Team:UC Davis/Parts

From 2009.igem.org

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<title>PARTS1</title>
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<span style="font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><o:p></o:p></span>
<span style="font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"><o:p></o:p></span>
<p class="freeform0" style="margin-bottom: 6pt; line-height: 19pt;"><a
<p class="freeform0" style="margin-bottom: 6pt; line-height: 19pt;"><a
-
name="INPNC"></a><b>INPNC:</b>The ice-nucleation protein (INP) from <i>Pseudomonas
+
name="INPNC"></a><b>INPNC:</b> The ice-nucleation protein (INP) from <i>Pseudomonas
-
syringae</i> is used by its natural host to nucleate ice formation and
+
syringae</i> (<a
-
is
+
href="https://2009.igem.org/Team:UC_Davis/Contacts_References">9</a>)
-
implicated in<i> P. syringae</i> associated pathogenesis<i>.&nbsp; </i>INP
+
is used by its natural host to nucleate ice formation and
 +
is implicated in<i> P.syringae</i>-associated pathogenesis<i>.&nbsp; </i>INP
and
and
a truncated derivative lacking the central domain (INPNC) have been
a truncated derivative lacking the central domain (INPNC) have been
used
used
-
extensively for displaying proteins on the surface of <i>E. coli (7)</i>.&nbsp;
+
extensively for displaying proteins on the surface of <i>E. coli </i>(<a
 +
href="https://2009.igem.org/Team:UC_Davis/Contacts_References">7</a>).&nbsp;
For instance, AldO and PhaZ1 have been successfully displayed on the
For instance, AldO and PhaZ1 have been successfully displayed on the
surface of
surface of
-
<i>E. coli </i>using INPNC (7, 15). <br>
+
<i>E.coli </i>using INPNC (<a
-
<u1:p></u1:p>Park <i>et al.</i> have shown that INPNC when fused to
+
href="https://2009.igem.org/Team:UC_Davis/Contacts_References">7, 15</a>).
 +
<br>
 +
<u1:p></u1:p>Park <i>et al.</i> have shown that when INPNC is fused to
the <i>phaZ1</i>
the <i>phaZ1</i>
-
gene, including its signal sequence, can serve as a suitable surface
+
gene and its signal sequence, it can serve as a suitable surface
delivery
delivery
-
and secretion device of the otherwise toxic <i>phaZ1</i> gene product<i>
+
and secretion device of the otherwise toxic <i>phaZ1</i> gene product(<a
-
</i>(15).&nbsp;
+
href="https://2009.igem.org/Team:UC_Davis/Contacts_References">15</a>).&nbsp;
<u1:p></u1:p>This part was synthesized by Mr. Gene (Regensburg,
<u1:p></u1:p>This part was synthesized by Mr. Gene (Regensburg,
Germany) with
Germany) with
codon optimization and subsequently transferred into vector (<span
codon optimization and subsequently transferred into vector (<span
-
style="background: rgb(255, 255, 51) none repeat scroll 0%; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;">part
+
style="background: rgb(255, 255, 51) none repeat scroll 0% 50%; color: black; -moz-background-clip: -moz-initial; -moz-background-origin: -moz-initial; -moz-background-inline-policy: -moz-initial;"></span>
-
name for AK vector).&nbsp;</span>
+
<a href="http://partsregistry.org/Part:pSB1AK3">pSB1AK3</a>). As it is
-
As it is expected that this part will be used in the context of the
+
expected that this part will be used in the context of the
fusion
fusion
protein, the prefix and suffix for this part are consistent with the <i>BBF
protein, the prefix and suffix for this part are consistent with the <i>BBF
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secrete
secrete
any target protein.&nbsp; <br>
any target protein.&nbsp; <br>
-
<u1:p></u1:p><i>We have modified this protein to be consistent with BBF
+
<u1:p></u1:p><i>We have modified this protein to be consistent with the
 +
BBF
RFC-12
RFC-12
Standard. We have submitted this part to the parts registry as part </i><a
Standard. We have submitted this part to the parts registry as part </i><a
href="http://partsregistry.org/wiki/index.php/Part:BBa_K265008"><i><span
href="http://partsregistry.org/wiki/index.php/Part:BBa_K265008"><i><span
-
style="color: rgb(0, 0, 153);">BBa_K265008</span></i></a><i>.<u1:p></u1:p></i><o:p></o:p></p>
+
style="color: rgb(0, 0, 153);">BBa_K265008</span></i></a><i>.<br>
 +
</i></p>
 +
<p class="freeform0" style="margin-bottom: 6pt; line-height: 19pt;"><br>
 +
<i><u1:p></u1:p></i><o:p></o:p></p>
<p class="freeform0" style="margin-bottom: 6pt; line-height: 19pt;"><a
<p class="freeform0" style="margin-bottom: 6pt; line-height: 19pt;"><a
-
name="SS"></a><b><u1:p></u1:p>SS:</b>The
+
name="SS"></a><b><u1:p></u1:p>SS:</b> The
signal sequence (SS) for the <i>phaZ1 </i>gene product of <i>Paucimonas
signal sequence (SS) for the <i>phaZ1 </i>gene product of <i>Paucimonas
-
lemoignei</i>, a polyhydroxybutyrate depolymerase (15).&nbsp; In the
+
lemoignei</i>, a polyhydroxybutyrate depolymerase (<a
 +
href="https://2009.igem.org/Team:UC_Davis/Contacts_References">15</a>).&nbsp;
 +
In the
native
native
protein the signal sequence is cleaved between residues Ala37 and
protein the signal sequence is cleaved between residues Ala37 and
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such as INPNC (<a
such as INPNC (<a
href="http://partsregistry.org/wiki/index.php/Part:BBa_K265008"><i><span
href="http://partsregistry.org/wiki/index.php/Part:BBa_K265008"><i><span
-
style="color: rgb(0, 0, 153);">BBa_K265008</span></i></a>) or OmpA (<i><span
+
style="color: rgb(0, 0, 153);">BBa_K265008</span></i></a>) or OmpA (<i><a
-
style="color: blue;">BBa_K103006</span>).<span
+
href="http://partsregistry.org/wiki/index.php/Part:BBa_K103006"><span
 +
style="color: blue;">BBa_K103006</span></a>).<span
style="color: rgb(0, 41, 57);"> </span></i>The
style="color: rgb(0, 41, 57);"> </span></i>The
proposed constructs would consists of a membrane anchor (INPNC or OmpA)
proposed constructs would consists of a membrane anchor (INPNC or OmpA)
Line 210: Line 221:
Standard. We have submitted this part to the part registry as part </i><a
Standard. We have submitted this part to the part registry as part </i><a
href="http://partsregistry.org/wiki/index.php/Part:BBa_K265002"><i><span
href="http://partsregistry.org/wiki/index.php/Part:BBa_K265002"><i><span
-
style="color: rgb(0, 0, 153);">BBa_K265002</span></i></a>.</p>
+
style="color: rgb(0, 0, 153);">BBa_K265002</span></i></a>.<br>
 +
<br>
 +
</p>
<u1:p></u1:p>
<u1:p></u1:p>
<p class="freeform0" style="margin-bottom: 6pt; line-height: 19pt;"><a
<p class="freeform0" style="margin-bottom: 6pt; line-height: 19pt;"><a
-
name="INPNCSS"></a><b>INPNC + SS:</b>Park <i>et al. </i>have showed
+
name="INPNCSS"></a><b>INPNC+SS:</b> Park <i>et al. </i>have showed
that the
that the
fusion of the complete <i>phaZ1 </i>gene (including SS) and a
fusion of the complete <i>phaZ1 </i>gene (including SS) and a
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style="color: rgb(0, 0, 153);">BBa_K265008</span></i></a>), could lead
style="color: rgb(0, 0, 153);">BBa_K265008</span></i></a>), could lead
to stable
to stable
-
expression and secretion of the <i>phaZ1</i> gene product (15).<br>
+
expression and secretion of the <i>phaZ1</i> gene product (<a
 +
href="https://2009.igem.org/Team:UC_Davis/Contacts_References">15</a>).<br>
<u1:p></u1:p>We propose that this system might be generally useful for
<u1:p></u1:p>We propose that this system might be generally useful for
the
the
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RFC-12 Standard </i>as part<i> </i><a
RFC-12 Standard </i>as part<i> </i><a
href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K265009"><i><span
href="http://partsregistry.org/wiki/index.php?title=Part:BBa_K265009"><i><span
-
style="color: rgb(0, 0, 153);">BBa_K265009</span></i></a>.</p>
+
style="color: rgb(0, 0, 153);">BBa_K265009</span></i></a>.<br>
 +
<br>
 +
</p>
<u1:p></u1:p>
<u1:p></u1:p>
<p class="freeform0" style="margin-bottom: 6pt; line-height: 19pt;"><a
<p class="freeform0" style="margin-bottom: 6pt; line-height: 19pt;"><a
-
name="OmpAss"></a><b>OmpA + SS:</b>Since OmpA is believed to function
+
name="OmpAss"></a><b>OmpA+SS:</b> Since OmpA is believed to function
similarly
similarly
to INPNC and Park <i>et al. </i>have showed that the fusion of the
to INPNC and Park <i>et al. </i>have showed that the fusion of the
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style="color: rgb(0, 0, 153);">BBa_K265008</span></i></a>), could lead
style="color: rgb(0, 0, 153);">BBa_K265008</span></i></a>), could lead
to stable
to stable
-
expression and secretion of the <i>phaZ1</i> gene product (15), we
+
expression and secretion of the <i>phaZ1</i> gene product (<a
 +
href="https://2009.igem.org/Team:UC_Davis/Contacts_References">15</a>),
 +
we
have decided
have decided
to test and see if OmpA's ability to secret increases when it is used
to test and see if OmpA's ability to secret increases when it is used
-
by a
+
with a
signal sequence.<br>
signal sequence.<br>
<u1:p></u1:p><i>We have modified this protein to be consistent with BBF
<u1:p></u1:p><i>We have modified this protein to be consistent with BBF
Line 270: Line 288:
<p class="MsoNormal"><a name="OmpA"></a><b>OmpA</b>: OmpA is one of the
<p class="MsoNormal"><a name="OmpA"></a><b>OmpA</b>: OmpA is one of the
proteins on
proteins on
-
the outer membrane of <i>E. coli</i> (13),it is used as a displaying
+
the outer membrane of <i>E. coli</i> (<a
 +
href="https://2009.igem.org/Team:UC_Davis/Contacts_References">13</a>),it
 +
is used as a displaying
fusion
fusion
protein on the cell surface . This part has already been documented on
protein on the cell surface . This part has already been documented on
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Note: “It has remained essentially unknown how proteins of E. coli
Note: “It has remained essentially unknown how proteins of E. coli
outer
outer
-
membrane are sorted and incorporated into this membrane” (10)</i> <i><br>
+
membrane are sorted to and incorporated into this membrane” (<a
 +
href="https://2009.igem.org/Team:UC_Davis/Contacts_References">10</a>)</i>
 +
<i><br>
For more information go to:<a
For more information go to:<a
href="http://partsregistry.org/wiki/index.php/Part:BBa_K103006"><u><span
href="http://partsregistry.org/wiki/index.php/Part:BBa_K103006"><u><span
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<hr align="center" size="2" width="100%"></div>
<hr align="center" size="2" width="100%"></div>
<p class="MsoNormal" style=""><a name="GFP"></a><b>GFP</b> <b>(Green
<p class="MsoNormal" style=""><a name="GFP"></a><b>GFP</b> <b>(Green
-
Fluorescent Protein)</b> : Mutant of GFP
+
Fluorescent Protein)</b>: Mutant of GFP
known to be very stable (superfolder), which will let this protein fold
known to be very stable (superfolder), which will let this protein fold
quickly
quickly
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<div class="MsoNormal" style="text-align: center;" align="center">
<div class="MsoNormal" style="text-align: center;" align="center">
<hr align="center" size="2" width="100%"></div>
<hr align="center" size="2" width="100%"></div>
-
<p class="MsoNormal" style=""><a name="LacI"></a><b>LacI</b>: One
+
<p class="MsoNormal" style=""><a name="LacI"></a><b>LacI</b>: An
-
inducible Promoter which was found in the part
+
inducible promoter that was found in the part
registry.<br>
registry.<br>
<i>For more information go to:<a
<i>For more information go to:<a
href="http://partsregistry.org/wiki/index.php/Part:BBa_R0010"><u><span
href="http://partsregistry.org/wiki/index.php/Part:BBa_R0010"><u><span
style="color: blue;"> BBa_R0010</span></u></a><br style="">
style="color: blue;"> BBa_R0010</span></u></a><br style="">
-
<!--[if !supportLineBreakNewLine]--><br style="">
 
<!--[endif]--></i></p>
<!--[endif]--></i></p>
<u1:p></u1:p>
<u1:p></u1:p>
<div class="MsoNormal" style="text-align: center;" align="center">
<div class="MsoNormal" style="text-align: center;" align="center">
<hr align="center" size="2" width="100%"></div>
<hr align="center" size="2" width="100%"></div>
-
<p class="MsoNormal" style=""><a name="His"></a><b>6-His Tag</b>:The
+
<p class="MsoNormal" style=""><a name="His"></a><b>6-His Tag</b>: The
6-Histidine Tag serves as a tag for Western
6-Histidine Tag serves as a tag for Western
Blotting if our fluorescent reporters are not expressed as highly as we
Blotting if our fluorescent reporters are not expressed as highly as we
-
would
+
would like. <br>
-
like. <br>
+
<i>Note: We are using this tag as an additional method for assay beside
-
<i>Note: We are using this tag, just in case if the GFP or Luciferase
+
fluorescence of GFP and Luciferase.</i> </p>
-
does not
+
-
work under a plate reader.</i> </p>
+
-
<u1:p></u1:p>
+
<div class="MsoNormal" style="text-align: center;" align="center">
<div class="MsoNormal" style="text-align: center;" align="center">
<hr align="center" size="2" width="100%"></div>
<hr align="center" size="2" width="100%"></div>
-
<p class="MsoNormal" style=""><a name="ChvI_promoter"></a><b>ChvI
+
<br>
-
promoter</b>: Gene fusion studies confirmed
+
more information go to: <a
-
that ChvI gene was induced by acidic conditions (1). This gene is one
+
-
of the
+
-
candidates to be use in our biological pH sensor as a promoter.</p>
+
-
<u1:p></u1:p>
+
-
<div class="MsoNormal" style="text-align: center;" align="center">
+
-
<hr align="center" size="2" width="100%"></div>
+
-
<p class="MsoNormal" style=""><a name="katA"></a><b>KatA promoter</b>:
+
-
This Chromosomal gene is located on the
+
-
linear chromosome (2) and it seems to be induced under an acidic
+
-
environment as
+
-
well as being involved in the <i>Agrobacterium tumorigenesis</i>
+
-
(2).Research
+
-
has suggested that ChvG is needed for "responsiveness of&nbsp; gene
+
-
expression to low pH "(2). This gene has become a candidate to complete
+
-
our pH sensor device from this evidence.</p>
+
-
<u1:p></u1:p>
+
-
<div class="MsoNormal" style="text-align: center;" align="center">
+
-
<hr align="center" size="2" width="100%"></div>
+
-
<p class="MsoNormal" style=""><a name="aopB"></a><b>AopB promoter</b>:
+
-
This Chromosomal gene located on the
+
-
circular chromosome (2) encodes an outer member protein exposed on the
+
-
bacterial cell surface (2). Also, ChvG was shown to be absolutely
+
-
required for
+
-
this gene expression (2)It seems to get induced under an acidic
+
-
environment as
+
-
well as being involved in the <i>Agrobacterium</i> <i>tumorigenesis </i>(2).
+
-
Therefore, we have chosen this gene to be one of our candidates to
+
-
complete our
+
-
pH sensor device.</p>
+
-
<u1:p></u1:p>
+
-
<div class="MsoNormal" style="text-align: center;" align="center">
+
-
<hr align="center" size="2" width="100%"></div>
+
-
<p class="MsoNormal" style=""><a name="PhoA"></a><b>PhoA promoter</b>:
+
-
There has been a suggestion that ChvI can
+
-
activate AP activity by activating transcription of this gene, PhoA
+
-
(3).
+
-
Therefore, this gene has become one of our candidates to complete our
+
-
pH sensor
+
-
device.</p>
+
-
<u1:p></u1:p>
+
-
<div class="MsoNormal" style="text-align: center;" align="center">
+
-
<hr align="center" size="2" width="100%"></div>
+
-
<p class="MsoNormal" style=""><a name="impA"></a><b>ImpA promoter:</b>Gene
+
-
fusion studies confirmed that impA
+
-
genes was induced by acidic conditions (1), therefore, this is one of
+
-
our
+
-
candidates to complete our pH sensor device.</p>
+
-
<div class="MsoNormal" style="text-align: center;" align="center">
+
-
<hr align="center" size="2" width="100%"></div>
+
-
<p class="MsoNormal" style=""><i>For
+
-
more information go to: </i><a
+
href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&amp;group=UC_Davis"><i><u><span
href="http://partsregistry.org/cgi/partsdb/pgroup.cgi?pgroup=iGEM2009&amp;group=UC_Davis"><i><u><span
-
style="color: blue;">UCDAVIS_Parts</span></u></i></a> </p>
+
style="color: blue;">UCDAVIS_Parts</span></u></i></a> <u1:p></u1:p>
-
<u1:p></u1:p>
+
<hr style="width: 100%; height: 2px;"><small style="font-weight: bold;"><span
<hr style="width: 100%; height: 2px;"><small style="font-weight: bold;"><span
style="font-size: 18pt; line-height: 115%; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"></span></small></div>
style="font-size: 18pt; line-height: 115%; font-family: &quot;Times New Roman&quot;,&quot;serif&quot;;"></span></small></div>

Latest revision as of 01:22, 15 December 2009

PARTS1

 
Parts:   
Parts related to secretion:                                                                                                                                 Parts related to pH sensor:
Proteins:
Promoters:
Others:
 New parts:
      Promoters:
Proteins:
 

New parts: 

INPNC: The ice-nucleation protein (INP) from Pseudomonas syringae (9) is used by its natural host to nucleate ice formation and is implicated in P.syringae-associated pathogenesisINP and a truncated derivative lacking the central domain (INPNC) have been used extensively for displaying proteins on the surface of E. coli (7).  For instance, AldO and PhaZ1 have been successfully displayed on the surface of E.coli using INPNC (7, 15).
Park et al. have shown that when INPNC is fused to the phaZ1 gene and its signal sequence, it can serve as a suitable surface delivery and secretion device of the otherwise toxic phaZ1 gene product(15).  This part was synthesized by Mr. Gene (Regensburg, Germany) with codon optimization and subsequently transferred into vector ( pSB1AK3). As it is expected that this part will be used in the context of the fusion protein, the prefix and suffix for this part are consistent with the BBF RCF-12 standard. 
We have proposed to build and test a general protein secretion system modeled after that developed by Park et al. in which a fusion of INPNC and the signal sequence from the phaZ1 gene are used to secrete any target protein. 
We have modified this protein to be consistent with the BBF RFC-12 Standard. We have submitted this part to the parts registry as part BBa_K265008.


SS: The signal sequence (SS) for the phaZ1 gene product of Paucimonas lemoignei, a polyhydroxybutyrate depolymerase (15).  In the native protein the signal sequence is cleaved between residues Ala37 and Leu38.  Park et al. have showed that the fusion of the complete phaZ1 gene (including SS) and a truncated ice nucleation protein from Pseudomonas syringae (BBa_K265008), could lead to stable expression and secretion of the phaZ1 gene product. 
We propose that the signal sequence might be generally useful as a cleavage tag in secretion systems that include a membrane anchor component, such as INPNC (BBa_K265008) or OmpA (BBa_K103006). The proposed constructs would consists of a membrane anchor (INPNC or OmpA) followed by the cleavable signal sequence and finally a target protein marked for secretion. 
Since we expect that this part will be used in the context of a fusion protein, we have modified this protein to be consistent with BBF RFC-12 Standard. We have submitted this part to the part registry as part BBa_K265002.

INPNC+SS: Park et al. have showed that the fusion of the complete phaZ1 gene (including SS) and a truncated ice nucleation protein from Pseudomonas syringae (BBa_K265008), could lead to stable expression and secretion of the phaZ1 gene product (15).
We propose that this system might be generally useful for the secretion of other target proteins in E. coli and have therefore created a fusion of parts BBa_K265008 (INPNC) and BBa_K265002 (SS) which is compatible with the BBF RFC-12 Standard.
During the construction of this part, two silent mutations were introduced in the coding region of INPNC (T324A and A348T) that differ from those in part BBa_K265008
We have submitted this part to the part registry in the BBF RFC-12 Standard as part BBa_K265009.

OmpA+SS: Since OmpA is believed to function similarly to INPNC and Park et al. have showed that the fusion of the complete phaZ1 gene (including SS) and a truncated ice nucleation protein from Pseudomonas syringae (BBa_K265008), could lead to stable expression and secretion of the phaZ1 gene product (15), we have decided to test and see if OmpA's ability to secret increases when it is used with a signal sequence.
We have modified this protein to be consistent with BBF RFC-12 Standard and have submitted this part to the part registry, BBa_K265011.


OmpA: OmpA is one of the proteins on the outer membrane of E. coli (13),it is used as a displaying fusion protein on the cell surface . This part has already been documented on the parts registry; however, it has not been tested as a compnent of secretion system (via fusion with a target protein linked with a cleavable signal sequence)
We have modified this protein to be consistent with BBF RFC-12 Standard.
Note: “It has remained essentially unknown how proteins of E. coli outer membrane are sorted to and incorporated into this membrane” (10)

For more information go to: BBa_K103006


RBS:  Ribosome Binding site number 32 (BBa_J61132) from the registry is being used in our secretion system.
For more information go to: BBa_J61132


Terminator: We are using BBa_B0015, a double terminator, as our terminator in both our secretion and pH system.
For more information go to: BBa_B0015


GFP (Green Fluorescent Protein): Mutant of GFP known to be very stable (superfolder), which will let this protein fold quickly so we can use either a fluorescent reader or UV light to detect it. Therefore it has been used as a reporter in our secretion system. It also serves as a small protein in testing our secretion system.
For more informaiton go to: BBa_K265003 


Luciferase: Luciferase is a firefly protein that also fluoresces, so it serves as a reporter as well as a testable large protein.
For more information go to: BBa_1712019


LacI: An inducible promoter that was found in the part registry.
For more information go to: BBa_R0010


6-His Tag: The 6-Histidine Tag serves as a tag for Western Blotting if our fluorescent reporters are not expressed as highly as we would like.
Note: We are using this tag as an additional method for assay beside fluorescence of GFP and Luciferase.



more information go to: UCDAVIS_Parts