<br />
|2007<br />
|U.Alon<br />
|Network motifs : theory and experimental approaches<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17510665 117510665]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|J.Stricker & J.Hasty<br />
|A Fast Robust and Tunable synthetic gene oscillator<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18971928 18971928]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Vesicle biophysics model<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 6]]<br />
|1977<br />
|Harbich et al<br />
|Optical observation of rotationally symmetric lecithin vesicle shapes<br />
|J. Physique, 38:727–729<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 4]]<br />
|1987<br />
|Ou-Yang & Helfrich<br />
|Instability and deformation of a spherical vesicle by pressure<br />
|Phys. Rev. Lett., 59:2486-2488 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 1]]<br />
|1991<br />
|Lipowsky<br />
|The conformation of membranes<br />
|Nature, 349(6309):475-481<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 5]]<br />
|1995 <br />
|Fattal et al <br />
|The vesicle-micelle transition in mixed lipid-surfactant<br />
|Langmuir, 11:1154-1161 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 3]]<br />
|1998<br />
|Zhou et al<br />
|On the origin of membrane vesicles in gram-negative bacteria<br />
|FEMS microbiology letters, 163(2):223-228 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 8]]<br />
|2005 <br />
|Kuehn & Kesty<br />
|Bacterial outer membrane vesicles and the host pathogen interaction<br />
|Genes & Dev, 19:2645-2655 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 2]]<br />
|2008<br />
|Park & Uehara<br />
|How bacteria consume their own exoskeletons<br />
|Microbiol Mol Biol Rev, 72(2):211-227 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 7]]<br />
|2009<br />
|Deatherage et al <br />
|Biogenesis of bacterial membrane vesicles,<br />
|Mol Microbiol, 72(6):1395-1407<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 9]]<br />
|2009<br />
|Kumaran & Losick<br />
|Negative membrane curvature as a cue for subcellular localization of a bacterial protein.<br />
|PNAS USA, 106(32):13541-13545 <br />
|}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/PapersTeam:Paris/Papers2009-10-22T03:34:05Z<p>Christophe.R: </p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Papers#bottom | Papers]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
==Bibliography==<br />
<br />
In order to class our reading, you can see here a part of it. Some sith the [X] symbol doe not figure in the wiki as support for the main parts. Every paper can be numeroted several time in different parts. Some reading does not figure here, but are link with all the information in its respective part. <br />
<br />
<br />
For the references of the Ethical part fo to the [https://2009.igem.org/Team:Paris/Ethics_Materials#top Material] or [https://2009.igem.org/Team:Paris/EthicalReportReferences#bottom References].<br />
<br />
==OMV Overview==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white; font-weight:bold; "<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px| [X]<br />
|1999<br />
|Terry J. Beveridge<br />
|Structures of gram-negative cell walls and their derived membrane vesicles.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93954 10438737]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Miller SI & Guina T.<br />
|Bacterial vesicle formation as a mechanism of protein transfer to animals.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14531993?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 14531993]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2005<br />
|Kuehn MJ & Kesty NC.<br />
|Bacterial outer membrane vesicles and the host-pathogen interaction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16291643?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16291643]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|McBroom AJ & Kuehn MJ.<br />
|Outer membrane vesicle production by Escherichia coli is independent of membrane instability.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16855227?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16855227]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 1]]<br />
|2007<br />
|McBroom AJ & Kuehn MJ.<br />
|Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17163978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17163978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 2]]<br />
|2009<br />
|Deatherage BL & Cookson BT.<br />
|Biogenesis of bacterial membrane vesicles<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19432795?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 19432795]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2009<br />
|Purnick PE & Weiss R.<br />
|The second wave of synthetic biology: from modules to systems.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19461664?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 19461664]<br />
|}<br />
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<br />
==OMV Production==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Mashburn-Warren L & Whiteley M.<br />
|Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18630345?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 18630345]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Addressing_overview4#top|[2]]]<br />
|2001<br />
|Arora A. & Tamm LK.<br />
|Structure of outer membrane protein A transmembrane domain by NMR spectroscopy.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11276254?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 11276254]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|2007<br />
|Brown EA & Hardwidge PR.<br />
|Biochemical characterization of the enterotoxigenic Escherichia coli LeoA protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17975086?ordinalpos=16&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17975086]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2008<br />
|Burgess NK & Fleming KG.<br />
|Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18641391?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 18641391]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Tol/Pal<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|1986<br />
|Robert CHEN & Ulf HENNING.<br />
|Nucleotide sequence of the gene for the peptidoglycan-associated lipoprotein of Escherichia coli K12<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=210680 210680]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[3]]]<br />
|1995<br />
|Lazzaroni & Geli -<br />
|Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179564 179564]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|1999<br />
|Derouiche & Loret<br />
|Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10380085 10380085]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[4]]]<br />
|2001<br />
|Lloubès & RJournet L.<br />
|The Tol-Pal proteins of the Escherichia coli cell envelope: an energized system required for outer membrane integrity?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11501670 11501670]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|2002<br />
|Dubuisson JF & Lazzaroni JC.<br />
|Mutational analysis of the TolA C-terminal domain of Escherichia coli and genetic evidence for an interaction between TolA and TolB.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12142433 12142433]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2003<br />
|Llamas M & ARamos JL.<br />
|Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12896989 12896989]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[5]]]<br />
|2004<br />
|Henry T & Lloubès R.<br />
|Improved methods for producing outer membrane vesicles in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15249060 15249060]<br />
|}<br />
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<br />
==OMV Adressing==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1997<br />
|Kadurugamuwa JL & Beveridge TJ.<br />
|Natural release of virulence factors in membrane vesicles by Pseudomonas aeruginosa and the effect of aminoglycoside antibiotics on their release.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9421308 9421308]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|1998<br />
|Santini CL & Wu LF.<br />
|A novel sec-independent periplasmic protein translocation pathway in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9427745 9427745]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Berks BC & Palmer T.<br />
|The Tat protein export pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10652088 10652088]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2001<br />
|Mishima Y & Murata K.<br />
|Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11731126 11731126]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2001<br />
|Sargent F & Berks BC.<br />
|Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11422364 11422364]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2001<br />
|Yahr TL & Wickner WT.<br />
|Functional reconstitution of bacterial Tat translocation in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11350936 11350936]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2004<br />
|Robinson C & Bolhuis A.<br />
|Tat-dependent protein targeting in prokaryotes and chloroplasts.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15546663 15546663]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Sargent F & Palmer T.<br />
|Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16445746 16445746]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Lee PA & Georgiou G.<br />
|The bacterial twin-arginine translocation pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16756481 16756481]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Maillard J & Sargent F.<br />
|Structural diversity in twin-arginine signal peptide-binding proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17901208 17901208]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Sargent F.<br />
|The twin-arginine transport system: moving folded proteins across membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17956229 17956229]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Ferrandez Y & Condemine G.<br />
|Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2009<br />
|Pradel N & Bonnet R<br />
|Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2009<br />
|de Marco A.<br />
|Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19442264 19442264]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | ClyA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 5]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 1]]<br />
|2008<br />
|Kim JY & DeLisa MP.<br />
|Engineered bacterial outer membrane vesicles with enhanced functionality.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 1]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 2]]<br />
|2009<br />
|Mueller M & Ban N.<br />
|The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[Team:Paris/Addressing_overview4#top|[1]]]<br />
|2002<br />
|Wang Y.<br />
|The function of OmpA in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Dramsi S & Arthur M.<br />
|Covalent attachment of proteins to peptidoglycan.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18266854 18266854]<br />
|}<br />
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<br />
==OMV Reception==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Adhesin<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1989<br />
|Smeal T & Karin M.<br />
|Different requirements for formation of Jun:Jun and Jun:Fos complexes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|1994<br />
|Heffernan EJ & Guiney DG.<br />
|Specificity of the complement resistance and cell association phenotypes encoded by the outer membrane protein genes rck from Salmonella typhimurium and ail from Yersinia enterocolitica.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7927803 7927803]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Veiga E & Fernández LA.<br />
|Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12949111 12949111]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 6]]<br />
|2004<br />
|Kesty NC & Kuehn MJ.<br />
|Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14578354 14578354]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | G3P<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1982<br />
|JEF D. BOEKE & PETER MODEL<br />
|A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 8]]<br />
|1999<br />
|Chatellier J & Riechmann L.<br />
|Interdomain interactions within the gene 3 protein of filamentous phage.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 9]]<br />
|1999<br />
|Lubkowski J & Wlodawer A.<br />
|Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 10]]<br />
|2002<br />
|Baek H & Cha S.<br />
|An improved helper phage system for efficient isolation of specific antibody molecules in phage display.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 11]]<br />
|2003<br />
|Karlsson F & Malmborg-Hager AC.<br />
|The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Snare<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 17]]<br />
|2000<br />
|Waters MG & Hughson FM.<br />
|Membrane tethering and fusion in the secretory and endocytic pathways.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Woodbury DJ & Rognlien K.<br />
|The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11067766 11067766]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2002<br />
|Bowen ME,Brunger AT.<br />
|Mutational analysis of synaptobrevin transmembrane domain oligomerization.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12501216 12501216]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Hu C & Rothman JE.<br />
|Fusion of cells by flipped SNAREs.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Weninger K & Brunger AT.<br />
|Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14657376 14657376]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006 <br />
|Giraudo CG & Rothman JE.<br />
|A clamping mechanism involved in SNARE-dependent exocytosis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16794037 16794037]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Low HH & Löwe J.<br />
|A bacterial dynamin-like protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17122778 17122778]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Weninger K & Brunger AT.<br />
|Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18275821 18275821]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Delevoye C & Subtil A.<br />
|SNARE protein mimicry by an intracellular bacterium.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18369472 18369472]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 18]]<br />
|2009<br />
|Giraudo CG & Rothman JE.<br />
|Alternative zippering as an on-off switch for SNARE-mediated fusion.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19164750 19164750]<br />
<br />
|}<br />
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==OMV Signal transduction==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|1984<br />
|Lopilato JE & Beckwith JR.<br />
|D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6327616 6327616]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1995<br />
|Härle C & Braun V.<br />
|Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7729419 7729419]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[1]]]<br />
|1998<br />
|Tomii K & Kanehisa M.<br />
|A comparative analysis of ABC transporters in complete microbial genomes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1999<br />
|De Wulf P & Lin EC.<br />
|The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10542180 10542180]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[6]]]<br />
|2000<br />
|Stock AM & Goudreau PN.<br />
|Two-component signal transduction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Yaron S & Matthews KR.<br />
|Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11010892 11010892]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2004<br />
|Dwyer MA & Hellinga HW.<br />
|Periplasmic binding proteins: a versatile superfamily for protein engineering.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15313245 15313245]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Braun V & Sauter A.<br />
|Gene regulation by transmembrane signaling.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16718597 16718597]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Baker MD & Stock JB<br />
|Signal transduction: networks and integrated circuits in bacterial cognition.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18054766 18054766]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Baker MD & Stock JB.<br />
|Systems biology of bacterial chemotaxis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16529985 16529985]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Ibrahim M & Monnet V.<br />
|Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17921293 17921293]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[9]]]<br />
|2009<br />
|Kyriakidis DA & Tiligada E.<br />
|Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2009<br />
|Tomii & Kanehisa<br />
|comparative analysis of ABC transporter<br />
|[http://genome.cshlp.org/content/8/10/1048.full.html#ref-list-1 pdf-link]<br />
|}<br />
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==Modelling==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Genetic Regulatory Network<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 1]]<br />
|1977<br />
|Gillespie Daniel T.<br />
|Exact Stochastic Simlation of Coupled Chemical Equations<br />
|[http://www.dna.caltech.edu/courses/cs191/paperscs191/gillespie2.pdf Gillespie1]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 3]]<br />
|1997<br />
|J.B. Andersen & S.Molin<br />
|New Stable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria<br />
|[http://aem.asm.org/cgi/reprint/64/6/2240.pdf LVA tag]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 6]]<br />
|1999<br />
|M.Ellowitz & S.Leibler<br />
|A Synthetic oscillatory network of transcriptionnal regulators <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10659856 10659856]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 2]]<br />
|1997<br />
|D.T.Gillespie<br />
|The Chemical Langevin Equation<br />
|[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000113000001000297000001&idtype=cvips&gifs=yes Gillespie2]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 5]]<br />
|2002<br />
|N.Rosenfold & U.Alon<br />
|Negative Autoregulation Speeds The Response TImes of Transcription Network <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12417193 2417193]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2002<br />
|M.B.Ellowitz & P.S.Swain<br />
|Stochastic Gene Expression In A Single Cell<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12183631 12183631]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 7]]<br />
|2003<br />
|S.Mangan & U.Alon<br />
|Structure and function ot the feed-forward Loop Network Motif<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14530388 14530388]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 4]]<br />
|2003<br />
|S.Basu & R.Weiss<br />
|Spatiotemporal control of gene expression with pulse-generating networks<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15096621 15096621]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 1]]<br />
|2005<br />
|S.Hooshangi & R.Weiss<br />
|Ultrasensitivity and noise propagation in a synthetic transcriptional cascade<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15738412 15738412]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 3]]<br />
|2006<br />
|H.Li & L.Petzold<br />
|Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems<br />
|[http://www.cs.ucsb.edu/~cse/Files/ldm0513.pdf Sto.Sim]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 2]]<br />
|2007<br />
|U.Alon<br />
|Network motifs : theory and experimental approaches<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17510665 117510665]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|J.Stricker & J.Hasty<br />
|A Fast Robust and Tunable synthetic gene oscillator<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18971928 18971928]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Vesicle biophysics model<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 6]]<br />
|1977<br />
|Harbich et al<br />
|Optical observation of rotationally symmetric lecithin vesicle shapes<br />
|J. Physique, 38:727–729<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 4]]<br />
|1987<br />
|Ou-Yang & Helfrich<br />
|Instability and deformation of a spherical vesicle by pressure<br />
|Phys. Rev. Lett., 59:2486-2488 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 1]]<br />
|1991<br />
|Lipowsky<br />
|The conformation of membranes<br />
|Nature, 349(6309):475-481<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 5]]<br />
|1995 <br />
|Fattal et al <br />
|The vesicle-micelle transition in mixed lipid-surfactant<br />
|Langmuir, 11:1154-1161 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 3]]<br />
|1998<br />
|Zhou et al<br />
|On the origin of membrane vesicles in gram-negative bacteria<br />
|FEMS microbiology letters, 163(2):223-228 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 8]]<br />
|2005 <br />
|Kuehn & Kesty<br />
|Bacterial outer membrane vesicles and the host pathogen interaction<br />
|Genes & Dev, 19:2645-2655 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 2]]<br />
|2008<br />
|Park & Uehara<br />
|How bacteria consume their own exoskeletons<br />
|Microbiol Mol Biol Rev, 72(2):211-227 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 7]]<br />
|2009<br />
|Deatherage et al <br />
|Biogenesis of bacterial membrane vesicles,<br />
|Mol Microbiol, 72(6):1395-1407<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 9]]<br />
|2009<br />
|Kumaran & Losick<br />
|Negative membrane curvature as a cue for subcellular localization of a bacterial protein.<br />
|PNAS USA, 106(32):13541-13545 <br />
|}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/PapersTeam:Paris/Papers2009-10-22T03:26:28Z<p>Christophe.R: </p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Papers#bottom | Papers]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
== '''OMV Overview''' ==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white; font-weight:bold; "<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px| [X]<br />
|1999<br />
|Terry J. Beveridge<br />
|Structures of gram-negative cell walls and their derived membrane vesicles.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93954 10438737]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Miller SI & Guina T.<br />
|Bacterial vesicle formation as a mechanism of protein transfer to animals.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14531993?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 14531993]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2005<br />
|Kuehn MJ & Kesty NC.<br />
|Bacterial outer membrane vesicles and the host-pathogen interaction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16291643?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16291643]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|McBroom AJ & Kuehn MJ.<br />
|Outer membrane vesicle production by Escherichia coli is independent of membrane instability.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16855227?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16855227]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 1]]<br />
|2007<br />
|McBroom AJ & Kuehn MJ.<br />
|Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17163978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17163978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 2]]<br />
|2009<br />
|Deatherage BL & Cookson BT.<br />
|Biogenesis of bacterial membrane vesicles<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19432795?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 19432795]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2009<br />
|Purnick PE & Weiss R.<br />
|The second wave of synthetic biology: from modules to systems.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19461664?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 19461664]<br />
|}<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
=='''OMV Production'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Mashburn-Warren L & Whiteley M.<br />
|Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18630345?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 18630345]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Addressing_overview4#top|[2]]]<br />
|2001<br />
|Arora A. & Tamm LK.<br />
|Structure of outer membrane protein A transmembrane domain by NMR spectroscopy.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11276254?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 11276254]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|2007<br />
|Brown EA & Hardwidge PR.<br />
|Biochemical characterization of the enterotoxigenic Escherichia coli LeoA protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17975086?ordinalpos=16&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17975086]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2008<br />
|Burgess NK & Fleming KG.<br />
|Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18641391?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 18641391]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Tol/Pal<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|1986<br />
|Robert CHEN & Ulf HENNING.<br />
|Nucleotide sequence of the gene for the peptidoglycan-associated lipoprotein of Escherichia coli K12<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=210680 210680]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[3]]]<br />
|1995<br />
|Lazzaroni & Geli -<br />
|Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179564 179564]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|1999<br />
|Derouiche & Loret<br />
|Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10380085 10380085]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[4]]]<br />
|2001<br />
|Lloubès & RJournet L.<br />
|The Tol-Pal proteins of the Escherichia coli cell envelope: an energized system required for outer membrane integrity?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11501670 11501670]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[X]<br />
|2002<br />
|Dubuisson JF & Lazzaroni JC.<br />
|Mutational analysis of the TolA C-terminal domain of Escherichia coli and genetic evidence for an interaction between TolA and TolB.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12142433 12142433]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[X]<br />
|2003<br />
|Llamas M & ARamos JL.<br />
|Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12896989 12896989]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[5]]]<br />
|2004<br />
|Henry T & Lloubès R.<br />
|Improved methods for producing outer membrane vesicles in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15249060 15249060]<br />
|}<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
==''' OMV Adressing '''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1997<br />
|Kadurugamuwa JL & Beveridge TJ.<br />
|Natural release of virulence factors in membrane vesicles by Pseudomonas aeruginosa and the effect of aminoglycoside antibiotics on their release.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9421308 9421308]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|1998<br />
|Santini CL & Wu LF.<br />
|A novel sec-independent periplasmic protein translocation pathway in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9427745 9427745]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Berks BC & Palmer T.<br />
|The Tat protein export pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10652088 10652088]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2001<br />
|Mishima Y & Murata K.<br />
|Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11731126 11731126]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2001<br />
|Sargent F & Berks BC.<br />
|Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11422364 11422364]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2001<br />
|Yahr TL & Wickner WT.<br />
|Functional reconstitution of bacterial Tat translocation in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11350936 11350936]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2004<br />
|Robinson C & Bolhuis A.<br />
|Tat-dependent protein targeting in prokaryotes and chloroplasts.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15546663 15546663]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Sargent F & Palmer T.<br />
|Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16445746 16445746]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Lee PA & Georgiou G.<br />
|The bacterial twin-arginine translocation pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16756481 16756481]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Maillard J & Sargent F.<br />
|Structural diversity in twin-arginine signal peptide-binding proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17901208 17901208]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Sargent F.<br />
|The twin-arginine transport system: moving folded proteins across membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17956229 17956229]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Ferrandez Y & Condemine G.<br />
|Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2009<br />
|Pradel N & Bonnet R<br />
|Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2009<br />
|de Marco A.<br />
|Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19442264 19442264]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | ClyA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 5]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 1]]<br />
|2008<br />
|Kim JY & DeLisa MP.<br />
|Engineered bacterial outer membrane vesicles with enhanced functionality.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 1]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 2]]<br />
|2009<br />
|Mueller M & Ban N.<br />
|The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[Team:Paris/Addressing_overview4#top|[1]]]<br />
|2002<br />
|Wang Y.<br />
|The function of OmpA in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Dramsi S & Arthur M.<br />
|Covalent attachment of proteins to peptidoglycan.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18266854 18266854]<br />
|}<br />
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==''' OMV Reception'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Adhesin<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1989<br />
|Smeal T & Karin M.<br />
|Different requirements for formation of Jun:Jun and Jun:Fos complexes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|1994<br />
|Heffernan EJ & Guiney DG.<br />
|Specificity of the complement resistance and cell association phenotypes encoded by the outer membrane protein genes rck from Salmonella typhimurium and ail from Yersinia enterocolitica.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7927803 7927803]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Veiga E & Fernández LA.<br />
|Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12949111 12949111]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 6]]<br />
|2004<br />
|Kesty NC & Kuehn MJ.<br />
|Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14578354 14578354]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | G3P<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1982<br />
|JEF D. BOEKE & PETER MODEL<br />
|A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 8]]<br />
|1999<br />
|Chatellier J & Riechmann L.<br />
|Interdomain interactions within the gene 3 protein of filamentous phage.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 9]]<br />
|1999<br />
|Lubkowski J & Wlodawer A.<br />
|Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 10]]<br />
|2002<br />
|Baek H & Cha S.<br />
|An improved helper phage system for efficient isolation of specific antibody molecules in phage display.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 11]]<br />
|2003<br />
|Karlsson F & Malmborg-Hager AC.<br />
|The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Snare<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 17]]<br />
|2000<br />
|Waters MG & Hughson FM.<br />
|Membrane tethering and fusion in the secretory and endocytic pathways.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Woodbury DJ & Rognlien K.<br />
|The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11067766 11067766]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2002<br />
|Bowen ME,Brunger AT.<br />
|Mutational analysis of synaptobrevin transmembrane domain oligomerization.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12501216 12501216]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Hu C & Rothman JE.<br />
|Fusion of cells by flipped SNAREs.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Weninger K & Brunger AT.<br />
|Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14657376 14657376]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006 <br />
|Giraudo CG & Rothman JE.<br />
|A clamping mechanism involved in SNARE-dependent exocytosis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16794037 16794037]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Low HH & Löwe J.<br />
|A bacterial dynamin-like protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17122778 17122778]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Weninger K & Brunger AT.<br />
|Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18275821 18275821]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Delevoye C & Subtil A.<br />
|SNARE protein mimicry by an intracellular bacterium.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18369472 18369472]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 18]]<br />
|2009<br />
|Giraudo CG & Rothman JE.<br />
|Alternative zippering as an on-off switch for SNARE-mediated fusion.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19164750 19164750]<br />
<br />
|}<br />
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<br />
==''' OMV Signal transduction'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|1984<br />
|Lopilato JE & Beckwith JR.<br />
|D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6327616 6327616]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1995<br />
|Härle C & Braun V.<br />
|Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7729419 7729419]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[1]]]<br />
|1998<br />
|Tomii K & Kanehisa M.<br />
|A comparative analysis of ABC transporters in complete microbial genomes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|1999<br />
|De Wulf P & Lin EC.<br />
|The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10542180 10542180]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[6]]]<br />
|2000<br />
|Stock AM & Goudreau PN.<br />
|Two-component signal transduction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Yaron S & Matthews KR.<br />
|Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11010892 11010892]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2004<br />
|Dwyer MA & Hellinga HW.<br />
|Periplasmic binding proteins: a versatile superfamily for protein engineering.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15313245 15313245]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Braun V & Sauter A.<br />
|Gene regulation by transmembrane signaling.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16718597 16718597]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Baker MD & Stock JB<br />
|Signal transduction: networks and integrated circuits in bacterial cognition.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18054766 18054766]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Baker MD & Stock JB.<br />
|Systems biology of bacterial chemotaxis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16529985 16529985]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Ibrahim M & Monnet V.<br />
|Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17921293 17921293]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[9]]]<br />
|2009<br />
|Kyriakidis DA & Tiligada E.<br />
|Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2009<br />
|Tomii & Kanehisa<br />
|comparative analysis of ABC transporter<br />
|[http://genome.cshlp.org/content/8/10/1048.full.html#ref-list-1 pdf-link]<br />
|}<br />
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<br />
=='''Modelling'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Genetic Regulatory Network<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 1]]<br />
|1977<br />
|Gillespie Daniel T.<br />
|Exact Stochastic Simlation of Coupled Chemical Equations<br />
|[http://www.dna.caltech.edu/courses/cs191/paperscs191/gillespie2.pdf Gillespie1]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 3]]<br />
|1997<br />
|J.B. Andersen & S.Molin<br />
|New Stable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria<br />
|[http://aem.asm.org/cgi/reprint/64/6/2240.pdf LVA tag]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 6]]<br />
|1999<br />
|M.Ellowitz & S.Leibler<br />
|A Synthetic oscillatory network of transcriptionnal regulators <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10659856 10659856]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 2]]<br />
|1997<br />
|D.T.Gillespie<br />
|The Chemical Langevin Equation<br />
|[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000113000001000297000001&idtype=cvips&gifs=yes Gillespie2]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 5]]<br />
|2002<br />
|N.Rosenfold & U.Alon<br />
|Negative Autoregulation Speeds The Response TImes of Transcription Network <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12417193 2417193]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2002<br />
|M.B.Ellowitz & P.S.Swain<br />
|Stochastic Gene Expression In A Single Cell<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12183631 12183631]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 7]]<br />
|2003<br />
|S.Mangan & U.Alon<br />
|Structure and function ot the feed-forward Loop Network Motif<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14530388 14530388]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 4]]<br />
|2003<br />
|S.Basu & R.Weiss<br />
|Spatiotemporal control of gene expression with pulse-generating networks<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15096621 15096621]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 1]]<br />
|2005<br />
|S.Hooshangi & R.Weiss<br />
|Ultrasensitivity and noise propagation in a synthetic transcriptional cascade<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15738412 15738412]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 3]]<br />
|2006<br />
|H.Li & L.Petzold<br />
|Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems<br />
|[http://www.cs.ucsb.edu/~cse/Files/ldm0513.pdf Sto.Sim]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 2]]<br />
|2007<br />
|U.Alon<br />
|Network motifs : theory and experimental approaches<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17510665 117510665]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|J.Stricker & J.Hasty<br />
|A Fast Robust and Tunable synthetic gene oscillator<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18971928 18971928]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Vesicle biophysics model<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 6]]<br />
|1977<br />
|Harbich et al<br />
|Optical observation of rotationally symmetric lecithin vesicle shapes<br />
|J. Physique, 38:727–729<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 4]]<br />
|1987<br />
|Ou-Yang & Helfrich<br />
|Instability and deformation of a spherical vesicle by pressure<br />
|Phys. Rev. Lett., 59:2486-2488 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 1]]<br />
|1991<br />
|Lipowsky<br />
|The conformation of membranes<br />
|Nature, 349(6309):475-481<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 5]]<br />
|1995 <br />
|Fattal et al <br />
|The vesicle-micelle transition in mixed lipid-surfactant<br />
|Langmuir, 11:1154-1161 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 3]]<br />
|1998<br />
|Zhou et al<br />
|On the origin of membrane vesicles in gram-negative bacteria<br />
|FEMS microbiology letters, 163(2):223-228 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 8]]<br />
|2005 <br />
|Kuehn & Kesty<br />
|Bacterial outer membrane vesicles and the host pathogen interaction<br />
|Genes & Dev, 19:2645-2655 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 2]]<br />
|2008<br />
|Park & Uehara<br />
|How bacteria consume their own exoskeletons<br />
|Microbiol Mol Biol Rev, 72(2):211-227 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 7]]<br />
|2009<br />
|Deatherage et al <br />
|Biogenesis of bacterial membrane vesicles,<br />
|Mol Microbiol, 72(6):1395-1407<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 9]]<br />
|2009<br />
|Kumaran & Losick<br />
|Negative membrane curvature as a cue for subcellular localization of a bacterial protein.<br />
|PNAS USA, 106(32):13541-13545 <br />
|}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/PapersTeam:Paris/Papers2009-10-22T03:21:16Z<p>Christophe.R: /* OMV Signal transduction */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Papers#bottom | Papers]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
== '''OMV Overview''' ==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white; font-weight:bold; "<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px| []<br />
|1999<br />
|Terry J. Beveridge<br />
|Structures of gram-negative cell walls and their derived membrane vesicles.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93954 10438737]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Miller SI & Guina T.<br />
|Bacterial vesicle formation as a mechanism of protein transfer to animals.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14531993?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 14531993]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2005<br />
|Kuehn MJ & Kesty NC.<br />
|Bacterial outer membrane vesicles and the host-pathogen interaction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16291643?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16291643]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|McBroom AJ & Kuehn MJ.<br />
|Outer membrane vesicle production by Escherichia coli is independent of membrane instability.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16855227?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16855227]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 1]]<br />
|2007<br />
|McBroom AJ & Kuehn MJ.<br />
|Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17163978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17163978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 2]]<br />
|2009<br />
|Deatherage BL & Cookson BT.<br />
|Biogenesis of bacterial membrane vesicles<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19432795?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 19432795]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2009<br />
|Purnick PE & Weiss R.<br />
|The second wave of synthetic biology: from modules to systems.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19461664?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 19461664]<br />
|}<br />
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=='''OMV Production'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Mashburn-Warren L & Whiteley M.<br />
|Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18630345?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 18630345]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Addressing_overview4#top|[2]]]<br />
|2001<br />
|Arora A. & Tamm LK.<br />
|Structure of outer membrane protein A transmembrane domain by NMR spectroscopy.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11276254?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 11276254]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|2007<br />
|Brown EA & Hardwidge PR.<br />
|Biochemical characterization of the enterotoxigenic Escherichia coli LeoA protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17975086?ordinalpos=16&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17975086]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2008<br />
|Burgess NK & Fleming KG.<br />
|Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18641391?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 18641391]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Tol/Pal<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|1986<br />
|Robert CHEN & Ulf HENNING.<br />
|Nucleotide sequence of the gene for the peptidoglycan-associated lipoprotein of Escherichia coli K12<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=210680 210680]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[3]]]<br />
|1995<br />
|Lazzaroni & Geli -<br />
|Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179564 179564]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|1999<br />
|Derouiche & Loret<br />
|Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10380085 10380085]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[4]]]<br />
|2001<br />
|Lloubès & RJournet L.<br />
|The Tol-Pal proteins of the Escherichia coli cell envelope: an energized system required for outer membrane integrity?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11501670 11501670]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|2002<br />
|Dubuisson JF & Lazzaroni JC.<br />
|Mutational analysis of the TolA C-terminal domain of Escherichia coli and genetic evidence for an interaction between TolA and TolB.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12142433 12142433]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2003<br />
|Llamas M & ARamos JL.<br />
|Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12896989 12896989]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[5]]]<br />
|2004<br />
|Henry T & Lloubès R.<br />
|Improved methods for producing outer membrane vesicles in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15249060 15249060]<br />
|}<br />
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==''' OMV Adressing '''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1997<br />
|Kadurugamuwa JL & Beveridge TJ.<br />
|Natural release of virulence factors in membrane vesicles by Pseudomonas aeruginosa and the effect of aminoglycoside antibiotics on their release.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9421308 9421308]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1998<br />
|Santini CL & Wu LF.<br />
|A novel sec-independent periplasmic protein translocation pathway in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9427745 9427745]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Berks BC & Palmer T.<br />
|The Tat protein export pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10652088 10652088]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Mishima Y & Murata K.<br />
|Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11731126 11731126]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Sargent F & Berks BC.<br />
|Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11422364 11422364]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Yahr TL & Wickner WT.<br />
|Functional reconstitution of bacterial Tat translocation in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11350936 11350936]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2004<br />
|Robinson C & Bolhuis A.<br />
|Tat-dependent protein targeting in prokaryotes and chloroplasts.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15546663 15546663]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Sargent F & Palmer T.<br />
|Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16445746 16445746]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Lee PA & Georgiou G.<br />
|The bacterial twin-arginine translocation pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16756481 16756481]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Maillard J & Sargent F.<br />
|Structural diversity in twin-arginine signal peptide-binding proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17901208 17901208]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Sargent F.<br />
|The twin-arginine transport system: moving folded proteins across membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17956229 17956229]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Ferrandez Y & Condemine G.<br />
|Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Pradel N & Bonnet R<br />
|Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|de Marco A.<br />
|Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19442264 19442264]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | ClyA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 5]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 1]]<br />
|2008<br />
|Kim JY & DeLisa MP.<br />
|Engineered bacterial outer membrane vesicles with enhanced functionality.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 1]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 2]]<br />
|2009<br />
|Mueller M & Ban N.<br />
|The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[Team:Paris/Addressing_overview4#top|[1]]]<br />
|2002<br />
|Wang Y.<br />
|The function of OmpA in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Dramsi S & Arthur M.<br />
|Covalent attachment of proteins to peptidoglycan.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18266854 18266854]<br />
|}<br />
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==''' OMV Reception'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Adhesin<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1989<br />
|Smeal T & Karin M.<br />
|Different requirements for formation of Jun:Jun and Jun:Fos complexes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1994<br />
|Heffernan EJ & Guiney DG.<br />
|Specificity of the complement resistance and cell association phenotypes encoded by the outer membrane protein genes rck from Salmonella typhimurium and ail from Yersinia enterocolitica.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7927803 7927803]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Veiga E & Fernández LA.<br />
|Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12949111 12949111]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 6]]<br />
|2004<br />
|Kesty NC & Kuehn MJ.<br />
|Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14578354 14578354]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | G3P<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1982<br />
|JEF D. BOEKE & PETER MODEL<br />
|A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 8]]<br />
|1999<br />
|Chatellier J & Riechmann L.<br />
|Interdomain interactions within the gene 3 protein of filamentous phage.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 9]]<br />
|1999<br />
|Lubkowski J & Wlodawer A.<br />
|Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 10]]<br />
|2002<br />
|Baek H & Cha S.<br />
|An improved helper phage system for efficient isolation of specific antibody molecules in phage display.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 11]]<br />
|2003<br />
|Karlsson F & Malmborg-Hager AC.<br />
|The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Snare<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 17]]<br />
|2000<br />
|Waters MG & Hughson FM.<br />
|Membrane tethering and fusion in the secretory and endocytic pathways.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Woodbury DJ & Rognlien K.<br />
|The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11067766 11067766]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2002<br />
|Bowen ME,Brunger AT.<br />
|Mutational analysis of synaptobrevin transmembrane domain oligomerization.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12501216 12501216]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Hu C & Rothman JE.<br />
|Fusion of cells by flipped SNAREs.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Weninger K & Brunger AT.<br />
|Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14657376 14657376]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006 <br />
|Giraudo CG & Rothman JE.<br />
|A clamping mechanism involved in SNARE-dependent exocytosis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16794037 16794037]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Low HH & Löwe J.<br />
|A bacterial dynamin-like protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17122778 17122778]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Weninger K & Brunger AT.<br />
|Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18275821 18275821]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Delevoye C & Subtil A.<br />
|SNARE protein mimicry by an intracellular bacterium.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18369472 18369472]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 18]]<br />
|2009<br />
|Giraudo CG & Rothman JE.<br />
|Alternative zippering as an on-off switch for SNARE-mediated fusion.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19164750 19164750]<br />
<br />
|}<br />
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==''' OMV Signal transduction'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1984<br />
|Lopilato JE & Beckwith JR.<br />
|D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6327616 6327616]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1995<br />
|Härle C & Braun V.<br />
|Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7729419 7729419]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[1]]]<br />
|1998<br />
|Tomii K & Kanehisa M.<br />
|A comparative analysis of ABC transporters in complete microbial genomes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1999<br />
|De Wulf P & Lin EC.<br />
|The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10542180 10542180]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[6]]]<br />
|2000<br />
|Stock AM & Goudreau PN.<br />
|Two-component signal transduction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Yaron S & Matthews KR.<br />
|Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11010892 11010892]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2004<br />
|Dwyer MA & Hellinga HW.<br />
|Periplasmic binding proteins: a versatile superfamily for protein engineering.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15313245 15313245]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Braun V & Sauter A.<br />
|Gene regulation by transmembrane signaling.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16718597 16718597]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Baker MD & Stock JB<br />
|Signal transduction: networks and integrated circuits in bacterial cognition.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18054766 18054766]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Baker MD & Stock JB.<br />
|Systems biology of bacterial chemotaxis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16529985 16529985]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Ibrahim M & Monnet V.<br />
|Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17921293 17921293]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[Team:Paris/Transduction_overview2_transduction#top|[9]]]<br />
|2009<br />
|Kyriakidis DA & Tiligada E.<br />
|Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Tomii & Kanehisa<br />
|comparative analysis of ABC transporter<br />
|[http://genome.cshlp.org/content/8/10/1048.full.html#ref-list-1 pdf-link]<br />
|}<br />
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=='''Modelling'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Genetic Regulatory Network<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 1]]<br />
|1977<br />
|Gillespie Daniel T.<br />
|Exact Stochastic Simlation of Coupled Chemical Equations<br />
|[http://www.dna.caltech.edu/courses/cs191/paperscs191/gillespie2.pdf Gillespie1]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 3]]<br />
|1997<br />
|J.B. Andersen & S.Molin<br />
|New Stable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria<br />
|[http://aem.asm.org/cgi/reprint/64/6/2240.pdf LVA tag]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 6]]<br />
|1999<br />
|M.Ellowitz & S.Leibler<br />
|A Synthetic oscillatory network of transcriptionnal regulators <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10659856 10659856]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 2]]<br />
|1997<br />
|D.T.Gillespie<br />
|The Chemical Langevin Equation<br />
|[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000113000001000297000001&idtype=cvips&gifs=yes Gillespie2]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 5]]<br />
|2002<br />
|N.Rosenfold & U.Alon<br />
|Negative Autoregulation Speeds The Response TImes of Transcription Network <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12417193 2417193]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|M.B.Ellowitz & P.S.Swain<br />
|Stochastic Gene Expression In A Single Cell<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12183631 12183631]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 7]]<br />
|2003<br />
|S.Mangan & U.Alon<br />
|Structure and function ot the feed-forward Loop Network Motif<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14530388 14530388]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 4]]<br />
|2003<br />
|S.Basu & R.Weiss<br />
|Spatiotemporal control of gene expression with pulse-generating networks<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15096621 15096621]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 1]]<br />
|2005<br />
|S.Hooshangi & R.Weiss<br />
|Ultrasensitivity and noise propagation in a synthetic transcriptional cascade<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15738412 15738412]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 3]]<br />
|2006<br />
|H.Li & L.Petzold<br />
|Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems<br />
|[http://www.cs.ucsb.edu/~cse/Files/ldm0513.pdf Sto.Sim]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 2]]<br />
|2007<br />
|U.Alon<br />
|Network motifs : theory and experimental approaches<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17510665 117510665]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|J.Stricker & J.Hasty<br />
|A Fast Robust and Tunable synthetic gene oscillator<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18971928 18971928]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Vesicle biophysics model<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 6]]<br />
|1977<br />
|Harbich et al<br />
|Optical observation of rotationally symmetric lecithin vesicle shapes<br />
|J. Physique, 38:727–729<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 4]]<br />
|1987<br />
|Ou-Yang & Helfrich<br />
|Instability and deformation of a spherical vesicle by pressure<br />
|Phys. Rev. Lett., 59:2486-2488 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 1]]<br />
|1991<br />
|Lipowsky<br />
|The conformation of membranes<br />
|Nature, 349(6309):475-481<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 5]]<br />
|1995 <br />
|Fattal et al <br />
|The vesicle-micelle transition in mixed lipid-surfactant<br />
|Langmuir, 11:1154-1161 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 3]]<br />
|1998<br />
|Zhou et al<br />
|On the origin of membrane vesicles in gram-negative bacteria<br />
|FEMS microbiology letters, 163(2):223-228 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 8]]<br />
|2005 <br />
|Kuehn & Kesty<br />
|Bacterial outer membrane vesicles and the host pathogen interaction<br />
|Genes & Dev, 19:2645-2655 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 2]]<br />
|2008<br />
|Park & Uehara<br />
|How bacteria consume their own exoskeletons<br />
|Microbiol Mol Biol Rev, 72(2):211-227 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 7]]<br />
|2009<br />
|Deatherage et al <br />
|Biogenesis of bacterial membrane vesicles,<br />
|Mol Microbiol, 72(6):1395-1407<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 9]]<br />
|2009<br />
|Kumaran & Losick<br />
|Negative membrane curvature as a cue for subcellular localization of a bacterial protein.<br />
|PNAS USA, 106(32):13541-13545 <br />
|}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview2_transductionTeam:Paris/Transduction overview2 transduction2009-10-22T03:16:05Z<p>Christophe.R: /* Two-component system */</p>
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<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview2#bottom | Transduction]]<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#bottom"> Transduction</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_construction#bottom"> Construction</a><br />
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<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#ABC_transporters"> ABC transporters</a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#Two-component_system"> Two-component system</a><br />
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In biology, signal transduction refers to any process by which a cell converts one kind of signal or stimulus into another. Most processes of signal transduction involve ordered sequences of biochemical reactions inside the cell, which are carried out by enzymes and sometimes activated by second messengers, resulting in a signal transduction pathway. <br />
<br />
<br />
Such processes are usually rapid, lasting on the order of milliseconds in the case of ion flux, or minutes for the activation of proteic cascades, but some can take hours, and even days (as is the case with gene expression), to complete. <br />
<br />
<br />
We must also refer to the amplification of the signal , in which a relative small stimulus can elicit a large response. It is often du to the increasing numbers of protein ativation<br />
implied in the transduction pathways. <br />
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==ABC transporters==<br />
<br />
[[Image:Tranduction_abc_transporter_b12.png|380px|right| fec operon induction]]<br />
The ABC transporter is a major class of cellular translocation machinery encoded in the largest set of paralogous genes <sup>[[Team:Paris/Transduction_overview2_transduction#References|[1]]]</sup>.<br />
<br />
<br />
ABC (ATP binding cassette) transporters are active transport systems of the cell, which is widespread in archaea, eubacteria, and eukaryotes. They require energy in the form of adenosine triphosphate (ATP) to translocate substrates across cell membranes. These proteins harness the energy of ATP binding and/or hydrolysis to drive conformational changes in the transmembrane domain (TMD) and consequently transports molecules <sup>[[Team:Paris/Transduction_overview2_transduction#References|[2]]]</sup>.<br />
ABC transporters are also known as the periplasmic binding protein-dependent transport system in Gram-negative bacteria and the binding-lipoprotein-dependent transport system in Gram positive bacteria. <br />
The transporter shows a common global organization with three types of molecular components. Typically, it consists of two integral membrane proteins (permeases) each having six transmembrane segments, two peripheral membrane proteins that bind and hydrolyze ATP, and a periplasmic (or lipoprotein) substrate-binding protein. The ATP-binding protein component is the most conserved, the TMD is somewhat less conserved, and the substrate-binding protein component is most divergent in terms of the sequence similarity. The ABC transporters form the largest group of paralogous genes in bacterial and archaeal genomes , and the genes for the three components frequently form an operon. <br />
<br />
<br />
====Uses====<br />
<br />
Bacterial ABC transporters are essential in cell viability, virulence, and pathogenicity <sup>[[Team:Paris/Transduction_overview2_transduction#References|[3]]]</sup> Iron ABC uptake systems, for example, are important effectors of virulence<br />
<sup>[[Team:Paris/Transduction_overview2_transduction#References|[4]]]</sup>.<br />
Prokaryotic ABC transporters utilize the energy of ATP hydrolysis to transport lot of different substrates across cellular membranes. They are divided into 2 functionnal categories :<br />
<br />
- '''importers''' : they mediate the uptake of amino-acids, peptids, sugar ... into the cell, so they allow the transport of protein directly into the cytolpasm to activate the transcription <sup>[[Team:Paris/Transduction_overview2_transduction#References|[5]]]</sup>. <br />
<br />
- '''exporters''' : they transport lipids and some polysaccharides from the cytoplasm to the periplasm.<br />
<br />
====Advantages/drawbacks====<br />
<br />
The import system of these transporters is really interesting and attractive four our project to transmit a "message" from vesicles to target cells.<br />
The main advantage is that the protein of interest is directly translocated in the cytoplasm and if it is a transcription factor it could activated immediatly the response. The communication is simple,fast and efficient.<br />
But this system is not perfect... One major drawback is that ABC transporter system is a nutriment uptake system. So, basically only (very) small molecules are able to pass thought the membranes.<br />
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==Two-component system==<br />
<br />
[[Image:Transduction_overview_tcs.png|350px|right| Tcs system (Atosc)]]<br />
<br />
The Two-Component System (TCS) can be considered as a widely spread class of biosensor knowing that adaptive signal transduction within microbial cells involving a multi-faceted regulated phosphotransfer mechanism that comprises structural rearrangements of sensor histidine kinases upon ligand-binding and phosphorylation-induced conformational changes in response regulators of versatile TCS, arisen early in bacterial evolution <sup>[[Team:Paris/Transduction_overview2_transduction#References|[6]]]</sup>, <sup>[[Team:Paris/Transduction_overview2_transduction#References|[7]]]</sup><br />
<br />
<br />
In most eubacteria, two-component proteins typically constitute 1% of encoded peptides. In pathogenic bacteria they control the expression of important pathogenetic factors, in addition to regulating basic housekeeping functions. The widespread distribution of two-component signal transduction systems in Bacteria and Achaea reflects their biological value as major sensing and response elements to a wide range of environmental insults that are tuned to respond from within milliseconds to hours <sup>[[Team:Paris/Transduction_overview2_transduction#References|[8]]]</sup>. Although TCSs are probably the most eficient means of adaptation to conventional stressful stimuli encountered by bacteria during their lifespan, the plasticity of some of these sophisticated systems may contribute to strain-specific cellular processes and to the acquisition of distinct features and phenotypes, particularly in pathogens <sup>[[Team:Paris/Transduction_overview2_transduction#References|[9]]]</sup>. <br />
<br />
<br />
To put the structure in a nutshell: A typical TCS consists of a transmembrane dimeric sensor histidine kinase (HK) and a cytoplasmic cognate response regulator (RR). In gram negative bacteria there is often a Periplasmic Binding Protein which optimize the detection of the molecule localized in the periplasm by a high affinity for the HK after binding the specific molecule. The following scheme shows a typical ABC mechanism : <br />
<br />
<br />
====Uses====<br />
<br />
Two-component systems serve as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions <sup>[[Team:Paris/Transduction_overview2_transduction#References|[6]]]</sup>.<br />
<br />
<br />
By transferring a packet of molecule synthesize by the donor but not present in the medium, <br />
the arrival could activate the transcription of gene of interest. This will allow us to check for the "bacterial communication"<br />
<br />
====Advantages/drawbacks====<br />
<br />
Most gene regulation proteins that were known were single proteins, often homodimers or homotetramers, which bound to two ligands, a metabolic intermediate or a cis-acting gene regulation element. The functional state of the regulatory protein was thus modified by binding to the metabolic intermediate. The consequence of ligand binding, an altered state of the regulatory protein, was directed to the appropriate gene(s) by the protein's DNA binding activity. <br />
<br />
<br />
The main advantage of TCS is that the mechanism is dedicated to the transcription of gene under a specific promoter. Four our project, the difficulty is to find an easily exportable and detectable signal. <br />
In contrats, most of the biosensor are generally sensible to high diffusible molecule for which the vesicles transport is useless, so using vesicules to transmit a message doesn't seems the best way to explore.<br />
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====References====<br />
<ol class="references"><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Kentaro Tomii and Minoru Kanehisa, A Comparative Analysis of ABC Transporters in Complete Microbial Genomes,Genome Res. 1998 Oct;8(10):1048-59. [http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Hollenstein, K.; R.J. Dawson; K.P. Locher. 2007. Structure and mechanism of ABC transporter proteins. Curr. Opin. Struct. Biol. 17, 412-418. [http://www.ncbi.nlm.nih.gov/pubmed/17723295 17723295] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Davidson, A.L.; E. Dassa; C. Orelle; and J. Chen. 2008. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72(2), 317-364.[http://www.ncbi.nlm.nih.gov/pubmed/18535149 18535149] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Henderson, D.P. and S.M. Payne. 1994. Vibrio cholerae iron transport system: roles of heme and siderophore iron transport in virulence and identification of a gene associated with multiple iron transport systems. Infect. Immun. 62, 5120-5125. [http://www.ncbi.nlm.nih.gov/pubmed/7927795 7927795] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]<br />
Davidson, A.L.; E. Dassa; C. Orelle; and J. Chen. 2008. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72(2), 317-364.[http://www.ncbi.nlm.nih.gov/pubmed/18535149 18535149]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Stock AM, Robinson VL, Goudreau PN. Two-component signal transduction.2000, Annu. Rev. Biochem. 69: 183–215.[http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Mascher T, Helmann JD, Unden G. Stimulus perception in bacterial signal-transducing histidine kinases. 2006. Microbiol. Mol. Biol. Rev. 70 (4): 910–38.[http://www.ncbi.nlm.nih.gov/pubmed/17158704 17158704] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]<br />
Attwood PV, Piggott MJ, Zu XL, Besant PG. Focus on phosphohistidine, 2007, Amino Acids 32 (1): 145–56. [http://www.ncbi.nlm.nih.gov/pubmed/17103118 17103118] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Kyriakidis DA, Tiligada E. Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm, 2009, Amino Acids.37(3):443-58. [http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978] </li><br />
</ol></div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview2_transductionTeam:Paris/Transduction overview2 transduction2009-10-22T03:15:46Z<p>Christophe.R: /* References */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview2#bottom | Transduction]]<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#bottom"> Transduction</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_construction#bottom"> Construction</a><br />
</center><br />
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<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#ABC_transporters"> ABC transporters</a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#Two-component_system"> Two-component system</a><br />
</center><br />
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<br />
In biology, signal transduction refers to any process by which a cell converts one kind of signal or stimulus into another. Most processes of signal transduction involve ordered sequences of biochemical reactions inside the cell, which are carried out by enzymes and sometimes activated by second messengers, resulting in a signal transduction pathway. <br />
<br />
<br />
Such processes are usually rapid, lasting on the order of milliseconds in the case of ion flux, or minutes for the activation of proteic cascades, but some can take hours, and even days (as is the case with gene expression), to complete. <br />
<br />
<br />
We must also refer to the amplification of the signal , in which a relative small stimulus can elicit a large response. It is often du to the increasing numbers of protein ativation<br />
implied in the transduction pathways. <br />
<br />
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<br />
==ABC transporters==<br />
<br />
[[Image:Tranduction_abc_transporter_b12.png|380px|right| fec operon induction]]<br />
The ABC transporter is a major class of cellular translocation machinery encoded in the largest set of paralogous genes <sup>[[Team:Paris/Transduction_overview2_transduction#References|[1]]]</sup>.<br />
<br />
<br />
ABC (ATP binding cassette) transporters are active transport systems of the cell, which is widespread in archaea, eubacteria, and eukaryotes. They require energy in the form of adenosine triphosphate (ATP) to translocate substrates across cell membranes. These proteins harness the energy of ATP binding and/or hydrolysis to drive conformational changes in the transmembrane domain (TMD) and consequently transports molecules <sup>[[Team:Paris/Transduction_overview2_transduction#References|[2]]]</sup>.<br />
ABC transporters are also known as the periplasmic binding protein-dependent transport system in Gram-negative bacteria and the binding-lipoprotein-dependent transport system in Gram positive bacteria. <br />
The transporter shows a common global organization with three types of molecular components. Typically, it consists of two integral membrane proteins (permeases) each having six transmembrane segments, two peripheral membrane proteins that bind and hydrolyze ATP, and a periplasmic (or lipoprotein) substrate-binding protein. The ATP-binding protein component is the most conserved, the TMD is somewhat less conserved, and the substrate-binding protein component is most divergent in terms of the sequence similarity. The ABC transporters form the largest group of paralogous genes in bacterial and archaeal genomes , and the genes for the three components frequently form an operon. <br />
<br />
<br />
====Uses====<br />
<br />
Bacterial ABC transporters are essential in cell viability, virulence, and pathogenicity <sup>[[Team:Paris/Transduction_overview2_transduction#References|[3]]]</sup> Iron ABC uptake systems, for example, are important effectors of virulence<br />
<sup>[[Team:Paris/Transduction_overview2_transduction#References|[4]]]</sup>.<br />
Prokaryotic ABC transporters utilize the energy of ATP hydrolysis to transport lot of different substrates across cellular membranes. They are divided into 2 functionnal categories :<br />
<br />
- '''importers''' : they mediate the uptake of amino-acids, peptids, sugar ... into the cell, so they allow the transport of protein directly into the cytolpasm to activate the transcription <sup>[[Team:Paris/Transduction_overview2_transduction#References|[5]]]</sup>. <br />
<br />
- '''exporters''' : they transport lipids and some polysaccharides from the cytoplasm to the periplasm.<br />
<br />
====Advantages/drawbacks====<br />
<br />
The import system of these transporters is really interesting and attractive four our project to transmit a "message" from vesicles to target cells.<br />
The main advantage is that the protein of interest is directly translocated in the cytoplasm and if it is a transcription factor it could activated immediatly the response. The communication is simple,fast and efficient.<br />
But this system is not perfect... One major drawback is that ABC transporter system is a nutriment uptake system. So, basically only (very) small molecules are able to pass thought the membranes.<br />
<br />
<br />
<br />
<br />
<br />
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==Two-component system==<br />
<br />
[[Image:Transduction_overview_tcs.png|350px|right| Tcs system (Atosc)]]<br />
<br />
The Two-Component System (TCS) can be considered as a widely spread class of biosensor knowing that adaptive signal transduction within microbial cells involving a multi-faceted regulated phosphotransfer mechanism that comprises structural rearrangements of sensor histidine kinases upon ligand-binding and phosphorylation-induced conformational changes in response regulators of versatile TCS, arisen early in bacterial evolution <sup>[[Team:Paris/Transduction_overview2_transduction#References|[6]]]</sup>, <sup>[[Team:Paris/Transduction_overview2_transduction#References|[7]]]</sup><br />
<br />
<br />
In most eubacteria, two-component proteins typically constitute 1% of encoded peptides. In pathogenic bacteria they control the expression of important pathogenetic factors, in addition to regulating basic housekeeping functions. The widespread distribution of two-component signal transduction systems in Bacteria and Achaea reflects their biological value as major sensing and response elements to a wide range of environmental insults that are tuned to respond from within milliseconds to hours <sup>[[Team:Paris/Transduction_overview2_transduction#References|[8]]]</sup>. Although TCSs are probably the most eficient means of adaptation to conventional stressful stimuli encountered by bacteria during their lifespan, the plasticity of some of these sophisticated systems may contribute to strain-specific cellular processes and to the acquisition of distinct features and phenotypes, particularly in pathogens <sup>[[Team:Paris/Transduction_overview2_transduction#References|[9]]]</sup>. <br />
<br />
<br />
To put the structure in a nutshell: A typical TCS consists of a transmembrane dimeric sensor histidine kinase (HK) and a cytoplasmic cognate response regulator (RR). In gram negative bacteria there is often a Periplasmic Binding Protein which optimize the detection of the molecule localized in the periplasm by a high affinity for the HK after binding the specific molecule. The following scheme shows a typical ABC mechanism : <br />
<br />
<br />
====Uses====<br />
<br />
Two-component systems serve as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions <sup>[[Team:Paris/Transduction_overview2_transduction#References|[6]]]</sup>.<br />
<br />
<br />
By transferring a packet of molecule synthesize by the donor but not present in the medium, <br />
the arrival could activate the transcription of gene of interest. This will allow us to check for the "bacterial communication"<br />
<br />
====Advantages/drawbacks====<br />
<br />
Most gene regulation proteins that were known were single proteins, often homodimers or homotetramers, which bound to two ligands, a metabolic intermediate or a cis-acting gene regulation element. The functional state of the regulatory protein was thus modified by binding to the metabolic intermediate. The consequence of ligand binding, an altered state of the regulatory protein, was directed to the appropriate gene(s) by the protein's DNA binding activity. <br />
<br />
<br />
The main advantage of TCS is that the mechanism is dedicated to the transcription of gene under a specific promoter. Four our project, the difficulty is to find an easily exportable and detectable signal. <br />
In contrats, most of the biosensor are generally sensible to high diffusible molecule for which the vesicles transport is useless, so using vesicules to transmit a message doesn't seems the best way to explore.<br />
<br />
<br />
{{Template:Paris2009_guided|Transduction_overview2#top.23top|Transduction_overview2_strategy#bottom}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview2_transductionTeam:Paris/Transduction overview2 transduction2009-10-22T03:15:19Z<p>Christophe.R: /* Two-component system */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview2#bottom | Transduction]]<br />
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==Transduction==<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#bottom"> Transduction</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
<div id="left-side2"></div><br />
<div id="middle-side2"><center><br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#ABC_transporters"> ABC transporters</a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#Two-component_system"> Two-component system</a><br />
</center><br />
</div><br />
<div id="right-side2"></div><br />
</html><br />
<br />
In biology, signal transduction refers to any process by which a cell converts one kind of signal or stimulus into another. Most processes of signal transduction involve ordered sequences of biochemical reactions inside the cell, which are carried out by enzymes and sometimes activated by second messengers, resulting in a signal transduction pathway. <br />
<br />
<br />
Such processes are usually rapid, lasting on the order of milliseconds in the case of ion flux, or minutes for the activation of proteic cascades, but some can take hours, and even days (as is the case with gene expression), to complete. <br />
<br />
<br />
We must also refer to the amplification of the signal , in which a relative small stimulus can elicit a large response. It is often du to the increasing numbers of protein ativation<br />
implied in the transduction pathways. <br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<span/ id="1"><br />
<br />
==ABC transporters==<br />
<br />
[[Image:Tranduction_abc_transporter_b12.png|380px|right| fec operon induction]]<br />
The ABC transporter is a major class of cellular translocation machinery encoded in the largest set of paralogous genes <sup>[[Team:Paris/Transduction_overview2_transduction#References|[1]]]</sup>.<br />
<br />
<br />
ABC (ATP binding cassette) transporters are active transport systems of the cell, which is widespread in archaea, eubacteria, and eukaryotes. They require energy in the form of adenosine triphosphate (ATP) to translocate substrates across cell membranes. These proteins harness the energy of ATP binding and/or hydrolysis to drive conformational changes in the transmembrane domain (TMD) and consequently transports molecules <sup>[[Team:Paris/Transduction_overview2_transduction#References|[2]]]</sup>.<br />
ABC transporters are also known as the periplasmic binding protein-dependent transport system in Gram-negative bacteria and the binding-lipoprotein-dependent transport system in Gram positive bacteria. <br />
The transporter shows a common global organization with three types of molecular components. Typically, it consists of two integral membrane proteins (permeases) each having six transmembrane segments, two peripheral membrane proteins that bind and hydrolyze ATP, and a periplasmic (or lipoprotein) substrate-binding protein. The ATP-binding protein component is the most conserved, the TMD is somewhat less conserved, and the substrate-binding protein component is most divergent in terms of the sequence similarity. The ABC transporters form the largest group of paralogous genes in bacterial and archaeal genomes , and the genes for the three components frequently form an operon. <br />
<br />
<br />
====Uses====<br />
<br />
Bacterial ABC transporters are essential in cell viability, virulence, and pathogenicity <sup>[[Team:Paris/Transduction_overview2_transduction#References|[3]]]</sup> Iron ABC uptake systems, for example, are important effectors of virulence<br />
<sup>[[Team:Paris/Transduction_overview2_transduction#References|[4]]]</sup>.<br />
Prokaryotic ABC transporters utilize the energy of ATP hydrolysis to transport lot of different substrates across cellular membranes. They are divided into 2 functionnal categories :<br />
<br />
- '''importers''' : they mediate the uptake of amino-acids, peptids, sugar ... into the cell, so they allow the transport of protein directly into the cytolpasm to activate the transcription <sup>[[Team:Paris/Transduction_overview2_transduction#References|[5]]]</sup>. <br />
<br />
- '''exporters''' : they transport lipids and some polysaccharides from the cytoplasm to the periplasm.<br />
<br />
====Advantages/drawbacks====<br />
<br />
The import system of these transporters is really interesting and attractive four our project to transmit a "message" from vesicles to target cells.<br />
The main advantage is that the protein of interest is directly translocated in the cytoplasm and if it is a transcription factor it could activated immediatly the response. The communication is simple,fast and efficient.<br />
But this system is not perfect... One major drawback is that ABC transporter system is a nutriment uptake system. So, basically only (very) small molecules are able to pass thought the membranes.<br />
<br />
<br />
<br />
<br />
<br />
====References====<br />
<ol class="references"><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Kentaro Tomii and Minoru Kanehisa, A Comparative Analysis of ABC Transporters in Complete Microbial Genomes,Genome Res. 1998 Oct;8(10):1048-59. [http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Hollenstein, K.; R.J. Dawson; K.P. Locher. 2007. Structure and mechanism of ABC transporter proteins. Curr. Opin. Struct. Biol. 17, 412-418. [http://www.ncbi.nlm.nih.gov/pubmed/17723295 17723295] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Davidson, A.L.; E. Dassa; C. Orelle; and J. Chen. 2008. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72(2), 317-364.[http://www.ncbi.nlm.nih.gov/pubmed/18535149 18535149] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Henderson, D.P. and S.M. Payne. 1994. Vibrio cholerae iron transport system: roles of heme and siderophore iron transport in virulence and identification of a gene associated with multiple iron transport systems. Infect. Immun. 62, 5120-5125. [http://www.ncbi.nlm.nih.gov/pubmed/7927795 7927795] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]<br />
Davidson, A.L.; E. Dassa; C. Orelle; and J. Chen. 2008. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72(2), 317-364.[http://www.ncbi.nlm.nih.gov/pubmed/18535149 18535149]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Stock AM, Robinson VL, Goudreau PN. Two-component signal transduction.2000, Annu. Rev. Biochem. 69: 183–215.[http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Mascher T, Helmann JD, Unden G. Stimulus perception in bacterial signal-transducing histidine kinases. 2006. Microbiol. Mol. Biol. Rev. 70 (4): 910–38.[http://www.ncbi.nlm.nih.gov/pubmed/17158704 17158704] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]<br />
Attwood PV, Piggott MJ, Zu XL, Besant PG. Focus on phosphohistidine, 2007, Amino Acids 32 (1): 145–56. [http://www.ncbi.nlm.nih.gov/pubmed/17103118 17103118] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Kyriakidis DA, Tiligada E. Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm, 2009, Amino Acids.37(3):443-58. [http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978] </li><br />
</ol><br />
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<br />
==Two-component system==<br />
<br />
[[Image:Transduction_overview_tcs.png|350px|right| Tcs system (Atosc)]]<br />
<br />
The Two-Component System (TCS) can be considered as a widely spread class of biosensor knowing that adaptive signal transduction within microbial cells involving a multi-faceted regulated phosphotransfer mechanism that comprises structural rearrangements of sensor histidine kinases upon ligand-binding and phosphorylation-induced conformational changes in response regulators of versatile TCS, arisen early in bacterial evolution <sup>[[Team:Paris/Transduction_overview2_transduction#References|[6]]]</sup>, <sup>[[Team:Paris/Transduction_overview2_transduction#References|[7]]]</sup><br />
<br />
<br />
In most eubacteria, two-component proteins typically constitute 1% of encoded peptides. In pathogenic bacteria they control the expression of important pathogenetic factors, in addition to regulating basic housekeeping functions. The widespread distribution of two-component signal transduction systems in Bacteria and Achaea reflects their biological value as major sensing and response elements to a wide range of environmental insults that are tuned to respond from within milliseconds to hours <sup>[[Team:Paris/Transduction_overview2_transduction#References|[8]]]</sup>. Although TCSs are probably the most eficient means of adaptation to conventional stressful stimuli encountered by bacteria during their lifespan, the plasticity of some of these sophisticated systems may contribute to strain-specific cellular processes and to the acquisition of distinct features and phenotypes, particularly in pathogens <sup>[[Team:Paris/Transduction_overview2_transduction#References|[9]]]</sup>. <br />
<br />
<br />
To put the structure in a nutshell: A typical TCS consists of a transmembrane dimeric sensor histidine kinase (HK) and a cytoplasmic cognate response regulator (RR). In gram negative bacteria there is often a Periplasmic Binding Protein which optimize the detection of the molecule localized in the periplasm by a high affinity for the HK after binding the specific molecule. The following scheme shows a typical ABC mechanism : <br />
<br />
<br />
====Uses====<br />
<br />
Two-component systems serve as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions <sup>[[Team:Paris/Transduction_overview2_transduction#References|[6]]]</sup>.<br />
<br />
<br />
By transferring a packet of molecule synthesize by the donor but not present in the medium, <br />
the arrival could activate the transcription of gene of interest. This will allow us to check for the "bacterial communication"<br />
<br />
====Advantages/drawbacks====<br />
<br />
Most gene regulation proteins that were known were single proteins, often homodimers or homotetramers, which bound to two ligands, a metabolic intermediate or a cis-acting gene regulation element. The functional state of the regulatory protein was thus modified by binding to the metabolic intermediate. The consequence of ligand binding, an altered state of the regulatory protein, was directed to the appropriate gene(s) by the protein's DNA binding activity. <br />
<br />
<br />
The main advantage of TCS is that the mechanism is dedicated to the transcription of gene under a specific promoter. Four our project, the difficulty is to find an easily exportable and detectable signal. <br />
In contrats, most of the biosensor are generally sensible to high diffusible molecule for which the vesicles transport is useless, so using vesicules to transmit a message doesn't seems the best way to explore.<br />
<br />
<br />
{{Template:Paris2009_guided|Transduction_overview2#top.23top|Transduction_overview2_strategy#bottom}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview2_transductionTeam:Paris/Transduction overview2 transduction2009-10-22T03:14:12Z<p>Christophe.R: /* References */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview2#bottom | Transduction]]<br />
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==Transduction==<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#bottom"> Transduction</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
<div id="left-side2"></div><br />
<div id="middle-side2"><center><br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#ABC_transporters"> ABC transporters</a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#Two-component_system"> Two-component system</a><br />
</center><br />
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<br />
In biology, signal transduction refers to any process by which a cell converts one kind of signal or stimulus into another. Most processes of signal transduction involve ordered sequences of biochemical reactions inside the cell, which are carried out by enzymes and sometimes activated by second messengers, resulting in a signal transduction pathway. <br />
<br />
<br />
Such processes are usually rapid, lasting on the order of milliseconds in the case of ion flux, or minutes for the activation of proteic cascades, but some can take hours, and even days (as is the case with gene expression), to complete. <br />
<br />
<br />
We must also refer to the amplification of the signal , in which a relative small stimulus can elicit a large response. It is often du to the increasing numbers of protein ativation<br />
implied in the transduction pathways. <br />
<br />
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<br />
==ABC transporters==<br />
<br />
[[Image:Tranduction_abc_transporter_b12.png|380px|right| fec operon induction]]<br />
The ABC transporter is a major class of cellular translocation machinery encoded in the largest set of paralogous genes <sup>[[Team:Paris/Transduction_overview2_transduction#References|[1]]]</sup>.<br />
<br />
<br />
ABC (ATP binding cassette) transporters are active transport systems of the cell, which is widespread in archaea, eubacteria, and eukaryotes. They require energy in the form of adenosine triphosphate (ATP) to translocate substrates across cell membranes. These proteins harness the energy of ATP binding and/or hydrolysis to drive conformational changes in the transmembrane domain (TMD) and consequently transports molecules <sup>[[Team:Paris/Transduction_overview2_transduction#References|[2]]]</sup>.<br />
ABC transporters are also known as the periplasmic binding protein-dependent transport system in Gram-negative bacteria and the binding-lipoprotein-dependent transport system in Gram positive bacteria. <br />
The transporter shows a common global organization with three types of molecular components. Typically, it consists of two integral membrane proteins (permeases) each having six transmembrane segments, two peripheral membrane proteins that bind and hydrolyze ATP, and a periplasmic (or lipoprotein) substrate-binding protein. The ATP-binding protein component is the most conserved, the TMD is somewhat less conserved, and the substrate-binding protein component is most divergent in terms of the sequence similarity. The ABC transporters form the largest group of paralogous genes in bacterial and archaeal genomes , and the genes for the three components frequently form an operon. <br />
<br />
<br />
====Uses====<br />
<br />
Bacterial ABC transporters are essential in cell viability, virulence, and pathogenicity <sup>[[Team:Paris/Transduction_overview2_transduction#References|[3]]]</sup> Iron ABC uptake systems, for example, are important effectors of virulence<br />
<sup>[[Team:Paris/Transduction_overview2_transduction#References|[4]]]</sup>.<br />
Prokaryotic ABC transporters utilize the energy of ATP hydrolysis to transport lot of different substrates across cellular membranes. They are divided into 2 functionnal categories :<br />
<br />
- '''importers''' : they mediate the uptake of amino-acids, peptids, sugar ... into the cell, so they allow the transport of protein directly into the cytolpasm to activate the transcription <sup>[[Team:Paris/Transduction_overview2_transduction#References|[5]]]</sup>. <br />
<br />
- '''exporters''' : they transport lipids and some polysaccharides from the cytoplasm to the periplasm.<br />
<br />
====Advantages/drawbacks====<br />
<br />
The import system of these transporters is really interesting and attractive four our project to transmit a "message" from vesicles to target cells.<br />
The main advantage is that the protein of interest is directly translocated in the cytoplasm and if it is a transcription factor it could activated immediatly the response. The communication is simple,fast and efficient.<br />
But this system is not perfect... One major drawback is that ABC transporter system is a nutriment uptake system. So, basically only (very) small molecules are able to pass thought the membranes.<br />
<br />
<br />
<br />
<br />
<br />
====References====<br />
<ol class="references"><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Kentaro Tomii and Minoru Kanehisa, A Comparative Analysis of ABC Transporters in Complete Microbial Genomes,Genome Res. 1998 Oct;8(10):1048-59. [http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Hollenstein, K.; R.J. Dawson; K.P. Locher. 2007. Structure and mechanism of ABC transporter proteins. Curr. Opin. Struct. Biol. 17, 412-418. [http://www.ncbi.nlm.nih.gov/pubmed/17723295 17723295] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Davidson, A.L.; E. Dassa; C. Orelle; and J. Chen. 2008. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72(2), 317-364.[http://www.ncbi.nlm.nih.gov/pubmed/18535149 18535149] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Henderson, D.P. and S.M. Payne. 1994. Vibrio cholerae iron transport system: roles of heme and siderophore iron transport in virulence and identification of a gene associated with multiple iron transport systems. Infect. Immun. 62, 5120-5125. [http://www.ncbi.nlm.nih.gov/pubmed/7927795 7927795] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]<br />
Davidson, A.L.; E. Dassa; C. Orelle; and J. Chen. 2008. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72(2), 317-364.[http://www.ncbi.nlm.nih.gov/pubmed/18535149 18535149]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Stock AM, Robinson VL, Goudreau PN. Two-component signal transduction.2000, Annu. Rev. Biochem. 69: 183–215.[http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Mascher T, Helmann JD, Unden G. Stimulus perception in bacterial signal-transducing histidine kinases. 2006. Microbiol. Mol. Biol. Rev. 70 (4): 910–38.[http://www.ncbi.nlm.nih.gov/pubmed/17158704 17158704] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]<br />
Attwood PV, Piggott MJ, Zu XL, Besant PG. Focus on phosphohistidine, 2007, Amino Acids 32 (1): 145–56. [http://www.ncbi.nlm.nih.gov/pubmed/17103118 17103118] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Kyriakidis DA, Tiligada E. Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm, 2009, Amino Acids.37(3):443-58. [http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978] </li><br />
</ol><br />
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==Two-component system==<br />
<br />
[[Image:Transduction_overview_tcs.png|350px|right| Tcs system (Atosc)]]<br />
<br />
The Two-Component System (TCS) can be considered as a widely spread class of biosensor knowing that adaptive signal transduction within microbial cells involving a multi-faceted regulated phosphotransfer mechanism that comprises structural rearrangements of sensor histidine kinases upon ligand-binding and phosphorylation-induced conformational changes in response regulators of versatile TCS, arisen early in bacterial evolution [http://www.ncbi.nlm.nih.gov/pubmed/10966457[1]], [http://www.ncbi.nlm.nih.gov/pubmed/17158704[2]]<br />
<br />
<br />
In most eubacteria, two-component proteins typically constitute 1% of encoded peptides. In pathogenic bacteria they control the expression of important pathogenetic factors, in addition to regulating basic housekeeping functions. The widespread distribution of two-component signal transduction systems in Bacteria and Achaea reflects their biological value as major sensing and response elements to a wide range of environmental insults that are tuned to respond from within milliseconds to hours [http://www.ncbi.nlm.nih.gov/pubmed/17103118[3]. Although TCSs are probably the most eficient means of adaptation to conventional stressful stimuli encountered by bacteria during their lifespan, the plasticity of some of these sophisticated systems may contribute to strain-specific cellular processes and to the acquisition of distinct features and phenotypes, particularly in pathogens [http://www.ncbi.nlm.nih.gov/pubmed/19198978[4]]. <br />
<br />
<br />
To put the structure in a nutshell: A typical TCS consists of a transmembrane dimeric sensor histidine kinase (HK) and a cytoplasmic cognate response regulator (RR). In gram negative bacteria there is often a Periplasmic Binding Protein which optimize the detection of the molecule localized in the periplasm by a high affinity for the HK after binding the specific molecule. The following scheme shows a typical ABC mechanism : <br />
<br />
<br />
====Uses====<br />
<br />
Two-component systems serve as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions [http://www.ncbi.nlm.nih.gov/pubmed/10966457[1]].<br />
<br />
<br />
By transferring a packet of molecule synthesize by the donor but not present in the medium, <br />
the arrival could activate the transcription of gene of interest. This will allow us to check for the "bacterial communication"<br />
<br />
====Advantages/drawbacks====<br />
<br />
Most gene regulation proteins that were known were single proteins, often homodimers or homotetramers, which bound to two ligands, a metabolic intermediate or a cis-acting gene regulation element. The functional state of the regulatory protein was thus modified by binding to the metabolic intermediate. The consequence of ligand binding, an altered state of the regulatory protein, was directed to the appropriate gene(s) by the protein's DNA binding activity. <br />
<br />
<br />
The main advantage of TCS is that the mechanism is dedicated to the transcription of gene under a specific promoter. Four our project, the difficulty is to find an easily exportable and detectable signal. <br />
In contrats, most of the biosensor are generally sensible to high diffusible molecule for which the vesicles transport is useless, so using vesicules to transmit a message doesn't seems the best way to explore.<br />
<br />
<br />
{{Template:Paris2009_guided|Transduction_overview2#top.23top|Transduction_overview2_strategy#bottom}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview2_transductionTeam:Paris/Transduction overview2 transduction2009-10-22T03:10:12Z<p>Christophe.R: /* Bibliography : */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview2#bottom | Transduction]]<br />
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==Transduction==<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#bottom"> Transduction</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
<div id="left-side2"></div><br />
<div id="middle-side2"><center><br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#ABC_transporters"> ABC transporters</a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#Two-component_system"> Two-component system</a><br />
</center><br />
</div><br />
<div id="right-side2"></div><br />
</html><br />
<br />
In biology, signal transduction refers to any process by which a cell converts one kind of signal or stimulus into another. Most processes of signal transduction involve ordered sequences of biochemical reactions inside the cell, which are carried out by enzymes and sometimes activated by second messengers, resulting in a signal transduction pathway. <br />
<br />
<br />
Such processes are usually rapid, lasting on the order of milliseconds in the case of ion flux, or minutes for the activation of proteic cascades, but some can take hours, and even days (as is the case with gene expression), to complete. <br />
<br />
<br />
We must also refer to the amplification of the signal , in which a relative small stimulus can elicit a large response. It is often du to the increasing numbers of protein ativation<br />
implied in the transduction pathways. <br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
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<span/ id="1"><br />
<br />
==ABC transporters==<br />
<br />
[[Image:Tranduction_abc_transporter_b12.png|380px|right| fec operon induction]]<br />
The ABC transporter is a major class of cellular translocation machinery encoded in the largest set of paralogous genes <sup>[[Team:Paris/Transduction_overview2_transduction#References|[1]]]</sup>.<br />
<br />
<br />
ABC (ATP binding cassette) transporters are active transport systems of the cell, which is widespread in archaea, eubacteria, and eukaryotes. They require energy in the form of adenosine triphosphate (ATP) to translocate substrates across cell membranes. These proteins harness the energy of ATP binding and/or hydrolysis to drive conformational changes in the transmembrane domain (TMD) and consequently transports molecules <sup>[[Team:Paris/Transduction_overview2_transduction#References|[2]]]</sup>.<br />
ABC transporters are also known as the periplasmic binding protein-dependent transport system in Gram-negative bacteria and the binding-lipoprotein-dependent transport system in Gram positive bacteria. <br />
The transporter shows a common global organization with three types of molecular components. Typically, it consists of two integral membrane proteins (permeases) each having six transmembrane segments, two peripheral membrane proteins that bind and hydrolyze ATP, and a periplasmic (or lipoprotein) substrate-binding protein. The ATP-binding protein component is the most conserved, the TMD is somewhat less conserved, and the substrate-binding protein component is most divergent in terms of the sequence similarity. The ABC transporters form the largest group of paralogous genes in bacterial and archaeal genomes , and the genes for the three components frequently form an operon. <br />
<br />
<br />
====Uses====<br />
<br />
Bacterial ABC transporters are essential in cell viability, virulence, and pathogenicity <sup>[[Team:Paris/Transduction_overview2_transduction#References|[3]]]</sup> Iron ABC uptake systems, for example, are important effectors of virulence<br />
<sup>[[Team:Paris/Transduction_overview2_transduction#References|[4]]]</sup>.<br />
Prokaryotic ABC transporters utilize the energy of ATP hydrolysis to transport lot of different substrates across cellular membranes. They are divided into 2 functionnal categories :<br />
<br />
- '''importers''' : they mediate the uptake of amino-acids, peptids, sugar ... into the cell, so they allow the transport of protein directly into the cytolpasm to activate the transcription <sup>[[Team:Paris/Transduction_overview2_transduction#References|[5]]]</sup>. <br />
<br />
- '''exporters''' : they transport lipids and some polysaccharides from the cytoplasm to the periplasm.<br />
<br />
====Advantages/drawbacks====<br />
<br />
The import system of these transporters is really interesting and attractive four our project to transmit a "message" from vesicles to target cells.<br />
The main advantage is that the protein of interest is directly translocated in the cytoplasm and if it is a transcription factor it could activated immediatly the response. The communication is simple,fast and efficient.<br />
But this system is not perfect... One major drawback is that ABC transporter system is a nutriment uptake system. So, basically only (very) small molecules are able to pass thought the membranes.<br />
<br />
<br />
<br />
<br />
<br />
====References====<br />
<ol class="references"><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Kentaro Tomii and Minoru Kanehisa, A Comparative Analysis of ABC Transporters in Complete Microbial Genomes,Genome Res. 1998 Oct;8(10):1048-59. [http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Hollenstein, K.; R.J. Dawson; K.P. Locher. 2007. Structure and mechanism of ABC transporter proteins. Curr. Opin. Struct. Biol. 17, 412-418. [http://www.ncbi.nlm.nih.gov/pubmed/17723295 17723295] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Davidson, A.L.; E. Dassa; C. Orelle; and J. Chen. 2008. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72(2), 317-364.[http://www.ncbi.nlm.nih.gov/pubmed/18535149 18535149] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Henderson, D.P. and S.M. Payne. 1994. Vibrio cholerae iron transport system: roles of heme and siderophore iron transport in virulence and identification of a gene associated with multiple iron transport systems. Infect. Immun. 62, 5120-5125. [http://www.ncbi.nlm.nih.gov/pubmed/7927795 7927795] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]<br />
Davidson, A.L.; E. Dassa; C. Orelle; and J. Chen. 2008. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72(2), 317-364.[http://www.ncbi.nlm.nih.gov/pubmed/18535149 18535149]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
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==Two-component system==<br />
<br />
[[Image:Transduction_overview_tcs.png|350px|right| Tcs system (Atosc)]]<br />
<br />
The Two-Component System (TCS) can be considered as a widely spread class of biosensor knowing that adaptive signal transduction within microbial cells involving a multi-faceted regulated phosphotransfer mechanism that comprises structural rearrangements of sensor histidine kinases upon ligand-binding and phosphorylation-induced conformational changes in response regulators of versatile TCS, arisen early in bacterial evolution [http://www.ncbi.nlm.nih.gov/pubmed/10966457[1]], [http://www.ncbi.nlm.nih.gov/pubmed/17158704[2]]<br />
<br />
<br />
In most eubacteria, two-component proteins typically constitute 1% of encoded peptides. In pathogenic bacteria they control the expression of important pathogenetic factors, in addition to regulating basic housekeeping functions. The widespread distribution of two-component signal transduction systems in Bacteria and Achaea reflects their biological value as major sensing and response elements to a wide range of environmental insults that are tuned to respond from within milliseconds to hours [http://www.ncbi.nlm.nih.gov/pubmed/17103118[3]. Although TCSs are probably the most eficient means of adaptation to conventional stressful stimuli encountered by bacteria during their lifespan, the plasticity of some of these sophisticated systems may contribute to strain-specific cellular processes and to the acquisition of distinct features and phenotypes, particularly in pathogens [http://www.ncbi.nlm.nih.gov/pubmed/19198978[4]]. <br />
<br />
<br />
To put the structure in a nutshell: A typical TCS consists of a transmembrane dimeric sensor histidine kinase (HK) and a cytoplasmic cognate response regulator (RR). In gram negative bacteria there is often a Periplasmic Binding Protein which optimize the detection of the molecule localized in the periplasm by a high affinity for the HK after binding the specific molecule. The following scheme shows a typical ABC mechanism : <br />
<br />
<br />
====Uses====<br />
<br />
Two-component systems serve as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions [http://www.ncbi.nlm.nih.gov/pubmed/10966457[1]].<br />
<br />
<br />
By transferring a packet of molecule synthesize by the donor but not present in the medium, <br />
the arrival could activate the transcription of gene of interest. This will allow us to check for the "bacterial communication"<br />
<br />
====Advantages/drawbacks====<br />
<br />
Most gene regulation proteins that were known were single proteins, often homodimers or homotetramers, which bound to two ligands, a metabolic intermediate or a cis-acting gene regulation element. The functional state of the regulatory protein was thus modified by binding to the metabolic intermediate. The consequence of ligand binding, an altered state of the regulatory protein, was directed to the appropriate gene(s) by the protein's DNA binding activity. <br />
<br />
<br />
The main advantage of TCS is that the mechanism is dedicated to the transcription of gene under a specific promoter. Four our project, the difficulty is to find an easily exportable and detectable signal. <br />
In contrats, most of the biosensor are generally sensible to high diffusible molecule for which the vesicles transport is useless, so using vesicules to transmit a message doesn't seems the best way to explore.<br />
<br />
<br />
{{Template:Paris2009_guided|Transduction_overview2#top.23top|Transduction_overview2_strategy#bottom}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview2_transductionTeam:Paris/Transduction overview2 transduction2009-10-22T03:09:21Z<p>Christophe.R: /* Transduction */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview2#bottom | Transduction]]<br />
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==Transduction==<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#bottom"> Transduction</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
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<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#ABC_transporters"> ABC transporters</a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#Two-component_system"> Two-component system</a><br />
</center><br />
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<br />
In biology, signal transduction refers to any process by which a cell converts one kind of signal or stimulus into another. Most processes of signal transduction involve ordered sequences of biochemical reactions inside the cell, which are carried out by enzymes and sometimes activated by second messengers, resulting in a signal transduction pathway. <br />
<br />
<br />
Such processes are usually rapid, lasting on the order of milliseconds in the case of ion flux, or minutes for the activation of proteic cascades, but some can take hours, and even days (as is the case with gene expression), to complete. <br />
<br />
<br />
We must also refer to the amplification of the signal , in which a relative small stimulus can elicit a large response. It is often du to the increasing numbers of protein ativation<br />
implied in the transduction pathways. <br />
<br />
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<br />
==ABC transporters==<br />
<br />
[[Image:Tranduction_abc_transporter_b12.png|380px|right| fec operon induction]]<br />
The ABC transporter is a major class of cellular translocation machinery encoded in the largest set of paralogous genes <sup>[[Team:Paris/Transduction_overview2_transduction#References|[1]]]</sup>.<br />
<br />
<br />
ABC (ATP binding cassette) transporters are active transport systems of the cell, which is widespread in archaea, eubacteria, and eukaryotes. They require energy in the form of adenosine triphosphate (ATP) to translocate substrates across cell membranes. These proteins harness the energy of ATP binding and/or hydrolysis to drive conformational changes in the transmembrane domain (TMD) and consequently transports molecules <sup>[[Team:Paris/Transduction_overview2_transduction#References|[2]]]</sup>.<br />
ABC transporters are also known as the periplasmic binding protein-dependent transport system in Gram-negative bacteria and the binding-lipoprotein-dependent transport system in Gram positive bacteria. <br />
The transporter shows a common global organization with three types of molecular components. Typically, it consists of two integral membrane proteins (permeases) each having six transmembrane segments, two peripheral membrane proteins that bind and hydrolyze ATP, and a periplasmic (or lipoprotein) substrate-binding protein. The ATP-binding protein component is the most conserved, the TMD is somewhat less conserved, and the substrate-binding protein component is most divergent in terms of the sequence similarity. The ABC transporters form the largest group of paralogous genes in bacterial and archaeal genomes , and the genes for the three components frequently form an operon. <br />
<br />
<br />
====Uses====<br />
<br />
Bacterial ABC transporters are essential in cell viability, virulence, and pathogenicity <sup>[[Team:Paris/Transduction_overview2_transduction#References|[3]]]</sup> Iron ABC uptake systems, for example, are important effectors of virulence<br />
<sup>[[Team:Paris/Transduction_overview2_transduction#References|[4]]]</sup>.<br />
Prokaryotic ABC transporters utilize the energy of ATP hydrolysis to transport lot of different substrates across cellular membranes. They are divided into 2 functionnal categories :<br />
<br />
- '''importers''' : they mediate the uptake of amino-acids, peptids, sugar ... into the cell, so they allow the transport of protein directly into the cytolpasm to activate the transcription <sup>[[Team:Paris/Transduction_overview2_transduction#References|[5]]]</sup>. <br />
<br />
- '''exporters''' : they transport lipids and some polysaccharides from the cytoplasm to the periplasm.<br />
<br />
====Advantages/drawbacks====<br />
<br />
The import system of these transporters is really interesting and attractive four our project to transmit a "message" from vesicles to target cells.<br />
The main advantage is that the protein of interest is directly translocated in the cytoplasm and if it is a transcription factor it could activated immediatly the response. The communication is simple,fast and efficient.<br />
But this system is not perfect... One major drawback is that ABC transporter system is a nutriment uptake system. So, basically only (very) small molecules are able to pass thought the membranes.<br />
<br />
<br />
<br />
<br />
<br />
====References====<br />
<ol class="references"><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Kentaro Tomii and Minoru Kanehisa, A Comparative Analysis of ABC Transporters in Complete Microbial Genomes,Genome Res. 1998 Oct;8(10):1048-59. [http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Hollenstein, K.; R.J. Dawson; K.P. Locher. 2007. Structure and mechanism of ABC transporter proteins. Curr. Opin. Struct. Biol. 17, 412-418. [http://www.ncbi.nlm.nih.gov/pubmed/17723295 17723295] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Davidson, A.L.; E. Dassa; C. Orelle; and J. Chen. 2008. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72(2), 317-364.[http://www.ncbi.nlm.nih.gov/pubmed/18535149 18535149] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Henderson, D.P. and S.M. Payne. 1994. Vibrio cholerae iron transport system: roles of heme and siderophore iron transport in virulence and identification of a gene associated with multiple iron transport systems. Infect. Immun. 62, 5120-5125. [http://www.ncbi.nlm.nih.gov/pubmed/7927795 7927795] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]<br />
Davidson, A.L.; E. Dassa; C. Orelle; and J. Chen. 2008. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72(2), 317-364.[http://www.ncbi.nlm.nih.gov/pubmed/18535149 18535149]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<br />
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<br />
<br />
<br />
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<br />
==Two-component system==<br />
<br />
[[Image:Transduction_overview_tcs.png|350px|right| Tcs system (Atosc)]]<br />
<br />
The Two-Component System (TCS) can be considered as a widely spread class of biosensor knowing that adaptive signal transduction within microbial cells involving a multi-faceted regulated phosphotransfer mechanism that comprises structural rearrangements of sensor histidine kinases upon ligand-binding and phosphorylation-induced conformational changes in response regulators of versatile TCS, arisen early in bacterial evolution [http://www.ncbi.nlm.nih.gov/pubmed/10966457[1]], [http://www.ncbi.nlm.nih.gov/pubmed/17158704[2]]<br />
<br />
<br />
In most eubacteria, two-component proteins typically constitute 1% of encoded peptides. In pathogenic bacteria they control the expression of important pathogenetic factors, in addition to regulating basic housekeeping functions. The widespread distribution of two-component signal transduction systems in Bacteria and Achaea reflects their biological value as major sensing and response elements to a wide range of environmental insults that are tuned to respond from within milliseconds to hours [http://www.ncbi.nlm.nih.gov/pubmed/17103118[3]. Although TCSs are probably the most eficient means of adaptation to conventional stressful stimuli encountered by bacteria during their lifespan, the plasticity of some of these sophisticated systems may contribute to strain-specific cellular processes and to the acquisition of distinct features and phenotypes, particularly in pathogens [http://www.ncbi.nlm.nih.gov/pubmed/19198978[4]]. <br />
<br />
<br />
To put the structure in a nutshell: A typical TCS consists of a transmembrane dimeric sensor histidine kinase (HK) and a cytoplasmic cognate response regulator (RR). In gram negative bacteria there is often a Periplasmic Binding Protein which optimize the detection of the molecule localized in the periplasm by a high affinity for the HK after binding the specific molecule. The following scheme shows a typical ABC mechanism : <br />
<br />
<br />
====Uses====<br />
<br />
Two-component systems serve as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions [http://www.ncbi.nlm.nih.gov/pubmed/10966457[1]].<br />
<br />
<br />
By transferring a packet of molecule synthesize by the donor but not present in the medium, <br />
the arrival could activate the transcription of gene of interest. This will allow us to check for the "bacterial communication"<br />
<br />
====Advantages/drawbacks====<br />
<br />
Most gene regulation proteins that were known were single proteins, often homodimers or homotetramers, which bound to two ligands, a metabolic intermediate or a cis-acting gene regulation element. The functional state of the regulatory protein was thus modified by binding to the metabolic intermediate. The consequence of ligand binding, an altered state of the regulatory protein, was directed to the appropriate gene(s) by the protein's DNA binding activity. <br />
<br />
<br />
The main advantage of TCS is that the mechanism is dedicated to the transcription of gene under a specific promoter. Four our project, the difficulty is to find an easily exportable and detectable signal. <br />
In contrats, most of the biosensor are generally sensible to high diffusible molecule for which the vesicles transport is useless, so using vesicules to transmit a message doesn't seems the best way to explore.<br />
<br />
<br />
{{Template:Paris2009_guided|Transduction_overview2#top.23top|Transduction_overview2_strategy#bottom}}<br />
<br />
<br />
====Bibliography :====<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/10966457[1]] Stock AM, Robinson VL, Goudreau PN. Two-component signal transduction.2000, Annu. Rev. Biochem. 69: 183–215<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/17158704[2]] Mascher T, Helmann JD, Unden G. Stimulus perception in bacterial signal-transducing histidine kinases. 2006. Microbiol. Mol. Biol. Rev. 70 (4): 910–38.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/17103118[3]] Attwood PV, Piggott MJ, Zu XL, Besant PG. Focus on phosphohistidine, 2007, Amino Acids 32 (1): 145–56.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19198978[4]] Kyriakidis DA, Tiligada E. Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm, 2009, Amino Acids.37(3):443-58</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview2_transductionTeam:Paris/Transduction overview2 transduction2009-10-22T03:08:49Z<p>Christophe.R: /* ABC transporters */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview2#bottom | Transduction]]<br />
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==Transduction==<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#bottom"> Transduction</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
<div id="left-side2"></div><br />
<div id="middle-side2"><center><br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#ABC_transporters"> ABC transporters</a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#Two-component_system"> Two-component system</a><br />
</center><br />
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<div id="right-side2"></div><br />
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<br />
In biology, signal transduction refers to any process by which a cell converts one kind of signal or stimulus into another. Most processes of signal transduction involve ordered sequences of biochemical reactions inside the cell, which are carried out by enzymes and sometimes activated by second messengers, resulting in a signal transduction pathway. <br />
<br />
<br />
Such processes are usually rapid, lasting on the order of milliseconds in the case of ion flux, or minutes for the activation of proteic cascades, but some can take hours, and even days (as is the case with gene expression), to complete. <br />
<br />
<br />
We must also refer to the amplification of the signal , in which a relative small stimulus can elicit a large response. It is often du to the increasing numbers of protein ativation<br />
implied in the transduction pathways. <br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
==ABC transporters==<br />
<br />
[[Image:Tranduction_abc_transporter_b12.png|380px|right| fec operon induction]]<br />
The ABC transporter is a major class of cellular translocation machinery encoded in the largest set of paralogous genes <sup>[[Team:Paris/Transduction_overview2_transduction#References|[1]]]</sup>.<br />
<br />
<br />
ABC (ATP binding cassette) transporters are active transport systems of the cell, which is widespread in archaea, eubacteria, and eukaryotes. They require energy in the form of adenosine triphosphate (ATP) to translocate substrates across cell membranes. These proteins harness the energy of ATP binding and/or hydrolysis to drive conformational changes in the transmembrane domain (TMD) and consequently transports molecules <sup>[[Team:Paris/Transduction_overview2_transduction#References|[2]]]</sup>.<br />
ABC transporters are also known as the periplasmic binding protein-dependent transport system in Gram-negative bacteria and the binding-lipoprotein-dependent transport system in Gram positive bacteria. <br />
The transporter shows a common global organization with three types of molecular components. Typically, it consists of two integral membrane proteins (permeases) each having six transmembrane segments, two peripheral membrane proteins that bind and hydrolyze ATP, and a periplasmic (or lipoprotein) substrate-binding protein. The ATP-binding protein component is the most conserved, the TMD is somewhat less conserved, and the substrate-binding protein component is most divergent in terms of the sequence similarity. The ABC transporters form the largest group of paralogous genes in bacterial and archaeal genomes , and the genes for the three components frequently form an operon. <br />
<br />
<br />
====Uses====<br />
<br />
Bacterial ABC transporters are essential in cell viability, virulence, and pathogenicity <sup>[[Team:Paris/Transduction_overview2_transduction#References|[3]]]</sup> Iron ABC uptake systems, for example, are important effectors of virulence<br />
<sup>[[Team:Paris/Transduction_overview2_transduction#References|[4]]]</sup>.<br />
Prokaryotic ABC transporters utilize the energy of ATP hydrolysis to transport lot of different substrates across cellular membranes. They are divided into 2 functionnal categories :<br />
<br />
- '''importers''' : they mediate the uptake of amino-acids, peptids, sugar ... into the cell, so they allow the transport of protein directly into the cytolpasm to activate the transcription <sup>[[Team:Paris/Transduction_overview2_transduction#References|[5]]]</sup>. <br />
<br />
- '''exporters''' : they transport lipids and some polysaccharides from the cytoplasm to the periplasm.<br />
<br />
====Advantages/drawbacks====<br />
<br />
The import system of these transporters is really interesting and attractive four our project to transmit a "message" from vesicles to target cells.<br />
The main advantage is that the protein of interest is directly translocated in the cytoplasm and if it is a transcription factor it could activated immediatly the response. The communication is simple,fast and efficient.<br />
But this system is not perfect... One major drawback is that ABC transporter system is a nutriment uptake system. So, basically only (very) small molecules are able to pass thought the membranes.<br />
<br />
<br />
<br />
<br />
<br />
====References====<br />
<ol class="references"><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Kentaro Tomii and Minoru Kanehisa, A Comparative Analysis of ABC Transporters in Complete Microbial Genomes,Genome Res. 1998 Oct;8(10):1048-59. [http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Hollenstein, K.; R.J. Dawson; K.P. Locher. 2007. Structure and mechanism of ABC transporter proteins. Curr. Opin. Struct. Biol. 17, 412-418. [http://www.ncbi.nlm.nih.gov/pubmed/17723295 17723295] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Davidson, A.L.; E. Dassa; C. Orelle; and J. Chen. 2008. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72(2), 317-364.[http://www.ncbi.nlm.nih.gov/pubmed/18535149 18535149] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Henderson, D.P. and S.M. Payne. 1994. Vibrio cholerae iron transport system: roles of heme and siderophore iron transport in virulence and identification of a gene associated with multiple iron transport systems. Infect. Immun. 62, 5120-5125. [http://www.ncbi.nlm.nih.gov/pubmed/7927795 7927795] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]<br />
Davidson, A.L.; E. Dassa; C. Orelle; and J. Chen. 2008. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72(2), 317-364.[http://www.ncbi.nlm.nih.gov/pubmed/18535149 18535149]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
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==Two-component system==<br />
<br />
[[Image:Transduction_overview_tcs.png|350px|right| Tcs system (Atosc)]]<br />
<br />
The Two-Component System (TCS) can be considered as a widely spread class of biosensor knowing that adaptive signal transduction within microbial cells involving a multi-faceted regulated phosphotransfer mechanism that comprises structural rearrangements of sensor histidine kinases upon ligand-binding and phosphorylation-induced conformational changes in response regulators of versatile TCS, arisen early in bacterial evolution [http://www.ncbi.nlm.nih.gov/pubmed/10966457[1]], [http://www.ncbi.nlm.nih.gov/pubmed/17158704[2]]<br />
<br />
<br />
In most eubacteria, two-component proteins typically constitute 1% of encoded peptides. In pathogenic bacteria they control the expression of important pathogenetic factors, in addition to regulating basic housekeeping functions. The widespread distribution of two-component signal transduction systems in Bacteria and Achaea reflects their biological value as major sensing and response elements to a wide range of environmental insults that are tuned to respond from within milliseconds to hours [http://www.ncbi.nlm.nih.gov/pubmed/17103118[3]. Although TCSs are probably the most eficient means of adaptation to conventional stressful stimuli encountered by bacteria during their lifespan, the plasticity of some of these sophisticated systems may contribute to strain-specific cellular processes and to the acquisition of distinct features and phenotypes, particularly in pathogens [http://www.ncbi.nlm.nih.gov/pubmed/19198978[4]]. <br />
<br />
<br />
To put the structure in a nutshell: A typical TCS consists of a transmembrane dimeric sensor histidine kinase (HK) and a cytoplasmic cognate response regulator (RR). In gram negative bacteria there is often a Periplasmic Binding Protein which optimize the detection of the molecule localized in the periplasm by a high affinity for the HK after binding the specific molecule. The following scheme shows a typical ABC mechanism : <br />
<br />
<br />
====Uses====<br />
<br />
Two-component systems serve as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions [http://www.ncbi.nlm.nih.gov/pubmed/10966457[1]].<br />
<br />
<br />
By transferring a packet of molecule synthesize by the donor but not present in the medium, <br />
the arrival could activate the transcription of gene of interest. This will allow us to check for the "bacterial communication"<br />
<br />
====Advantages/drawbacks====<br />
<br />
Most gene regulation proteins that were known were single proteins, often homodimers or homotetramers, which bound to two ligands, a metabolic intermediate or a cis-acting gene regulation element. The functional state of the regulatory protein was thus modified by binding to the metabolic intermediate. The consequence of ligand binding, an altered state of the regulatory protein, was directed to the appropriate gene(s) by the protein's DNA binding activity. <br />
<br />
<br />
The main advantage of TCS is that the mechanism is dedicated to the transcription of gene under a specific promoter. Four our project, the difficulty is to find an easily exportable and detectable signal. <br />
In contrats, most of the biosensor are generally sensible to high diffusible molecule for which the vesicles transport is useless, so using vesicules to transmit a message doesn't seems the best way to explore.<br />
<br />
<br />
{{Template:Paris2009_guided|Transduction_overview2#top.23top|Transduction_overview2_strategy#bottom}}<br />
<br />
<br />
====Bibliography :====<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/10966457[1]] Stock AM, Robinson VL, Goudreau PN. Two-component signal transduction.2000, Annu. Rev. Biochem. 69: 183–215<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/17158704[2]] Mascher T, Helmann JD, Unden G. Stimulus perception in bacterial signal-transducing histidine kinases. 2006. Microbiol. Mol. Biol. Rev. 70 (4): 910–38.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/17103118[3]] Attwood PV, Piggott MJ, Zu XL, Besant PG. Focus on phosphohistidine, 2007, Amino Acids 32 (1): 145–56.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19198978[4]] Kyriakidis DA, Tiligada E. Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm, 2009, Amino Acids.37(3):443-58</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview2_transductionTeam:Paris/Transduction overview2 transduction2009-10-22T03:07:14Z<p>Christophe.R: /* Bibliography : */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview2#bottom | Transduction]]<br />
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==Transduction==<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#bottom"> Transduction</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_construction#bottom"> Construction</a><br />
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<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#ABC_transporters"> ABC transporters</a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#Two-component_system"> Two-component system</a><br />
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In biology, signal transduction refers to any process by which a cell converts one kind of signal or stimulus into another. Most processes of signal transduction involve ordered sequences of biochemical reactions inside the cell, which are carried out by enzymes and sometimes activated by second messengers, resulting in a signal transduction pathway. <br />
<br />
<br />
Such processes are usually rapid, lasting on the order of milliseconds in the case of ion flux, or minutes for the activation of proteic cascades, but some can take hours, and even days (as is the case with gene expression), to complete. <br />
<br />
<br />
We must also refer to the amplification of the signal , in which a relative small stimulus can elicit a large response. It is often du to the increasing numbers of protein ativation<br />
implied in the transduction pathways. <br />
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==ABC transporters==<br />
<br />
[[Image:Tranduction_abc_transporter_b12.png|380px|right| fec operon induction]]<br />
The ABC transporter is a major class of cellular translocation machinery encoded in the largest set of paralogous genes [http://www.ncbi.nlm.nih.gov/pubmed/9799792[1]].<br />
<br />
<br />
ABC (ATP binding cassette) transporters are active transport systems of the cell, which is widespread in archaea, eubacteria, and eukaryotes. They require energy in the form of adenosine triphosphate (ATP) to translocate substrates across cell membranes. These proteins harness the energy of ATP binding and/or hydrolysis to drive conformational changes in the transmembrane domain (TMD) and consequently transports molecules [http://www.ncbi.nlm.nih.gov/pubmed/17723295[2]].<br />
ABC transporters are also known as the periplasmic binding protein-dependent transport system in Gram-negative bacteria and the binding-lipoprotein-dependent transport system in Gram positive bacteria. <br />
The transporter shows a common global organization with three types of molecular components. Typically, it consists of two integral membrane proteins (permeases) each having six transmembrane segments, two peripheral membrane proteins that bind and hydrolyze ATP, and a periplasmic (or lipoprotein) substrate-binding protein. The ATP-binding protein component is the most conserved, the TMD is somewhat less conserved, and the substrate-binding protein component is most divergent in terms of the sequence similarity. The ABC transporters form the largest group of paralogous genes in bacterial and archaeal genomes , and the genes for the three components frequently form an operon. <br />
<br />
<br />
====Uses====<br />
<br />
Bacterial ABC transporters are essential in cell viability, virulence, and pathogenicity [http://www.ncbi.nlm.nih.gov/pubmed/18535149[3]] Iron ABC uptake systems, for example, are important effectors of virulence<br />
[http://www.ncbi.nlm.nih.gov/pubmed/7927795[4]].<br />
Prokaryotic ABC transporters utilize the energy of ATP hydrolysis to transport lot of different substrates across cellular membranes. They are divided into 2 functionnal categories :<br />
<br />
- '''importers''' : they mediate the uptake of amino-acids, peptids, sugar ... into the cell, so they allow the transport of protein directly into the cytolpasm to activate the transcription [http://www.ncbi.nlm.nih.gov/pubmed/18535149[5]]. <br />
<br />
- '''exporters''' : they transport lipids and some polysaccharides from the cytoplasm to the periplasm.<br />
<br />
====Advantages/drawbacks====<br />
<br />
The import system of these transporters is really interesting and attractive four our project to transmit a "message" from vesicles to target cells.<br />
The main advantage is that the protein of interest is directly translocated in the cytoplasm and if it is a transcription factor it could activated immediatly the response. The communication is simple,fast and efficient.<br />
But this system is not perfect... One major drawback is that ABC transporter system is a nutriment uptake system. So, basically only (very) small molecules are able to pass thought the membranes.<br />
<br />
<br />
<br />
<br />
<br />
====References====<br />
<ol class="references"><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Kentaro Tomii and Minoru Kanehisa, A Comparative Analysis of ABC Transporters in Complete Microbial Genomes,Genome Res. 1998 Oct;8(10):1048-59. [http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Hollenstein, K.; R.J. Dawson; K.P. Locher. 2007. Structure and mechanism of ABC transporter proteins. Curr. Opin. Struct. Biol. 17, 412-418. [http://www.ncbi.nlm.nih.gov/pubmed/17723295 17723295] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Davidson, A.L.; E. Dassa; C. Orelle; and J. Chen. 2008. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72(2), 317-364.[http://www.ncbi.nlm.nih.gov/pubmed/18535149 18535149] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]Henderson, D.P. and S.M. Payne. 1994. Vibrio cholerae iron transport system: roles of heme and siderophore iron transport in virulence and identification of a gene associated with multiple iron transport systems. Infect. Immun. 62, 5120-5125. [http://www.ncbi.nlm.nih.gov/pubmed/7927795 7927795] </li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]<br />
Davidson, A.L.; E. Dassa; C. Orelle; and J. Chen. 2008. Structure, function, and evolution of bacterial ATP-binding cassette systems. Microbiol. Mol. Biol. Rev. 72(2), 317-364.[http://www.ncbi.nlm.nih.gov/pubmed/18535149 18535149]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<li> [[Team:Paris/Transduction_overview2_transduction#1 | ^]]</li><br />
<br />
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<br />
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==Two-component system==<br />
<br />
[[Image:Transduction_overview_tcs.png|350px|right| Tcs system (Atosc)]]<br />
<br />
The Two-Component System (TCS) can be considered as a widely spread class of biosensor knowing that adaptive signal transduction within microbial cells involving a multi-faceted regulated phosphotransfer mechanism that comprises structural rearrangements of sensor histidine kinases upon ligand-binding and phosphorylation-induced conformational changes in response regulators of versatile TCS, arisen early in bacterial evolution [http://www.ncbi.nlm.nih.gov/pubmed/10966457[1]], [http://www.ncbi.nlm.nih.gov/pubmed/17158704[2]]<br />
<br />
<br />
In most eubacteria, two-component proteins typically constitute 1% of encoded peptides. In pathogenic bacteria they control the expression of important pathogenetic factors, in addition to regulating basic housekeeping functions. The widespread distribution of two-component signal transduction systems in Bacteria and Achaea reflects their biological value as major sensing and response elements to a wide range of environmental insults that are tuned to respond from within milliseconds to hours [http://www.ncbi.nlm.nih.gov/pubmed/17103118[3]. Although TCSs are probably the most eficient means of adaptation to conventional stressful stimuli encountered by bacteria during their lifespan, the plasticity of some of these sophisticated systems may contribute to strain-specific cellular processes and to the acquisition of distinct features and phenotypes, particularly in pathogens [http://www.ncbi.nlm.nih.gov/pubmed/19198978[4]]. <br />
<br />
<br />
To put the structure in a nutshell: A typical TCS consists of a transmembrane dimeric sensor histidine kinase (HK) and a cytoplasmic cognate response regulator (RR). In gram negative bacteria there is often a Periplasmic Binding Protein which optimize the detection of the molecule localized in the periplasm by a high affinity for the HK after binding the specific molecule. The following scheme shows a typical ABC mechanism : <br />
<br />
<br />
====Uses====<br />
<br />
Two-component systems serve as a basic stimulus-response coupling mechanism to allow organisms to sense and respond to changes in many different environmental conditions [http://www.ncbi.nlm.nih.gov/pubmed/10966457[1]].<br />
<br />
<br />
By transferring a packet of molecule synthesize by the donor but not present in the medium, <br />
the arrival could activate the transcription of gene of interest. This will allow us to check for the "bacterial communication"<br />
<br />
====Advantages/drawbacks====<br />
<br />
Most gene regulation proteins that were known were single proteins, often homodimers or homotetramers, which bound to two ligands, a metabolic intermediate or a cis-acting gene regulation element. The functional state of the regulatory protein was thus modified by binding to the metabolic intermediate. The consequence of ligand binding, an altered state of the regulatory protein, was directed to the appropriate gene(s) by the protein's DNA binding activity. <br />
<br />
<br />
The main advantage of TCS is that the mechanism is dedicated to the transcription of gene under a specific promoter. Four our project, the difficulty is to find an easily exportable and detectable signal. <br />
In contrats, most of the biosensor are generally sensible to high diffusible molecule for which the vesicles transport is useless, so using vesicules to transmit a message doesn't seems the best way to explore.<br />
<br />
<br />
{{Template:Paris2009_guided|Transduction_overview2#top.23top|Transduction_overview2_strategy#bottom}}<br />
<br />
<br />
====Bibliography :====<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/10966457[1]] Stock AM, Robinson VL, Goudreau PN. Two-component signal transduction.2000, Annu. Rev. Biochem. 69: 183–215<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/17158704[2]] Mascher T, Helmann JD, Unden G. Stimulus perception in bacterial signal-transducing histidine kinases. 2006. Microbiol. Mol. Biol. Rev. 70 (4): 910–38.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/17103118[3]] Attwood PV, Piggott MJ, Zu XL, Besant PG. Focus on phosphohistidine, 2007, Amino Acids 32 (1): 145–56.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19198978[4]] Kyriakidis DA, Tiligada E. Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm, 2009, Amino Acids.37(3):443-58</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview2Team:Paris/Transduction overview22009-10-22T03:04:28Z<p>Christophe.R: </p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview#bottom | Transduction]]<br />
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== Signal transduction: Main ==<br />
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<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview2#bottom"> Main </a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Transduction_overview2_transduction#bottom"> Transduction</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview2_construction#bottom"> Construction</a><br />
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This part of the project was focus on the following point:<br />
<br />
<br />
*[[Team:Paris/Transduction_overview2_transduction#bottom |The activation of the transcription of a genetic construction after fusionning the OMVs with the outer membrane of the receiving bacterium.]] <br />
<br />
<br />
The sinequanone conditions : we tried to achieve this aim without sacrifying important proprieties of our message : specific, repeatable , multidirectional.<br />
<br />
<br />
It seems that we have two possible ways : the ABC transporters or the two component systems.<br />
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ABC transporters and two component systems are natural transport systems (export or import) of nutriments or toxines, and even information but the mecanism is mostly unknown so the DNA-containing OMVs would have been a useful mean of information transport if it would not be so unknown. Here for information about [[Team:Paris/Transduction_overview_transduction#B.1_ABC_transporters | ABC transporter ]] and [[Team:Paris/Transduction_overview_transduction#B.2 Two-component system| Two Component System]].<br />
<br />
<br />
[[Team:Paris/Transduction_overview2_strategy#bottom | Our strategy]] and [[Team:Paris/Transduction_overview_construction#bottom | Construction]] part explains our aim in this OMV production system. <br />
<br />
<br />
{{Template:Paris2009_guided|Transduction_overview_strategy#bottom|Transduction_overview2_transduction#bottom}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Addressing_overview2_strategyTeam:Paris/Addressing overview2 strategy2009-10-22T02:59:07Z<p>Christophe.R: </p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Addressing_overview2#top | ClyA]] > [[Team:Paris/Addressing_overview2_strategy#bottom | Our strategy]]<br />
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==Addressing the message in the membrane : Our strategy==<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2#bottom"> Main </a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Addressing_overview3#bottom"> ClyA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview4#bottom"> OmpA</a>|<br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview_Construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
</html><br />
<br />
Our strategy is to use clyA to export a protein to the outer-membrane of the cell. The protein fused to clyA will be incorporated into the vesicle during the vesiculation process and it's also express on the surface. ClyA contain the signal peptide required for the exportation process from the cytoplasm to the periplasm. The overall idea is to fused the protein of interest to clyA. <br />
<br />
So in a first time in order to see if our ClyA are localize in OMVs, we fused it we a RFP. For that we add a poly glycine linker to ClyA biobrick to improve ClyA-RFP fusion. Moreover if we put RFP before ClyA, it seem that there is more fluorescence than ClyA before RFP under <sup>[[Team:Paris/Addressing_overview2#References|[1]]]</sup>. You can see the contruction [https://2009.igem.org/Team:Paris/Addressing_overview_Construction#Overview here]<br />
<br />
Then if this test work, we could replace the RFP by the protein of interest for signal transduction, moreover this system couple to fec system can transduct a signal from outer membran to the cytoplasm.<br />
<br />
<br />
{{Template:Paris2009_guided|Addressing_overview4#bottom|Production_overview#top}}<br />
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====References====<br />
<ol class="references"><br />
<li>[[Team:Paris/Addressing_overview2#1| ^]]J.Y. Kim, A.M. Doody, D. J. Chen, G.H. Cremona, M.L. Shuler, D.Putnam,and M.P. DeLisa.Engineered. Bacterial Outer Membrane Vesicles with Enhanced Functionality, 2008, J. Mol. Biol. 380, 51–66. [http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]</li><br />
</ol></div>Christophe.Rhttp://2009.igem.org/Team:Paris/Addressing_overview2_strategyTeam:Paris/Addressing overview2 strategy2009-10-22T02:58:44Z<p>Christophe.R: /* Addressing the message in the membrane : Our strategy */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Addressing_overview2#top | ClyA]] > [[Team:Paris/Addressing_overview2_strategy#bottom | Our strategy]]<br />
{{Template:Paris2009}}<br />
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==Addressing the message in the membrane : Our strategy==<br />
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<div id="left-side"></div><br />
<div id="middle-side"><center><br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2#bottom"> Main </a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Addressing_overview3#bottom"> ClyA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview4#bottom"> OmpA</a>|<br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview_Construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
</html><br />
<br />
Our strategy is to use clyA to export a protein to the outer-membrane of the cell. The protein fused to clyA will be incorporated into the vesicle during the vesiculation process and it's also express on the surface. ClyA contain the signal peptide required for the exportation process from the cytoplasm to the periplasm. The overall idea is to fused the protein of interest to clyA. <br />
<br />
So in a first time in order to see if our ClyA are localize in OMVs, we fused it we a RFP. For that we add a poly glycine linker to ClyA biobrick to improve ClyA-RFP fusion. Moreover if we put RFP before ClyA, it seem that there is more fluorescence than ClyA before RFP under <sup>[[Team:Paris/Addressing_overview2#References|[1]]]</sup>. You can see the contruction [https://2009.igem.org/Team:Paris/Addressing_overview_Construction#Overview here]<br />
<br />
Then if this test work, we could replace the RFP by the protein of interest for signal transduction, moreover this system couple to fec system can transduct a signal from outer membran to the cytoplasm.<br />
<br />
<br />
{{Template:Paris2009_guided|Addressing_overview4#bottom|Production_overview#top}}<br />
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</div><br />
<div id="paris_content_boxtop"><br />
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<div id="paris_content"><br />
</html><br />
====References====<br />
<ol class="references"><br />
<li>[[Team:Paris/Addressing_overview2#1| ^]]J.Y. Kim, A.M. Doody, D. J. Chen, G.H. Cremona, M.L. Shuler, D.Putnam,and M.P. DeLisa.Engineered. Bacterial Outer Membrane Vesicles with Enhanced Functionality, 2008, J. Mol. Biol. 380, 51–66. [http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]</li><br />
</ol></div>Christophe.Rhttp://2009.igem.org/Team:Paris/PapersTeam:Paris/Papers2009-10-22T02:55:55Z<p>Christophe.R: /* OMV Production */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Papers#bottom | Papers]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
== '''OMV Overview''' ==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white; font-weight:bold; "<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px| []<br />
|1999<br />
|Terry J. Beveridge<br />
|Structures of gram-negative cell walls and their derived membrane vesicles.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93954 10438737]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Miller SI & Guina T.<br />
|Bacterial vesicle formation as a mechanism of protein transfer to animals.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14531993?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 14531993]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2005<br />
|Kuehn MJ & Kesty NC.<br />
|Bacterial outer membrane vesicles and the host-pathogen interaction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16291643?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16291643]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|McBroom AJ & Kuehn MJ.<br />
|Outer membrane vesicle production by Escherichia coli is independent of membrane instability.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16855227?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16855227]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 1]]<br />
|2007<br />
|McBroom AJ & Kuehn MJ.<br />
|Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17163978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17163978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 2]]<br />
|2009<br />
|Deatherage BL & Cookson BT.<br />
|Biogenesis of bacterial membrane vesicles<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19432795?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 19432795]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2009<br />
|Purnick PE & Weiss R.<br />
|The second wave of synthetic biology: from modules to systems.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19461664?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 19461664]<br />
|}<br />
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<br />
=='''OMV Production'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Mashburn-Warren L & Whiteley M.<br />
|Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18630345?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 18630345]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Addressing_overview4#top|[2]]]<br />
|2001<br />
|Arora A. & Tamm LK.<br />
|Structure of outer membrane protein A transmembrane domain by NMR spectroscopy.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11276254?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 11276254]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|2007<br />
|Brown EA & Hardwidge PR.<br />
|Biochemical characterization of the enterotoxigenic Escherichia coli LeoA protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17975086?ordinalpos=16&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17975086]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2008<br />
|Burgess NK & Fleming KG.<br />
|Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18641391?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 18641391]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Tol/Pal<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|1986<br />
|Robert CHEN & Ulf HENNING.<br />
|Nucleotide sequence of the gene for the peptidoglycan-associated lipoprotein of Escherichia coli K12<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=210680 210680]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[3]]]<br />
|1995<br />
|Lazzaroni & Geli -<br />
|Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179564 179564]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|1999<br />
|Derouiche & Loret<br />
|Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10380085 10380085]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[4]]]<br />
|2001<br />
|Lloubès & RJournet L.<br />
|The Tol-Pal proteins of the Escherichia coli cell envelope: an energized system required for outer membrane integrity?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11501670 11501670]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|2002<br />
|Dubuisson JF & Lazzaroni JC.<br />
|Mutational analysis of the TolA C-terminal domain of Escherichia coli and genetic evidence for an interaction between TolA and TolB.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12142433 12142433]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2003<br />
|Llamas M & ARamos JL.<br />
|Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12896989 12896989]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[5]]]<br />
|2004<br />
|Henry T & Lloubès R.<br />
|Improved methods for producing outer membrane vesicles in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15249060 15249060]<br />
|}<br />
<br />
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<div id="paris_content_boxtop"><br />
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<div id="paris_content"><br />
</html><br />
<br />
==''' OMV Adressing '''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1997<br />
|Kadurugamuwa JL & Beveridge TJ.<br />
|Natural release of virulence factors in membrane vesicles by Pseudomonas aeruginosa and the effect of aminoglycoside antibiotics on their release.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9421308 9421308]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1998<br />
|Santini CL & Wu LF.<br />
|A novel sec-independent periplasmic protein translocation pathway in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9427745 9427745]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Berks BC & Palmer T.<br />
|The Tat protein export pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10652088 10652088]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Mishima Y & Murata K.<br />
|Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11731126 11731126]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Sargent F & Berks BC.<br />
|Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11422364 11422364]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Yahr TL & Wickner WT.<br />
|Functional reconstitution of bacterial Tat translocation in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11350936 11350936]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2004<br />
|Robinson C & Bolhuis A.<br />
|Tat-dependent protein targeting in prokaryotes and chloroplasts.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15546663 15546663]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Sargent F & Palmer T.<br />
|Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16445746 16445746]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Lee PA & Georgiou G.<br />
|The bacterial twin-arginine translocation pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16756481 16756481]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Maillard J & Sargent F.<br />
|Structural diversity in twin-arginine signal peptide-binding proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17901208 17901208]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Sargent F.<br />
|The twin-arginine transport system: moving folded proteins across membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17956229 17956229]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Ferrandez Y & Condemine G.<br />
|Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Pradel N & Bonnet R<br />
|Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|de Marco A.<br />
|Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19442264 19442264]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | ClyA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 5]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 1]]<br />
|2008<br />
|Kim JY & DeLisa MP.<br />
|Engineered bacterial outer membrane vesicles with enhanced functionality.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 1]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 2]]<br />
|2009<br />
|Mueller M & Ban N.<br />
|The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[Team:Paris/Addressing_overview4#top|[1]]]<br />
|2002<br />
|Wang Y.<br />
|The function of OmpA in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Dramsi S & Arthur M.<br />
|Covalent attachment of proteins to peptidoglycan.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18266854 18266854]<br />
|}<br />
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==''' OMV Reception'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Adhesin<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1989<br />
|Smeal T & Karin M.<br />
|Different requirements for formation of Jun:Jun and Jun:Fos complexes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1994<br />
|Heffernan EJ & Guiney DG.<br />
|Specificity of the complement resistance and cell association phenotypes encoded by the outer membrane protein genes rck from Salmonella typhimurium and ail from Yersinia enterocolitica.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7927803 7927803]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Veiga E & Fernández LA.<br />
|Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12949111 12949111]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 6]]<br />
|2004<br />
|Kesty NC & Kuehn MJ.<br />
|Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14578354 14578354]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | G3P<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1982<br />
|JEF D. BOEKE & PETER MODEL<br />
|A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 8]]<br />
|1999<br />
|Chatellier J & Riechmann L.<br />
|Interdomain interactions within the gene 3 protein of filamentous phage.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 9]]<br />
|1999<br />
|Lubkowski J & Wlodawer A.<br />
|Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 10]]<br />
|2002<br />
|Baek H & Cha S.<br />
|An improved helper phage system for efficient isolation of specific antibody molecules in phage display.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 11]]<br />
|2003<br />
|Karlsson F & Malmborg-Hager AC.<br />
|The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Snare<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 17]]<br />
|2000<br />
|Waters MG & Hughson FM.<br />
|Membrane tethering and fusion in the secretory and endocytic pathways.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Woodbury DJ & Rognlien K.<br />
|The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11067766 11067766]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2002<br />
|Bowen ME,Brunger AT.<br />
|Mutational analysis of synaptobrevin transmembrane domain oligomerization.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12501216 12501216]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Hu C & Rothman JE.<br />
|Fusion of cells by flipped SNAREs.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Weninger K & Brunger AT.<br />
|Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14657376 14657376]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006 <br />
|Giraudo CG & Rothman JE.<br />
|A clamping mechanism involved in SNARE-dependent exocytosis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16794037 16794037]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Low HH & Löwe J.<br />
|A bacterial dynamin-like protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17122778 17122778]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Weninger K & Brunger AT.<br />
|Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18275821 18275821]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Delevoye C & Subtil A.<br />
|SNARE protein mimicry by an intracellular bacterium.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18369472 18369472]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 18]]<br />
|2009<br />
|Giraudo CG & Rothman JE.<br />
|Alternative zippering as an on-off switch for SNARE-mediated fusion.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19164750 19164750]<br />
<br />
|}<br />
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<br />
==''' OMV Signal transduction'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1984<br />
|Lopilato JE & Beckwith JR.<br />
|D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6327616 6327616]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1995<br />
|Härle C & Braun V.<br />
|Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7729419 7729419]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1998<br />
|Tomii K & Kanehisa M.<br />
|A comparative analysis of ABC transporters in complete microbial genomes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1999<br />
|De Wulf P & Lin EC.<br />
|The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10542180 10542180]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Stock AM & Goudreau PN.<br />
|Two-component signal transduction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Yaron S & Matthews KR.<br />
|Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11010892 11010892]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2004<br />
|Dwyer MA & Hellinga HW.<br />
|Periplasmic binding proteins: a versatile superfamily for protein engineering.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15313245 15313245]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Braun V & Sauter A.<br />
|Gene regulation by transmembrane signaling.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16718597 16718597]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Baker MD & Stock JB<br />
|Signal transduction: networks and integrated circuits in bacterial cognition.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18054766 18054766]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Baker MD & Stock JB.<br />
|Systems biology of bacterial chemotaxis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16529985 16529985]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Ibrahim M & Monnet V.<br />
|Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17921293 17921293]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Kyriakidis DA & Tiligada E.<br />
|Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Tomii & Kanehisa<br />
|comparative analysis of ABC transporter<br />
|[http://genome.cshlp.org/content/8/10/1048.full.html#ref-list-1 pdf-link]<br />
|}<br />
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=='''Modelling'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Genetic Regulatory Network<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 1]]<br />
|1977<br />
|Gillespie Daniel T.<br />
|Exact Stochastic Simlation of Coupled Chemical Equations<br />
|[http://www.dna.caltech.edu/courses/cs191/paperscs191/gillespie2.pdf Gillespie1]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 3]]<br />
|1997<br />
|J.B. Andersen & S.Molin<br />
|New Stable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria<br />
|[http://aem.asm.org/cgi/reprint/64/6/2240.pdf LVA tag]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 6]]<br />
|1999<br />
|M.Ellowitz & S.Leibler<br />
|A Synthetic oscillatory network of transcriptionnal regulators <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10659856 10659856]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 2]]<br />
|1997<br />
|D.T.Gillespie<br />
|The Chemical Langevin Equation<br />
|[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000113000001000297000001&idtype=cvips&gifs=yes Gillespie2]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 5]]<br />
|2002<br />
|N.Rosenfold & U.Alon<br />
|Negative Autoregulation Speeds The Response TImes of Transcription Network <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12417193 2417193]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|M.B.Ellowitz & P.S.Swain<br />
|Stochastic Gene Expression In A Single Cell<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12183631 12183631]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 7]]<br />
|2003<br />
|S.Mangan & U.Alon<br />
|Structure and function ot the feed-forward Loop Network Motif<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14530388 14530388]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 4]]<br />
|2003<br />
|S.Basu & R.Weiss<br />
|Spatiotemporal control of gene expression with pulse-generating networks<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15096621 15096621]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 1]]<br />
|2005<br />
|S.Hooshangi & R.Weiss<br />
|Ultrasensitivity and noise propagation in a synthetic transcriptional cascade<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15738412 15738412]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 3]]<br />
|2006<br />
|H.Li & L.Petzold<br />
|Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems<br />
|[http://www.cs.ucsb.edu/~cse/Files/ldm0513.pdf Sto.Sim]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 2]]<br />
|2007<br />
|U.Alon<br />
|Network motifs : theory and experimental approaches<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17510665 117510665]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|J.Stricker & J.Hasty<br />
|A Fast Robust and Tunable synthetic gene oscillator<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18971928 18971928]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Vesicle biophysics model<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 6]]<br />
|1977<br />
|Harbich et al<br />
|Optical observation of rotationally symmetric lecithin vesicle shapes<br />
|J. Physique, 38:727–729<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 4]]<br />
|1987<br />
|Ou-Yang & Helfrich<br />
|Instability and deformation of a spherical vesicle by pressure<br />
|Phys. Rev. Lett., 59:2486-2488 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 1]]<br />
|1991<br />
|Lipowsky<br />
|The conformation of membranes<br />
|Nature, 349(6309):475-481<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 5]]<br />
|1995 <br />
|Fattal et al <br />
|The vesicle-micelle transition in mixed lipid-surfactant<br />
|Langmuir, 11:1154-1161 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 3]]<br />
|1998<br />
|Zhou et al<br />
|On the origin of membrane vesicles in gram-negative bacteria<br />
|FEMS microbiology letters, 163(2):223-228 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 8]]<br />
|2005 <br />
|Kuehn & Kesty<br />
|Bacterial outer membrane vesicles and the host pathogen interaction<br />
|Genes & Dev, 19:2645-2655 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 2]]<br />
|2008<br />
|Park & Uehara<br />
|How bacteria consume their own exoskeletons<br />
|Microbiol Mol Biol Rev, 72(2):211-227 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 7]]<br />
|2009<br />
|Deatherage et al <br />
|Biogenesis of bacterial membrane vesicles,<br />
|Mol Microbiol, 72(6):1395-1407<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 9]]<br />
|2009<br />
|Kumaran & Losick<br />
|Negative membrane curvature as a cue for subcellular localization of a bacterial protein.<br />
|PNAS USA, 106(32):13541-13545 <br />
|}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/PapersTeam:Paris/Papers2009-10-22T02:55:06Z<p>Christophe.R: /* OMV Adressing */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Papers#bottom | Papers]]<br />
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<br />
== '''OMV Overview''' ==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white; font-weight:bold; "<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px| []<br />
|1999<br />
|Terry J. Beveridge<br />
|Structures of gram-negative cell walls and their derived membrane vesicles.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93954 10438737]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Miller SI & Guina T.<br />
|Bacterial vesicle formation as a mechanism of protein transfer to animals.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14531993?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 14531993]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2005<br />
|Kuehn MJ & Kesty NC.<br />
|Bacterial outer membrane vesicles and the host-pathogen interaction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16291643?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16291643]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|McBroom AJ & Kuehn MJ.<br />
|Outer membrane vesicle production by Escherichia coli is independent of membrane instability.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16855227?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16855227]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 1]]<br />
|2007<br />
|McBroom AJ & Kuehn MJ.<br />
|Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17163978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17163978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 2]]<br />
|2009<br />
|Deatherage BL & Cookson BT.<br />
|Biogenesis of bacterial membrane vesicles<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19432795?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 19432795]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2009<br />
|Purnick PE & Weiss R.<br />
|The second wave of synthetic biology: from modules to systems.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19461664?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 19461664]<br />
|}<br />
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=='''OMV Production'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Mashburn-Warren L & Whiteley M.<br />
|Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18630345?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 18630345]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2001<br />
|Arora A. & Tamm LK.<br />
|Structure of outer membrane protein A transmembrane domain by NMR spectroscopy.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11276254?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 11276254]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|2007<br />
|Brown EA & Hardwidge PR.<br />
|Biochemical characterization of the enterotoxigenic Escherichia coli LeoA protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17975086?ordinalpos=16&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17975086]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2008<br />
|Burgess NK & Fleming KG.<br />
|Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18641391?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 18641391]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Tol/Pal<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|1986<br />
|Robert CHEN & Ulf HENNING.<br />
|Nucleotide sequence of the gene for the peptidoglycan-associated lipoprotein of Escherichia coli K12<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=210680 210680]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[3]]]<br />
|1995<br />
|Lazzaroni & Geli -<br />
|Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179564 179564]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|1999<br />
|Derouiche & Loret<br />
|Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10380085 10380085]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[4]]]<br />
|2001<br />
|Lloubès & RJournet L.<br />
|The Tol-Pal proteins of the Escherichia coli cell envelope: an energized system required for outer membrane integrity?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11501670 11501670]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|2002<br />
|Dubuisson JF & Lazzaroni JC.<br />
|Mutational analysis of the TolA C-terminal domain of Escherichia coli and genetic evidence for an interaction between TolA and TolB.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12142433 12142433]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2003<br />
|Llamas M & ARamos JL.<br />
|Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12896989 12896989]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[5]]]<br />
|2004<br />
|Henry T & Lloubès R.<br />
|Improved methods for producing outer membrane vesicles in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15249060 15249060]<br />
|}<br />
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==''' OMV Adressing '''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1997<br />
|Kadurugamuwa JL & Beveridge TJ.<br />
|Natural release of virulence factors in membrane vesicles by Pseudomonas aeruginosa and the effect of aminoglycoside antibiotics on their release.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9421308 9421308]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1998<br />
|Santini CL & Wu LF.<br />
|A novel sec-independent periplasmic protein translocation pathway in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9427745 9427745]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Berks BC & Palmer T.<br />
|The Tat protein export pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10652088 10652088]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Mishima Y & Murata K.<br />
|Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11731126 11731126]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Sargent F & Berks BC.<br />
|Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11422364 11422364]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Yahr TL & Wickner WT.<br />
|Functional reconstitution of bacterial Tat translocation in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11350936 11350936]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2004<br />
|Robinson C & Bolhuis A.<br />
|Tat-dependent protein targeting in prokaryotes and chloroplasts.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15546663 15546663]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Sargent F & Palmer T.<br />
|Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16445746 16445746]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Lee PA & Georgiou G.<br />
|The bacterial twin-arginine translocation pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16756481 16756481]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Maillard J & Sargent F.<br />
|Structural diversity in twin-arginine signal peptide-binding proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17901208 17901208]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Sargent F.<br />
|The twin-arginine transport system: moving folded proteins across membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17956229 17956229]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Ferrandez Y & Condemine G.<br />
|Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Pradel N & Bonnet R<br />
|Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|de Marco A.<br />
|Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19442264 19442264]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | ClyA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 5]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 1]]<br />
|2008<br />
|Kim JY & DeLisa MP.<br />
|Engineered bacterial outer membrane vesicles with enhanced functionality.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 1]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 2]]<br />
|2009<br />
|Mueller M & Ban N.<br />
|The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[Team:Paris/Addressing_overview4#top|[1]]]<br />
|2002<br />
|Wang Y.<br />
|The function of OmpA in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Dramsi S & Arthur M.<br />
|Covalent attachment of proteins to peptidoglycan.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18266854 18266854]<br />
|}<br />
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==''' OMV Reception'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Adhesin<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1989<br />
|Smeal T & Karin M.<br />
|Different requirements for formation of Jun:Jun and Jun:Fos complexes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1994<br />
|Heffernan EJ & Guiney DG.<br />
|Specificity of the complement resistance and cell association phenotypes encoded by the outer membrane protein genes rck from Salmonella typhimurium and ail from Yersinia enterocolitica.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7927803 7927803]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Veiga E & Fernández LA.<br />
|Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12949111 12949111]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 6]]<br />
|2004<br />
|Kesty NC & Kuehn MJ.<br />
|Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14578354 14578354]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | G3P<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1982<br />
|JEF D. BOEKE & PETER MODEL<br />
|A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 8]]<br />
|1999<br />
|Chatellier J & Riechmann L.<br />
|Interdomain interactions within the gene 3 protein of filamentous phage.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 9]]<br />
|1999<br />
|Lubkowski J & Wlodawer A.<br />
|Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 10]]<br />
|2002<br />
|Baek H & Cha S.<br />
|An improved helper phage system for efficient isolation of specific antibody molecules in phage display.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 11]]<br />
|2003<br />
|Karlsson F & Malmborg-Hager AC.<br />
|The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Snare<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 17]]<br />
|2000<br />
|Waters MG & Hughson FM.<br />
|Membrane tethering and fusion in the secretory and endocytic pathways.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Woodbury DJ & Rognlien K.<br />
|The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11067766 11067766]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2002<br />
|Bowen ME,Brunger AT.<br />
|Mutational analysis of synaptobrevin transmembrane domain oligomerization.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12501216 12501216]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Hu C & Rothman JE.<br />
|Fusion of cells by flipped SNAREs.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Weninger K & Brunger AT.<br />
|Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14657376 14657376]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006 <br />
|Giraudo CG & Rothman JE.<br />
|A clamping mechanism involved in SNARE-dependent exocytosis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16794037 16794037]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Low HH & Löwe J.<br />
|A bacterial dynamin-like protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17122778 17122778]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Weninger K & Brunger AT.<br />
|Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18275821 18275821]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Delevoye C & Subtil A.<br />
|SNARE protein mimicry by an intracellular bacterium.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18369472 18369472]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 18]]<br />
|2009<br />
|Giraudo CG & Rothman JE.<br />
|Alternative zippering as an on-off switch for SNARE-mediated fusion.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19164750 19164750]<br />
<br />
|}<br />
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==''' OMV Signal transduction'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1984<br />
|Lopilato JE & Beckwith JR.<br />
|D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6327616 6327616]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1995<br />
|Härle C & Braun V.<br />
|Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7729419 7729419]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1998<br />
|Tomii K & Kanehisa M.<br />
|A comparative analysis of ABC transporters in complete microbial genomes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1999<br />
|De Wulf P & Lin EC.<br />
|The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10542180 10542180]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Stock AM & Goudreau PN.<br />
|Two-component signal transduction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Yaron S & Matthews KR.<br />
|Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11010892 11010892]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2004<br />
|Dwyer MA & Hellinga HW.<br />
|Periplasmic binding proteins: a versatile superfamily for protein engineering.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15313245 15313245]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Braun V & Sauter A.<br />
|Gene regulation by transmembrane signaling.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16718597 16718597]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Baker MD & Stock JB<br />
|Signal transduction: networks and integrated circuits in bacterial cognition.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18054766 18054766]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Baker MD & Stock JB.<br />
|Systems biology of bacterial chemotaxis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16529985 16529985]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Ibrahim M & Monnet V.<br />
|Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17921293 17921293]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Kyriakidis DA & Tiligada E.<br />
|Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Tomii & Kanehisa<br />
|comparative analysis of ABC transporter<br />
|[http://genome.cshlp.org/content/8/10/1048.full.html#ref-list-1 pdf-link]<br />
|}<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
=='''Modelling'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Genetic Regulatory Network<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 1]]<br />
|1977<br />
|Gillespie Daniel T.<br />
|Exact Stochastic Simlation of Coupled Chemical Equations<br />
|[http://www.dna.caltech.edu/courses/cs191/paperscs191/gillespie2.pdf Gillespie1]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 3]]<br />
|1997<br />
|J.B. Andersen & S.Molin<br />
|New Stable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria<br />
|[http://aem.asm.org/cgi/reprint/64/6/2240.pdf LVA tag]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 6]]<br />
|1999<br />
|M.Ellowitz & S.Leibler<br />
|A Synthetic oscillatory network of transcriptionnal regulators <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10659856 10659856]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 2]]<br />
|1997<br />
|D.T.Gillespie<br />
|The Chemical Langevin Equation<br />
|[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000113000001000297000001&idtype=cvips&gifs=yes Gillespie2]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 5]]<br />
|2002<br />
|N.Rosenfold & U.Alon<br />
|Negative Autoregulation Speeds The Response TImes of Transcription Network <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12417193 2417193]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|M.B.Ellowitz & P.S.Swain<br />
|Stochastic Gene Expression In A Single Cell<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12183631 12183631]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 7]]<br />
|2003<br />
|S.Mangan & U.Alon<br />
|Structure and function ot the feed-forward Loop Network Motif<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14530388 14530388]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 4]]<br />
|2003<br />
|S.Basu & R.Weiss<br />
|Spatiotemporal control of gene expression with pulse-generating networks<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15096621 15096621]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 1]]<br />
|2005<br />
|S.Hooshangi & R.Weiss<br />
|Ultrasensitivity and noise propagation in a synthetic transcriptional cascade<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15738412 15738412]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 3]]<br />
|2006<br />
|H.Li & L.Petzold<br />
|Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems<br />
|[http://www.cs.ucsb.edu/~cse/Files/ldm0513.pdf Sto.Sim]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 2]]<br />
|2007<br />
|U.Alon<br />
|Network motifs : theory and experimental approaches<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17510665 117510665]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|J.Stricker & J.Hasty<br />
|A Fast Robust and Tunable synthetic gene oscillator<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18971928 18971928]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Vesicle biophysics model<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 6]]<br />
|1977<br />
|Harbich et al<br />
|Optical observation of rotationally symmetric lecithin vesicle shapes<br />
|J. Physique, 38:727–729<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 4]]<br />
|1987<br />
|Ou-Yang & Helfrich<br />
|Instability and deformation of a spherical vesicle by pressure<br />
|Phys. Rev. Lett., 59:2486-2488 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 1]]<br />
|1991<br />
|Lipowsky<br />
|The conformation of membranes<br />
|Nature, 349(6309):475-481<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 5]]<br />
|1995 <br />
|Fattal et al <br />
|The vesicle-micelle transition in mixed lipid-surfactant<br />
|Langmuir, 11:1154-1161 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 3]]<br />
|1998<br />
|Zhou et al<br />
|On the origin of membrane vesicles in gram-negative bacteria<br />
|FEMS microbiology letters, 163(2):223-228 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 8]]<br />
|2005 <br />
|Kuehn & Kesty<br />
|Bacterial outer membrane vesicles and the host pathogen interaction<br />
|Genes & Dev, 19:2645-2655 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 2]]<br />
|2008<br />
|Park & Uehara<br />
|How bacteria consume their own exoskeletons<br />
|Microbiol Mol Biol Rev, 72(2):211-227 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 7]]<br />
|2009<br />
|Deatherage et al <br />
|Biogenesis of bacterial membrane vesicles,<br />
|Mol Microbiol, 72(6):1395-1407<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 9]]<br />
|2009<br />
|Kumaran & Losick<br />
|Negative membrane curvature as a cue for subcellular localization of a bacterial protein.<br />
|PNAS USA, 106(32):13541-13545 <br />
|}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Addressing_overview4Team:Paris/Addressing overview42009-10-22T02:51:55Z<p>Christophe.R: </p>
<hr />
<div>{{Template:Paris2009}}<br />
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==Addressing the message to the outer membrane : OmpA==<br />
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<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Addressing_overview3#bottom"> ClyA</a>|<br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Addressing_overview4#bottom"> OmpA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview_Construction#bottom"> Construction</a><br />
</center><br />
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<br />
<br />
Outer membrane protein A (OmpA) as previously been used in protein fusion to expose heterologuous protein domains to the surface of ''Escherichia coli''. As an outer membrane protein, ompA could be incorporated into vesicles and is similarly to clyA also a good candidate for adressing protein domains to vesicles. <br />
<br />
<br />
<br />
[[Image:OmpA1.JPG|250px|left]][[Image:OmpA2.JPG|250px|right]]<br />
<br />
OmpA is a major protein in the Escherichia coli outer membrane. OmpA plays a vital structural role in ''E. coli'', and suggested that a perfect β-barrel structure of OmpA is important for outer membrane stability <sup>[[Team:Paris/Addressing_overview4#References|[1]]]</sup>. OmpA is the most well-studied outer membrane protein in ''E. coli''. This 325-residue protein was thought to contain two domains. The classic N-terminal domain, consisting of 171 amino acid residues, was shown to cross the membrane eight times in antiparallel β-strands with four relatively large and hydrophilic surface-exposed loops and short periplasmic turns<sup>[[Team:Paris/Addressing_overview4#References|[2]]]</sup>. The C-terminal domain is located in the periplasm, and binds to the peptidoglycan thus connecting it to the outer membrane<sup>[[Team:Paris/Addressing_overview4#References|[3]]]</sup>. The function of OmpA is thought to contribute to the structural integrity of the outer membrane<br />
along with murein lipoprotein<sup>[[Team:Paris/Addressing_overview4#References|[4]]]</sup> and peptidoglycanassociated lipoprotein . In addition to its structural role, OmpA serves as a receptor of colicin and several phages<sup>[[Team:Paris/Addressing_overview4#References|[5]]]</sup>, and it's required in F-conjugation<sup>[[Team:Paris/Addressing_overview4#References|[6]]]</sup>,<sup>[[Team:Paris/Addressing_overview4#References|[7]]]</sup><br />
<br />
<br />
<br />
<br />
<br />
<br />
{{Template:Paris2009_guided|Addressing_overview3#bottom|Addressing_overview2_strategy#bottom}}<br />
<br />
<br />
====References====<br />
<ol class="references"><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]Ying Wang, (2002) The Function of OmpA in Escherichia coli, Biochem Biophys Res Commun.292(2):396-401. [http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]Arora, A., Abildgaard, F., Bushweller, J. H., and Tamm, L. K. (2001) Structure of outer membrane protein A transmembrane domain by NMR spectroscopy. Nat. Struct. Biol 8, 334–338. [http://www.ncbi.nlm.nih.gov/pubmed/11276254 11276254] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]<br />
Koebnik, R. (1995) Proposal for a peptidoglycan associating alpha-helical motif in the C-terminal regions of some bacterial cell-surface proteins. Mol. Microbiol. 16, 1269–1270. [http://www.ncbi.nlm.nih.gov/pubmed/8577259 8577259] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]<br />
Braun, V., and Bosch, V. (1972) Sequence of the mureinlipoprotein and the attachment site of the lipid. Eur. J. Biochem. 28, 51–69. [http://www.ncbi.nlm.nih.gov/pubmed/4261992 4261992] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]<br />
Lazzaroni, J.-C., and Portalier, R. (1992) The excC gene of Escherichia coli K-12 required for cell envelope integrity encodes the peptidoglycan-associated lipoprotein. Mol. Microbiol. 6, 735–742. [http://www.ncbi.nlm.nih.gov/pubmed/1574003 1574003] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]Schweizer, M., and Henning, U. (1977) Action of major outer cell envelope membrane protein in conjugation of Escherichia coli K-12. J. Bacteriol. 129, 1651–1652. [http://www.ncbi.nlm.nih.gov/pubmed/321438 321438]</li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]Koebnik, R. (1999) Structural and functional roles of the surfaceexposed loops of the β-barrel membrane protein OmpA from Escherichia coli. J. Bacteriol. 181, 3688–3694.[http://www.ncbi.nlm.nih.gov/pubmed/10368142 10368142] </li><br />
</ol></div>Christophe.Rhttp://2009.igem.org/Team:Paris/Addressing_overview4Team:Paris/Addressing overview42009-10-22T02:51:29Z<p>Christophe.R: /* Addressing the message to the outer membrane : OmpA */</p>
<hr />
<div>{{Template:Paris2009}}<br />
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==Addressing the message to the outer membrane : OmpA==<br />
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<div id="left-side"></div><br />
<div id="middle-side"><center><br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2#bottom"> Main </a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Addressing_overview3#bottom"> ClyA</a>|<br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Addressing_overview4#bottom"> OmpA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview_Construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
</html><br />
<br />
<br />
Outer membrane protein A (OmpA) as previously been used in protein fusion to expose heterologuous protein domains to the surface of ''Escherichia coli''. As an outer membrane protein, ompA could be incorporated into vesicles and is similarly to clyA also a good candidate for adressing protein domains to vesicles. <br />
<br />
<br />
<br />
[[Image:OmpA1.JPG|250px|left]][[Image:OmpA2.JPG|250px|right]]<br />
<br />
OmpA is a major protein in the Escherichia coli outer membrane. OmpA plays a vital structural role in ''E. coli'', and suggested that a perfect β-barrel structure of OmpA is important for outer membrane stability <sup>[[Team:Paris/Addressing_overview4#References|[1]]]</sup>. OmpA is the most well-studied outer membrane protein in ''E. coli''. This 325-residue protein was thought to contain two domains. The classic N-terminal domain, consisting of 171 amino acid residues, was shown to cross the membrane eight times in antiparallel β-strands with four relatively large and hydrophilic surface-exposed loops and short periplasmic turns<sup>[[Team:Paris/Addressing_overview4#References|[2]]]</sup>. The C-terminal domain is located in the periplasm, and binds to the peptidoglycan thus connecting it to the outer membrane<sup>[[Team:Paris/Addressing_overview4#References|[3]]]</sup>. The function of OmpA is thought to contribute to the structural integrity of the outer membrane<br />
along with murein lipoprotein<sup>[[Team:Paris/Addressing_overview4#References|[4]]]</sup> and peptidoglycanassociated lipoprotein . In addition to its structural role, OmpA serves as a receptor of colicin and several phages<sup>[[Team:Paris/Addressing_overview4#References|[5]]]</sup>, and it's required in F-conjugation<sup>[[Team:Paris/Addressing_overview4#References|[6]]]</sup>,<sup>[[Team:Paris/Addressing_overview4#References|[7]]]</sup><br />
<br />
<br />
<br />
<br />
<br />
<br />
{{Template:Paris2009_guided|Addressing_overview3#bottom|Addressing_overview2_strategy#bottom}}<br />
<br />
<br />
====References====<br />
<ol class="references"><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]Ying Wang, (2002) The Function of OmpA in Escherichia coli, Biochem Biophys Res Commun.292(2):396-401. [http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]Arora, A., Abildgaard, F., Bushweller, J. H., and Tamm, L. K. (2001) Structure of outer membrane protein A transmembrane domain by NMR spectroscopy. Nat. Struct. Biol 8, 334–338. [http://www.ncbi.nlm.nih.gov/pubmed/11276254 11276254] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]<br />
Koebnik, R. (1995) Proposal for a peptidoglycan associating alpha-helical motif in the C-terminal regions of some bacterial cell-surface proteins. Mol. Microbiol. 16, 1269–1270. [http://www.ncbi.nlm.nih.gov/pubmed/8577259 8577259] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]<br />
Braun, V., and Bosch, V. (1972) Sequence of the mureinlipoprotein and the attachment site of the lipid. Eur. J. Biochem. 28, 51–69. [http://www.ncbi.nlm.nih.gov/pubmed/4261992 4261992] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]<br />
Lazzaroni, J.-C., and Portalier, R. (1992) The excC gene of Escherichia coli K-12 required for cell envelope integrity encodes the peptidoglycan-associated lipoprotein. Mol. Microbiol. 6, 735–742. [http://www.ncbi.nlm.nih.gov/pubmed/1574003 1574003] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]Schweizer, M., and Henning, U. (1977) Action of major outer cell envelope membrane protein in conjugation of Escherichia coli K-12. J. Bacteriol. 129, 1651–1652. [http://www.ncbi.nlm.nih.gov/pubmed/321438 321438]</li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]Koebnik, R. (1999) Structural and functional roles of the surfaceexposed loops of the β-barrel membrane protein OmpA from Escherichia coli. J. Bacteriol. 181, 3688–3694.[http://www.ncbi.nlm.nih.gov/pubmed/10368142 10368142] </li><br />
</ol></div>Christophe.Rhttp://2009.igem.org/Team:Paris/Addressing_overview3Team:Paris/Addressing overview32009-10-22T02:49:24Z<p>Christophe.R: </p>
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Addressing_overview3#bottom"> ClyA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview4#bottom"> OmpA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview_Construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
</html><br />
<br />
We work on the cell-cell communication using vesicle:<br />
<br><br />
In this part we look into adressing a protein into the sender outer membrane that could be incoporated into outer membrane vesicles (OMVs). This protein would then be able to transmit a message after the fusion of OMVs with a receiver cell.<br />
<br />
In this direction ClyA (the cytolysine A of E.Coli) seems to be a good candidate. ClyA is one of the proteins that has been previously detected into OMVs and is known to be specificly exported to the outer membrane <sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>. ClyA is thus expressed on bacteria and OMVs surface. Moreover, when ClyA is overproduced, it is accumulated into the periplasmic space<sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>.<br />
<br />
<br />
However there is an inconvenient to use this protein. ClyA is an alpha-Pore Forming Toxin (PFT). PFT are widely distributed proteins which form lesions in biological membranes. They exhibit their toxic effect in different manner. The first one is that ClyA allows the destruction of membrane permeability barrier. Furthermore, the toxic effect of ClyA could be explain by its capacity to deliver toxic component after the assembly of 8 or 13 of its subunits. PFTs can be subdivided into two classes; α-PFTs and β-PFTs, depending on the suspected mode of membrane integration, either by α-helical or β-sheet elements.<sup>[[Team:Paris/Addressing_overview3#References|[2]]]</sup><br />
<br />
[[Image:Clya_simple.jpg|ClyA subunit|150px|left]] [[Image:Clya_structure.jpg|ClyA assembled|150px|right]] [[Image:ClyA.jpg|ClyA are assembling in outer membrane of a host cell|150px|center]]<br />
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<br />
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Some article argue that E.Coli K12 use this ClyA to lyse other cell (specially mamalian cell or eurcaryote cell<sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>). But E. coli cells expressing clyA do not lyse each other.<br />
<br />
<br />
<br />
Kim et al. have successfully fused clyA to GFP in order to observe vesicles <sup>[[Team:Paris/Addressing_overview3#References|[1]]]</sup>, so we know that we can try to fuse clyA to a protein domain that would induce a signal transduction into the receiver cell. To see how we want to exploite clyA properties see [https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#Overview our strategy].<br />
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====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Kim, J.-Y. & DeLisa, M.P. Engineered bacterial outer membrane vesicles with enhanced functionality J.Mol. Biol. (2008) 380, 51–66. [http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]</li><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Muller, M. & Ban, N. The structure of a cytolytic a-helical toxin pore reveals its assembly mechanism Nature (4 June 2009) 459, 726-730. [http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]</li><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Wai, S.N. & Lindmark, B. Vesicle-Mediated Export and Assembly of Pore-Forming Oligomers of the Enterobacterial ClyA Cytotoxin Cell (October 2003), 115,25-35. [http://www.ncbi.nlm.nih.gov/pubmed/14532000 14532000]</li><br />
</ol></div>Christophe.Rhttp://2009.igem.org/Team:Paris/Addressing_overview3Team:Paris/Addressing overview32009-10-22T02:49:11Z<p>Christophe.R: </p>
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Addressing_overview3#bottom"> ClyA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview4#bottom"> OmpA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview_Construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
</html><br />
<br />
We work on the cell-cell communication using vesicle:<br />
<br><br />
In this part we look into adressing a protein into the sender outer membrane that could be incoporated into outer membrane vesicles (OMVs). This protein would then be able to transmit a message after the fusion of OMVs with a receiver cell.<br />
<br />
In this direction ClyA (the cytolysine A of E.Coli) seems to be a good candidate. ClyA is one of the proteins that has been previously detected into OMVs and is known to be specificly exported to the outer membrane <sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>. ClyA is thus expressed on bacteria and OMVs surface. Moreover, when ClyA is overproduced, it is accumulated into the periplasmic space<sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>.<br />
<br />
<br />
However there is an inconvenient to use this protein. ClyA is an alpha-Pore Forming Toxin (PFT). PFT are widely distributed proteins which form lesions in biological membranes. They exhibit their toxic effect in different manner. The first one is that ClyA allows the destruction of membrane permeability barrier. Furthermore, the toxic effect of ClyA could be explain by its capacity to deliver toxic component after the assembly of 8 or 13 of its subunits. PFTs can be subdivided into two classes; α-PFTs and β-PFTs, depending on the suspected mode of membrane integration, either by α-helical or β-sheet elements.<sup>[[Team:Paris/Addressing_overview3#References|[2]]]</sup><br />
<br />
[[Image:Clya_simple.jpg|ClyA subunit|150px|left]] [[Image:Clya_structure.jpg|ClyA assembled|150px|right]] [[Image:ClyA.jpg|ClyA are assembling in outer membrane of a host cell|150px|center]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Some article argue that E.Coli K12 use this ClyA to lyse other cell (specially mamalian cell or eurcaryote cell<sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>). But E. coli cells expressing clyA do not lyse each other.<br />
<br />
<br />
<br />
Kim et al. have successfully fused clyA to GFP in order to observe vesicles <sup>[[Team:Paris/Addressing_overview3#References|[1]]]</sup>, so we know that we can try to fuse clyA to a protein domain that would induce a signal transduction into the receiver cell. To see how we want to exploite clyA properties see [https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#Overview our strategy].<br />
<br />
<br />
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<br />
====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Kim, J.-Y. & DeLisa, M.P. Engineered bacterial outer membrane vesicles with enhanced functionality J.Mol. Biol. (2008) 380, 51–66. [http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]</li><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Muller, M. & Ban, N. The structure of a cytolytic a-helical toxin pore reveals its assembly mechanism Nature (4 June 2009) 459, 726-730. [http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]</li><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Wai, S.N. & Lindmark, B. Vesicle-Mediated Export and Assembly of Pore-Forming Oligomers of the Enterobacterial ClyA Cytotoxin Cell (October 2003), 115,25-35. [http://www.ncbi.nlm.nih.gov/pubmed/14532000 14532000]</li><br />
</ol></div>Christophe.Rhttp://2009.igem.org/Team:Paris/Addressing_overview4Team:Paris/Addressing overview42009-10-22T02:48:36Z<p>Christophe.R: /* Bibliography: */</p>
<hr />
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==Addressing the message to the outer membrane : OmpA==<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2#bottom"> Main </a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Addressing_overview3#bottom"> ClyA</a>|<br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Addressing_overview4#bottom"> OmpA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview_Construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
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<br />
Outer membrane protein A (OmpA) as previously been used in protein fusion to expose heterologuous protein domains to the surface of ''Escherichia coli''. As an outer membrane protein, ompA could be incorporated into vesicles and is similarly to clyA also a good candidate for adressing protein domains to vesicles. <br />
<br />
<br />
<br />
[[Image:OmpA1.JPG|250px|left]][[Image:OmpA2.JPG|250px|right]]<br />
<br />
OmpA is a major protein in the Escherichia coli outer membrane. OmpA plays a vital structural role in ''E. coli'', and suggested that a perfect β-barrel structure of OmpA is important for outer membrane stability[http://www.ncbi.nlm.nih.gov/pubmed/11906175[1]]. OmpA is the most well-studied outer membrane protein in ''E. coli''. This 325-residue protein was thought to contain two domains. The classic N-terminal domain, consisting of 171 amino acid residues, was shown to cross the membrane eight times in antiparallel β-strands with four relatively large and hydrophilic surface-exposed loops and short periplasmic turns[http://www.ncbi.nlm.nih.gov/pubmed/11276254[2]]. The C-terminal domain is located in the periplasm, and binds to the peptidoglycan thus connecting it to the outer membrane[http://www.ncbi.nlm.nih.gov/pubmed/8577259[3]]. The function of OmpA is thought to contribute to the structural integrity of the outer membrane<br />
along with murein lipoprotein[http://www.ncbi.nlm.nih.gov/pubmed/4261992[4]] and peptidoglycanassociated lipoprotein . In addition to its structural role, OmpA serves as a receptor of colicin and several phages[http://www.ncbi.nlm.nih.gov/pubmed/1574003[5]], and it's required in F-conjugation[http://www.ncbi.nlm.nih.gov/pubmed/321438[6]],[http://www.ncbi.nlm.nih.gov/pubmed/10368142[7]]<br />
<br />
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{{Template:Paris2009_guided|Addressing_overview3#bottom|Addressing_overview2_strategy#bottom}}<br />
<br />
<br />
====References====<br />
<ol class="references"><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]Ying Wang, (2002) The Function of OmpA in Escherichia coli, Biochem Biophys Res Commun.292(2):396-401. [http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]Arora, A., Abildgaard, F., Bushweller, J. H., and Tamm, L. K. (2001) Structure of outer membrane protein A transmembrane domain by NMR spectroscopy. Nat. Struct. Biol 8, 334–338. [http://www.ncbi.nlm.nih.gov/pubmed/11276254 11276254] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]<br />
Koebnik, R. (1995) Proposal for a peptidoglycan associating alpha-helical motif in the C-terminal regions of some bacterial cell-surface proteins. Mol. Microbiol. 16, 1269–1270. [http://www.ncbi.nlm.nih.gov/pubmed/8577259 8577259] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]<br />
Braun, V., and Bosch, V. (1972) Sequence of the mureinlipoprotein and the attachment site of the lipid. Eur. J. Biochem. 28, 51–69. [http://www.ncbi.nlm.nih.gov/pubmed/4261992 4261992] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]<br />
Lazzaroni, J.-C., and Portalier, R. (1992) The excC gene of Escherichia coli K-12 required for cell envelope integrity encodes the peptidoglycan-associated lipoprotein. Mol. Microbiol. 6, 735–742. [http://www.ncbi.nlm.nih.gov/pubmed/1574003 1574003] </li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]Schweizer, M., and Henning, U. (1977) Action of major outer cell envelope membrane protein in conjugation of Escherichia coli K-12. J. Bacteriol. 129, 1651–1652. [http://www.ncbi.nlm.nih.gov/pubmed/321438 321438]</li><br />
<li>[[Team:Paris/Addressing_overview4#1| ^]]Koebnik, R. (1999) Structural and functional roles of the surfaceexposed loops of the β-barrel membrane protein OmpA from Escherichia coli. J. Bacteriol. 181, 3688–3694.[http://www.ncbi.nlm.nih.gov/pubmed/10368142 10368142] </li><br />
</ol></div>Christophe.Rhttp://2009.igem.org/Team:Paris/PapersTeam:Paris/Papers2009-10-22T02:44:55Z<p>Christophe.R: /* OMV Adressing */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Papers#bottom | Papers]]<br />
{{Template:Paris2009}}<br />
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<br />
== '''OMV Overview''' ==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white; font-weight:bold; "<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px| []<br />
|1999<br />
|Terry J. Beveridge<br />
|Structures of gram-negative cell walls and their derived membrane vesicles.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93954 10438737]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Miller SI & Guina T.<br />
|Bacterial vesicle formation as a mechanism of protein transfer to animals.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14531993?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 14531993]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2005<br />
|Kuehn MJ & Kesty NC.<br />
|Bacterial outer membrane vesicles and the host-pathogen interaction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16291643?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16291643]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|McBroom AJ & Kuehn MJ.<br />
|Outer membrane vesicle production by Escherichia coli is independent of membrane instability.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16855227?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16855227]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 1]]<br />
|2007<br />
|McBroom AJ & Kuehn MJ.<br />
|Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17163978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17163978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 2]]<br />
|2009<br />
|Deatherage BL & Cookson BT.<br />
|Biogenesis of bacterial membrane vesicles<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19432795?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 19432795]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2009<br />
|Purnick PE & Weiss R.<br />
|The second wave of synthetic biology: from modules to systems.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19461664?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 19461664]<br />
|}<br />
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=='''OMV Production'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Mashburn-Warren L & Whiteley M.<br />
|Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18630345?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 18630345]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2001<br />
|Arora A. & Tamm LK.<br />
|Structure of outer membrane protein A transmembrane domain by NMR spectroscopy.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11276254?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 11276254]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|2007<br />
|Brown EA & Hardwidge PR.<br />
|Biochemical characterization of the enterotoxigenic Escherichia coli LeoA protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17975086?ordinalpos=16&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17975086]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2008<br />
|Burgess NK & Fleming KG.<br />
|Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18641391?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 18641391]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Tol/Pal<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|1986<br />
|Robert CHEN & Ulf HENNING.<br />
|Nucleotide sequence of the gene for the peptidoglycan-associated lipoprotein of Escherichia coli K12<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=210680 210680]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[3]]]<br />
|1995<br />
|Lazzaroni & Geli -<br />
|Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179564 179564]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|1999<br />
|Derouiche & Loret<br />
|Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10380085 10380085]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[4]]]<br />
|2001<br />
|Lloubès & RJournet L.<br />
|The Tol-Pal proteins of the Escherichia coli cell envelope: an energized system required for outer membrane integrity?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11501670 11501670]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|2002<br />
|Dubuisson JF & Lazzaroni JC.<br />
|Mutational analysis of the TolA C-terminal domain of Escherichia coli and genetic evidence for an interaction between TolA and TolB.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12142433 12142433]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2003<br />
|Llamas M & ARamos JL.<br />
|Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12896989 12896989]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[5]]]<br />
|2004<br />
|Henry T & Lloubès R.<br />
|Improved methods for producing outer membrane vesicles in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15249060 15249060]<br />
|}<br />
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==''' OMV Adressing '''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1997<br />
|Kadurugamuwa JL & Beveridge TJ.<br />
|Natural release of virulence factors in membrane vesicles by Pseudomonas aeruginosa and the effect of aminoglycoside antibiotics on their release.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9421308 9421308]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1998<br />
|Santini CL & Wu LF.<br />
|A novel sec-independent periplasmic protein translocation pathway in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9427745 9427745]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Berks BC & Palmer T.<br />
|The Tat protein export pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10652088 10652088]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Mishima Y & Murata K.<br />
|Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11731126 11731126]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Sargent F & Berks BC.<br />
|Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11422364 11422364]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Yahr TL & Wickner WT.<br />
|Functional reconstitution of bacterial Tat translocation in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11350936 11350936]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2004<br />
|Robinson C & Bolhuis A.<br />
|Tat-dependent protein targeting in prokaryotes and chloroplasts.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15546663 15546663]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Sargent F & Palmer T.<br />
|Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16445746 16445746]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Lee PA & Georgiou G.<br />
|The bacterial twin-arginine translocation pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16756481 16756481]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Maillard J & Sargent F.<br />
|Structural diversity in twin-arginine signal peptide-binding proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17901208 17901208]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Sargent F.<br />
|The twin-arginine transport system: moving folded proteins across membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17956229 17956229]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Ferrandez Y & Condemine G.<br />
|Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Pradel N & Bonnet R<br />
|Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|de Marco A.<br />
|Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19442264 19442264]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | ClyA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 5]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 1]]<br />
|2008<br />
|Kim JY & DeLisa MP.<br />
|Engineered bacterial outer membrane vesicles with enhanced functionality.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 1]] [[https://2009.igem.org/Team:Paris/Addressing_overview3#top 2]]<br />
|2009<br />
|Mueller M & Ban N.<br />
|The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|Wang Y.<br />
|The function of OmpA in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Dramsi S & Arthur M.<br />
|Covalent attachment of proteins to peptidoglycan.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18266854 18266854]<br />
|}<br />
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==''' OMV Reception'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Adhesin<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1989<br />
|Smeal T & Karin M.<br />
|Different requirements for formation of Jun:Jun and Jun:Fos complexes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1994<br />
|Heffernan EJ & Guiney DG.<br />
|Specificity of the complement resistance and cell association phenotypes encoded by the outer membrane protein genes rck from Salmonella typhimurium and ail from Yersinia enterocolitica.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7927803 7927803]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Veiga E & Fernández LA.<br />
|Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12949111 12949111]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 6]]<br />
|2004<br />
|Kesty NC & Kuehn MJ.<br />
|Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14578354 14578354]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | G3P<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1982<br />
|JEF D. BOEKE & PETER MODEL<br />
|A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 8]]<br />
|1999<br />
|Chatellier J & Riechmann L.<br />
|Interdomain interactions within the gene 3 protein of filamentous phage.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 9]]<br />
|1999<br />
|Lubkowski J & Wlodawer A.<br />
|Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 10]]<br />
|2002<br />
|Baek H & Cha S.<br />
|An improved helper phage system for efficient isolation of specific antibody molecules in phage display.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 11]]<br />
|2003<br />
|Karlsson F & Malmborg-Hager AC.<br />
|The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Snare<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 17]]<br />
|2000<br />
|Waters MG & Hughson FM.<br />
|Membrane tethering and fusion in the secretory and endocytic pathways.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Woodbury DJ & Rognlien K.<br />
|The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11067766 11067766]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2002<br />
|Bowen ME,Brunger AT.<br />
|Mutational analysis of synaptobrevin transmembrane domain oligomerization.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12501216 12501216]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Hu C & Rothman JE.<br />
|Fusion of cells by flipped SNAREs.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Weninger K & Brunger AT.<br />
|Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14657376 14657376]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006 <br />
|Giraudo CG & Rothman JE.<br />
|A clamping mechanism involved in SNARE-dependent exocytosis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16794037 16794037]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Low HH & Löwe J.<br />
|A bacterial dynamin-like protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17122778 17122778]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Weninger K & Brunger AT.<br />
|Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18275821 18275821]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Delevoye C & Subtil A.<br />
|SNARE protein mimicry by an intracellular bacterium.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18369472 18369472]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 18]]<br />
|2009<br />
|Giraudo CG & Rothman JE.<br />
|Alternative zippering as an on-off switch for SNARE-mediated fusion.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19164750 19164750]<br />
<br />
|}<br />
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==''' OMV Signal transduction'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1984<br />
|Lopilato JE & Beckwith JR.<br />
|D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6327616 6327616]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1995<br />
|Härle C & Braun V.<br />
|Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7729419 7729419]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1998<br />
|Tomii K & Kanehisa M.<br />
|A comparative analysis of ABC transporters in complete microbial genomes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1999<br />
|De Wulf P & Lin EC.<br />
|The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10542180 10542180]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Stock AM & Goudreau PN.<br />
|Two-component signal transduction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Yaron S & Matthews KR.<br />
|Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11010892 11010892]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2004<br />
|Dwyer MA & Hellinga HW.<br />
|Periplasmic binding proteins: a versatile superfamily for protein engineering.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15313245 15313245]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Braun V & Sauter A.<br />
|Gene regulation by transmembrane signaling.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16718597 16718597]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Baker MD & Stock JB<br />
|Signal transduction: networks and integrated circuits in bacterial cognition.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18054766 18054766]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Baker MD & Stock JB.<br />
|Systems biology of bacterial chemotaxis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16529985 16529985]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Ibrahim M & Monnet V.<br />
|Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17921293 17921293]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Kyriakidis DA & Tiligada E.<br />
|Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Tomii & Kanehisa<br />
|comparative analysis of ABC transporter<br />
|[http://genome.cshlp.org/content/8/10/1048.full.html#ref-list-1 pdf-link]<br />
|}<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
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<br />
=='''Modelling'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Genetic Regulatory Network<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 1]]<br />
|1977<br />
|Gillespie Daniel T.<br />
|Exact Stochastic Simlation of Coupled Chemical Equations<br />
|[http://www.dna.caltech.edu/courses/cs191/paperscs191/gillespie2.pdf Gillespie1]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 3]]<br />
|1997<br />
|J.B. Andersen & S.Molin<br />
|New Stable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria<br />
|[http://aem.asm.org/cgi/reprint/64/6/2240.pdf LVA tag]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 6]]<br />
|1999<br />
|M.Ellowitz & S.Leibler<br />
|A Synthetic oscillatory network of transcriptionnal regulators <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10659856 10659856]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 2]]<br />
|1997<br />
|D.T.Gillespie<br />
|The Chemical Langevin Equation<br />
|[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000113000001000297000001&idtype=cvips&gifs=yes Gillespie2]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 5]]<br />
|2002<br />
|N.Rosenfold & U.Alon<br />
|Negative Autoregulation Speeds The Response TImes of Transcription Network <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12417193 2417193]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|M.B.Ellowitz & P.S.Swain<br />
|Stochastic Gene Expression In A Single Cell<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12183631 12183631]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 7]]<br />
|2003<br />
|S.Mangan & U.Alon<br />
|Structure and function ot the feed-forward Loop Network Motif<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14530388 14530388]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 4]]<br />
|2003<br />
|S.Basu & R.Weiss<br />
|Spatiotemporal control of gene expression with pulse-generating networks<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15096621 15096621]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 1]]<br />
|2005<br />
|S.Hooshangi & R.Weiss<br />
|Ultrasensitivity and noise propagation in a synthetic transcriptional cascade<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15738412 15738412]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 3]]<br />
|2006<br />
|H.Li & L.Petzold<br />
|Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems<br />
|[http://www.cs.ucsb.edu/~cse/Files/ldm0513.pdf Sto.Sim]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 2]]<br />
|2007<br />
|U.Alon<br />
|Network motifs : theory and experimental approaches<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17510665 117510665]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|J.Stricker & J.Hasty<br />
|A Fast Robust and Tunable synthetic gene oscillator<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18971928 18971928]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Vesicle biophysics model<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 6]]<br />
|1977<br />
|Harbich et al<br />
|Optical observation of rotationally symmetric lecithin vesicle shapes<br />
|J. Physique, 38:727–729<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 4]]<br />
|1987<br />
|Ou-Yang & Helfrich<br />
|Instability and deformation of a spherical vesicle by pressure<br />
|Phys. Rev. Lett., 59:2486-2488 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 1]]<br />
|1991<br />
|Lipowsky<br />
|The conformation of membranes<br />
|Nature, 349(6309):475-481<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 5]]<br />
|1995 <br />
|Fattal et al <br />
|The vesicle-micelle transition in mixed lipid-surfactant<br />
|Langmuir, 11:1154-1161 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 3]]<br />
|1998<br />
|Zhou et al<br />
|On the origin of membrane vesicles in gram-negative bacteria<br />
|FEMS microbiology letters, 163(2):223-228 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 8]]<br />
|2005 <br />
|Kuehn & Kesty<br />
|Bacterial outer membrane vesicles and the host pathogen interaction<br />
|Genes & Dev, 19:2645-2655 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 2]]<br />
|2008<br />
|Park & Uehara<br />
|How bacteria consume their own exoskeletons<br />
|Microbiol Mol Biol Rev, 72(2):211-227 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 7]]<br />
|2009<br />
|Deatherage et al <br />
|Biogenesis of bacterial membrane vesicles,<br />
|Mol Microbiol, 72(6):1395-1407<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 9]]<br />
|2009<br />
|Kumaran & Losick<br />
|Negative membrane curvature as a cue for subcellular localization of a bacterial protein.<br />
|PNAS USA, 106(32):13541-13545 <br />
|}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Addressing_overview3Team:Paris/Addressing overview32009-10-22T02:43:30Z<p>Christophe.R: /* Addressing the message in the outer membrane : ClyA */</p>
<hr />
<div>{{Template:Paris2009}}<br />
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<br />
==Addressing the message in the outer membrane : ClyA==<br />
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<div id="middle-side"><center><br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Addressing_overview3#bottom"> ClyA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview4#bottom"> OmpA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview_Construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
</html><br />
<br />
We work on the cell-cell communication using vesicle:<br />
<br><br />
In this part we look into adressing a protein into the sender outer membrane that could be incoporated into outer membrane vesicles (OMVs). This protein would then be able to transmit a message after the fusion of OMVs with a receiver cell.<br />
<br />
In this direction ClyA (the cytolysine A of E.Coli) seems to be a good candidate. ClyA is one of the proteins that has been previously detected into OMVs and is known to be specificly exported to the outer membrane <sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>. ClyA is thus expressed on bacteria and OMVs surface. Moreover, when ClyA is overproduced, it is accumulated into the periplasmic space<sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>.<br />
<br />
<br />
However there is an inconvenient to use this protein. ClyA is an alpha-Pore Forming Toxin (PFT). PFT are widely distributed proteins which form lesions in biological membranes. They exhibit their toxic effect in different manner. The first one is that ClyA allows the destruction of membrane permeability barrier. Furthermore, the toxic effect of ClyA could be explain by its capacity to deliver toxic component after the assembly of 8 or 13 of its subunits. PFTs can be subdivided into two classes; α-PFTs and β-PFTs, depending on the suspected mode of membrane integration, either by α-helical or β-sheet elements.<sup>[[Team:Paris/Addressing_overview3#References|[2]]]</sup><br />
<br />
[[Image:Clya_simple.jpg|ClyA subunit|150px|left]] [[Image:Clya_structure.jpg|ClyA assembled|150px|right]] [[Image:ClyA.jpg|ClyA are assembling in outer membrane of a host cell|150px|center]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Some article argue that E.Coli K12 use this ClyA to lyse other cell (specially mamalian cell or eurcaryote cell<sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>). But E. coli cells expressing clyA do not lyse each other.<br />
<br />
<br />
<br />
Kim et al. have successfully fused clyA to GFP in order to observe vesicles <sup>[[Team:Paris/Addressing_overview3#References|[1]]]</sup>, so we know that we can try to fuse clyA to a protein domain that would induce a signal transduction into the receiver cell. To see how we want to exploite clyA properties see [https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#Overview our strategy].<br />
<br />
<br />
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<br />
====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Kim, J.-Y. & DeLisa, M.P. Engineered bacterial outer membrane vesicles with enhanced functionality J.Mol. Biol. (2008) 380, 51–66. [http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]</li><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Muller, M. & Ban, N. The structure of a cytolytic a-helical toxin pore reveals its assembly mechanism Nature (4 June 2009) 459, 726-730. [http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]</li><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Wai, S.N. & Lindmark, B. Vesicle-Mediated Export and Assembly of Pore-Forming Oligomers of the Enterobacterial ClyA Cytotoxin Cell (October 2003), 115,25-35. [http://www.ncbi.nlm.nih.gov/pubmed/14532000 14532000]</li><br />
</ol></div>Christophe.Rhttp://2009.igem.org/Team:Paris/Addressing_overview3Team:Paris/Addressing overview32009-10-22T02:43:16Z<p>Christophe.R: /* References */</p>
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==Addressing the message in the outer membrane : ClyA==<br />
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<div id="left-side"></div><br />
<div id="middle-side"><center><br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Addressing_overview3#bottom"> ClyA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview4#bottom"> OmpA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview_Construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
</html><br />
<br />
We work on the cell-cell communication using vesicle:<br />
<br><br />
In this part we look into adressing a protein into the sender outer membrane that could be incoporated into outer membrane vesicles (OMVs). This protein would then be able to transmit a message after the fusion of OMVs with a receiver cell.<br />
<br />
In this direction ClyA (the cytolysine A of E.Coli) seems to be a good candidate. ClyA is one of the proteins that has been previously detected into OMVs and is known to be specificly exported to the outer membrane <sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>. ClyA is thus expressed on bacteria and OMVs surface. Moreover, when ClyA is overproduced, it is accumulated into the periplasmic space<sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>.<br />
<br />
<br />
However there is an inconvenient to use this protein. ClyA is an alpha-Pore Forming Toxin (PFT). PFT are widely distributed proteins which form lesions in biological membranes. They exhibit their toxic effect in different manner. The first one is that ClyA allows the destruction of membrane permeability barrier. Furthermore, the toxic effect of ClyA could be explain by its capacity to deliver toxic component after the assembly of 8 or 13 of its subunits. PFTs can be subdivided into two classes; α-PFTs and β-PFTs, depending on the suspected mode of membrane integration, either by α-helical or β-sheet elements.<sup>[[Team:Paris/Addressing_overview3#References|[2]]]</sup><br />
<br />
[[Image:Clya_simple.jpg|ClyA subunit|150px|left]] [[Image:Clya_structure.jpg|ClyA assembled|150px|right]] [[Image:ClyA.jpg|ClyA are assembling in outer membrane of a host cell|150px|center]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Some article argue that E.Coli K12 use this ClyA to lyse other cell (specially mamalian cell or eurcaryote cell<sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>). But E. coli cells expressing clyA do not lyse each other.<br />
<br />
<br />
<br />
Kim et al. have successfully fused clyA to GFP in order to observe vesicles <sup>[[Team:Paris/Addressing_overview3#References|[1]]]</sup>, so we know that we can try to fuse clyA to a protein domain that would induce a signal transduction into the receiver cell. To see how we want to exploite clyA properties see [https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#Overview our strategy].<br />
<br />
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<div id="paris_content_boxtop"><br />
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<div id="paris_content"><br />
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<br />
====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Kim, J.-Y. & DeLisa, M.P. Engineered bacterial outer membrane vesicles with enhanced functionality J.Mol. Biol. (2008) 380, 51–66. [http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]</li><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Muller, M. & Ban, N. The structure of a cytolytic a-helical toxin pore reveals its assembly mechanism Nature (4 June 2009) 459, 726-730. [http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]</li><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Wai, S.N. & Lindmark, B. Vesicle-Mediated Export and Assembly of Pore-Forming Oligomers of the Enterobacterial ClyA Cytotoxin Cell (October 2003), 115,25-35. [http://www.ncbi.nlm.nih.gov/pubmed/14532000 14532000]</li><br />
</ol></div>Christophe.Rhttp://2009.igem.org/Team:Paris/Addressing_overview3Team:Paris/Addressing overview32009-10-22T02:42:57Z<p>Christophe.R: </p>
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==Addressing the message in the outer membrane : ClyA==<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Addressing_overview3#bottom"> ClyA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview4#bottom"> OmpA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview_Construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
</html><br />
<br />
We work on the cell-cell communication using vesicle:<br />
<br><br />
In this part we look into adressing a protein into the sender outer membrane that could be incoporated into outer membrane vesicles (OMVs). This protein would then be able to transmit a message after the fusion of OMVs with a receiver cell.<br />
<br />
In this direction ClyA (the cytolysine A of E.Coli) seems to be a good candidate. ClyA is one of the proteins that has been previously detected into OMVs and is known to be specificly exported to the outer membrane <sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>. ClyA is thus expressed on bacteria and OMVs surface. Moreover, when ClyA is overproduced, it is accumulated into the periplasmic space<sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>.<br />
<br />
<br />
However there is an inconvenient to use this protein. ClyA is an alpha-Pore Forming Toxin (PFT). PFT are widely distributed proteins which form lesions in biological membranes. They exhibit their toxic effect in different manner. The first one is that ClyA allows the destruction of membrane permeability barrier. Furthermore, the toxic effect of ClyA could be explain by its capacity to deliver toxic component after the assembly of 8 or 13 of its subunits. PFTs can be subdivided into two classes; α-PFTs and β-PFTs, depending on the suspected mode of membrane integration, either by α-helical or β-sheet elements.<sup>[[Team:Paris/Addressing_overview3#References|[2]]]</sup><br />
<br />
[[Image:Clya_simple.jpg|ClyA subunit|150px|left]] [[Image:Clya_structure.jpg|ClyA assembled|150px|right]] [[Image:ClyA.jpg|ClyA are assembling in outer membrane of a host cell|150px|center]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Some article argue that E.Coli K12 use this ClyA to lyse other cell (specially mamalian cell or eurcaryote cell<sup>[[Team:Paris/Addressing_overview3#References|[3]]]</sup>). But E. coli cells expressing clyA do not lyse each other.<br />
<br />
<br />
<br />
Kim et al. have successfully fused clyA to GFP in order to observe vesicles <sup>[[Team:Paris/Addressing_overview3#References|[1]]]</sup>, so we know that we can try to fuse clyA to a protein domain that would induce a signal transduction into the receiver cell. To see how we want to exploite clyA properties see [https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#Overview our strategy].<br />
<br />
<br />
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</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
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<br />
<br />
====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Kim, J.-Y. & DeLisa, M.P. Engineered bacterial outer membrane vesicles with enhanced functionality J.Mol. Biol. (2008) 380, 51–66. [http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]</li><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Muller, M. & Ban, N. The structure of a cytolytic a-helical toxin pore reveals its assembly mechanism Nature (4 June 2009) 459, 726-730. [http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]</li><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Wai, S.N. & Lindmark, B. Vesicle-Mediated Export and Assembly of Pore-Forming Oligomers of the Enterobacterial ClyA Cytotoxin Cell (October 2003), 115,25-35. [http://www.ncbi.nlm.nih.gov/pubmed/14532000 14532000]</li><br />
</ol><br />
<br />
<br />
<br />
<br />
<br />
<br />
{{Template:Paris2009_guided|Addressing_overview2#bottom|Addressing_overview4#bottom}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Addressing_overview3Team:Paris/Addressing overview32009-10-22T02:41:47Z<p>Christophe.R: </p>
<hr />
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==Addressing the message in the outer membrane : ClyA==<br />
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<div id="left-side"></div><br />
<div id="middle-side"><center><br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Addressing_overview3#bottom"> ClyA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview4#bottom"> OmpA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview_Construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
</html><br />
<br />
We work on the cell-cell communication using vesicle:<br />
<br><br />
In this part we look into adressing a protein into the sender outer membrane that could be incoporated into outer membrane vesicles (OMVs). This protein would then be able to transmit a message after the fusion of OMVs with a receiver cell.<br />
<br />
In this direction ClyA (the cytolysine A of E.Coli) seems to be a good candidate. ClyA is one of the proteins that has been previously detected into OMVs and is known to be specificly exported to the outer membrane <sup>[[Team:Paris//Addressing_overview3#References|[3]]]</sup>. ClyA is thus expressed on bacteria and OMVs surface. Moreover, when ClyA is overproduced, it is accumulated into the periplasmic space [http://www.ncbi.nlm.nih.gov/pubmed/14532000 [3]].<br />
<br />
<br />
However there is an inconvenient to use this protein. ClyA is an alpha-Pore Forming Toxin (PFT). PFT are widely distributed proteins which form lesions in biological membranes. They exhibit their toxic effect in different manner. The first one is that ClyA allows the destruction of membrane permeability barrier. Furthermore, the toxic effect of ClyA could be explain by its capacity to deliver toxic component after the assembly of 8 or 13 of its subunits. PFTs can be subdivided into two classes; α-PFTs and β-PFTs, depending on the suspected mode of membrane integration, either by α-helical or β-sheet elements.<sup>[[Team:Paris//Addressing_overview3#References|[2]]]</sup><br />
<br />
[[Image:Clya_simple.jpg|ClyA subunit|150px|left]] [[Image:Clya_structure.jpg|ClyA assembled|150px|right]] [[Image:ClyA.jpg|ClyA are assembling in outer membrane of a host cell|150px|center]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Some article argue that E.Coli K12 use this ClyA to lyse other cell (specially mamalian cell or eurcaryote cell<sup>[[Team:Paris//Addressing_overview3#References|[3]]]</sup>). But E. coli cells expressing clyA do not lyse each other.<br />
<br />
<br />
<br />
Kim et al. have successfully fused clyA to GFP in order to observe vesicles <sup>[[Team:Paris//Addressing_overview3#References|[1]]]</sup>, so we know that we can try to fuse clyA to a protein domain that would induce a signal transduction into the receiver cell. To see how we want to exploite clyA properties see [https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#Overview our strategy].<br />
<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
<br />
====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Kim, J.-Y. & DeLisa, M.P. Engineered bacterial outer membrane vesicles with enhanced functionality J.Mol. Biol. (2008) 380, 51–66. [http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]</li><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Muller, M. & Ban, N. The structure of a cytolytic a-helical toxin pore reveals its assembly mechanism Nature (4 June 2009) 459, 726-730. [http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]</li><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Wai, S.N. & Lindmark, B. Vesicle-Mediated Export and Assembly of Pore-Forming Oligomers of the Enterobacterial ClyA Cytotoxin Cell (October 2003), 115,25-35. [http://www.ncbi.nlm.nih.gov/pubmed/14532000 14532000]</li><br />
</ol><br />
<br />
<br />
<br />
<br />
<br />
<br />
{{Template:Paris2009_guided|Addressing_overview2#bottom|Addressing_overview4#bottom}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Addressing_overview3Team:Paris/Addressing overview32009-10-22T02:39:36Z<p>Christophe.R: /* Bibliography : */</p>
<hr />
<div>{{Template:Paris2009}}<br />
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<br />
==Addressing the message in the outer membrane : ClyA==<br />
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</style><br />
<div id="left-side"></div><br />
<div id="middle-side"><center><br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2#bottom"> Main </a>|<br />
<a class="menu_sub_active" href="https://2009.igem.org/Team:Paris/Addressing_overview3#bottom"> ClyA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview4#bottom"> OmpA</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Addressing_overview_Construction#bottom"> Construction</a><br />
</center><br />
</div><br />
<div id="right-side"></div><br />
</html><br />
<br />
We work on the cell-cell communication using vesicle:<br />
<br><br />
In this part we look into adressing a protein into the sender outer membrane that could be incoporated into outer membrane vesicles (OMVs). This protein would then be able to transmit a message after the fusion of OMVs with a receiver cell.<br />
<br />
In this direction ClyA (the cytolysine A of E.Coli) seems to be a good candidate. ClyA is one of the proteins that has been previously detected into OMVs and is known to be specificly exported to the outer membrane [http://www.ncbi.nlm.nih.gov/pubmed/14532000 [3]]. ClyA is thus expressed on bacteria and OMVs surface. Moreover, when ClyA is overproduced, it is accumulated into the periplasmic space [http://www.ncbi.nlm.nih.gov/pubmed/14532000 [3]].<br />
<br />
<br />
However there is an inconvenient to use this protein. ClyA is an alpha-Pore Forming Toxin (PFT). PFT are widely distributed proteins which form lesions in biological membranes. They exhibit their toxic effect in different manner. The first one is that ClyA allows the destruction of membrane permeability barrier. Furthermore, the toxic effect of ClyA could be explain by its capacity to deliver toxic component after the assembly of 8 or 13 of its subunits. PFTs can be subdivided into two classes; α-PFTs and β-PFTs, depending on the suspected mode of membrane integration, either by α-helical or β-sheet elements.[http://www.ncbi.nlm.nih.gov/pubmed/19421192 [2]]<br />
<br />
[[Image:Clya_simple.jpg|ClyA subunit|150px|left]] [[Image:Clya_structure.jpg|ClyA assembled|150px|right]] [[Image:ClyA.jpg|ClyA are assembling in outer membrane of a host cell|150px|center]]<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
<br />
Some article argue that E.Coli K12 use this ClyA to lyse other cell (specially mamalian cell or eurcaryote cell[http://www.ncbi.nlm.nih.gov/pubmed/14532000 [3]]). But E. coli cells expressing clyA do not lyse each other.<br />
<br />
<br />
<br />
Kim et al. have successfully fused clyA to GFP in order to observe vesicles [http://www.ncbi.nlm.nih.gov/pubmed/18511069 [1]], so we know that we can try to fuse clyA to a protein domain that would induce a signal transduction into the receiver cell. To see how we want to exploite clyA properties see [https://2009.igem.org/Team:Paris/Addressing_overview2_strategy#Overview our strategy].<br />
<br />
<br />
<br />
<br />
<br />
====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Kim, J.-Y. & DeLisa, M.P. Engineered bacterial outer membrane vesicles with enhanced functionality J.Mol. Biol. (2008) 380, 51–66. [http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]</li><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Muller, M. & Ban, N. The structure of a cytolytic a-helical toxin pore reveals its assembly mechanism Nature (4 June 2009) 459, 726-730. [http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]</li><br />
<li>[[Team:Paris/Addressing_overview3#1| ^]]Wai, S.N. & Lindmark, B. Vesicle-Mediated Export and Assembly of Pore-Forming Oligomers of the Enterobacterial ClyA Cytotoxin Cell (October 2003), 115,25-35. [http://www.ncbi.nlm.nih.gov/pubmed/14532000 14532000]</li><br />
</ol><br />
<br />
<br />
<br />
<br />
<br />
<br />
{{Template:Paris2009_guided|Addressing_overview2#bottom|Addressing_overview4#bottom}}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/PapersTeam:Paris/Papers2009-10-22T02:37:14Z<p>Christophe.R: /* OMV Reception */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Papers#bottom | Papers]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
== '''OMV Overview''' ==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white; font-weight:bold; "<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px| []<br />
|1999<br />
|Terry J. Beveridge<br />
|Structures of gram-negative cell walls and their derived membrane vesicles.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93954 10438737]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Miller SI & Guina T.<br />
|Bacterial vesicle formation as a mechanism of protein transfer to animals.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14531993?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 14531993]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2005<br />
|Kuehn MJ & Kesty NC.<br />
|Bacterial outer membrane vesicles and the host-pathogen interaction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16291643?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16291643]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|McBroom AJ & Kuehn MJ.<br />
|Outer membrane vesicle production by Escherichia coli is independent of membrane instability.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16855227?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16855227]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 1]]<br />
|2007<br />
|McBroom AJ & Kuehn MJ.<br />
|Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17163978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17163978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 2]]<br />
|2009<br />
|Deatherage BL & Cookson BT.<br />
|Biogenesis of bacterial membrane vesicles<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19432795?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 19432795]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2009<br />
|Purnick PE & Weiss R.<br />
|The second wave of synthetic biology: from modules to systems.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19461664?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 19461664]<br />
|}<br />
<br />
<html><br />
</div><br />
<div id="paris_content_boxtop"><br />
</div><br />
<div id="paris_content"><br />
</html><br />
<br />
=='''OMV Production'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Mashburn-Warren L & Whiteley M.<br />
|Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18630345?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 18630345]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2001<br />
|Arora A. & Tamm LK.<br />
|Structure of outer membrane protein A transmembrane domain by NMR spectroscopy.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11276254?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 11276254]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|2007<br />
|Brown EA & Hardwidge PR.<br />
|Biochemical characterization of the enterotoxigenic Escherichia coli LeoA protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17975086?ordinalpos=16&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17975086]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2008<br />
|Burgess NK & Fleming KG.<br />
|Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18641391?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 18641391]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Tol/Pal<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|1986<br />
|Robert CHEN & Ulf HENNING.<br />
|Nucleotide sequence of the gene for the peptidoglycan-associated lipoprotein of Escherichia coli K12<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=210680 210680]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[3]]]<br />
|1995<br />
|Lazzaroni & Geli -<br />
|Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179564 179564]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|1999<br />
|Derouiche & Loret<br />
|Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10380085 10380085]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[4]]]<br />
|2001<br />
|Lloubès & RJournet L.<br />
|The Tol-Pal proteins of the Escherichia coli cell envelope: an energized system required for outer membrane integrity?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11501670 11501670]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|2002<br />
|Dubuisson JF & Lazzaroni JC.<br />
|Mutational analysis of the TolA C-terminal domain of Escherichia coli and genetic evidence for an interaction between TolA and TolB.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12142433 12142433]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2003<br />
|Llamas M & ARamos JL.<br />
|Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12896989 12896989]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[5]]]<br />
|2004<br />
|Henry T & Lloubès R.<br />
|Improved methods for producing outer membrane vesicles in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15249060 15249060]<br />
|}<br />
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==''' OMV Adressing '''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1997<br />
|Kadurugamuwa JL & Beveridge TJ.<br />
|Natural release of virulence factors in membrane vesicles by Pseudomonas aeruginosa and the effect of aminoglycoside antibiotics on their release.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9421308 9421308]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1998<br />
|Santini CL & Wu LF.<br />
|A novel sec-independent periplasmic protein translocation pathway in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9427745 9427745]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Berks BC & Palmer T.<br />
|The Tat protein export pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10652088 10652088]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Mishima Y & Murata K.<br />
|Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11731126 11731126]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Sargent F & Berks BC.<br />
|Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11422364 11422364]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Yahr TL & Wickner WT.<br />
|Functional reconstitution of bacterial Tat translocation in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11350936 11350936]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2004<br />
|Robinson C & Bolhuis A.<br />
|Tat-dependent protein targeting in prokaryotes and chloroplasts.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15546663 15546663]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Sargent F & Palmer T.<br />
|Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16445746 16445746]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Lee PA & Georgiou G.<br />
|The bacterial twin-arginine translocation pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16756481 16756481]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Maillard J & Sargent F.<br />
|Structural diversity in twin-arginine signal peptide-binding proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17901208 17901208]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Sargent F.<br />
|The twin-arginine transport system: moving folded proteins across membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17956229 17956229]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Ferrandez Y & Condemine G.<br />
|Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Pradel N & Bonnet R<br />
|Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|de Marco A.<br />
|Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19442264 19442264]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | ClyA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 5]]<br />
|2008<br />
|Kim JY & DeLisa MP.<br />
|Engineered bacterial outer membrane vesicles with enhanced functionality.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 1]]<br />
|2009<br />
|Mueller M & Ban N.<br />
|The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|Wang Y.<br />
|The function of OmpA in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Dramsi S & Arthur M.<br />
|Covalent attachment of proteins to peptidoglycan.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18266854 18266854]<br />
|}<br />
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==''' OMV Reception'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Adhesin<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1989<br />
|Smeal T & Karin M.<br />
|Different requirements for formation of Jun:Jun and Jun:Fos complexes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1994<br />
|Heffernan EJ & Guiney DG.<br />
|Specificity of the complement resistance and cell association phenotypes encoded by the outer membrane protein genes rck from Salmonella typhimurium and ail from Yersinia enterocolitica.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7927803 7927803]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Veiga E & Fernández LA.<br />
|Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12949111 12949111]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 6]]<br />
|2004<br />
|Kesty NC & Kuehn MJ.<br />
|Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14578354 14578354]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | G3P<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1982<br />
|JEF D. BOEKE & PETER MODEL<br />
|A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 8]]<br />
|1999<br />
|Chatellier J & Riechmann L.<br />
|Interdomain interactions within the gene 3 protein of filamentous phage.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 9]]<br />
|1999<br />
|Lubkowski J & Wlodawer A.<br />
|Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 10]]<br />
|2002<br />
|Baek H & Cha S.<br />
|An improved helper phage system for efficient isolation of specific antibody molecules in phage display.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 11]]<br />
|2003<br />
|Karlsson F & Malmborg-Hager AC.<br />
|The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Snare<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 17]]<br />
|2000<br />
|Waters MG & Hughson FM.<br />
|Membrane tethering and fusion in the secretory and endocytic pathways.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2000<br />
|Woodbury DJ & Rognlien K.<br />
|The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11067766 11067766]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2002<br />
|Bowen ME,Brunger AT.<br />
|Mutational analysis of synaptobrevin transmembrane domain oligomerization.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12501216 12501216]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Hu C & Rothman JE.<br />
|Fusion of cells by flipped SNAREs.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2003<br />
|Weninger K & Brunger AT.<br />
|Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14657376 14657376]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2006 <br />
|Giraudo CG & Rothman JE.<br />
|A clamping mechanism involved in SNARE-dependent exocytosis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16794037 16794037]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2006<br />
|Low HH & Löwe J.<br />
|A bacterial dynamin-like protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17122778 17122778]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[X]<br />
|2007<br />
|Weninger K & Brunger AT.<br />
|Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18275821 18275821]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[X]<br />
|2008<br />
|Delevoye C & Subtil A.<br />
|SNARE protein mimicry by an intracellular bacterium.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18369472 18369472]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_overview_fusion#top 18]]<br />
|2009<br />
|Giraudo CG & Rothman JE.<br />
|Alternative zippering as an on-off switch for SNARE-mediated fusion.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19164750 19164750]<br />
<br />
|}<br />
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==''' OMV Signal transduction'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1984<br />
|Lopilato JE & Beckwith JR.<br />
|D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6327616 6327616]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1995<br />
|Härle C & Braun V.<br />
|Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7729419 7729419]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1998<br />
|Tomii K & Kanehisa M.<br />
|A comparative analysis of ABC transporters in complete microbial genomes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1999<br />
|De Wulf P & Lin EC.<br />
|The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10542180 10542180]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Stock AM & Goudreau PN.<br />
|Two-component signal transduction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Yaron S & Matthews KR.<br />
|Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11010892 11010892]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2004<br />
|Dwyer MA & Hellinga HW.<br />
|Periplasmic binding proteins: a versatile superfamily for protein engineering.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15313245 15313245]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Braun V & Sauter A.<br />
|Gene regulation by transmembrane signaling.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16718597 16718597]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Baker MD & Stock JB<br />
|Signal transduction: networks and integrated circuits in bacterial cognition.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18054766 18054766]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Baker MD & Stock JB.<br />
|Systems biology of bacterial chemotaxis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16529985 16529985]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Ibrahim M & Monnet V.<br />
|Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17921293 17921293]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Kyriakidis DA & Tiligada E.<br />
|Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Tomii & Kanehisa<br />
|comparative analysis of ABC transporter<br />
|[http://genome.cshlp.org/content/8/10/1048.full.html#ref-list-1 pdf-link]<br />
|}<br />
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=='''Modelling'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Genetic Regulatory Network<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 1]]<br />
|1977<br />
|Gillespie Daniel T.<br />
|Exact Stochastic Simlation of Coupled Chemical Equations<br />
|[http://www.dna.caltech.edu/courses/cs191/paperscs191/gillespie2.pdf Gillespie1]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 3]]<br />
|1997<br />
|J.B. Andersen & S.Molin<br />
|New Stable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria<br />
|[http://aem.asm.org/cgi/reprint/64/6/2240.pdf LVA tag]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 6]]<br />
|1999<br />
|M.Ellowitz & S.Leibler<br />
|A Synthetic oscillatory network of transcriptionnal regulators <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10659856 10659856]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 2]]<br />
|1997<br />
|D.T.Gillespie<br />
|The Chemical Langevin Equation<br />
|[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000113000001000297000001&idtype=cvips&gifs=yes Gillespie2]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 5]]<br />
|2002<br />
|N.Rosenfold & U.Alon<br />
|Negative Autoregulation Speeds The Response TImes of Transcription Network <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12417193 2417193]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|M.B.Ellowitz & P.S.Swain<br />
|Stochastic Gene Expression In A Single Cell<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12183631 12183631]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 7]]<br />
|2003<br />
|S.Mangan & U.Alon<br />
|Structure and function ot the feed-forward Loop Network Motif<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14530388 14530388]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 4]]<br />
|2003<br />
|S.Basu & R.Weiss<br />
|Spatiotemporal control of gene expression with pulse-generating networks<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15096621 15096621]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 1]]<br />
|2005<br />
|S.Hooshangi & R.Weiss<br />
|Ultrasensitivity and noise propagation in a synthetic transcriptional cascade<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15738412 15738412]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 3]]<br />
|2006<br />
|H.Li & L.Petzold<br />
|Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems<br />
|[http://www.cs.ucsb.edu/~cse/Files/ldm0513.pdf Sto.Sim]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 2]]<br />
|2007<br />
|U.Alon<br />
|Network motifs : theory and experimental approaches<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17510665 117510665]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|J.Stricker & J.Hasty<br />
|A Fast Robust and Tunable synthetic gene oscillator<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18971928 18971928]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Vesicle biophysics model<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 6]]<br />
|1977<br />
|Harbich et al<br />
|Optical observation of rotationally symmetric lecithin vesicle shapes<br />
|J. Physique, 38:727–729<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 4]]<br />
|1987<br />
|Ou-Yang & Helfrich<br />
|Instability and deformation of a spherical vesicle by pressure<br />
|Phys. Rev. Lett., 59:2486-2488 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 1]]<br />
|1991<br />
|Lipowsky<br />
|The conformation of membranes<br />
|Nature, 349(6309):475-481<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 5]]<br />
|1995 <br />
|Fattal et al <br />
|The vesicle-micelle transition in mixed lipid-surfactant<br />
|Langmuir, 11:1154-1161 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 3]]<br />
|1998<br />
|Zhou et al<br />
|On the origin of membrane vesicles in gram-negative bacteria<br />
|FEMS microbiology letters, 163(2):223-228 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 8]]<br />
|2005 <br />
|Kuehn & Kesty<br />
|Bacterial outer membrane vesicles and the host pathogen interaction<br />
|Genes & Dev, 19:2645-2655 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 2]]<br />
|2008<br />
|Park & Uehara<br />
|How bacteria consume their own exoskeletons<br />
|Microbiol Mol Biol Rev, 72(2):211-227 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 7]]<br />
|2009<br />
|Deatherage et al <br />
|Biogenesis of bacterial membrane vesicles,<br />
|Mol Microbiol, 72(6):1395-1407<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 9]]<br />
|2009<br />
|Kumaran & Losick<br />
|Negative membrane curvature as a cue for subcellular localization of a bacterial protein.<br />
|PNAS USA, 106(32):13541-13545 <br />
|}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview_fusionTeam:Paris/Transduction overview fusion2009-10-22T02:29:32Z<p>Christophe.R: /* Using SNAREs in Bacteria : not so easy ... */</p>
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<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview_fusion#bottom | Fusion]]<br />
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==Fusion: Jun/Fos and AIDA==<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview#bottom"> Main </a>|<br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#bottom"> Fusion</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_construction#bottom"> Construction</a><br />
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<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_Jun.2FFos_and_AIDA"> Jun/Fos </a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_G3P"> G3P</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_SNAREs"> SNAREs</a><br />
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===Jun and Fos===<br />
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Fos and Jun, the protein products of the nuclear proto-oncogenes c-fos and c-jun, associate preferentially to form a heterodimer. Both Fos and Jun contain a single leucine zipper region. Previous studies <sup>[[Team:Paris/Transduction_overview_fusion#References|[1]]]</sup>,<sup>[[Team:Paris/Transduction_overview_fusion#References|[2]]]</sup> have shown that the leucine zippers of Fos and Jun are necessary and sufficient to mediate preferential heterodimer formation and that Jun : Fos heterodimers have higher stability than Jun homodimers <br />
<br />
<br />
In our project we would like to be sure that vesicles are going to recognize target bacteria. In this direction we decided to use the Jun and Fos recognition system. The problem was that Jun is able to form an homodimer and an heterodimer with Fos, so the specific interaction between vesicles and receiver cell is not specific. An article demonstrated that 2 mutations in the leucine-zipper allow the Jun/Fos dimerisation but abolished the Jun/Jun dimer formation <sup>[[Team:Paris/Transduction_overview_fusion#References|[3]]]</sup>. <br />
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===AIDA===<br />
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The cell envelope of gram-negative bacteria consists of two membranes, the cytoplasmic or inner membrane and the outer membrane. Transport of proteins across the inner membrane in most cases follows the general secretory pathway (GSP) <sup>[[Team:Paris/Transduction_overview_fusion#References|[4]]]</sup>. Therefore, in gram-negative bacteria, proteins end up in the periplasm. To translocate proteins to the outer surface or into the supernatant, gram-negative bacteria have developed several distinct mechanisms. In contrast to the secretory systems that require a variety of specialized accessory proteins that, often in combination with the GSP, are responsible for the export of one or several passenger proteins into the supernatant, the '''autotransporter''' protein family members carry the export signal and machinery within a single polypeptide chain.<br />
The adhesin-involved-in-diffuse-adherence (AIDA) autotransporter has been identified as a virulence factor of the enteropathogenic Escherichia coli strain 2787 <sup>[[Team:Paris/Transduction_overview_fusion#References|[5]]]</sup> and predicted to be a member of the autotransporter protein family <sup>[[Team:Paris/Transduction_overview_fusion#References|[6]]]</sup><br />
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This AIDA autotransporter is using to translocate Jun and Fos to the outer membrane of bacteria (Jun for the donnor, Fos for the receiver).<br />
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==Fusion: g3p==<br />
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What is the g3p and how could it be a key part in the vesicles-bacteria fusion ?<br />
<span/ id="7"><br />
====Description of g3p====<br />
<br />
Infection of Escherichia coli by filamentous bacteriophages as M13, fd, f1, is mediated by the phage gene 3 protein (g3p or pIII). This protein of 406 amino acid residues, has a signal peptide, two N-terminal domains and one C-terminal domain, separated by two flexible glycin-rich linkers. All three domains are indispensable for phage infectivity.<br><br />
g3p could be also found in phage helper like M13KO7 <sup>[[Team:Paris/Transduction_overview_fusion#References|[10]]]</sup><br><br />
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* The signal peptide (1-18aa) address the protein to the cell membrane before being cleaved. We deleted it because we fusione g3p to OmpA-Linker (BBa_K103996).<br><br />
<br />
* The first N-terminal domain (N1) binds to the bacterial periplasmatic domain of TolA ([http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG11007 TolAIII]), receptor presumably at the inner face of the outer membrane <sup>[[Team:Paris/Transduction_overview_fusion#References|[9]]]</sup>.<br><br />
<br />
* The second N-terminal domain (N2) gives recognition of the host cell by binding the F-pilus on the surface of E. coli. F-pilus is encode by the F episome of male E. coli, and is the primary receptor of the host cell <sup>[[Team:Paris/Transduction_overview_fusion#References|[12]]]</sup>.<br><br />
<br />
* In fact, N1 and N2 interact with each other to form a blocked di-domain (N1G1N2). The binding of N2 to the tip of the bacterial F-pilus releases N1, which becomes free to interact with its receptor TolA (TolAIII) <sup>[[Team:Paris/Transduction_overview_fusion#References|[8]]]</sup><sup>[[Team:Paris/Transduction_overview_fusion#References|[11]]]</sup>.<br><br />
<br />
* The C terminus (CT) of g3p anchors the g3p in the phage coat by interacting with phage coat protein 6, at the tip of the phage. Its seem that phages are released from the bacterial membrane by a two-step mechanism involving a short C-terminal fragment of g3p <sup>[[Team:Paris/Transduction_overview_fusion#References|[7]]]</sup>.<br><br />
<br />
* N1, N2 and N3 domain are linked by flexible glycin-rich domains (G1 and G2). G1 is composed of four tandem copies of the sequence Glu-Gly-Gly-Gly-Ser. In a recent study it has been showed that it may have an active role in F-pilus-dependent infection.<br><br />
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* Fusion of peptides or proteins to the N-terminus of intact g3p does not compromise infectivity of the phage, but insertion of polypeptides between N2 and N3 appear to reduce the infectivity.<br><br />
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====Our use====<br />
<br />
The viral protein known as g3p is naturally exposed at the surface of the filamentous bacteriophage which enable it to get in the bacteria. The M13 phage has a high affinity for E.coli, and if we could place its g3p on the surface of the vesicles it could activate the fusion with the Outer membrane of the targeted bacteria.<br><br />
<br />
To be sure to target the receiving bacteria, we separe the donnor from the receiver with the criterium of the presence or not of pilli, because the g3p need a pillus to start its incorporation process. So the donnor would be pillus negative and the receiver pillus positive.<br><br />
<br />
OmpA-Linker is the second protein required because it is a protein that target any protein that is fuse to it to the surface of the Outer membrane, consequently we fuse G3P with OmpA-Linker.<br><br />
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==Fusion: SNAREs==<br />
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SNARE proteins are a large protein superfamily consisting of more than 60 members in yeast and mammalian cells.<br />
<br />
<br />
The primary role of SNARE proteins is to mediate vesicle fusion, that is, the exocytosis of cellular transport vesicles with the cell membrane at the porosome or with a target compartment (such as a lysosome).<br />
<br />
<br />
SNAREs can be divided into two categories: vesicle-SNAREs (or v-SNAREs), which are incorporated into the membranes of transport vesicles during budding, and target-SNAREs (or t-SNAREs), which are located in the membranes of target compartments.<br />
<br />
<br />
The core of any functionnal SNARE complex is composed by four α-helices provided by the synaptobrevin (for one helix) by the syntaxin (for another helix) and by two SNAP-25 ( for the last two helices) : <br />
<br />
<br />
''Synaptobrevin'' : is a small integral membrane protein of secretory vesicles with molecular weight of 18 kilodalton (kDa) that is part of the vesicle-associated membrane protein (VAMP) family <br />
<br />
<br />
''Syntaxin'' : Syntaxin 1A was initially identified as a 35 kDa protein in the plasma membrane of amacrine cells <sup>[[Team:Paris/Transduction_overview_fusion#References|[13]]]</sup>, as a subunit of Ca2+ channels <sup>[[Team:Paris/Transduction_overview_fusion#References|[14]]]</sup>,<sup>[[Team:Paris/Transduction_overview_fusion#References|[15]]]</sup> and as a synaptotagmin-binding protein <sup>[[Team:Paris/Transduction_overview_fusion#References|[16]]]</sup>. Since these initial reports, the function of syntaxin as a central component in the synaptic vesicle membrane fusion machinery has been well established.<br />
<br />
<br />
''SNAP 25'' : SNAP-25 is a membrane bound protein anchored to the cytosolic face of membranes via palmitoyl side chains in the middle of the molecule. SNAP-25 is a protein contributing two α-helices in the formation of the exocytotic fusion complex in neurons where it assembles with syntaxin-1 and synaptobrevin. <br />
<br />
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[[Image:Exocytosis-machinery.jpg|center]]<br />
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''Legend : Molecular machinery driving vesicle fusion in neuromediator release. The core SNARE complex is formed by four α-helices contributed by synaptobrevin, syntaxin and two SNAP-25.''<br />
''Synaptotagmin serves as a calcium sensor and regulates intimately the SNARE zipping''<br />
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<br />
===Using SNAREs in Bacteria : not so easy ... ===<br />
<br />
Our first idea was to use SNAREs to perform the fusion between vesicles and target bacteria. The main problem is that the 3D structure of the SNARE complex is crucial for the fusion to proceed <sup>[[Team:Paris/Transduction_overview_fusion#References|[16]]]</sup>, <sup>[[Team:Paris/Transduction_overview_fusion#References|[17]]]</sup>, <sup>[[Team:Paris/Transduction_overview_fusion#References|[18]]]</sup>. As SNAREs don't exist in bacteria we have to clone these genes (into bacteria) and we have to merge the SNAREs protein with a bacterial protein which is localized in the outer membrane (to allow the localization of SNARE protein to the surface of cell). In this direction we weren't sure to obtain the correct conformation of both v- (for the donnor) and t- (for the receiver) SNAREs after their exportation to the bacterial membrane, so we weren't sure that this mechanism will perform. We decided to focus our effort on the Jun/Fos strategy.<br />
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====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Kouzarides, T. and E. Ziff. 1988. The role of the leucine zipper in the fos-jun interaction. Nature 336: 646-656. [http://www.ncbi.nlm.nih.gov/pubmed/2974122 2974122] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Gentz, R., F.J. Rauscher III, C. Abate, and T. Curran. 1989. Parallel association of Fos and Jun leucine zippers juxtaposes DNA-binding domains. Science 243:16951699.[http://www.ncbi.nlm.nih.gov/pubmed/2494702 2494702]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]<br />
Tod Smeal, Peter Angel, Jennifer Meek, and Michael Karin 1989. Different requirements for formation of Jun: Jun and Jun : Fos complexes. GENES & DEVELOPMENT 3:2091-2100. [http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Benz, I., and M. A. Schmidt. 1989. Cloning and expression of an adhesin (AIDA-I) involved in diffuse adherence of enteropathogenic Escherichia coli. Infect. Immun. 57:1506–1511. [http://www.ncbi.nlm.nih.gov/pubmed/2565291 2565291]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Murphy, C., W. Prinz, M. Pohlschroder, A. Derman, and J. Beckwith. 1995. Essential features of the pathway for protein translocation across the Escherichia coli cytoplasmic membrane. Cold Spring Harbor Symp. Quant. Biol. 60:277–283. [http://www.ncbi.nlm.nih.gov/pubmed/8824401 8824401]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Klauser, T., J. Pohlner, and T. F. Meyer. 1990. Extracellular transport of cholera toxin B subunit using Neisseria IgA protease beta-domain: conformation- dependent outer membrane translocation. EMBO J. 9:1991–1999. [http://www.ncbi.nlm.nih.gov/pubmed/2189728 2189728]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Jef D.Boeke & Peter Model. A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane. 1982.[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Chatellier J & Riechmann L. Interdomain interactions within the gene 3 protein of filamentous phage. 1999.[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]<br />
Lubkowski J & Wlodawer A. Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA. 1999.[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Baek H & Cha S. An improved helper phage system for efficient isolation of specific antibody molecules in phage display. 2002.[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]<br />
Karlsson F & Malmborg-Hager AC. The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains. 2003.[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Caro LG, Schnös M. The attachment of the male-specific bacteriophage F1 to sensitive strains of Escherichia coli. 1966.[http://www.ncbi.nlm.nih.gov/pubmed/5338586 5338586]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#8| ^]]Barnstable C. J.Hofstein R.,Akagawa K. A marker of early amacrine cell development in rat retina.(1985) Brain Res 352:286–290.[http://www.ncbi.nlm.nih.gov/pubmed/3896407 3896407] <br />
</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#8| ^]]Inoue A.Obata K.Akagawa K.(1992)Cloning and sequence analysis of cDNA for a neuronal cell membrane antigen, HPC-1 J. Biol. Chem. 267:10613–10619. [http://www.ncbi.nlm.nih.gov/pubmed/1587842 1587842] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#8| ^]]Yoshida A.,Oho C.,Omori A.,Kuwahara R.,Ito T.,Takahashi M.(1992)HPC-1 is associated with synaptotagmin and omega-conotoxin receptor J. Biol. Chem. 267:24925–24928. [http://www.ncbi.nlm.nih.gov/pubmed/1334074 1334074] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#8| ^]]Bennett M. K.,Calakos N.,Scheller R. H(1992). Syntaxin: a synaptic protein implicated in docking of synaptic vesicles at presynaptic active zones. Science 257:255–259. [http://www.ncbi.nlm.nih.gov/pubmed/1321498 1321498]Hu C, Ahmed M, Melia TJ, Söllner TH, Mayer T, Rothman JE. Fusion of cells by flipped SNAREs. Science. 2003 Jun 13;300(5626):1745-9. [http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#8| ^]]Waters MG, Hughson FM. Membrane tethering and fusion in the secretory and endocytic pathways. Traffic. 2000 Aug;1(8):588-97. [http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#8| ^]]Giraudo CG, Garcia-Diaz A, Eng WS, Chen Y, Hendrickson WA, Melia TJ, Rothman JE. Alternative zippering as an on-off switch for SNARE-mediated fusion. Science. 2009 Jan 23;323(5913):512-6. [http://www.ncbi.nlm.nih.gov/pubmed/19164750 19164750] </li><br />
</ol></div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview_fusionTeam:Paris/Transduction overview fusion2009-10-22T02:28:45Z<p>Christophe.R: </p>
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<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview_fusion#bottom | Fusion]]<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview#bottom"> Main </a>|<br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#bottom"> Fusion</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_construction#bottom"> Construction</a><br />
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<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_Jun.2FFos_and_AIDA"> Jun/Fos </a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_G3P"> G3P</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_SNAREs"> SNAREs</a><br />
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===Jun and Fos===<br />
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Fos and Jun, the protein products of the nuclear proto-oncogenes c-fos and c-jun, associate preferentially to form a heterodimer. Both Fos and Jun contain a single leucine zipper region. Previous studies <sup>[[Team:Paris/Transduction_overview_fusion#References|[1]]]</sup>,<sup>[[Team:Paris/Transduction_overview_fusion#References|[2]]]</sup> have shown that the leucine zippers of Fos and Jun are necessary and sufficient to mediate preferential heterodimer formation and that Jun : Fos heterodimers have higher stability than Jun homodimers <br />
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In our project we would like to be sure that vesicles are going to recognize target bacteria. In this direction we decided to use the Jun and Fos recognition system. The problem was that Jun is able to form an homodimer and an heterodimer with Fos, so the specific interaction between vesicles and receiver cell is not specific. An article demonstrated that 2 mutations in the leucine-zipper allow the Jun/Fos dimerisation but abolished the Jun/Jun dimer formation <sup>[[Team:Paris/Transduction_overview_fusion#References|[3]]]</sup>. <br />
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===AIDA===<br />
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The cell envelope of gram-negative bacteria consists of two membranes, the cytoplasmic or inner membrane and the outer membrane. Transport of proteins across the inner membrane in most cases follows the general secretory pathway (GSP) <sup>[[Team:Paris/Transduction_overview_fusion#References|[4]]]</sup>. Therefore, in gram-negative bacteria, proteins end up in the periplasm. To translocate proteins to the outer surface or into the supernatant, gram-negative bacteria have developed several distinct mechanisms. In contrast to the secretory systems that require a variety of specialized accessory proteins that, often in combination with the GSP, are responsible for the export of one or several passenger proteins into the supernatant, the '''autotransporter''' protein family members carry the export signal and machinery within a single polypeptide chain.<br />
The adhesin-involved-in-diffuse-adherence (AIDA) autotransporter has been identified as a virulence factor of the enteropathogenic Escherichia coli strain 2787 <sup>[[Team:Paris/Transduction_overview_fusion#References|[5]]]</sup> and predicted to be a member of the autotransporter protein family <sup>[[Team:Paris/Transduction_overview_fusion#References|[6]]]</sup><br />
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This AIDA autotransporter is using to translocate Jun and Fos to the outer membrane of bacteria (Jun for the donnor, Fos for the receiver).<br />
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==Fusion: g3p==<br />
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What is the g3p and how could it be a key part in the vesicles-bacteria fusion ?<br />
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====Description of g3p====<br />
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Infection of Escherichia coli by filamentous bacteriophages as M13, fd, f1, is mediated by the phage gene 3 protein (g3p or pIII). This protein of 406 amino acid residues, has a signal peptide, two N-terminal domains and one C-terminal domain, separated by two flexible glycin-rich linkers. All three domains are indispensable for phage infectivity.<br><br />
g3p could be also found in phage helper like M13KO7 <sup>[[Team:Paris/Transduction_overview_fusion#References|[10]]]</sup><br><br />
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* The signal peptide (1-18aa) address the protein to the cell membrane before being cleaved. We deleted it because we fusione g3p to OmpA-Linker (BBa_K103996).<br><br />
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* The first N-terminal domain (N1) binds to the bacterial periplasmatic domain of TolA ([http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG11007 TolAIII]), receptor presumably at the inner face of the outer membrane <sup>[[Team:Paris/Transduction_overview_fusion#References|[9]]]</sup>.<br><br />
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* The second N-terminal domain (N2) gives recognition of the host cell by binding the F-pilus on the surface of E. coli. F-pilus is encode by the F episome of male E. coli, and is the primary receptor of the host cell <sup>[[Team:Paris/Transduction_overview_fusion#References|[12]]]</sup>.<br><br />
<br />
* In fact, N1 and N2 interact with each other to form a blocked di-domain (N1G1N2). The binding of N2 to the tip of the bacterial F-pilus releases N1, which becomes free to interact with its receptor TolA (TolAIII) <sup>[[Team:Paris/Transduction_overview_fusion#References|[8]]]</sup><sup>[[Team:Paris/Transduction_overview_fusion#References|[11]]]</sup>.<br><br />
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* The C terminus (CT) of g3p anchors the g3p in the phage coat by interacting with phage coat protein 6, at the tip of the phage. Its seem that phages are released from the bacterial membrane by a two-step mechanism involving a short C-terminal fragment of g3p <sup>[[Team:Paris/Transduction_overview_fusion#References|[7]]]</sup>.<br><br />
<br />
* N1, N2 and N3 domain are linked by flexible glycin-rich domains (G1 and G2). G1 is composed of four tandem copies of the sequence Glu-Gly-Gly-Gly-Ser. In a recent study it has been showed that it may have an active role in F-pilus-dependent infection.<br><br />
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* Fusion of peptides or proteins to the N-terminus of intact g3p does not compromise infectivity of the phage, but insertion of polypeptides between N2 and N3 appear to reduce the infectivity.<br><br />
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====Our use====<br />
<br />
The viral protein known as g3p is naturally exposed at the surface of the filamentous bacteriophage which enable it to get in the bacteria. The M13 phage has a high affinity for E.coli, and if we could place its g3p on the surface of the vesicles it could activate the fusion with the Outer membrane of the targeted bacteria.<br><br />
<br />
To be sure to target the receiving bacteria, we separe the donnor from the receiver with the criterium of the presence or not of pilli, because the g3p need a pillus to start its incorporation process. So the donnor would be pillus negative and the receiver pillus positive.<br><br />
<br />
OmpA-Linker is the second protein required because it is a protein that target any protein that is fuse to it to the surface of the Outer membrane, consequently we fuse G3P with OmpA-Linker.<br><br />
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==Fusion: SNAREs==<br />
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SNARE proteins are a large protein superfamily consisting of more than 60 members in yeast and mammalian cells.<br />
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The primary role of SNARE proteins is to mediate vesicle fusion, that is, the exocytosis of cellular transport vesicles with the cell membrane at the porosome or with a target compartment (such as a lysosome).<br />
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<br />
SNAREs can be divided into two categories: vesicle-SNAREs (or v-SNAREs), which are incorporated into the membranes of transport vesicles during budding, and target-SNAREs (or t-SNAREs), which are located in the membranes of target compartments.<br />
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<br />
The core of any functionnal SNARE complex is composed by four α-helices provided by the synaptobrevin (for one helix) by the syntaxin (for another helix) and by two SNAP-25 ( for the last two helices) : <br />
<br />
<br />
''Synaptobrevin'' : is a small integral membrane protein of secretory vesicles with molecular weight of 18 kilodalton (kDa) that is part of the vesicle-associated membrane protein (VAMP) family <br />
<br />
<br />
''Syntaxin'' : Syntaxin 1A was initially identified as a 35 kDa protein in the plasma membrane of amacrine cells <sup>[[Team:Paris/Transduction_overview_fusion#References|[13]]]</sup>, as a subunit of Ca2+ channels <sup>[[Team:Paris/Transduction_overview_fusion#References|[14]]]</sup>,<sup>[[Team:Paris/Transduction_overview_fusion#References|[15]]]</sup> and as a synaptotagmin-binding protein <sup>[[Team:Paris/Transduction_overview_fusion#References|[16]]]</sup>. Since these initial reports, the function of syntaxin as a central component in the synaptic vesicle membrane fusion machinery has been well established.<br />
<br />
<br />
''SNAP 25'' : SNAP-25 is a membrane bound protein anchored to the cytosolic face of membranes via palmitoyl side chains in the middle of the molecule. SNAP-25 is a protein contributing two α-helices in the formation of the exocytotic fusion complex in neurons where it assembles with syntaxin-1 and synaptobrevin. <br />
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[[Image:Exocytosis-machinery.jpg|center]]<br />
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''Legend : Molecular machinery driving vesicle fusion in neuromediator release. The core SNARE complex is formed by four α-helices contributed by synaptobrevin, syntaxin and two SNAP-25.''<br />
''Synaptotagmin serves as a calcium sensor and regulates intimately the SNARE zipping''<br />
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===Using SNAREs in Bacteria : not so easy ... ===<br />
<br />
Our first idea was to use SNAREs to perform the fusion between vesicles and target bacteria. The main problem is that the 3D structure of the SNARE complex is crucial for the fusion to proceed <sup>[[Team:Paris/Transduction_overview_fusion#References|[17]]]</sup>, <sup>[[Team:Paris/Transduction_overview_fusion#References|[18]]]</sup>, <sup>[[Team:Paris/Transduction_overview_fusion#References|[19]]]</sup>. As SNAREs don't exist in bacteria we have to clone these genes (into bacteria) and we have to merge the SNAREs protein with a bacterial protein which is localized in the outer membrane (to allow the localization of SNARE protein to the surface of cell). In this direction we weren't sure to obtain the correct conformation of both v- (for the donnor) and t- (for the receiver) SNAREs after their exportation to the bacterial membrane, so we weren't sure that this mechanism will perform. We decided to focus our effort on the Jun/Fos strategy.<br />
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====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Kouzarides, T. and E. Ziff. 1988. The role of the leucine zipper in the fos-jun interaction. Nature 336: 646-656. [http://www.ncbi.nlm.nih.gov/pubmed/2974122 2974122] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Gentz, R., F.J. Rauscher III, C. Abate, and T. Curran. 1989. Parallel association of Fos and Jun leucine zippers juxtaposes DNA-binding domains. Science 243:16951699.[http://www.ncbi.nlm.nih.gov/pubmed/2494702 2494702]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]<br />
Tod Smeal, Peter Angel, Jennifer Meek, and Michael Karin 1989. Different requirements for formation of Jun: Jun and Jun : Fos complexes. GENES & DEVELOPMENT 3:2091-2100. [http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Benz, I., and M. A. Schmidt. 1989. Cloning and expression of an adhesin (AIDA-I) involved in diffuse adherence of enteropathogenic Escherichia coli. Infect. Immun. 57:1506–1511. [http://www.ncbi.nlm.nih.gov/pubmed/2565291 2565291]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Murphy, C., W. Prinz, M. Pohlschroder, A. Derman, and J. Beckwith. 1995. Essential features of the pathway for protein translocation across the Escherichia coli cytoplasmic membrane. Cold Spring Harbor Symp. Quant. Biol. 60:277–283. [http://www.ncbi.nlm.nih.gov/pubmed/8824401 8824401]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Klauser, T., J. Pohlner, and T. F. Meyer. 1990. Extracellular transport of cholera toxin B subunit using Neisseria IgA protease beta-domain: conformation- dependent outer membrane translocation. EMBO J. 9:1991–1999. [http://www.ncbi.nlm.nih.gov/pubmed/2189728 2189728]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Jef D.Boeke & Peter Model. A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane. 1982.[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Chatellier J & Riechmann L. Interdomain interactions within the gene 3 protein of filamentous phage. 1999.[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]<br />
Lubkowski J & Wlodawer A. Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA. 1999.[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Baek H & Cha S. An improved helper phage system for efficient isolation of specific antibody molecules in phage display. 2002.[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]<br />
Karlsson F & Malmborg-Hager AC. The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains. 2003.[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Caro LG, Schnös M. The attachment of the male-specific bacteriophage F1 to sensitive strains of Escherichia coli. 1966.[http://www.ncbi.nlm.nih.gov/pubmed/5338586 5338586]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#8| ^]]Barnstable C. J.Hofstein R.,Akagawa K. A marker of early amacrine cell development in rat retina.(1985) Brain Res 352:286–290.[http://www.ncbi.nlm.nih.gov/pubmed/3896407 3896407] <br />
</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#8| ^]]Inoue A.Obata K.Akagawa K.(1992)Cloning and sequence analysis of cDNA for a neuronal cell membrane antigen, HPC-1 J. Biol. Chem. 267:10613–10619. [http://www.ncbi.nlm.nih.gov/pubmed/1587842 1587842] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#8| ^]]Yoshida A.,Oho C.,Omori A.,Kuwahara R.,Ito T.,Takahashi M.(1992)HPC-1 is associated with synaptotagmin and omega-conotoxin receptor J. Biol. Chem. 267:24925–24928. [http://www.ncbi.nlm.nih.gov/pubmed/1334074 1334074] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#8| ^]]Bennett M. K.,Calakos N.,Scheller R. H(1992). Syntaxin: a synaptic protein implicated in docking of synaptic vesicles at presynaptic active zones. Science 257:255–259. [http://www.ncbi.nlm.nih.gov/pubmed/1321498 1321498]Hu C, Ahmed M, Melia TJ, Söllner TH, Mayer T, Rothman JE. Fusion of cells by flipped SNAREs. Science. 2003 Jun 13;300(5626):1745-9. [http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#8| ^]]Waters MG, Hughson FM. Membrane tethering and fusion in the secretory and endocytic pathways. Traffic. 2000 Aug;1(8):588-97. [http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#8| ^]]Giraudo CG, Garcia-Diaz A, Eng WS, Chen Y, Hendrickson WA, Melia TJ, Rothman JE. Alternative zippering as an on-off switch for SNARE-mediated fusion. Science. 2009 Jan 23;323(5913):512-6. [http://www.ncbi.nlm.nih.gov/pubmed/19164750 19164750] </li><br />
</ol></div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview_fusionTeam:Paris/Transduction overview fusion2009-10-22T02:20:52Z<p>Christophe.R: /* Our use */</p>
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<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview_fusion#bottom | Fusion]]<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview#bottom"> Main </a>|<br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#bottom"> Fusion</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_construction#bottom"> Construction</a><br />
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<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_Jun.2FFos_and_AIDA"> Jun/Fos </a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_G3P"> G3P</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_SNAREs"> SNAREs</a><br />
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===Jun and Fos===<br />
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<br />
Fos and Jun, the protein products of the nuclear proto-oncogenes c-fos and c-jun, associate preferentially to form a heterodimer. Both Fos and Jun contain a single leucine zipper region. Previous studies <sup>[[Team:Paris/Transduction_overview_fusion#References|[1]]]</sup>,<sup>[[Team:Paris/Transduction_overview_fusion#References|[2]]]</sup> have shown that the leucine zippers of Fos and Jun are necessary and sufficient to mediate preferential heterodimer formation and that Jun : Fos heterodimers have higher stability than Jun homodimers <br />
<br />
<br />
In our project we would like to be sure that vesicles are going to recognize target bacteria. In this direction we decided to use the Jun and Fos recognition system. The problem was that Jun is able to form an homodimer and an heterodimer with Fos, so the specific interaction between vesicles and receiver cell is not specific. An article demonstrated that 2 mutations in the leucine-zipper allow the Jun/Fos dimerisation but abolished the Jun/Jun dimer formation <sup>[[Team:Paris/Transduction_overview_fusion#References|[3]]]</sup>. <br />
<br />
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===AIDA===<br />
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<br />
The cell envelope of gram-negative bacteria consists of two membranes, the cytoplasmic or inner membrane and the outer membrane. Transport of proteins across the inner membrane in most cases follows the general secretory pathway (GSP) <sup>[[Team:Paris/Transduction_overview_fusion#References|[4]]]</sup>. Therefore, in gram-negative bacteria, proteins end up in the periplasm. To translocate proteins to the outer surface or into the supernatant, gram-negative bacteria have developed several distinct mechanisms. In contrast to the secretory systems that require a variety of specialized accessory proteins that, often in combination with the GSP, are responsible for the export of one or several passenger proteins into the supernatant, the '''autotransporter''' protein family members carry the export signal and machinery within a single polypeptide chain.<br />
The adhesin-involved-in-diffuse-adherence (AIDA) autotransporter has been identified as a virulence factor of the enteropathogenic Escherichia coli strain 2787 <sup>[[Team:Paris/Transduction_overview_fusion#References|[5]]]</sup> and predicted to be a member of the autotransporter protein family <sup>[[Team:Paris/Transduction_overview_fusion#References|[6]]]</sup><br />
<br />
This AIDA autotransporter is using to translocate Jun and Fos to the outer membrane of bacteria (Jun for the donnor, Fos for the receiver).<br />
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====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Kouzarides, T. and E. Ziff. 1988. The role of the leucine zipper in the fos-jun interaction. Nature 336: 646-656. [http://www.ncbi.nlm.nih.gov/pubmed/2974122 2974122] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Gentz, R., F.J. Rauscher III, C. Abate, and T. Curran. 1989. Parallel association of Fos and Jun leucine zippers juxtaposes DNA-binding domains. Science 243:16951699.[http://www.ncbi.nlm.nih.gov/pubmed/2494702 2494702]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]<br />
Tod Smeal, Peter Angel, Jennifer Meek, and Michael Karin 1989. Different requirements for formation of Jun: Jun and Jun : Fos complexes. GENES & DEVELOPMENT 3:2091-2100. [http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Benz, I., and M. A. Schmidt. 1989. Cloning and expression of an adhesin (AIDA-I) involved in diffuse adherence of enteropathogenic Escherichia coli. Infect. Immun. 57:1506–1511. [http://www.ncbi.nlm.nih.gov/pubmed/2565291 2565291]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Murphy, C., W. Prinz, M. Pohlschroder, A. Derman, and J. Beckwith. 1995. Essential features of the pathway for protein translocation across the Escherichia coli cytoplasmic membrane. Cold Spring Harbor Symp. Quant. Biol. 60:277–283. [http://www.ncbi.nlm.nih.gov/pubmed/8824401 8824401]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Klauser, T., J. Pohlner, and T. F. Meyer. 1990. Extracellular transport of cholera toxin B subunit using Neisseria IgA protease beta-domain: conformation- dependent outer membrane translocation. EMBO J. 9:1991–1999. [http://www.ncbi.nlm.nih.gov/pubmed/2189728 2189728]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Jef D.Boeke & Peter Model. A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane. 1982.[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Chatellier J & Riechmann L. Interdomain interactions within the gene 3 protein of filamentous phage. 1999.[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]<br />
Lubkowski J & Wlodawer A. Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA. 1999.[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Baek H & Cha S. An improved helper phage system for efficient isolation of specific antibody molecules in phage display. 2002.[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]<br />
Karlsson F & Malmborg-Hager AC. The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains. 2003.[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Caro LG, Schnös M. The attachment of the male-specific bacteriophage F1 to sensitive strains of Escherichia coli. 1966.[http://www.ncbi.nlm.nih.gov/pubmed/5338586 5338586]</li><br />
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==Fusion: g3p==<br />
<br />
What is the g3p and how could it be a key part in the vesicles-bacteria fusion ?<br />
<br />
====Description of g3p====<br />
<br />
Infection of Escherichia coli by filamentous bacteriophages as M13, fd, f1, is mediated by the phage gene 3 protein (g3p or pIII). This protein of 406 amino acid residues, has a signal peptide, two N-terminal domains and one C-terminal domain, separated by two flexible glycin-rich linkers. All three domains are indispensable for phage infectivity.<br><br />
g3p could be also found in phage helper like M13KO7 <sup>[[Team:Paris/Transduction_overview_fusion#References|[10]]]</sup><br><br />
<br />
* The signal peptide (1-18aa) address the protein to the cell membrane before being cleaved. We deleted it because we fusione g3p to OmpA-Linker (BBa_K103996).<br><br />
<br />
* The first N-terminal domain (N1) binds to the bacterial periplasmatic domain of TolA ([http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG11007 TolAIII]), receptor presumably at the inner face of the outer membrane <sup>[[Team:Paris/Transduction_overview_fusion#References|[9]]]</sup>.<br><br />
<br />
* The second N-terminal domain (N2) gives recognition of the host cell by binding the F-pilus on the surface of E. coli. F-pilus is encode by the F episome of male E. coli, and is the primary receptor of the host cell <sup>[[Team:Paris/Transduction_overview_fusion#References|[12]]]</sup>.<br><br />
<br />
* In fact, N1 and N2 interact with each other to form a blocked di-domain (N1G1N2). The binding of N2 to the tip of the bacterial F-pilus releases N1, which becomes free to interact with its receptor TolA (TolAIII) <sup>[[Team:Paris/Transduction_overview_fusion#References|[8]]]</sup><sup>[[Team:Paris/Transduction_overview_fusion#References|[11]]]</sup>.<br><br />
<br />
* The C terminus (CT) of g3p anchors the g3p in the phage coat by interacting with phage coat protein 6, at the tip of the phage. Its seem that phages are released from the bacterial membrane by a two-step mechanism involving a short C-terminal fragment of g3p <sup>[[Team:Paris/Transduction_overview_fusion#References|[7]]]</sup>.<br><br />
<br />
* N1, N2 and N3 domain are linked by flexible glycin-rich domains (G1 and G2). G1 is composed of four tandem copies of the sequence Glu-Gly-Gly-Gly-Ser. In a recent study it has been showed that it may have an active role in F-pilus-dependent infection.<br><br />
<br />
* Fusion of peptides or proteins to the N-terminus of intact g3p does not compromise infectivity of the phage, but insertion of polypeptides between N2 and N3 appear to reduce the infectivity.<br><br />
<br />
====Our use====<br />
<br />
The viral protein known as g3p is naturally exposed at the surface of the filamentous bacteriophage which enable it to get in the bacteria. The M13 phage has a high affinity for E.coli, and if we could place its g3p on the surface of the vesicles it could activate the fusion with the Outer membrane of the targeted bacteria.<br><br />
<br />
To be sure to target the receiving bacteria, we separe the donnor from the receiver with the criterium of the presence or not of pilli, because the g3p need a pillus to start its incorporation process. So the donnor would be pillus negative and the receiver pillus positive.<br><br />
<br />
OmpA-Linker is the second protein required because it is a protein that target any protein that is fuse to it to the surface of the Outer membrane, consequently we fuse G3P with OmpA-Linker.<br><br />
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==Fusion: SNAREs==<br />
<br />
SNARE proteins are a large protein superfamily consisting of more than 60 members in yeast and mammalian cells.<br />
<br />
<br />
The primary role of SNARE proteins is to mediate vesicle fusion, that is, the exocytosis of cellular transport vesicles with the cell membrane at the porosome or with a target compartment (such as a lysosome).<br />
<br />
<br />
SNAREs can be divided into two categories: vesicle-SNAREs (or v-SNAREs), which are incorporated into the membranes of transport vesicles during budding, and target-SNAREs (or t-SNAREs), which are located in the membranes of target compartments.<br />
<br />
<br />
The core of any functionnal SNARE complex is composed by four α-helices provided by the synaptobrevin (for one helix) by the syntaxin (for another helix) and by two SNAP-25 ( for the last two helices) : <br />
<br />
<br />
''Synaptobrevin'' : is a small integral membrane protein of secretory vesicles with molecular weight of 18 kilodalton (kDa) that is part of the vesicle-associated membrane protein (VAMP) family <br />
<br />
<br />
''Syntaxin'' : Syntaxin 1A was initially identified as a 35 kDa protein in the plasma membrane of amacrine cells [http://www.ncbi.nlm.nih.gov/pubmed/3896407[1]], as a subunit of Ca2+ channels [http://www.ncbi.nlm.nih.gov/pubmed/1587842[2]],[http://www.ncbi.nlm.nih.gov/pubmed/1334074[3]] and as a synaptotagmin-binding protein [http://www.ncbi.nlm.nih.gov/pubmed/1321498[4]]. Since these initial reports, the function of syntaxin as a central component in the synaptic vesicle membrane fusion machinery has been well established.<br />
<br />
<br />
''SNAP 25'' : SNAP-25 is a membrane bound protein anchored to the cytosolic face of membranes via palmitoyl side chains in the middle of the molecule. SNAP-25 is a protein contributing two α-helices in the formation of the exocytotic fusion complex in neurons where it assembles with syntaxin-1 and synaptobrevin. <br />
<br />
<br />
<br />
<br />
[[Image:Exocytosis-machinery.jpg|center]]<br />
<br />
<br />
''Legend : Molecular machinery driving vesicle fusion in neuromediator release. The core SNARE complex is formed by four α-helices contributed by synaptobrevin, syntaxin and two SNAP-25.''<br />
''Synaptotagmin serves as a calcium sensor and regulates intimately the SNARE zipping''<br />
<br />
<br />
<br />
<br />
===Using SNAREs in Bacteria : not so easy ... ===<br />
<br />
Our first idea was to use SNAREs to perform the fusion between vesicles and target bacteria. The main problem is that the 3D structure of the SNARE complex is crucial for the fusion to proceed [http://www.ncbi.nlm.nih.gov/pubmed/12805548 [5]], [http://www.ncbi.nlm.nih.gov/pubmed/11208146[6]], [http://www.ncbi.nlm.nih.gov/pubmed/19164750 [7]]. As SNAREs don't exist in bacteria we have to clone these genes (into bacteria) and we have to merge the SNAREs protein with a bacterial protein which is localized in the outer membrane (to allow the localization of SNARE protein to the surface of cell). In this direction we weren't sure to obtain the correct conformation of both v- (for the donnor) and t- (for the receiver) SNAREs after their exportation to the bacterial membrane, so we weren't sure that this mechanism will perform. We decided to focus our effort on the Jun/Fos strategy.<br />
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<br />
====Bibliography====<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/3896407[1]] Barnstable C. J.Hofstein R.,Akagawa K. A marker of early amacrine cell development in rat retina.(1985) Brain Res 352:286–290<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/1587842[2]] Inoue A.Obata K.Akagawa K.(1992)Cloning and sequence analysis of cDNA for a neuronal cell membrane antigen, HPC-1 J. Biol. Chem. 267:10613–10619<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/1334074[3]] Yoshida A.,Oho C.,Omori A.,Kuwahara R.,Ito T.,Takahashi M.(1992)HPC-1 is associated with synaptotagmin and omega-conotoxin receptor J. Biol. Chem. 267:24925–24928<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/1321498[4]] Bennett M. K.,Calakos N.,Scheller R. H(1992). Syntaxin: a synaptic protein implicated in docking of synaptic vesicles at presynaptic active zones. Science 257:255–259.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/12805548 [5]] Hu C, Ahmed M, Melia TJ, Söllner TH, Mayer T, Rothman JE. Fusion of cells by flipped SNAREs. Science. 2003 Jun 13;300(5626):1745-9.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/11208146[6]] Waters MG, Hughson FM. Membrane tethering and fusion in the secretory and endocytic pathways. Traffic. 2000 Aug;1(8):588-97.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19164750 [7]] Giraudo CG, Garcia-Diaz A, Eng WS, Chen Y, Hendrickson WA, Melia TJ, Rothman JE. Alternative zippering as an on-off switch for SNARE-mediated fusion. Science. 2009 Jan 23;323(5913):512-6.</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview_fusionTeam:Paris/Transduction overview fusion2009-10-22T02:20:30Z<p>Christophe.R: /* Bibliography */</p>
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<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview_fusion#bottom | Fusion]]<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview#bottom"> Main </a>|<br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#bottom"> Fusion</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_strategy#bottom"> Our strategy</a>|<br />
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<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_Jun.2FFos_and_AIDA"> Jun/Fos </a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_G3P"> G3P</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_SNAREs"> SNAREs</a><br />
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===Jun and Fos===<br />
<br />
<br />
Fos and Jun, the protein products of the nuclear proto-oncogenes c-fos and c-jun, associate preferentially to form a heterodimer. Both Fos and Jun contain a single leucine zipper region. Previous studies <sup>[[Team:Paris/Transduction_overview_fusion#References|[1]]]</sup>,<sup>[[Team:Paris/Transduction_overview_fusion#References|[2]]]</sup> have shown that the leucine zippers of Fos and Jun are necessary and sufficient to mediate preferential heterodimer formation and that Jun : Fos heterodimers have higher stability than Jun homodimers <br />
<br />
<br />
In our project we would like to be sure that vesicles are going to recognize target bacteria. In this direction we decided to use the Jun and Fos recognition system. The problem was that Jun is able to form an homodimer and an heterodimer with Fos, so the specific interaction between vesicles and receiver cell is not specific. An article demonstrated that 2 mutations in the leucine-zipper allow the Jun/Fos dimerisation but abolished the Jun/Jun dimer formation <sup>[[Team:Paris/Transduction_overview_fusion#References|[3]]]</sup>. <br />
<br />
<br />
<br />
<span/ id="4"><br />
===AIDA===<br />
<br />
<br />
The cell envelope of gram-negative bacteria consists of two membranes, the cytoplasmic or inner membrane and the outer membrane. Transport of proteins across the inner membrane in most cases follows the general secretory pathway (GSP) <sup>[[Team:Paris/Transduction_overview_fusion#References|[4]]]</sup>. Therefore, in gram-negative bacteria, proteins end up in the periplasm. To translocate proteins to the outer surface or into the supernatant, gram-negative bacteria have developed several distinct mechanisms. In contrast to the secretory systems that require a variety of specialized accessory proteins that, often in combination with the GSP, are responsible for the export of one or several passenger proteins into the supernatant, the '''autotransporter''' protein family members carry the export signal and machinery within a single polypeptide chain.<br />
The adhesin-involved-in-diffuse-adherence (AIDA) autotransporter has been identified as a virulence factor of the enteropathogenic Escherichia coli strain 2787 <sup>[[Team:Paris/Transduction_overview_fusion#References|[5]]]</sup> and predicted to be a member of the autotransporter protein family <sup>[[Team:Paris/Transduction_overview_fusion#References|[6]]]</sup><br />
<br />
This AIDA autotransporter is using to translocate Jun and Fos to the outer membrane of bacteria (Jun for the donnor, Fos for the receiver).<br />
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====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Kouzarides, T. and E. Ziff. 1988. The role of the leucine zipper in the fos-jun interaction. Nature 336: 646-656. [http://www.ncbi.nlm.nih.gov/pubmed/2974122 2974122] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Gentz, R., F.J. Rauscher III, C. Abate, and T. Curran. 1989. Parallel association of Fos and Jun leucine zippers juxtaposes DNA-binding domains. Science 243:16951699.[http://www.ncbi.nlm.nih.gov/pubmed/2494702 2494702]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]<br />
Tod Smeal, Peter Angel, Jennifer Meek, and Michael Karin 1989. Different requirements for formation of Jun: Jun and Jun : Fos complexes. GENES & DEVELOPMENT 3:2091-2100. [http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Benz, I., and M. A. Schmidt. 1989. Cloning and expression of an adhesin (AIDA-I) involved in diffuse adherence of enteropathogenic Escherichia coli. Infect. Immun. 57:1506–1511. [http://www.ncbi.nlm.nih.gov/pubmed/2565291 2565291]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Murphy, C., W. Prinz, M. Pohlschroder, A. Derman, and J. Beckwith. 1995. Essential features of the pathway for protein translocation across the Escherichia coli cytoplasmic membrane. Cold Spring Harbor Symp. Quant. Biol. 60:277–283. [http://www.ncbi.nlm.nih.gov/pubmed/8824401 8824401]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Klauser, T., J. Pohlner, and T. F. Meyer. 1990. Extracellular transport of cholera toxin B subunit using Neisseria IgA protease beta-domain: conformation- dependent outer membrane translocation. EMBO J. 9:1991–1999. [http://www.ncbi.nlm.nih.gov/pubmed/2189728 2189728]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Jef D.Boeke & Peter Model. A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane. 1982.[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Chatellier J & Riechmann L. Interdomain interactions within the gene 3 protein of filamentous phage. 1999.[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]<br />
Lubkowski J & Wlodawer A. Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA. 1999.[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Baek H & Cha S. An improved helper phage system for efficient isolation of specific antibody molecules in phage display. 2002.[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]<br />
Karlsson F & Malmborg-Hager AC. The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains. 2003.[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Caro LG, Schnös M. The attachment of the male-specific bacteriophage F1 to sensitive strains of Escherichia coli. 1966.[http://www.ncbi.nlm.nih.gov/pubmed/5338586 5338586]</li><br />
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==Fusion: g3p==<br />
<br />
What is the g3p and how could it be a key part in the vesicles-bacteria fusion ?<br />
<br />
====Description of g3p====<br />
<br />
Infection of Escherichia coli by filamentous bacteriophages as M13, fd, f1, is mediated by the phage gene 3 protein (g3p or pIII). This protein of 406 amino acid residues, has a signal peptide, two N-terminal domains and one C-terminal domain, separated by two flexible glycin-rich linkers. All three domains are indispensable for phage infectivity.<br><br />
g3p could be also found in phage helper like M13KO7 <sup>[[Team:Paris/Transduction_overview_fusion#References|[10]]]</sup><br><br />
<br />
* The signal peptide (1-18aa) address the protein to the cell membrane before being cleaved. We deleted it because we fusione g3p to OmpA-Linker (BBa_K103996).<br><br />
<br />
* The first N-terminal domain (N1) binds to the bacterial periplasmatic domain of TolA ([http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG11007 TolAIII]), receptor presumably at the inner face of the outer membrane <sup>[[Team:Paris/Transduction_overview_fusion#References|[9]]]</sup>.<br><br />
<br />
* The second N-terminal domain (N2) gives recognition of the host cell by binding the F-pilus on the surface of E. coli. F-pilus is encode by the F episome of male E. coli, and is the primary receptor of the host cell <sup>[[Team:Paris/Transduction_overview_fusion#References|[12]]]</sup>.<br><br />
<br />
* In fact, N1 and N2 interact with each other to form a blocked di-domain (N1G1N2). The binding of N2 to the tip of the bacterial F-pilus releases N1, which becomes free to interact with its receptor TolA (TolAIII) <sup>[[Team:Paris/Transduction_overview_fusion#References|[8]]]</sup><sup>[[Team:Paris/Transduction_overview_fusion#References|[11]]]</sup>.<br><br />
<br />
* The C terminus (CT) of g3p anchors the g3p in the phage coat by interacting with phage coat protein 6, at the tip of the phage. Its seem that phages are released from the bacterial membrane by a two-step mechanism involving a short C-terminal fragment of g3p <sup>[[Team:Paris/Transduction_overview_fusion#References|[7]]]</sup>.<br><br />
<br />
* N1, N2 and N3 domain are linked by flexible glycin-rich domains (G1 and G2). G1 is composed of four tandem copies of the sequence Glu-Gly-Gly-Gly-Ser. In a recent study it has been showed that it may have an active role in F-pilus-dependent infection.<br><br />
<br />
* Fusion of peptides or proteins to the N-terminus of intact g3p does not compromise infectivity of the phage, but insertion of polypeptides between N2 and N3 appear to reduce the infectivity.<br><br />
<br />
====Our use====<br />
<br />
The viral protein known as g3p is naturally exposed at the surface of the filamentous bacteriophage which enable it to get in the bacteria. The M13 phage has a high affinity for E.coli, and if we could place its g3p on the surface of the vesicles it could activate the fusion with the Outer membrane of the targeted bacteria.<br><br />
<br />
To be sure to target the receiving bacteria, we separe the donnor from the receiver with the criterium of the presence or not of pilli, because the g3p need a pillus to start its incorporation process. So the donnor would be pillus negative and the receiver pillus positive.<br><br />
<br />
OmpA-Linker is the second protein required because it is a protein that target any protein that is fuse to it to the surface of the Outer membrane, consequently we fuse G3P with OmpA-Linker.<br><br />
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==Fusion: SNAREs==<br />
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SNARE proteins are a large protein superfamily consisting of more than 60 members in yeast and mammalian cells.<br />
<br />
<br />
The primary role of SNARE proteins is to mediate vesicle fusion, that is, the exocytosis of cellular transport vesicles with the cell membrane at the porosome or with a target compartment (such as a lysosome).<br />
<br />
<br />
SNAREs can be divided into two categories: vesicle-SNAREs (or v-SNAREs), which are incorporated into the membranes of transport vesicles during budding, and target-SNAREs (or t-SNAREs), which are located in the membranes of target compartments.<br />
<br />
<br />
The core of any functionnal SNARE complex is composed by four α-helices provided by the synaptobrevin (for one helix) by the syntaxin (for another helix) and by two SNAP-25 ( for the last two helices) : <br />
<br />
<br />
''Synaptobrevin'' : is a small integral membrane protein of secretory vesicles with molecular weight of 18 kilodalton (kDa) that is part of the vesicle-associated membrane protein (VAMP) family <br />
<br />
<br />
''Syntaxin'' : Syntaxin 1A was initially identified as a 35 kDa protein in the plasma membrane of amacrine cells [http://www.ncbi.nlm.nih.gov/pubmed/3896407[1]], as a subunit of Ca2+ channels [http://www.ncbi.nlm.nih.gov/pubmed/1587842[2]],[http://www.ncbi.nlm.nih.gov/pubmed/1334074[3]] and as a synaptotagmin-binding protein [http://www.ncbi.nlm.nih.gov/pubmed/1321498[4]]. Since these initial reports, the function of syntaxin as a central component in the synaptic vesicle membrane fusion machinery has been well established.<br />
<br />
<br />
''SNAP 25'' : SNAP-25 is a membrane bound protein anchored to the cytosolic face of membranes via palmitoyl side chains in the middle of the molecule. SNAP-25 is a protein contributing two α-helices in the formation of the exocytotic fusion complex in neurons where it assembles with syntaxin-1 and synaptobrevin. <br />
<br />
<br />
<br />
<br />
[[Image:Exocytosis-machinery.jpg|center]]<br />
<br />
<br />
''Legend : Molecular machinery driving vesicle fusion in neuromediator release. The core SNARE complex is formed by four α-helices contributed by synaptobrevin, syntaxin and two SNAP-25.''<br />
''Synaptotagmin serves as a calcium sensor and regulates intimately the SNARE zipping''<br />
<br />
<br />
<br />
<br />
===Using SNAREs in Bacteria : not so easy ... ===<br />
<br />
Our first idea was to use SNAREs to perform the fusion between vesicles and target bacteria. The main problem is that the 3D structure of the SNARE complex is crucial for the fusion to proceed [http://www.ncbi.nlm.nih.gov/pubmed/12805548 [5]], [http://www.ncbi.nlm.nih.gov/pubmed/11208146[6]], [http://www.ncbi.nlm.nih.gov/pubmed/19164750 [7]]. As SNAREs don't exist in bacteria we have to clone these genes (into bacteria) and we have to merge the SNAREs protein with a bacterial protein which is localized in the outer membrane (to allow the localization of SNARE protein to the surface of cell). In this direction we weren't sure to obtain the correct conformation of both v- (for the donnor) and t- (for the receiver) SNAREs after their exportation to the bacterial membrane, so we weren't sure that this mechanism will perform. We decided to focus our effort on the Jun/Fos strategy.<br />
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<br />
====Bibliography====<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/3896407[1]] Barnstable C. J.Hofstein R.,Akagawa K. A marker of early amacrine cell development in rat retina.(1985) Brain Res 352:286–290<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/1587842[2]] Inoue A.Obata K.Akagawa K.(1992)Cloning and sequence analysis of cDNA for a neuronal cell membrane antigen, HPC-1 J. Biol. Chem. 267:10613–10619<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/1334074[3]] Yoshida A.,Oho C.,Omori A.,Kuwahara R.,Ito T.,Takahashi M.(1992)HPC-1 is associated with synaptotagmin and omega-conotoxin receptor J. Biol. Chem. 267:24925–24928<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/1321498[4]] Bennett M. K.,Calakos N.,Scheller R. H(1992). Syntaxin: a synaptic protein implicated in docking of synaptic vesicles at presynaptic active zones. Science 257:255–259.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/12805548 [5]] Hu C, Ahmed M, Melia TJ, Söllner TH, Mayer T, Rothman JE. Fusion of cells by flipped SNAREs. Science. 2003 Jun 13;300(5626):1745-9.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/11208146[6]] Waters MG, Hughson FM. Membrane tethering and fusion in the secretory and endocytic pathways. Traffic. 2000 Aug;1(8):588-97.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19164750 [7]] Giraudo CG, Garcia-Diaz A, Eng WS, Chen Y, Hendrickson WA, Melia TJ, Rothman JE. Alternative zippering as an on-off switch for SNARE-mediated fusion. Science. 2009 Jan 23;323(5913):512-6.</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview_fusionTeam:Paris/Transduction overview fusion2009-10-22T02:19:50Z<p>Christophe.R: </p>
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<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview_fusion#bottom | Fusion]]<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview#bottom"> Main </a>|<br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#bottom"> Fusion</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_strategy#bottom"> Our strategy</a>|<br />
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<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_Jun.2FFos_and_AIDA"> Jun/Fos </a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_G3P"> G3P</a>|<br />
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===Jun and Fos===<br />
<br />
<br />
Fos and Jun, the protein products of the nuclear proto-oncogenes c-fos and c-jun, associate preferentially to form a heterodimer. Both Fos and Jun contain a single leucine zipper region. Previous studies <sup>[[Team:Paris/Transduction_overview_fusion#References|[1]]]</sup>,<sup>[[Team:Paris/Transduction_overview_fusion#References|[2]]]</sup> have shown that the leucine zippers of Fos and Jun are necessary and sufficient to mediate preferential heterodimer formation and that Jun : Fos heterodimers have higher stability than Jun homodimers <br />
<br />
<br />
In our project we would like to be sure that vesicles are going to recognize target bacteria. In this direction we decided to use the Jun and Fos recognition system. The problem was that Jun is able to form an homodimer and an heterodimer with Fos, so the specific interaction between vesicles and receiver cell is not specific. An article demonstrated that 2 mutations in the leucine-zipper allow the Jun/Fos dimerisation but abolished the Jun/Jun dimer formation <sup>[[Team:Paris/Transduction_overview_fusion#References|[3]]]</sup>. <br />
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===AIDA===<br />
<br />
<br />
The cell envelope of gram-negative bacteria consists of two membranes, the cytoplasmic or inner membrane and the outer membrane. Transport of proteins across the inner membrane in most cases follows the general secretory pathway (GSP) <sup>[[Team:Paris/Transduction_overview_fusion#References|[4]]]</sup>. Therefore, in gram-negative bacteria, proteins end up in the periplasm. To translocate proteins to the outer surface or into the supernatant, gram-negative bacteria have developed several distinct mechanisms. In contrast to the secretory systems that require a variety of specialized accessory proteins that, often in combination with the GSP, are responsible for the export of one or several passenger proteins into the supernatant, the '''autotransporter''' protein family members carry the export signal and machinery within a single polypeptide chain.<br />
The adhesin-involved-in-diffuse-adherence (AIDA) autotransporter has been identified as a virulence factor of the enteropathogenic Escherichia coli strain 2787 <sup>[[Team:Paris/Transduction_overview_fusion#References|[5]]]</sup> and predicted to be a member of the autotransporter protein family <sup>[[Team:Paris/Transduction_overview_fusion#References|[6]]]</sup><br />
<br />
This AIDA autotransporter is using to translocate Jun and Fos to the outer membrane of bacteria (Jun for the donnor, Fos for the receiver).<br />
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====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Kouzarides, T. and E. Ziff. 1988. The role of the leucine zipper in the fos-jun interaction. Nature 336: 646-656. [http://www.ncbi.nlm.nih.gov/pubmed/2974122 2974122] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Gentz, R., F.J. Rauscher III, C. Abate, and T. Curran. 1989. Parallel association of Fos and Jun leucine zippers juxtaposes DNA-binding domains. Science 243:16951699.[http://www.ncbi.nlm.nih.gov/pubmed/2494702 2494702]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]<br />
Tod Smeal, Peter Angel, Jennifer Meek, and Michael Karin 1989. Different requirements for formation of Jun: Jun and Jun : Fos complexes. GENES & DEVELOPMENT 3:2091-2100. [http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Benz, I., and M. A. Schmidt. 1989. Cloning and expression of an adhesin (AIDA-I) involved in diffuse adherence of enteropathogenic Escherichia coli. Infect. Immun. 57:1506–1511. [http://www.ncbi.nlm.nih.gov/pubmed/2565291 2565291]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Murphy, C., W. Prinz, M. Pohlschroder, A. Derman, and J. Beckwith. 1995. Essential features of the pathway for protein translocation across the Escherichia coli cytoplasmic membrane. Cold Spring Harbor Symp. Quant. Biol. 60:277–283. [http://www.ncbi.nlm.nih.gov/pubmed/8824401 8824401]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#4| ^]]Klauser, T., J. Pohlner, and T. F. Meyer. 1990. Extracellular transport of cholera toxin B subunit using Neisseria IgA protease beta-domain: conformation- dependent outer membrane translocation. EMBO J. 9:1991–1999. [http://www.ncbi.nlm.nih.gov/pubmed/2189728 2189728]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Jef D.Boeke & Peter Model. A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane. 1982.[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Chatellier J & Riechmann L. Interdomain interactions within the gene 3 protein of filamentous phage. 1999.[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]<br />
Lubkowski J & Wlodawer A. Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA. 1999.[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Baek H & Cha S. An improved helper phage system for efficient isolation of specific antibody molecules in phage display. 2002.[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]<br />
Karlsson F & Malmborg-Hager AC. The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains. 2003.[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#7| ^]]Caro LG, Schnös M. The attachment of the male-specific bacteriophage F1 to sensitive strains of Escherichia coli. 1966.[http://www.ncbi.nlm.nih.gov/pubmed/5338586 5338586]</li><br />
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==Fusion: g3p==<br />
<br />
What is the g3p and how could it be a key part in the vesicles-bacteria fusion ?<br />
<br />
====Description of g3p====<br />
<br />
Infection of Escherichia coli by filamentous bacteriophages as M13, fd, f1, is mediated by the phage gene 3 protein (g3p or pIII). This protein of 406 amino acid residues, has a signal peptide, two N-terminal domains and one C-terminal domain, separated by two flexible glycin-rich linkers. All three domains are indispensable for phage infectivity.<br><br />
g3p could be also found in phage helper like M13KO7 <sup>[[Team:Paris/Transduction_overview_fusion#References|[10]]]</sup><br><br />
<br />
* The signal peptide (1-18aa) address the protein to the cell membrane before being cleaved. We deleted it because we fusione g3p to OmpA-Linker (BBa_K103996).<br><br />
<br />
* The first N-terminal domain (N1) binds to the bacterial periplasmatic domain of TolA ([http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG11007 TolAIII]), receptor presumably at the inner face of the outer membrane <sup>[[Team:Paris/Transduction_overview_fusion#References|[9]]]</sup>.<br><br />
<br />
* The second N-terminal domain (N2) gives recognition of the host cell by binding the F-pilus on the surface of E. coli. F-pilus is encode by the F episome of male E. coli, and is the primary receptor of the host cell <sup>[[Team:Paris/Transduction_overview_fusion#References|[12]]]</sup>.<br><br />
<br />
* In fact, N1 and N2 interact with each other to form a blocked di-domain (N1G1N2). The binding of N2 to the tip of the bacterial F-pilus releases N1, which becomes free to interact with its receptor TolA (TolAIII) <sup>[[Team:Paris/Transduction_overview_fusion#References|[8]]]</sup><sup>[[Team:Paris/Transduction_overview_fusion#References|[11]]]</sup>.<br><br />
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* The C terminus (CT) of g3p anchors the g3p in the phage coat by interacting with phage coat protein 6, at the tip of the phage. Its seem that phages are released from the bacterial membrane by a two-step mechanism involving a short C-terminal fragment of g3p <sup>[[Team:Paris/Transduction_overview_fusion#References|[7]]]</sup>.<br><br />
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* N1, N2 and N3 domain are linked by flexible glycin-rich domains (G1 and G2). G1 is composed of four tandem copies of the sequence Glu-Gly-Gly-Gly-Ser. In a recent study it has been showed that it may have an active role in F-pilus-dependent infection.<br><br />
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* Fusion of peptides or proteins to the N-terminus of intact g3p does not compromise infectivity of the phage, but insertion of polypeptides between N2 and N3 appear to reduce the infectivity.<br><br />
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====Our use====<br />
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The viral protein known as g3p is naturally exposed at the surface of the filamentous bacteriophage which enable it to get in the bacteria. The M13 phage has a high affinity for E.coli, and if we could place its g3p on the surface of the vesicles it could activate the fusion with the Outer membrane of the targeted bacteria.<br><br />
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To be sure to target the receiving bacteria, we separe the donnor from the receiver with the criterium of the presence or not of pilli, because the g3p need a pillus to start its incorporation process. So the donnor would be pillus negative and the receiver pillus positive.<br><br />
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OmpA-Linker is the second protein required because it is a protein that target any protein that is fuse to it to the surface of the Outer membrane, consequently we fuse G3P with OmpA-Linker.<br><br />
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====Bibliography====<br />
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==Fusion: SNAREs==<br />
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SNARE proteins are a large protein superfamily consisting of more than 60 members in yeast and mammalian cells.<br />
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The primary role of SNARE proteins is to mediate vesicle fusion, that is, the exocytosis of cellular transport vesicles with the cell membrane at the porosome or with a target compartment (such as a lysosome).<br />
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SNAREs can be divided into two categories: vesicle-SNAREs (or v-SNAREs), which are incorporated into the membranes of transport vesicles during budding, and target-SNAREs (or t-SNAREs), which are located in the membranes of target compartments.<br />
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The core of any functionnal SNARE complex is composed by four α-helices provided by the synaptobrevin (for one helix) by the syntaxin (for another helix) and by two SNAP-25 ( for the last two helices) : <br />
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''Synaptobrevin'' : is a small integral membrane protein of secretory vesicles with molecular weight of 18 kilodalton (kDa) that is part of the vesicle-associated membrane protein (VAMP) family <br />
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''Syntaxin'' : Syntaxin 1A was initially identified as a 35 kDa protein in the plasma membrane of amacrine cells [http://www.ncbi.nlm.nih.gov/pubmed/3896407[1]], as a subunit of Ca2+ channels [http://www.ncbi.nlm.nih.gov/pubmed/1587842[2]],[http://www.ncbi.nlm.nih.gov/pubmed/1334074[3]] and as a synaptotagmin-binding protein [http://www.ncbi.nlm.nih.gov/pubmed/1321498[4]]. Since these initial reports, the function of syntaxin as a central component in the synaptic vesicle membrane fusion machinery has been well established.<br />
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''SNAP 25'' : SNAP-25 is a membrane bound protein anchored to the cytosolic face of membranes via palmitoyl side chains in the middle of the molecule. SNAP-25 is a protein contributing two α-helices in the formation of the exocytotic fusion complex in neurons where it assembles with syntaxin-1 and synaptobrevin. <br />
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[[Image:Exocytosis-machinery.jpg|center]]<br />
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''Legend : Molecular machinery driving vesicle fusion in neuromediator release. The core SNARE complex is formed by four α-helices contributed by synaptobrevin, syntaxin and two SNAP-25.''<br />
''Synaptotagmin serves as a calcium sensor and regulates intimately the SNARE zipping''<br />
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===Using SNAREs in Bacteria : not so easy ... ===<br />
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Our first idea was to use SNAREs to perform the fusion between vesicles and target bacteria. The main problem is that the 3D structure of the SNARE complex is crucial for the fusion to proceed [http://www.ncbi.nlm.nih.gov/pubmed/12805548 [5]], [http://www.ncbi.nlm.nih.gov/pubmed/11208146[6]], [http://www.ncbi.nlm.nih.gov/pubmed/19164750 [7]]. As SNAREs don't exist in bacteria we have to clone these genes (into bacteria) and we have to merge the SNAREs protein with a bacterial protein which is localized in the outer membrane (to allow the localization of SNARE protein to the surface of cell). In this direction we weren't sure to obtain the correct conformation of both v- (for the donnor) and t- (for the receiver) SNAREs after their exportation to the bacterial membrane, so we weren't sure that this mechanism will perform. We decided to focus our effort on the Jun/Fos strategy.<br />
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====Bibliography====<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/3896407[1]] Barnstable C. J.Hofstein R.,Akagawa K. A marker of early amacrine cell development in rat retina.(1985) Brain Res 352:286–290<br />
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[http://www.ncbi.nlm.nih.gov/pubmed/1587842[2]] Inoue A.Obata K.Akagawa K.(1992)Cloning and sequence analysis of cDNA for a neuronal cell membrane antigen, HPC-1 J. Biol. Chem. 267:10613–10619<br />
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[http://www.ncbi.nlm.nih.gov/pubmed/1334074[3]] Yoshida A.,Oho C.,Omori A.,Kuwahara R.,Ito T.,Takahashi M.(1992)HPC-1 is associated with synaptotagmin and omega-conotoxin receptor J. Biol. Chem. 267:24925–24928<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/1321498[4]] Bennett M. K.,Calakos N.,Scheller R. H(1992). Syntaxin: a synaptic protein implicated in docking of synaptic vesicles at presynaptic active zones. Science 257:255–259.<br />
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[http://www.ncbi.nlm.nih.gov/pubmed/12805548 [5]] Hu C, Ahmed M, Melia TJ, Söllner TH, Mayer T, Rothman JE. Fusion of cells by flipped SNAREs. Science. 2003 Jun 13;300(5626):1745-9.<br />
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[http://www.ncbi.nlm.nih.gov/pubmed/11208146[6]] Waters MG, Hughson FM. Membrane tethering and fusion in the secretory and endocytic pathways. Traffic. 2000 Aug;1(8):588-97.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19164750 [7]] Giraudo CG, Garcia-Diaz A, Eng WS, Chen Y, Hendrickson WA, Melia TJ, Rothman JE. Alternative zippering as an on-off switch for SNARE-mediated fusion. Science. 2009 Jan 23;323(5913):512-6.</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Production_overviewTeam:Paris/Production overview2009-10-22T02:08:09Z<p>Christophe.R: /* Vesicle production system : Tol/Pal */</p>
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<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Production_overview#bottom"> Main </a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Production_overview#Vesicle_production_system_:_Tol.2FPal"> Tol/Pal</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Production_overview#Vesicle_production_system_:_Our_strategy"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Production_overview_Construction#bottom"> Construction</a><br />
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Several gram-negative bacteria - including ''E. coli'' - have been shown to produce vesicles for various hypothetical reasons<sup>[[Team:Paris/Production_overview#References|[1]]]</sup><sup>[[Team:Paris/Production_overview#References|[2]]]</sup> (stress response, host-pathogen interaction...). In our project, we want to optimize vesicle production to develop a long distance communication system between gram-negative bacteria. Outer membrane vesicles (OMVs) production can be enhanced through the destabilization of the outer-membrane. We found in the literature that the Tol/Pal system could be a good target for this purpose<sup>[[Team:Paris/Production_overview#References|[3]]]</sup>.<br />
The Tol/Pal system of ''Escherichia Coli'' is involved in anchoring the outer- to the inner-membrane and to the peptidoglycan layer. It is thus essential in maintaining membrane integrity. The system is composed of five membrane proteins (TolA, TolB, TolQ, TolR and Pal) associating in two complexes.<sup>[[Team:Paris/Production_overview#References|[4]]]</sup><sup>[[Team:Paris/Production_overview#References|[5]]]</sup><br />
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See [[Team:Paris/Production_overview#Vesicle_production_system_:_Tol.2FPal|Tol/Pal]] part for more information and why we choose this system. [[Team:Paris/Production_overview#Vesicle_production_system_:_Our_strategy|Strategy]] and [[Team:Paris/Production_overview_Construction#bottom|Construction]] part explains our aim in this OMV production system. <br />
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==Vesicle production system : Tol/Pal==<br />
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''E. Coli'' is gram-. Its membrane is a complex that included: the inner membrane and the outer membrane. Between both, there is a layer of peptidoglycan.<br />
The outer membrane presents lipo-polysaccharides (LPS). We find also porins and other proteins. There are receivers for the entrance of nourishing elements, receivers in pili (bacterial conjugation), receivers where settles bacteriophage. It has properties of selective permeability, protection and support. This complex of proteins is in place to maintain the stability between the inner membrane and the outer membrane.<br />
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In particular the system called Tol-Pal consisted of five proteins, TolA, TolB, TolQ, TolR and Pal<sup>[[Team:Paris/Production_overview#References|[3]]]</sup><sup>[[Team:Paris/Production_overview#References|[4]]]</sup>. This complex allows to maintain the integrity of the membrane. Studies showed that if we destabilize this system, we also destabilize the membrane, leading then a production of vesicles. But when the membrane of the bacteria stays for such a long time to this state of destabilization, the bacteria produces too many vesicles and go in state of lysis<sup>[[Team:Paris/Production_overview#References|[4]]]</sup>.<br />
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What is Tol-Pal complex ?<br />
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Five proteins organised this complex<sup>[[Team:Paris/Production_overview#References|[5]]]</sup>.<br />
The TolA/Q/R proteins form a protein complex in the inner membrane. TolB is a periplasmic protein associated with Pal, a lipoprotein. Pal is anchored to the outer membrane and interacts with the peptidoglycan layer. There are interactions with TolA–Pal and TolA–TolB.<br />
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[[Image:TolPal.jpg|250px|center| Tol-Pal system]]<br />
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==Vesicle production system : Our strategy==<br />
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We want to destabilize the outer membrane to create outer membrane vesicles (OMVs). <br />
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OMVs were formed upon periplasmic overproduction of soluble TolA and TolR domains, since these two short periplasmic domains (both less than 100 residues) have been previously found to disturb the Tol–Pal system<sup>[[Team:Paris/Production_overview#References|[6]]]</sup><sup>[[Team:Paris/Production_overview#References|[7]]]</sup>. (TolA and TolR have three domains: Nterminal, central and Cterminal domains)<br />
An other study<sup>[[Team:Paris/Production_overview#References|[5]]]</sup> focused on the development of a gene expression system able to induce production of large amounts of OMVs when they used different domains of these two proteins of Tol-Pal system. This team <sup>[[Team:Paris/Production_overview#References|[5]]]</sup> send us their plasmid and we were able to begin our work quickly.<br />
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To achieve our goal, we decided to do like the Lloubès Team<sup><[[Team:Paris/Production_overview#References|[5]]]</sup> and take advantage of the soluble central domain of TolR (TolRII). We don’t use the third domain of TolA because, it doesn’t work so well and TolAIII have lot of PstI domain in his sequence. In order to achieve our project, we will over express specifically designed biobricks containing TolRII fused with OmpA signal which allows it to migrate in the periplasm<sup>[[Team:Paris/Production_overview#References|[4]]]</sup>. So Tol-Pal system will become bad and the membrane integrity will be destabilised. Lot of vesicle could be creating. <br />
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If bacteria stay in this conformation, there is lysis. We try to create an ON/OFF system to stop the vesicles creation.<br />
In the same framework, we could also over express various Tol ligand (like colicin) to destabilize the membrane. But it doesn’t work very well.<sup>[[Team:Paris/Production_overview#References|[5]]]</sup> <br />
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BioBrick TolR domain II N-term fusion : [http://partsregistry.org/wiki/index.php?title=Part:BBa_K257005 Bba K257005]<br />
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BioBrick ompA sequence signal : [http://partsregistry.org/wiki/index.php?title=Part:BBa_K257006 Bba_K257006]<br />
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You can see now our [[Team:Paris/Production_overview_Construction#bottom|Construction]].<br />
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====References====<br />
<ol class="references"><br />
<li> [[Team:Paris/Production_overview#1 | ^]]Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response. McBroom AJ & Kuehn MJ 2007 - [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=17163978 17163978]</li><br />
<li> [[Team:Paris/Production_overview#1 | ^]]Biogenesis of bacterial membrane vesicles. Deatherage BL & Cookson BT 2009 - [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=19432795 19432795]</li><br />
<li> [[Team:Paris/Production_overview#1 | ^]]Transmembrane a-helix interactions are required for the functional assembly of the escherichia coli Tol complex. Lazzaroni & Geli 1995 - [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179564 179564]</li><br />
<li> [[Team:Paris/Production_overview#1 | ^]]The Tol-Pal proteins of the Escherichia coli cell envelope an energized system required for outer membrane integrity. Lloubès & Journet 2001 - [http://www.ncbi.nlm.nih.gov/pubmed/11501670 11501670]</li><br />
<li> [[Team:Paris/Production_overview#1 | ^]]Improved methods for producing outer membrane vesicles in gram-negative bacteria. Henry & Lloubès 2004 - [http://www.ncbi.nlm.nih.gov/pubmed/15249060 15249060]</li><br />
<li> [[Team:Paris/Production_overview#6 | ^]]Role of TolR N-terminal, central, and C-terminal domains in dimerization and interaction with TolA and tolQ. Journet L & Bénédetti H. 1999 - [http://www.ncbi.nlm.nih.gov/pubmed/10419942 10419942]</li><br />
<li> [[Team:Paris/Production_overview#6 | ^]]Role of the carboxyl-terminal domain of TolA in protein import and integrity of the outer membrane. Levengood-Freyermuth SK & Webster RE. 1993 - [http://www.ncbi.nlm.nih.gov/pubmed/8416897 8416897]</li><br />
</ol></div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview_fusionTeam:Paris/Transduction overview fusion2009-10-22T02:06:03Z<p>Christophe.R: /* AIDA */</p>
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===Jun and Fos===<br />
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Fos and Jun, the protein products of the nuclear proto-oncogenes c-fos and c-jun, associate preferentially to form a heterodimer. Both Fos and Jun contain a single leucine zipper region. Previous studies [http://www.ncbi.nlm.nih.gov/pubmed/2974122[1]],[http://www.ncbi.nlm.nih.gov/pubmed/2494702[2]] have shown that the leucine zippers of Fos and Jun are necessary and sufficient to mediate preferential heterodimer formation and that Jun : Fos heterodimers have higher stability than Jun homodimers <br />
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In our project we would like to be sure that vesicles are going to recognize target bacteria. In this direction we decided to use the Jun and Fos recognition system. The problem was that Jun is able to form an homodimer and an heterodimer with Fos, so the specific interaction between vesicles and receiver cell is not specific. An article demonstrated that 2 mutations in the leucine-zipper allow the Jun/Fos dimerisation but abolished the Jun/Jun dimer formation [http://www.ncbi.nlm.nih.gov/pubmed/2516828[3]]. <br />
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===AIDA===<br />
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<sup>[[Team:Paris/Transduction_overview_fusion#References [1]]]</sup><br />
The cell envelope of gram-negative bacteria consists of two membranes, the cytoplasmic or inner membrane and the outer membrane. Transport of proteins across the inner membrane in most cases follows the general secretory pathway (GSP) [http://www.ncbi.nlm.nih.gov/pubmed/2565291[4]]. Therefore, in gram-negative bacteria, proteins end up in the periplasm. To translocate proteins to the outer surface or into the supernatant, gram-negative bacteria have developed several distinct mechanisms. In contrast to the secretory systems that require a variety of specialized accessory proteins that, often in combination with the GSP, are responsible for the export of one or several passenger proteins into the supernatant, the '''autotransporter''' protein family members carry the export signal and machinery within a single polypeptide chain.<br />
The adhesin-involved-in-diffuse-adherence (AIDA) autotransporter has been identified as a virulence factor of the enteropathogenic Escherichia coli strain 2787 [http://www.ncbi.nlm.nih.gov/pubmed/8824401[5]] and predicted to be a member of the autotransporter protein family [http://www.ncbi.nlm.nih.gov/pubmed/2189728[6]]<br />
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This AIDA autotransporter is using to translocate Jun and Fos to the outer membrane of bacteria (Jun for the donnor, Fos for the receiver).<br />
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====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Kouzarides, T. and E. Ziff. 1988. The role of the leucine zipper in the fos-jun interaction. Nature 336: 646-656. [http://www.ncbi.nlm.nih.gov/pubmed/2974122 2974122] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Gentz, R., F.J. Rauscher III, C. Abate, and T. Curran. 1989. Parallel association of Fos and Jun leucine zippers juxtaposes DNA-binding domains. Science 243:16951699.[http://www.ncbi.nlm.nih.gov/pubmed/2494702 2494702]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]<br />
Tod Smeal, Peter Angel, Jennifer Meek, and Michael Karin 1989. Different requirements for formation of Jun: Jun and Jun : Fos complexes. GENES & DEVELOPMENT 3:2091-2100. [http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Benz, I., and M. A. Schmidt. 1989. Cloning and expression of an adhesin (AIDA-I) involved in diffuse adherence of enteropathogenic Escherichia coli. Infect. Immun. 57:1506–1511. [http://www.ncbi.nlm.nih.gov/pubmed/2565291 2565291]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Murphy, C., W. Prinz, M. Pohlschroder, A. Derman, and J. Beckwith. 1995. Essential features of the pathway for protein translocation across the Escherichia coli cytoplasmic membrane. Cold Spring Harbor Symp. Quant. Biol. 60:277–283. [http://www.ncbi.nlm.nih.gov/pubmed/8824401 8824401]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Klauser, T., J. Pohlner, and T. F. Meyer. 1990. Extracellular transport of cholera toxin B subunit using Neisseria IgA protease beta-domain: conformation- dependent outer membrane translocation. EMBO J. 9:1991–1999. [http://www.ncbi.nlm.nih.gov/pubmed/2189728 2189728]</li><br />
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==Fusion: g3p==<br />
<br />
What is the g3p and how could it be a key part in the vesicles-bacteria fusion ?<br />
<br />
====Description of g3p====<br />
<br />
Infection of Escherichia coli by filamentous bacteriophages as M13, fd, f1, is mediated by the phage gene 3 protein (g3p or pIII). This protein of 406 amino acid residues, has a signal peptide, two N-terminal domains and one C-terminal domain, separated by two flexible glycin-rich linkers. All three domains are indispensable for phage infectivity.<br><br />
g3p could be also found in phage helper like M13KO7 [http://www.ncbi.nlm.nih.gov/pubmed/11861923[4]]<br><br />
<br />
* The signal peptide (1-18aa) address the protein to the cell membrane before being cleaved. We deleted it because we fusione g3p to OmpA-Linker (BBa_K103996).<br><br />
<br />
* The first N-terminal domain (N1) binds to the bacterial periplasmatic domain of TolA ([http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG11007 TolAIII]), receptor presumably at the inner face of the outer membrane [http://www.ncbi.nlm.nih.gov/pubmed/10404600[3]].<br><br />
<br />
* The second N-terminal domain (N2) gives recognition of the host cell by binding the F-pilus on the surface of E. coli. F-pilus is encode by the F episome of male E. coli, and is the primary receptor of the host cell [http://www.ncbi.nlm.nih.gov/pubmed/5338586[6]].<br><br />
<br />
* In fact, N1 and N2 interact with each other to form a blocked di-domain (N1G1N2). The binding of N2 to the tip of the bacterial F-pilus releases N1, which becomes free to interact with its receptor TolA (TolAIII) [http://www.ncbi.nlm.nih.gov/pubmed/10606756[2]][http://www.ncbi.nlm.nih.gov/pubmed/12670988[5]].<br><br />
<br />
* The C terminus (CT) of g3p anchors the g3p in the phage coat by interacting with phage coat protein 6, at the tip of the phage. Its seem that phages are released from the bacterial membrane by a two-step mechanism involving a short C-terminal fragment of g3p [http://www.ncbi.nlm.nih.gov/pubmed/6291030[1]].<br><br />
<br />
* N1, N2 and N3 domain are linked by flexible glycin-rich domains (G1 and G2). G1 is composed of four tandem copies of the sequence Glu-Gly-Gly-Gly-Ser. In a recent study it has been showed that it may have an active role in F-pilus-dependent infection.<br><br />
<br />
* Fusion of peptides or proteins to the N-terminus of intact g3p does not compromise infectivity of the phage, but insertion of polypeptides between N2 and N3 appear to reduce the infectivity.<br><br />
<br />
====Our use====<br />
<br />
The viral protein known as g3p is naturally exposed at the surface of the filamentous bacteriophage which enable it to get in the bacteria. The M13 phage has a high affinity for E.coli, and if we could place its g3p on the surface of the vesicles it could activate the fusion with the Outer membrane of the targeted bacteria.<br><br />
<br />
To be sure to target the receiving bacteria, we separe the donnor from the receiver with the criterium of the presence or not of pilli, because the g3p need a pillus to start its incorporation process. So the donnor would be pillus negative and the receiver pillus positive.<br><br />
<br />
OmpA-Linker is the second protein required because it is a protein that target any protein that is fuse to it to the surface of the Outer membrane, consequently we fuse G3P with OmpA-Linker.<br><br />
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====Bibliography====<br />
[http://www.ncbi.nlm.nih.gov/pubmed/6291030[1]] Jef D.Boeke & Peter Model. A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane. 1982.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/10606756[2]] Chatellier J & Riechmann L. Interdomain interactions within the gene 3 protein of filamentous phage. 1999.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/10404600[3]] Lubkowski J & Wlodawer A. Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA. 1999.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/11861923[4]] Baek H & Cha S. An improved helper phage system for efficient isolation of specific antibody molecules in phage display. 2002.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/12670988[5]] Karlsson F & Malmborg-Hager AC. The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains. 2003.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/5338586[6]] Caro LG, Schnös M. The attachment of the male-specific bacteriophage F1 to sensitive strains of Escherichia coli. 1966.<br />
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==Fusion: SNAREs==<br />
<br />
SNARE proteins are a large protein superfamily consisting of more than 60 members in yeast and mammalian cells.<br />
<br />
<br />
The primary role of SNARE proteins is to mediate vesicle fusion, that is, the exocytosis of cellular transport vesicles with the cell membrane at the porosome or with a target compartment (such as a lysosome).<br />
<br />
<br />
SNAREs can be divided into two categories: vesicle-SNAREs (or v-SNAREs), which are incorporated into the membranes of transport vesicles during budding, and target-SNAREs (or t-SNAREs), which are located in the membranes of target compartments.<br />
<br />
<br />
The core of any functionnal SNARE complex is composed by four α-helices provided by the synaptobrevin (for one helix) by the syntaxin (for another helix) and by two SNAP-25 ( for the last two helices) : <br />
<br />
<br />
''Synaptobrevin'' : is a small integral membrane protein of secretory vesicles with molecular weight of 18 kilodalton (kDa) that is part of the vesicle-associated membrane protein (VAMP) family <br />
<br />
<br />
''Syntaxin'' : Syntaxin 1A was initially identified as a 35 kDa protein in the plasma membrane of amacrine cells [http://www.ncbi.nlm.nih.gov/pubmed/3896407[1]], as a subunit of Ca2+ channels [http://www.ncbi.nlm.nih.gov/pubmed/1587842[2]],[http://www.ncbi.nlm.nih.gov/pubmed/1334074[3]] and as a synaptotagmin-binding protein [http://www.ncbi.nlm.nih.gov/pubmed/1321498[4]]. Since these initial reports, the function of syntaxin as a central component in the synaptic vesicle membrane fusion machinery has been well established.<br />
<br />
<br />
''SNAP 25'' : SNAP-25 is a membrane bound protein anchored to the cytosolic face of membranes via palmitoyl side chains in the middle of the molecule. SNAP-25 is a protein contributing two α-helices in the formation of the exocytotic fusion complex in neurons where it assembles with syntaxin-1 and synaptobrevin. <br />
<br />
<br />
<br />
<br />
[[Image:Exocytosis-machinery.jpg|center]]<br />
<br />
<br />
''Legend : Molecular machinery driving vesicle fusion in neuromediator release. The core SNARE complex is formed by four α-helices contributed by synaptobrevin, syntaxin and two SNAP-25.''<br />
''Synaptotagmin serves as a calcium sensor and regulates intimately the SNARE zipping''<br />
<br />
<br />
<br />
<br />
===Using SNAREs in Bacteria : not so easy ... ===<br />
<br />
Our first idea was to use SNAREs to perform the fusion between vesicles and target bacteria. The main problem is that the 3D structure of the SNARE complex is crucial for the fusion to proceed [http://www.ncbi.nlm.nih.gov/pubmed/12805548 [5]], [http://www.ncbi.nlm.nih.gov/pubmed/11208146[6]], [http://www.ncbi.nlm.nih.gov/pubmed/19164750 [7]]. As SNAREs don't exist in bacteria we have to clone these genes (into bacteria) and we have to merge the SNAREs protein with a bacterial protein which is localized in the outer membrane (to allow the localization of SNARE protein to the surface of cell). In this direction we weren't sure to obtain the correct conformation of both v- (for the donnor) and t- (for the receiver) SNAREs after their exportation to the bacterial membrane, so we weren't sure that this mechanism will perform. We decided to focus our effort on the Jun/Fos strategy.<br />
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<br />
====Bibliography====<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/3896407[1]] Barnstable C. J.Hofstein R.,Akagawa K. A marker of early amacrine cell development in rat retina.(1985) Brain Res 352:286–290<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/1587842[2]] Inoue A.Obata K.Akagawa K.(1992)Cloning and sequence analysis of cDNA for a neuronal cell membrane antigen, HPC-1 J. Biol. Chem. 267:10613–10619<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/1334074[3]] Yoshida A.,Oho C.,Omori A.,Kuwahara R.,Ito T.,Takahashi M.(1992)HPC-1 is associated with synaptotagmin and omega-conotoxin receptor J. Biol. Chem. 267:24925–24928<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/1321498[4]] Bennett M. K.,Calakos N.,Scheller R. H(1992). Syntaxin: a synaptic protein implicated in docking of synaptic vesicles at presynaptic active zones. Science 257:255–259.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/12805548 [5]] Hu C, Ahmed M, Melia TJ, Söllner TH, Mayer T, Rothman JE. Fusion of cells by flipped SNAREs. Science. 2003 Jun 13;300(5626):1745-9.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/11208146[6]] Waters MG, Hughson FM. Membrane tethering and fusion in the secretory and endocytic pathways. Traffic. 2000 Aug;1(8):588-97.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19164750 [7]] Giraudo CG, Garcia-Diaz A, Eng WS, Chen Y, Hendrickson WA, Melia TJ, Rothman JE. Alternative zippering as an on-off switch for SNARE-mediated fusion. Science. 2009 Jan 23;323(5913):512-6.</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview_fusionTeam:Paris/Transduction overview fusion2009-10-22T02:05:47Z<p>Christophe.R: /* AIDA */</p>
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<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview_fusion#bottom | Fusion]]<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview#bottom"> Main </a>|<br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#bottom"> Fusion</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_strategy#bottom"> Our strategy</a>|<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_G3P"> G3P</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_SNAREs"> SNAREs</a><br />
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===Jun and Fos===<br />
<br />
<br />
Fos and Jun, the protein products of the nuclear proto-oncogenes c-fos and c-jun, associate preferentially to form a heterodimer. Both Fos and Jun contain a single leucine zipper region. Previous studies [http://www.ncbi.nlm.nih.gov/pubmed/2974122[1]],[http://www.ncbi.nlm.nih.gov/pubmed/2494702[2]] have shown that the leucine zippers of Fos and Jun are necessary and sufficient to mediate preferential heterodimer formation and that Jun : Fos heterodimers have higher stability than Jun homodimers <br />
<br />
<br />
In our project we would like to be sure that vesicles are going to recognize target bacteria. In this direction we decided to use the Jun and Fos recognition system. The problem was that Jun is able to form an homodimer and an heterodimer with Fos, so the specific interaction between vesicles and receiver cell is not specific. An article demonstrated that 2 mutations in the leucine-zipper allow the Jun/Fos dimerisation but abolished the Jun/Jun dimer formation [http://www.ncbi.nlm.nih.gov/pubmed/2516828[3]]. <br />
<br />
<br />
<br />
<br />
===AIDA===<br />
<br />
<sup>[Team:Paris/Transduction_overview_fusion#References [1]]</sup><br />
The cell envelope of gram-negative bacteria consists of two membranes, the cytoplasmic or inner membrane and the outer membrane. Transport of proteins across the inner membrane in most cases follows the general secretory pathway (GSP) [http://www.ncbi.nlm.nih.gov/pubmed/2565291[4]]. Therefore, in gram-negative bacteria, proteins end up in the periplasm. To translocate proteins to the outer surface or into the supernatant, gram-negative bacteria have developed several distinct mechanisms. In contrast to the secretory systems that require a variety of specialized accessory proteins that, often in combination with the GSP, are responsible for the export of one or several passenger proteins into the supernatant, the '''autotransporter''' protein family members carry the export signal and machinery within a single polypeptide chain.<br />
The adhesin-involved-in-diffuse-adherence (AIDA) autotransporter has been identified as a virulence factor of the enteropathogenic Escherichia coli strain 2787 [http://www.ncbi.nlm.nih.gov/pubmed/8824401[5]] and predicted to be a member of the autotransporter protein family [http://www.ncbi.nlm.nih.gov/pubmed/2189728[6]]<br />
<br />
This AIDA autotransporter is using to translocate Jun and Fos to the outer membrane of bacteria (Jun for the donnor, Fos for the receiver).<br />
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====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Kouzarides, T. and E. Ziff. 1988. The role of the leucine zipper in the fos-jun interaction. Nature 336: 646-656. [http://www.ncbi.nlm.nih.gov/pubmed/2974122 2974122] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Gentz, R., F.J. Rauscher III, C. Abate, and T. Curran. 1989. Parallel association of Fos and Jun leucine zippers juxtaposes DNA-binding domains. Science 243:16951699.[http://www.ncbi.nlm.nih.gov/pubmed/2494702 2494702]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]<br />
Tod Smeal, Peter Angel, Jennifer Meek, and Michael Karin 1989. Different requirements for formation of Jun: Jun and Jun : Fos complexes. GENES & DEVELOPMENT 3:2091-2100. [http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Benz, I., and M. A. Schmidt. 1989. Cloning and expression of an adhesin (AIDA-I) involved in diffuse adherence of enteropathogenic Escherichia coli. Infect. Immun. 57:1506–1511. [http://www.ncbi.nlm.nih.gov/pubmed/2565291 2565291]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Murphy, C., W. Prinz, M. Pohlschroder, A. Derman, and J. Beckwith. 1995. Essential features of the pathway for protein translocation across the Escherichia coli cytoplasmic membrane. Cold Spring Harbor Symp. Quant. Biol. 60:277–283. [http://www.ncbi.nlm.nih.gov/pubmed/8824401 8824401]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Klauser, T., J. Pohlner, and T. F. Meyer. 1990. Extracellular transport of cholera toxin B subunit using Neisseria IgA protease beta-domain: conformation- dependent outer membrane translocation. EMBO J. 9:1991–1999. [http://www.ncbi.nlm.nih.gov/pubmed/2189728 2189728]</li><br />
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==Fusion: g3p==<br />
<br />
What is the g3p and how could it be a key part in the vesicles-bacteria fusion ?<br />
<br />
====Description of g3p====<br />
<br />
Infection of Escherichia coli by filamentous bacteriophages as M13, fd, f1, is mediated by the phage gene 3 protein (g3p or pIII). This protein of 406 amino acid residues, has a signal peptide, two N-terminal domains and one C-terminal domain, separated by two flexible glycin-rich linkers. All three domains are indispensable for phage infectivity.<br><br />
g3p could be also found in phage helper like M13KO7 [http://www.ncbi.nlm.nih.gov/pubmed/11861923[4]]<br><br />
<br />
* The signal peptide (1-18aa) address the protein to the cell membrane before being cleaved. We deleted it because we fusione g3p to OmpA-Linker (BBa_K103996).<br><br />
<br />
* The first N-terminal domain (N1) binds to the bacterial periplasmatic domain of TolA ([http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG11007 TolAIII]), receptor presumably at the inner face of the outer membrane [http://www.ncbi.nlm.nih.gov/pubmed/10404600[3]].<br><br />
<br />
* The second N-terminal domain (N2) gives recognition of the host cell by binding the F-pilus on the surface of E. coli. F-pilus is encode by the F episome of male E. coli, and is the primary receptor of the host cell [http://www.ncbi.nlm.nih.gov/pubmed/5338586[6]].<br><br />
<br />
* In fact, N1 and N2 interact with each other to form a blocked di-domain (N1G1N2). The binding of N2 to the tip of the bacterial F-pilus releases N1, which becomes free to interact with its receptor TolA (TolAIII) [http://www.ncbi.nlm.nih.gov/pubmed/10606756[2]][http://www.ncbi.nlm.nih.gov/pubmed/12670988[5]].<br><br />
<br />
* The C terminus (CT) of g3p anchors the g3p in the phage coat by interacting with phage coat protein 6, at the tip of the phage. Its seem that phages are released from the bacterial membrane by a two-step mechanism involving a short C-terminal fragment of g3p [http://www.ncbi.nlm.nih.gov/pubmed/6291030[1]].<br><br />
<br />
* N1, N2 and N3 domain are linked by flexible glycin-rich domains (G1 and G2). G1 is composed of four tandem copies of the sequence Glu-Gly-Gly-Gly-Ser. In a recent study it has been showed that it may have an active role in F-pilus-dependent infection.<br><br />
<br />
* Fusion of peptides or proteins to the N-terminus of intact g3p does not compromise infectivity of the phage, but insertion of polypeptides between N2 and N3 appear to reduce the infectivity.<br><br />
<br />
====Our use====<br />
<br />
The viral protein known as g3p is naturally exposed at the surface of the filamentous bacteriophage which enable it to get in the bacteria. The M13 phage has a high affinity for E.coli, and if we could place its g3p on the surface of the vesicles it could activate the fusion with the Outer membrane of the targeted bacteria.<br><br />
<br />
To be sure to target the receiving bacteria, we separe the donnor from the receiver with the criterium of the presence or not of pilli, because the g3p need a pillus to start its incorporation process. So the donnor would be pillus negative and the receiver pillus positive.<br><br />
<br />
OmpA-Linker is the second protein required because it is a protein that target any protein that is fuse to it to the surface of the Outer membrane, consequently we fuse G3P with OmpA-Linker.<br><br />
<br />
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</html><br />
<br />
====Bibliography====<br />
[http://www.ncbi.nlm.nih.gov/pubmed/6291030[1]] Jef D.Boeke & Peter Model. A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane. 1982.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/10606756[2]] Chatellier J & Riechmann L. Interdomain interactions within the gene 3 protein of filamentous phage. 1999.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/10404600[3]] Lubkowski J & Wlodawer A. Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA. 1999.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/11861923[4]] Baek H & Cha S. An improved helper phage system for efficient isolation of specific antibody molecules in phage display. 2002.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/12670988[5]] Karlsson F & Malmborg-Hager AC. The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains. 2003.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/5338586[6]] Caro LG, Schnös M. The attachment of the male-specific bacteriophage F1 to sensitive strains of Escherichia coli. 1966.<br />
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==Fusion: SNAREs==<br />
<br />
SNARE proteins are a large protein superfamily consisting of more than 60 members in yeast and mammalian cells.<br />
<br />
<br />
The primary role of SNARE proteins is to mediate vesicle fusion, that is, the exocytosis of cellular transport vesicles with the cell membrane at the porosome or with a target compartment (such as a lysosome).<br />
<br />
<br />
SNAREs can be divided into two categories: vesicle-SNAREs (or v-SNAREs), which are incorporated into the membranes of transport vesicles during budding, and target-SNAREs (or t-SNAREs), which are located in the membranes of target compartments.<br />
<br />
<br />
The core of any functionnal SNARE complex is composed by four α-helices provided by the synaptobrevin (for one helix) by the syntaxin (for another helix) and by two SNAP-25 ( for the last two helices) : <br />
<br />
<br />
''Synaptobrevin'' : is a small integral membrane protein of secretory vesicles with molecular weight of 18 kilodalton (kDa) that is part of the vesicle-associated membrane protein (VAMP) family <br />
<br />
<br />
''Syntaxin'' : Syntaxin 1A was initially identified as a 35 kDa protein in the plasma membrane of amacrine cells [http://www.ncbi.nlm.nih.gov/pubmed/3896407[1]], as a subunit of Ca2+ channels [http://www.ncbi.nlm.nih.gov/pubmed/1587842[2]],[http://www.ncbi.nlm.nih.gov/pubmed/1334074[3]] and as a synaptotagmin-binding protein [http://www.ncbi.nlm.nih.gov/pubmed/1321498[4]]. Since these initial reports, the function of syntaxin as a central component in the synaptic vesicle membrane fusion machinery has been well established.<br />
<br />
<br />
''SNAP 25'' : SNAP-25 is a membrane bound protein anchored to the cytosolic face of membranes via palmitoyl side chains in the middle of the molecule. SNAP-25 is a protein contributing two α-helices in the formation of the exocytotic fusion complex in neurons where it assembles with syntaxin-1 and synaptobrevin. <br />
<br />
<br />
<br />
<br />
[[Image:Exocytosis-machinery.jpg|center]]<br />
<br />
<br />
''Legend : Molecular machinery driving vesicle fusion in neuromediator release. The core SNARE complex is formed by four α-helices contributed by synaptobrevin, syntaxin and two SNAP-25.''<br />
''Synaptotagmin serves as a calcium sensor and regulates intimately the SNARE zipping''<br />
<br />
<br />
<br />
<br />
===Using SNAREs in Bacteria : not so easy ... ===<br />
<br />
Our first idea was to use SNAREs to perform the fusion between vesicles and target bacteria. The main problem is that the 3D structure of the SNARE complex is crucial for the fusion to proceed [http://www.ncbi.nlm.nih.gov/pubmed/12805548 [5]], [http://www.ncbi.nlm.nih.gov/pubmed/11208146[6]], [http://www.ncbi.nlm.nih.gov/pubmed/19164750 [7]]. As SNAREs don't exist in bacteria we have to clone these genes (into bacteria) and we have to merge the SNAREs protein with a bacterial protein which is localized in the outer membrane (to allow the localization of SNARE protein to the surface of cell). In this direction we weren't sure to obtain the correct conformation of both v- (for the donnor) and t- (for the receiver) SNAREs after their exportation to the bacterial membrane, so we weren't sure that this mechanism will perform. We decided to focus our effort on the Jun/Fos strategy.<br />
<br />
<br />
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<br />
====Bibliography====<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/3896407[1]] Barnstable C. J.Hofstein R.,Akagawa K. A marker of early amacrine cell development in rat retina.(1985) Brain Res 352:286–290<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/1587842[2]] Inoue A.Obata K.Akagawa K.(1992)Cloning and sequence analysis of cDNA for a neuronal cell membrane antigen, HPC-1 J. Biol. Chem. 267:10613–10619<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/1334074[3]] Yoshida A.,Oho C.,Omori A.,Kuwahara R.,Ito T.,Takahashi M.(1992)HPC-1 is associated with synaptotagmin and omega-conotoxin receptor J. Biol. Chem. 267:24925–24928<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/1321498[4]] Bennett M. K.,Calakos N.,Scheller R. H(1992). Syntaxin: a synaptic protein implicated in docking of synaptic vesicles at presynaptic active zones. Science 257:255–259.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/12805548 [5]] Hu C, Ahmed M, Melia TJ, Söllner TH, Mayer T, Rothman JE. Fusion of cells by flipped SNAREs. Science. 2003 Jun 13;300(5626):1745-9.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/11208146[6]] Waters MG, Hughson FM. Membrane tethering and fusion in the secretory and endocytic pathways. Traffic. 2000 Aug;1(8):588-97.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19164750 [7]] Giraudo CG, Garcia-Diaz A, Eng WS, Chen Y, Hendrickson WA, Melia TJ, Rothman JE. Alternative zippering as an on-off switch for SNARE-mediated fusion. Science. 2009 Jan 23;323(5913):512-6.</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Transduction_overview_fusionTeam:Paris/Transduction overview fusion2009-10-22T02:03:35Z<p>Christophe.R: /* Bibliography */</p>
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<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Transduction_overview#top | Receiving the message]] > [[Team:Paris/Transduction_overview_fusion#bottom | Fusion]]<br />
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==Fusion: Jun/Fos and AIDA==<br />
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<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview#bottom"> Main </a>|<br />
<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#bottom"> Fusion</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_strategy#bottom"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_construction#bottom"> Construction</a><br />
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<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_Jun.2FFos_and_AIDA"> Jun/Fos </a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_G3P"> G3P</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#Fusion:_SNAREs"> SNAREs</a><br />
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===Jun and Fos===<br />
<br />
<br />
Fos and Jun, the protein products of the nuclear proto-oncogenes c-fos and c-jun, associate preferentially to form a heterodimer. Both Fos and Jun contain a single leucine zipper region. Previous studies [http://www.ncbi.nlm.nih.gov/pubmed/2974122[1]],[http://www.ncbi.nlm.nih.gov/pubmed/2494702[2]] have shown that the leucine zippers of Fos and Jun are necessary and sufficient to mediate preferential heterodimer formation and that Jun : Fos heterodimers have higher stability than Jun homodimers <br />
<br />
<br />
In our project we would like to be sure that vesicles are going to recognize target bacteria. In this direction we decided to use the Jun and Fos recognition system. The problem was that Jun is able to form an homodimer and an heterodimer with Fos, so the specific interaction between vesicles and receiver cell is not specific. An article demonstrated that 2 mutations in the leucine-zipper allow the Jun/Fos dimerisation but abolished the Jun/Jun dimer formation [http://www.ncbi.nlm.nih.gov/pubmed/2516828[3]]. <br />
<br />
<br />
<br />
<br />
===AIDA===<br />
<br />
<br />
The cell envelope of gram-negative bacteria consists of two membranes, the cytoplasmic or inner membrane and the outer membrane. Transport of proteins across the inner membrane in most cases follows the general secretory pathway (GSP) [http://www.ncbi.nlm.nih.gov/pubmed/2565291[4]]. Therefore, in gram-negative bacteria, proteins end up in the periplasm. To translocate proteins to the outer surface or into the supernatant, gram-negative bacteria have developed several distinct mechanisms. In contrast to the secretory systems that require a variety of specialized accessory proteins that, often in combination with the GSP, are responsible for the export of one or several passenger proteins into the supernatant, the '''autotransporter''' protein family members carry the export signal and machinery within a single polypeptide chain.<br />
The adhesin-involved-in-diffuse-adherence (AIDA) autotransporter has been identified as a virulence factor of the enteropathogenic Escherichia coli strain 2787 [http://www.ncbi.nlm.nih.gov/pubmed/8824401[5]] and predicted to be a member of the autotransporter protein family [http://www.ncbi.nlm.nih.gov/pubmed/2189728[6]]<br />
<br />
This AIDA autotransporter is using to translocate Jun and Fos to the outer membrane of bacteria (Jun for the donnor, Fos for the receiver).<br />
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====References====<br />
<br />
<ol class="references"><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Kouzarides, T. and E. Ziff. 1988. The role of the leucine zipper in the fos-jun interaction. Nature 336: 646-656. [http://www.ncbi.nlm.nih.gov/pubmed/2974122 2974122] </li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Gentz, R., F.J. Rauscher III, C. Abate, and T. Curran. 1989. Parallel association of Fos and Jun leucine zippers juxtaposes DNA-binding domains. Science 243:16951699.[http://www.ncbi.nlm.nih.gov/pubmed/2494702 2494702]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]<br />
Tod Smeal, Peter Angel, Jennifer Meek, and Michael Karin 1989. Different requirements for formation of Jun: Jun and Jun : Fos complexes. GENES & DEVELOPMENT 3:2091-2100. [http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Benz, I., and M. A. Schmidt. 1989. Cloning and expression of an adhesin (AIDA-I) involved in diffuse adherence of enteropathogenic Escherichia coli. Infect. Immun. 57:1506–1511. [http://www.ncbi.nlm.nih.gov/pubmed/2565291 2565291]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Murphy, C., W. Prinz, M. Pohlschroder, A. Derman, and J. Beckwith. 1995. Essential features of the pathway for protein translocation across the Escherichia coli cytoplasmic membrane. Cold Spring Harbor Symp. Quant. Biol. 60:277–283. [http://www.ncbi.nlm.nih.gov/pubmed/8824401 8824401]</li><br />
<li>[[Team:Paris/Transduction_overview_fusion#1| ^]]Klauser, T., J. Pohlner, and T. F. Meyer. 1990. Extracellular transport of cholera toxin B subunit using Neisseria IgA protease beta-domain: conformation- dependent outer membrane translocation. EMBO J. 9:1991–1999. [http://www.ncbi.nlm.nih.gov/pubmed/2189728 2189728]</li><br />
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==Fusion: g3p==<br />
<br />
What is the g3p and how could it be a key part in the vesicles-bacteria fusion ?<br />
<br />
====Description of g3p====<br />
<br />
Infection of Escherichia coli by filamentous bacteriophages as M13, fd, f1, is mediated by the phage gene 3 protein (g3p or pIII). This protein of 406 amino acid residues, has a signal peptide, two N-terminal domains and one C-terminal domain, separated by two flexible glycin-rich linkers. All three domains are indispensable for phage infectivity.<br><br />
g3p could be also found in phage helper like M13KO7 [http://www.ncbi.nlm.nih.gov/pubmed/11861923[4]]<br><br />
<br />
* The signal peptide (1-18aa) address the protein to the cell membrane before being cleaved. We deleted it because we fusione g3p to OmpA-Linker (BBa_K103996).<br><br />
<br />
* The first N-terminal domain (N1) binds to the bacterial periplasmatic domain of TolA ([http://biocyc.org/ECOLI/NEW-IMAGE?type=GENE&object=EG11007 TolAIII]), receptor presumably at the inner face of the outer membrane [http://www.ncbi.nlm.nih.gov/pubmed/10404600[3]].<br><br />
<br />
* The second N-terminal domain (N2) gives recognition of the host cell by binding the F-pilus on the surface of E. coli. F-pilus is encode by the F episome of male E. coli, and is the primary receptor of the host cell [http://www.ncbi.nlm.nih.gov/pubmed/5338586[6]].<br><br />
<br />
* In fact, N1 and N2 interact with each other to form a blocked di-domain (N1G1N2). The binding of N2 to the tip of the bacterial F-pilus releases N1, which becomes free to interact with its receptor TolA (TolAIII) [http://www.ncbi.nlm.nih.gov/pubmed/10606756[2]][http://www.ncbi.nlm.nih.gov/pubmed/12670988[5]].<br><br />
<br />
* The C terminus (CT) of g3p anchors the g3p in the phage coat by interacting with phage coat protein 6, at the tip of the phage. Its seem that phages are released from the bacterial membrane by a two-step mechanism involving a short C-terminal fragment of g3p [http://www.ncbi.nlm.nih.gov/pubmed/6291030[1]].<br><br />
<br />
* N1, N2 and N3 domain are linked by flexible glycin-rich domains (G1 and G2). G1 is composed of four tandem copies of the sequence Glu-Gly-Gly-Gly-Ser. In a recent study it has been showed that it may have an active role in F-pilus-dependent infection.<br><br />
<br />
* Fusion of peptides or proteins to the N-terminus of intact g3p does not compromise infectivity of the phage, but insertion of polypeptides between N2 and N3 appear to reduce the infectivity.<br><br />
<br />
====Our use====<br />
<br />
The viral protein known as g3p is naturally exposed at the surface of the filamentous bacteriophage which enable it to get in the bacteria. The M13 phage has a high affinity for E.coli, and if we could place its g3p on the surface of the vesicles it could activate the fusion with the Outer membrane of the targeted bacteria.<br><br />
<br />
To be sure to target the receiving bacteria, we separe the donnor from the receiver with the criterium of the presence or not of pilli, because the g3p need a pillus to start its incorporation process. So the donnor would be pillus negative and the receiver pillus positive.<br><br />
<br />
OmpA-Linker is the second protein required because it is a protein that target any protein that is fuse to it to the surface of the Outer membrane, consequently we fuse G3P with OmpA-Linker.<br><br />
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</html><br />
<br />
====Bibliography====<br />
[http://www.ncbi.nlm.nih.gov/pubmed/6291030[1]] Jef D.Boeke & Peter Model. A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane. 1982.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/10606756[2]] Chatellier J & Riechmann L. Interdomain interactions within the gene 3 protein of filamentous phage. 1999.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/10404600[3]] Lubkowski J & Wlodawer A. Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA. 1999.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/11861923[4]] Baek H & Cha S. An improved helper phage system for efficient isolation of specific antibody molecules in phage display. 2002.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/12670988[5]] Karlsson F & Malmborg-Hager AC. The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains. 2003.<br><br />
[http://www.ncbi.nlm.nih.gov/pubmed/5338586[6]] Caro LG, Schnös M. The attachment of the male-specific bacteriophage F1 to sensitive strains of Escherichia coli. 1966.<br />
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==Fusion: SNAREs==<br />
<br />
SNARE proteins are a large protein superfamily consisting of more than 60 members in yeast and mammalian cells.<br />
<br />
<br />
The primary role of SNARE proteins is to mediate vesicle fusion, that is, the exocytosis of cellular transport vesicles with the cell membrane at the porosome or with a target compartment (such as a lysosome).<br />
<br />
<br />
SNAREs can be divided into two categories: vesicle-SNAREs (or v-SNAREs), which are incorporated into the membranes of transport vesicles during budding, and target-SNAREs (or t-SNAREs), which are located in the membranes of target compartments.<br />
<br />
<br />
The core of any functionnal SNARE complex is composed by four α-helices provided by the synaptobrevin (for one helix) by the syntaxin (for another helix) and by two SNAP-25 ( for the last two helices) : <br />
<br />
<br />
''Synaptobrevin'' : is a small integral membrane protein of secretory vesicles with molecular weight of 18 kilodalton (kDa) that is part of the vesicle-associated membrane protein (VAMP) family <br />
<br />
<br />
''Syntaxin'' : Syntaxin 1A was initially identified as a 35 kDa protein in the plasma membrane of amacrine cells [http://www.ncbi.nlm.nih.gov/pubmed/3896407[1]], as a subunit of Ca2+ channels [http://www.ncbi.nlm.nih.gov/pubmed/1587842[2]],[http://www.ncbi.nlm.nih.gov/pubmed/1334074[3]] and as a synaptotagmin-binding protein [http://www.ncbi.nlm.nih.gov/pubmed/1321498[4]]. Since these initial reports, the function of syntaxin as a central component in the synaptic vesicle membrane fusion machinery has been well established.<br />
<br />
<br />
''SNAP 25'' : SNAP-25 is a membrane bound protein anchored to the cytosolic face of membranes via palmitoyl side chains in the middle of the molecule. SNAP-25 is a protein contributing two α-helices in the formation of the exocytotic fusion complex in neurons where it assembles with syntaxin-1 and synaptobrevin. <br />
<br />
<br />
<br />
<br />
[[Image:Exocytosis-machinery.jpg|center]]<br />
<br />
<br />
''Legend : Molecular machinery driving vesicle fusion in neuromediator release. The core SNARE complex is formed by four α-helices contributed by synaptobrevin, syntaxin and two SNAP-25.''<br />
''Synaptotagmin serves as a calcium sensor and regulates intimately the SNARE zipping''<br />
<br />
<br />
<br />
<br />
===Using SNAREs in Bacteria : not so easy ... ===<br />
<br />
Our first idea was to use SNAREs to perform the fusion between vesicles and target bacteria. The main problem is that the 3D structure of the SNARE complex is crucial for the fusion to proceed [http://www.ncbi.nlm.nih.gov/pubmed/12805548 [5]], [http://www.ncbi.nlm.nih.gov/pubmed/11208146[6]], [http://www.ncbi.nlm.nih.gov/pubmed/19164750 [7]]. As SNAREs don't exist in bacteria we have to clone these genes (into bacteria) and we have to merge the SNAREs protein with a bacterial protein which is localized in the outer membrane (to allow the localization of SNARE protein to the surface of cell). In this direction we weren't sure to obtain the correct conformation of both v- (for the donnor) and t- (for the receiver) SNAREs after their exportation to the bacterial membrane, so we weren't sure that this mechanism will perform. We decided to focus our effort on the Jun/Fos strategy.<br />
<br />
<br />
<br />
<html><br />
<a href="https://2009.igem.org/Team:Paris/Transduction_overview_fusion#bottom"><img style="width:40px; height:40px;" src="https://static.igem.org/mediawiki/2009/1/10/Paris_Up.png"/></a><br />
</html><br />
<br />
<br />
====Bibliography====<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/3896407[1]] Barnstable C. J.Hofstein R.,Akagawa K. A marker of early amacrine cell development in rat retina.(1985) Brain Res 352:286–290<br />
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[http://www.ncbi.nlm.nih.gov/pubmed/1587842[2]] Inoue A.Obata K.Akagawa K.(1992)Cloning and sequence analysis of cDNA for a neuronal cell membrane antigen, HPC-1 J. Biol. Chem. 267:10613–10619<br />
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[http://www.ncbi.nlm.nih.gov/pubmed/1334074[3]] Yoshida A.,Oho C.,Omori A.,Kuwahara R.,Ito T.,Takahashi M.(1992)HPC-1 is associated with synaptotagmin and omega-conotoxin receptor J. Biol. Chem. 267:24925–24928<br />
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[http://www.ncbi.nlm.nih.gov/pubmed/1321498[4]] Bennett M. K.,Calakos N.,Scheller R. H(1992). Syntaxin: a synaptic protein implicated in docking of synaptic vesicles at presynaptic active zones. Science 257:255–259.<br />
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[http://www.ncbi.nlm.nih.gov/pubmed/12805548 [5]] Hu C, Ahmed M, Melia TJ, Söllner TH, Mayer T, Rothman JE. Fusion of cells by flipped SNAREs. Science. 2003 Jun 13;300(5626):1745-9.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/11208146[6]] Waters MG, Hughson FM. Membrane tethering and fusion in the secretory and endocytic pathways. Traffic. 2000 Aug;1(8):588-97.<br />
<br />
[http://www.ncbi.nlm.nih.gov/pubmed/19164750 [7]] Giraudo CG, Garcia-Diaz A, Eng WS, Chen Y, Hendrickson WA, Melia TJ, Rothman JE. Alternative zippering as an on-off switch for SNARE-mediated fusion. Science. 2009 Jan 23;323(5913):512-6.</div>Christophe.Rhttp://2009.igem.org/Team:Paris/PapersTeam:Paris/Papers2009-10-22T01:59:10Z<p>Christophe.R: /* OMV Production */</p>
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<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Papers#bottom | Papers]]<br />
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<br />
== '''OMV Overview''' ==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white; font-weight:bold; "<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px| []<br />
|1999<br />
|Terry J. Beveridge<br />
|Structures of gram-negative cell walls and their derived membrane vesicles.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93954 10438737]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Miller SI & Guina T.<br />
|Bacterial vesicle formation as a mechanism of protein transfer to animals.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14531993?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 14531993]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2005<br />
|Kuehn MJ & Kesty NC.<br />
|Bacterial outer membrane vesicles and the host-pathogen interaction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16291643?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16291643]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|McBroom AJ & Kuehn MJ.<br />
|Outer membrane vesicle production by Escherichia coli is independent of membrane instability.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16855227?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16855227]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 1]]<br />
|2007<br />
|McBroom AJ & Kuehn MJ.<br />
|Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17163978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17163978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 2]]<br />
|2009<br />
|Deatherage BL & Cookson BT.<br />
|Biogenesis of bacterial membrane vesicles<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19432795?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 19432795]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2009<br />
|Purnick PE & Weiss R.<br />
|The second wave of synthetic biology: from modules to systems.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19461664?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 19461664]<br />
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=='''OMV Production'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Mashburn-Warren L & Whiteley M.<br />
|Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18630345?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 18630345]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2001<br />
|Arora A. & Tamm LK.<br />
|Structure of outer membrane protein A transmembrane domain by NMR spectroscopy.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11276254?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 11276254]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|2007<br />
|Brown EA & Hardwidge PR.<br />
|Biochemical characterization of the enterotoxigenic Escherichia coli LeoA protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17975086?ordinalpos=16&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17975086]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2008<br />
|Burgess NK & Fleming KG.<br />
|Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18641391?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 18641391]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Tol/Pal<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|1986<br />
|Robert CHEN & Ulf HENNING.<br />
|Nucleotide sequence of the gene for the peptidoglycan-associated lipoprotein of Escherichia coli K12<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=210680 210680]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[3]]]<br />
|1995<br />
|Lazzaroni & Geli -<br />
|Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179564 179564]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|1999<br />
|Derouiche & Loret<br />
|Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10380085 10380085]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[4]]]<br />
|2001<br />
|Lloubès & RJournet L.<br />
|The Tol-Pal proteins of the Escherichia coli cell envelope: an energized system required for outer membrane integrity?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11501670 11501670]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|2002<br />
|Dubuisson JF & Lazzaroni JC.<br />
|Mutational analysis of the TolA C-terminal domain of Escherichia coli and genetic evidence for an interaction between TolA and TolB.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12142433 12142433]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2003<br />
|Llamas M & ARamos JL.<br />
|Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12896989 12896989]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#top|[5]]]<br />
|2004<br />
|Henry T & Lloubès R.<br />
|Improved methods for producing outer membrane vesicles in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15249060 15249060]<br />
|}<br />
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==''' OMV Adressing '''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1997<br />
|Kadurugamuwa JL & Beveridge TJ.<br />
|Natural release of virulence factors in membrane vesicles by Pseudomonas aeruginosa and the effect of aminoglycoside antibiotics on their release.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9421308 9421308]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1998<br />
|Santini CL & Wu LF.<br />
|A novel sec-independent periplasmic protein translocation pathway in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9427745 9427745]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Berks BC & Palmer T.<br />
|The Tat protein export pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10652088 10652088]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Mishima Y & Murata K.<br />
|Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11731126 11731126]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Sargent F & Berks BC.<br />
|Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11422364 11422364]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Yahr TL & Wickner WT.<br />
|Functional reconstitution of bacterial Tat translocation in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11350936 11350936]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2004<br />
|Robinson C & Bolhuis A.<br />
|Tat-dependent protein targeting in prokaryotes and chloroplasts.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15546663 15546663]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Sargent F & Palmer T.<br />
|Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16445746 16445746]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Lee PA & Georgiou G.<br />
|The bacterial twin-arginine translocation pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16756481 16756481]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Maillard J & Sargent F.<br />
|Structural diversity in twin-arginine signal peptide-binding proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17901208 17901208]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Sargent F.<br />
|The twin-arginine transport system: moving folded proteins across membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17956229 17956229]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Ferrandez Y & Condemine G.<br />
|Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Pradel N & Bonnet R<br />
|Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|de Marco A.<br />
|Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19442264 19442264]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | ClyA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 5]]<br />
|2008<br />
|Kim JY & DeLisa MP.<br />
|Engineered bacterial outer membrane vesicles with enhanced functionality.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 1]]<br />
|2009<br />
|Mueller M & Ban N.<br />
|The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|Wang Y.<br />
|The function of OmpA in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Dramsi S & Arthur M.<br />
|Covalent attachment of proteins to peptidoglycan.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18266854 18266854]<br />
|}<br />
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==''' OMV Reception'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Adhesin<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1989<br />
|Smeal T & Karin M.<br />
|Different requirements for formation of Jun:Jun and Jun:Fos complexes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1994<br />
|Heffernan EJ & Guiney DG.<br />
|Specificity of the complement resistance and cell association phenotypes encoded by the outer membrane protein genes rck from Salmonella typhimurium and ail from Yersinia enterocolitica.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7927803 7927803]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Veiga E & Fernández LA.<br />
|Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12949111 12949111]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 6]]<br />
|2004<br />
|Kesty NC & Kuehn MJ.<br />
|Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14578354 14578354]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | G3P<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1982<br />
|JEF D. BOEKE & PETER MODEL<br />
|A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1999<br />
|Chatellier J & Riechmann L.<br />
|Interdomain interactions within the gene 3 protein of filamentous phage.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1999<br />
|Lubkowski J & Wlodawer A.<br />
|Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|Baek H & Cha S.<br />
|An improved helper phage system for efficient isolation of specific antibody molecules in phage display.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Karlsson F & Malmborg-Hager AC.<br />
|The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Snare<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Waters MG & Hughson FM.<br />
|Membrane tethering and fusion in the secretory and endocytic pathways.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Woodbury DJ & Rognlien K.<br />
|The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11067766 11067766]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|Bowen ME,Brunger AT.<br />
|Mutational analysis of synaptobrevin transmembrane domain oligomerization.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12501216 12501216]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Hu C & Rothman JE.<br />
|Fusion of cells by flipped SNAREs.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Weninger K & Brunger AT.<br />
|Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14657376 14657376]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006 <br />
|Giraudo CG & Rothman JE.<br />
|A clamping mechanism involved in SNARE-dependent exocytosis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16794037 16794037]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Low HH & Löwe J.<br />
|A bacterial dynamin-like protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17122778 17122778]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Weninger K & Brunger AT.<br />
|Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18275821 18275821]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Delevoye C & Subtil A.<br />
|SNARE protein mimicry by an intracellular bacterium.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18369472 18369472]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Giraudo CG & Rothman JE.<br />
|Alternative zippering as an on-off switch for SNARE-mediated fusion.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19164750 19164750]<br />
<br />
|}<br />
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<br />
==''' OMV Signal transduction'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1984<br />
|Lopilato JE & Beckwith JR.<br />
|D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6327616 6327616]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1995<br />
|Härle C & Braun V.<br />
|Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7729419 7729419]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1998<br />
|Tomii K & Kanehisa M.<br />
|A comparative analysis of ABC transporters in complete microbial genomes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1999<br />
|De Wulf P & Lin EC.<br />
|The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10542180 10542180]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Stock AM & Goudreau PN.<br />
|Two-component signal transduction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Yaron S & Matthews KR.<br />
|Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11010892 11010892]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2004<br />
|Dwyer MA & Hellinga HW.<br />
|Periplasmic binding proteins: a versatile superfamily for protein engineering.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15313245 15313245]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Braun V & Sauter A.<br />
|Gene regulation by transmembrane signaling.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16718597 16718597]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Baker MD & Stock JB<br />
|Signal transduction: networks and integrated circuits in bacterial cognition.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18054766 18054766]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Baker MD & Stock JB.<br />
|Systems biology of bacterial chemotaxis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16529985 16529985]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Ibrahim M & Monnet V.<br />
|Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17921293 17921293]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Kyriakidis DA & Tiligada E.<br />
|Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Tomii & Kanehisa<br />
|comparative analysis of ABC transporter<br />
|[http://genome.cshlp.org/content/8/10/1048.full.html#ref-list-1 pdf-link]<br />
|}<br />
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<br />
=='''Modelling'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Genetic Regulatory Network<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 1]]<br />
|1977<br />
|Gillespie Daniel T.<br />
|Exact Stochastic Simlation of Coupled Chemical Equations<br />
|[http://www.dna.caltech.edu/courses/cs191/paperscs191/gillespie2.pdf Gillespie1]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 3]]<br />
|1997<br />
|J.B. Andersen & S.Molin<br />
|New Stable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria<br />
|[http://aem.asm.org/cgi/reprint/64/6/2240.pdf LVA tag]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 6]]<br />
|1999<br />
|M.Ellowitz & S.Leibler<br />
|A Synthetic oscillatory network of transcriptionnal regulators <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10659856 10659856]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 2]]<br />
|1997<br />
|D.T.Gillespie<br />
|The Chemical Langevin Equation<br />
|[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000113000001000297000001&idtype=cvips&gifs=yes Gillespie2]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 5]]<br />
|2002<br />
|N.Rosenfold & U.Alon<br />
|Negative Autoregulation Speeds The Response TImes of Transcription Network <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12417193 2417193]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|M.B.Ellowitz & P.S.Swain<br />
|Stochastic Gene Expression In A Single Cell<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12183631 12183631]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 7]]<br />
|2003<br />
|S.Mangan & U.Alon<br />
|Structure and function ot the feed-forward Loop Network Motif<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14530388 14530388]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 4]]<br />
|2003<br />
|S.Basu & R.Weiss<br />
|Spatiotemporal control of gene expression with pulse-generating networks<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15096621 15096621]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 1]]<br />
|2005<br />
|S.Hooshangi & R.Weiss<br />
|Ultrasensitivity and noise propagation in a synthetic transcriptional cascade<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15738412 15738412]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 3]]<br />
|2006<br />
|H.Li & L.Petzold<br />
|Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems<br />
|[http://www.cs.ucsb.edu/~cse/Files/ldm0513.pdf Sto.Sim]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 2]]<br />
|2007<br />
|U.Alon<br />
|Network motifs : theory and experimental approaches<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17510665 117510665]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|J.Stricker & J.Hasty<br />
|A Fast Robust and Tunable synthetic gene oscillator<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18971928 18971928]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Vesicle biophysics model<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 6]]<br />
|1977<br />
|Harbich et al<br />
|Optical observation of rotationally symmetric lecithin vesicle shapes<br />
|J. Physique, 38:727–729<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 4]]<br />
|1987<br />
|Ou-Yang & Helfrich<br />
|Instability and deformation of a spherical vesicle by pressure<br />
|Phys. Rev. Lett., 59:2486-2488 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 1]]<br />
|1991<br />
|Lipowsky<br />
|The conformation of membranes<br />
|Nature, 349(6309):475-481<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 5]]<br />
|1995 <br />
|Fattal et al <br />
|The vesicle-micelle transition in mixed lipid-surfactant<br />
|Langmuir, 11:1154-1161 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 3]]<br />
|1998<br />
|Zhou et al<br />
|On the origin of membrane vesicles in gram-negative bacteria<br />
|FEMS microbiology letters, 163(2):223-228 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 8]]<br />
|2005 <br />
|Kuehn & Kesty<br />
|Bacterial outer membrane vesicles and the host pathogen interaction<br />
|Genes & Dev, 19:2645-2655 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 2]]<br />
|2008<br />
|Park & Uehara<br />
|How bacteria consume their own exoskeletons<br />
|Microbiol Mol Biol Rev, 72(2):211-227 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 7]]<br />
|2009<br />
|Deatherage et al <br />
|Biogenesis of bacterial membrane vesicles,<br />
|Mol Microbiol, 72(6):1395-1407<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 9]]<br />
|2009<br />
|Kumaran & Losick<br />
|Negative membrane curvature as a cue for subcellular localization of a bacterial protein.<br />
|PNAS USA, 106(32):13541-13545 <br />
|}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/PapersTeam:Paris/Papers2009-10-22T01:55:52Z<p>Christophe.R: /* OMV Overview */</p>
<hr />
<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Papers#bottom | Papers]]<br />
{{Template:Paris2009}}<br />
{{Template:Paris2009_menu}}<br />
<br />
== '''OMV Overview''' ==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white; font-weight:bold; "<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px| []<br />
|1999<br />
|Terry J. Beveridge<br />
|Structures of gram-negative cell walls and their derived membrane vesicles.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=93954 10438737]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Miller SI & Guina T.<br />
|Bacterial vesicle formation as a mechanism of protein transfer to animals.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14531993?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 14531993]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2005<br />
|Kuehn MJ & Kesty NC.<br />
|Bacterial outer membrane vesicles and the host-pathogen interaction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16291643?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16291643]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|McBroom AJ & Kuehn MJ.<br />
|Outer membrane vesicle production by Escherichia coli is independent of membrane instability.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16855227?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 16855227]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 1]]<br />
|2007<br />
|McBroom AJ & Kuehn MJ.<br />
|Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17163978?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17163978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_overview#top 2]]<br />
|2009<br />
|Deatherage BL & Cookson BT.<br />
|Biogenesis of bacterial membrane vesicles<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19432795?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 19432795]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2009<br />
|Purnick PE & Weiss R.<br />
|The second wave of synthetic biology: from modules to systems.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19461664?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 19461664]<br />
|}<br />
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<br />
=='''OMV Production'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Mashburn-Warren L & Whiteley M.<br />
|Interaction of quorum signals with outer membrane lipids: insights into prokaryotic membrane vesicle formation.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18630345?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 18630345]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2001<br />
|Arora A. & Tamm LK.<br />
|Structure of outer membrane protein A transmembrane domain by NMR spectroscopy.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11276254?ordinalpos=8&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 11276254]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|2007<br />
|Brown EA & Hardwidge PR.<br />
|Biochemical characterization of the enterotoxigenic Escherichia coli LeoA protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17975086?ordinalpos=16&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum 17975086]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2008<br />
|Burgess NK & Fleming KG.<br />
|Beta-barrel proteins that reside in the Escherichia coli outer membrane in vivo demonstrate varied folding behavior in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18641391?ordinalpos=&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.SmartSearch&log$=citationsensor 18641391]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Tol/Pal<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|1986<br />
|Robert CHEN & Ulf HENNING.<br />
|Nucleotide sequence of the gene for the peptidoglycan-associated lipoprotein of Escherichia coli K12<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=210680 210680]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#1|[1]]]<br />
|1995<br />
|Lazzaroni & Geli -<br />
|Transmembrane alpha-helix interactions are required for the functional assembly of the Escherichia coli Tol complex.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179564 179564]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|1999<br />
|Derouiche & Loret<br />
|Circular dichroism and molecular modeling of the E. coli TolA periplasmic domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10380085 10380085]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#2|[2]]]<br />
|2001<br />
|Lloubès & RJournet L.<br />
|The Tol-Pal proteins of the Escherichia coli cell envelope: an energized system required for outer membrane integrity?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11501670 11501670]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[]<br />
|2002<br />
|Dubuisson JF & Lazzaroni JC.<br />
|Mutational analysis of the TolA C-terminal domain of Escherichia coli and genetic evidence for an interaction between TolA and TolB.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12142433 12142433]<br />
<br />
|- style="background: #bebebe; text-align: center;" <br />
|height=40px|[]<br />
|2003<br />
|Llamas M & ARamos JL.<br />
|Role of Pseudomonas putida tol-oprL gene products in uptake of solutes through the cytoplasmic membrane.<br />
|[http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12896989 12896989]<br />
<br />
|- style="background: #d8d8d8; text-align: center;" <br />
|height=40px|[[Team:Paris/Production_overview#3|[3]]]<br />
|2004<br />
|Henry T & Lloubès R.<br />
|Improved methods for producing outer membrane vesicles in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15249060 15249060]<br />
|}<br />
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<br />
==''' OMV Adressing '''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1997<br />
|Kadurugamuwa JL & Beveridge TJ.<br />
|Natural release of virulence factors in membrane vesicles by Pseudomonas aeruginosa and the effect of aminoglycoside antibiotics on their release.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9421308 9421308]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1998<br />
|Santini CL & Wu LF.<br />
|A novel sec-independent periplasmic protein translocation pathway in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9427745 9427745]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Berks BC & Palmer T.<br />
|The Tat protein export pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10652088 10652088]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Mishima Y & Murata K.<br />
|Super-channel in bacteria: function and structure of the macromolecule import system mediated by a pit-dependent ABC transporter.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11731126 11731126]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Sargent F & Berks BC.<br />
|Purified components of the Escherichia coli Tat protein transport system form a double-layered ring structure.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11422364 11422364]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2001<br />
|Yahr TL & Wickner WT.<br />
|Functional reconstitution of bacterial Tat translocation in vitro.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11350936 11350936]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2004<br />
|Robinson C & Bolhuis A.<br />
|Tat-dependent protein targeting in prokaryotes and chloroplasts.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15546663 15546663]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Sargent F & Palmer T.<br />
|Pathfinders and trailblazers: a prokaryotic targeting system for transport of folded proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16445746 16445746]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Lee PA & Georgiou G.<br />
|The bacterial twin-arginine translocation pathway.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16756481 16756481]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Maillard J & Sargent F.<br />
|Structural diversity in twin-arginine signal peptide-binding proteins.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17901208 17901208]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Sargent F.<br />
|The twin-arginine transport system: moving folded proteins across membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17956229 17956229]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Ferrandez Y & Condemine G.<br />
|Novel mechanism of outer membrane targeting of proteins in Gram-negative bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Pradel N & Bonnet R<br />
|Sec- and Tat-dependent translocation of beta-lactamases across the Escherichia coli inner membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18643934 18643934]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|de Marco A.<br />
|Strategies for successful recombinant expression of disulfide bond-dependent proteins in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19442264 19442264]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | ClyA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 5]]<br />
|2008<br />
|Kim JY & DeLisa MP.<br />
|Engineered bacterial outer membrane vesicles with enhanced functionality.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18511069 18511069]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 1]]<br />
|2009<br />
|Mueller M & Ban N.<br />
|The structure of a cytolytic alpha-helical toxin pore reveals its assembly mechanism.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19421192 19421192]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | OmpA<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|Wang Y.<br />
|The function of OmpA in Escherichia coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11906175 11906175]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Dramsi S & Arthur M.<br />
|Covalent attachment of proteins to peptidoglycan.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18266854 18266854]<br />
|}<br />
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==''' OMV Reception'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Adhesin<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1989<br />
|Smeal T & Karin M.<br />
|Different requirements for formation of Jun:Jun and Jun:Fos complexes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/2516828 2516828]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1994<br />
|Heffernan EJ & Guiney DG.<br />
|Specificity of the complement resistance and cell association phenotypes encoded by the outer membrane protein genes rck from Salmonella typhimurium and ail from Yersinia enterocolitica.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7927803 7927803]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Veiga E & Fernández LA.<br />
|Autotransporters as scaffolds for novel bacterial adhesins: surface properties of Escherichia coli cells displaying Jun/Fos dimerization domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12949111 12949111]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Addressing_overview2#top 6]]<br />
|2004<br />
|Kesty NC & Kuehn MJ.<br />
|Incorporation of heterologous outer membrane and periplasmic proteins into Escherichia coli outer membrane vesicles.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14578354 14578354]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | G3P<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1982<br />
|JEF D. BOEKE & PETER MODEL<br />
|A prokaryotic membrane anchor sequence: carboxyl terminus of bacteriophage f1 gene III protein retains it in the membrane.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6291030 6291030]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1999<br />
|Chatellier J & Riechmann L.<br />
|Interdomain interactions within the gene 3 protein of filamentous phage.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10606756 10606756]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1999<br />
|Lubkowski J & Wlodawer A.<br />
|Filamentous phage infection: crystal structure of g3p in complex with its coreceptor, the C-terminal domain of TolA.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10404600 10404600]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|Baek H & Cha S.<br />
|An improved helper phage system for efficient isolation of specific antibody molecules in phage display.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11861923 11861923]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Karlsson F & Malmborg-Hager AC.<br />
|The mechanism of bacterial infection by filamentous phages involves molecular interactions between TolA and phage protein 3 domains.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12670988 12670988]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Snare<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Waters MG & Hughson FM.<br />
|Membrane tethering and fusion in the secretory and endocytic pathways.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11208146 11208146]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Woodbury DJ & Rognlien K.<br />
|The t-SNARE syntaxin is sufficient for spontaneous fusion of synaptic vesicles to planar membranes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11067766 11067766]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|Bowen ME,Brunger AT.<br />
|Mutational analysis of synaptobrevin transmembrane domain oligomerization.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12501216 12501216]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Hu C & Rothman JE.<br />
|Fusion of cells by flipped SNAREs.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12805548 12805548]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2003<br />
|Weninger K & Brunger AT.<br />
|Single-molecule studies of SNARE complex assembly reveal parallel and antiparallel configurations.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14657376 14657376]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006 <br />
|Giraudo CG & Rothman JE.<br />
|A clamping mechanism involved in SNARE-dependent exocytosis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16794037 16794037]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Low HH & Löwe J.<br />
|A bacterial dynamin-like protein.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17122778 17122778]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Weninger K & Brunger AT.<br />
|Accessory proteins stabilize the acceptor complex for synaptobrevin, the 1:1 syntaxin/SNAP-25 complex.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18275821 18275821]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Delevoye C & Subtil A.<br />
|SNARE protein mimicry by an intracellular bacterium.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18369472 18369472]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Giraudo CG & Rothman JE.<br />
|Alternative zippering as an on-off switch for SNARE-mediated fusion.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19164750 19164750]<br />
<br />
|}<br />
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==''' OMV Signal transduction'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1984<br />
|Lopilato JE & Beckwith JR.<br />
|D-ribose metabolism in Escherichia coli K-12: genetics, regulation, and transport.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/6327616 6327616]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1995<br />
|Härle C & Braun V.<br />
|Signal transfer through three compartments: transcription initiation of the Escherichia coli ferric citrate transport system from the cell surface.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/7729419 7729419]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|1998<br />
|Tomii K & Kanehisa M.<br />
|A comparative analysis of ABC transporters in complete microbial genomes.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/9799792 9799792]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|1999<br />
|De Wulf P & Lin EC.<br />
|The CpxRA signal transduction system of Escherichia coli: growth-related autoactivation and control of unanticipated target operons.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10542180 10542180]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Stock AM & Goudreau PN.<br />
|Two-component signal transduction.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10966457 10966457]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2000<br />
|Yaron S & Matthews KR.<br />
|Vesicle-mediated transfer of virulence genes from Escherichia coli O157:H7 to other enteric bacteria.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/11010892 11010892]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2004<br />
|Dwyer MA & Hellinga HW.<br />
|Periplasmic binding proteins: a versatile superfamily for protein engineering.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15313245 15313245]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|Braun V & Sauter A.<br />
|Gene regulation by transmembrane signaling.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16718597 16718597]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Baker MD & Stock JB<br />
|Signal transduction: networks and integrated circuits in bacterial cognition.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18054766 18054766]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Baker MD & Stock JB.<br />
|Systems biology of bacterial chemotaxis.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/16529985 16529985]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2007<br />
|Ibrahim M & Monnet V.<br />
|Control of the transcription of a short gene encoding a cyclic peptide in Streptococcus thermophilus: a new quorum-sensing system?<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17921293 17921293]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2008<br />
|Thie H & Hust M.<br />
|SRP and Sec pathway leader peptides for antibody phage display and antibody fragment production in E. coli.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18504019 18504019]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Kyriakidis DA & Tiligada E.<br />
|Signal transduction and adaptive regulation through bacterial two-component systems: the Escherichia coli AtoSC paradigm.<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/19198978 19198978]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2009<br />
|Tomii & Kanehisa<br />
|comparative analysis of ABC transporter<br />
|[http://genome.cshlp.org/content/8/10/1048.full.html#ref-list-1 pdf-link]<br />
|}<br />
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=='''Modelling'''==<br />
<br />
{|<br />
|- style="background: #0a3585; text-align: center; color:white;"<br />
|width=30px height=50px| N°<br />
|width= 40px| Date<br />
|width=100px| Authors<br />
|width=560px| Article<br />
|width=80px| Pubmed<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Genetic Regulatory Network<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 1]]<br />
|1977<br />
|Gillespie Daniel T.<br />
|Exact Stochastic Simlation of Coupled Chemical Equations<br />
|[http://www.dna.caltech.edu/courses/cs191/paperscs191/gillespie2.pdf Gillespie1]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 3]]<br />
|1997<br />
|J.B. Andersen & S.Molin<br />
|New Stable Variants of Green Fluorescent Protein for Studies of Transient Gene Expression in Bacteria<br />
|[http://aem.asm.org/cgi/reprint/64/6/2240.pdf LVA tag]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 6]]<br />
|1999<br />
|M.Ellowitz & S.Leibler<br />
|A Synthetic oscillatory network of transcriptionnal regulators <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/10659856 10659856]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 2]]<br />
|1997<br />
|D.T.Gillespie<br />
|The Chemical Langevin Equation<br />
|[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=JCPSA6000113000001000297000001&idtype=cvips&gifs=yes Gillespie2]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 5]]<br />
|2002<br />
|N.Rosenfold & U.Alon<br />
|Negative Autoregulation Speeds The Response TImes of Transcription Network <br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12417193 2417193]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2002<br />
|M.B.Ellowitz & P.S.Swain<br />
|Stochastic Gene Expression In A Single Cell<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/12183631 12183631]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 7]]<br />
|2003<br />
|S.Mangan & U.Alon<br />
|Structure and function ot the feed-forward Loop Network Motif<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/14530388 14530388]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 4]]<br />
|2003<br />
|S.Basu & R.Weiss<br />
|Spatiotemporal control of gene expression with pulse-generating networks<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15096621 15096621]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 1]]<br />
|2005<br />
|S.Hooshangi & R.Weiss<br />
|Ultrasensitivity and noise propagation in a synthetic transcriptional cascade<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/15738412 15738412]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Transduction_modeling#top 3]]<br />
|2006<br />
|H.Li & L.Petzold<br />
|Logarithmic Direct Method for Discrete Stochastic Simulation of Chemically Reacting Systems<br />
|[http://www.cs.ucsb.edu/~cse/Files/ldm0513.pdf Sto.Sim]<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling#top 2]]<br />
|2007<br />
|U.Alon<br />
|Network motifs : theory and experimental approaches<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/17510665 117510665]<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[]<br />
|2006<br />
|J.Stricker & J.Hasty<br />
|A Fast Robust and Tunable synthetic gene oscillator<br />
|[http://www.ncbi.nlm.nih.gov/pubmed/18971928 18971928]<br />
<br />
|- style="background: #ccccff; text-align: center;"<br />
! colspan="5" style="background: #ccccff;" | Vesicle biophysics model<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 6]]<br />
|1977<br />
|Harbich et al<br />
|Optical observation of rotationally symmetric lecithin vesicle shapes<br />
|J. Physique, 38:727–729<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 4]]<br />
|1987<br />
|Ou-Yang & Helfrich<br />
|Instability and deformation of a spherical vesicle by pressure<br />
|Phys. Rev. Lett., 59:2486-2488 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 1]]<br />
|1991<br />
|Lipowsky<br />
|The conformation of membranes<br />
|Nature, 349(6309):475-481<br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 5]]<br />
|1995 <br />
|Fattal et al <br />
|The vesicle-micelle transition in mixed lipid-surfactant<br />
|Langmuir, 11:1154-1161 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 3]]<br />
|1998<br />
|Zhou et al<br />
|On the origin of membrane vesicles in gram-negative bacteria<br />
|FEMS microbiology letters, 163(2):223-228 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 8]]<br />
|2005 <br />
|Kuehn & Kesty<br />
|Bacterial outer membrane vesicles and the host pathogen interaction<br />
|Genes & Dev, 19:2645-2655 <br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 2]]<br />
|2008<br />
|Park & Uehara<br />
|How bacteria consume their own exoskeletons<br />
|Microbiol Mol Biol Rev, 72(2):211-227 <br />
<br />
|- style="background: #d8d8d8; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 7]]<br />
|2009<br />
|Deatherage et al <br />
|Biogenesis of bacterial membrane vesicles,<br />
|Mol Microbiol, 72(6):1395-1407<br />
<br />
|- style="background: #bebebe; text-align: center;"<br />
|height=40px|[[https://2009.igem.org/Team:Paris/Production_modeling2#top 9]]<br />
|2009<br />
|Kumaran & Losick<br />
|Negative membrane curvature as a cue for subcellular localization of a bacterial protein.<br />
|PNAS USA, 106(32):13541-13545 <br />
|}</div>Christophe.Rhttp://2009.igem.org/Team:Paris/Production_overviewTeam:Paris/Production overview2009-10-22T01:51:20Z<p>Christophe.R: /* Vesicle production system : Tol/Pal */</p>
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<div><span/ id="bottom">[https://2009.igem.org/ iGEM ] > [[Team:Paris#top | Paris]] > [[Team:Paris/Production_overview#top | Vesicle production system]] > [[Team:Paris/Production_overview#bottom | Overview]]<br />
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==Vesicle production system : Main==<br />
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<a class="menu_sub_active"href="https://2009.igem.org/Team:Paris/Production_overview#bottom"> Main </a>|<br />
<a class="menu_sub" href="https://2009.igem.org/Team:Paris/Production_overview#Vesicle_production_system_:_Tol.2FPal"> Tol/Pal</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Production_overview#Vesicle_production_system_:_Our_strategy"> Our strategy</a>|<br />
<a class="menu_sub"href="https://2009.igem.org/Team:Paris/Production_overview_Construction#bottom"> Construction</a><br />
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Several gram-negative bacteria - including ''E. coli'' - have been shown to produce vesicles for various hypothetical reasons<sup>[[Team:Paris/Production_overview#References|[1]]]</sup><sup>[[Team:Paris/Production_overview#References|[2]]]</sup> (stress response, host-pathogen interaction...). In our project, we want to optimize vesicle production to develop a long distance communication system between gram-negative bacteria. Outer membrane vesicles (OMVs) production can be enhanced through the destabilization of the outer-membrane. We found in the literature that the Tol/Pal system could be a good target for this purpose<sup>[[Team:Paris/Production_overview#References|[3]]]</sup>.<br />
The Tol/Pal system of ''Escherichia Coli'' is involved in anchoring the outer- to the inner-membrane and to the peptidoglycan layer. It is thus essential in maintaining membrane integrity. The system is composed of five membrane proteins (TolA, TolB, TolQ, TolR and Pal) associating in two complexes.<sup>[[Team:Paris/Production_overview#References|[4]]]</sup><sup>[[Team:Paris/Production_overview#References|[5]]]</sup><br />
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See [[Team:Paris/Production_overview#Vesicle_production_system_:_Tol.2FPal|Tol/Pal]] part for more information and why we choose this system. [[Team:Paris/Production_overview#Vesicle_production_system_:_Our_strategy|Strategy]] and [[Team:Paris/Production_overview_Construction#bottom|Construction]] part explains our aim in this OMV production system. <br />
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==Vesicle production system : Tol/Pal==<br />
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''E. Coli'' is gram-. Its membrane is a complex that included: the inner membrane and the outer membrane. Between both, there is a layer of peptidoglycan.<br />
The outer membrane presents lipo-polysaccharides (LPS). We find also porins and other proteins. There are receivers for the entrance of nourishing elements, receivers in pili (bacterial conjugation), receivers where settles bacteriophage. It has properties of selective permeability, protection and support. This complex of proteins is in place to maintain the stability between the inner membrane and the outer membrane.<br />
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In particular the system called Tol-Pal consisted of five proteins, TolA, TolB, TolQ, TolR and Pal<sup>[[Team:Paris/Production_overview#References|[3]]]</sup><sup>[[Team:Paris/Production_overview#References|[4]]]</span></sup>. This complex allows to maintain the integrity of the membrane. Studies showed that if we destabilize this system, we also destabilize the membrane, leading then a production of vesicles. But when the membrane of the bacteria stays for such a long time to this state of destabilization, the bacteria produces too many vesicles and go in state of lysis<sup>[[Team:Paris/Production_overview#References|[4]]]</sup>.<br />
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What is Tol-Pal complex ?<br />
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Five proteins organised this complex<sup>[[Team:Paris/Production_overview#References|[5]]]</sup>.<br />
The TolA/Q/R proteins form a protein complex in the inner membrane. TolB is a periplasmic protein associated with Pal, a lipoprotein. Pal is anchored to the outer membrane and interacts with the peptidoglycan layer. There are interactions with TolA–Pal and TolA–TolB.<br />
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[[Image:TolPal.jpg|250px|center| Tol-Pal system]]<br />
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==Vesicle production system : Our strategy==<br />
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We want to destabilize the outer membrane to create outer membrane vesicles (OMVs). <br />
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OMVs were formed upon periplasmic overproduction of soluble TolA and TolR domains, since these two short periplasmic domains (both less than 100 residues) have been previously found to disturb the Tol–Pal system<sup>[[Team:Paris/Production_overview#References|[6]]]</sup><sup>[[Team:Paris/Production_overview#References|[7]]]</sup>. (TolA and TolR have three domains: Nterminal, central and Cterminal domains)<br />
An other study<sup>[[Team:Paris/Production_overview#References|[5]]]</sup> focused on the development of a gene expression system able to induce production of large amounts of OMVs when they used different domains of these two proteins of Tol-Pal system. This team <sup>[[Team:Paris/Production_overview#References|[5]]]</sup> send us their plasmid and we were able to begin our work quickly.<br />
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To achieve our goal, we decided to do like the Lloubès Team<sup><[[Team:Paris/Production_overview#References|[5]]]</sup> and take advantage of the soluble central domain of TolR (TolRII). We don’t use the third domain of TolA because, it doesn’t work so well and TolAIII have lot of PstI domain in his sequence. In order to achieve our project, we will over express specifically designed biobricks containing TolRII fused with OmpA signal which allows it to migrate in the periplasm<sup>[[Team:Paris/Production_overview#References|[4]]]</sup>. So Tol-Pal system will become bad and the membrane integrity will be destabilised. Lot of vesicle could be creating. <br />
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<br />
If bacteria stay in this conformation, there is lysis. We try to create an ON/OFF system to stop the vesicles creation.<br />
In the same framework, we could also over express various Tol ligand (like colicin) to destabilize the membrane. But it doesn’t work very well.<sup>[[Team:Paris/Production_overview#References|[5]]]</sup> <br />
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BioBrick TolR domain II N-term fusion : [http://partsregistry.org/wiki/index.php?title=Part:BBa_K257005 Bba K257005]<br />
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BioBrick ompA sequence signal : [http://partsregistry.org/wiki/index.php?title=Part:BBa_K257006 Bba_K257006]<br />
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You can see now our [[Team:Paris/Production_overview_Construction#bottom|Construction]].<br />
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====References====<br />
<ol class="references"><br />
<li> [[Team:Paris/Production_overview#1 | ^]]Release of outer membrane vesicles by Gram-negative bacteria is a novel envelope stress response. McBroom AJ & Kuehn MJ 2007 - [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=17163978 17163978]</li><br />
<li> [[Team:Paris/Production_overview#1 | ^]]Biogenesis of bacterial membrane vesicles. Deatherage BL & Cookson BT 2009 - [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=19432795 19432795]</li><br />
<li> [[Team:Paris/Production_overview#1 | ^]]Transmembrane a-helix interactions are required for the functional assembly of the escherichia coli Tol complex. Lazzaroni & Geli 1995 - [http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=179564 179564]</li><br />
<li> [[Team:Paris/Production_overview#1 | ^]]The Tol-Pal proteins of the Escherichia coli cell envelope an energized system required for outer membrane integrity. Lloubès & Journet 2001 - [http://www.ncbi.nlm.nih.gov/pubmed/11501670 11501670]</li><br />
<li> [[Team:Paris/Production_overview#1 | ^]]Improved methods for producing outer membrane vesicles in gram-negative bacteria. Henry & Lloubès 2004 - [http://www.ncbi.nlm.nih.gov/pubmed/15249060 15249060]</li><br />
<li> [[Team:Paris/Production_overview#6 | ^]]Role of TolR N-terminal, central, and C-terminal domains in dimerization and interaction with TolA and tolQ. Journet L & Bénédetti H. 1999 - [http://www.ncbi.nlm.nih.gov/pubmed/10419942 10419942]</li><br />
<li> [[Team:Paris/Production_overview#6 | ^]]Role of the carboxyl-terminal domain of TolA in protein import and integrity of the outer membrane. Levengood-Freyermuth SK & Webster RE. 1993 - [http://www.ncbi.nlm.nih.gov/pubmed/8416897 8416897]</li><br />
</ol></div>Christophe.R