Team:Imperial College London/M2/genes

From 2009.igem.org

(Difference between revisions)
Line 75: Line 75:
===<b>General Protective:</b>===
===<b>General Protective:</b>===
 +
 +
 +
 +
<html>
 +
 +
<p class="ecoparagraph">
 +
<map name="MAP91783">
 +
<area coords="17,55,48,72" onmouseover="return overlib('RcsB-Pasp trancriptional activator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -41.5 (ranging from -35 to -48)<br><b>Evidence:</b> Gene expression analysis [Boulanger05], Human inference based on similarity to consensus sequences [Boulanger05]');" onmouseout="return nd();">
 +
<area coords="101,41,162,72" onmouseover="return overlib(' <b>Gene:</b>  osmB    EG10679    b1283    ECK1278<br><b>Location:</b> 1,341,134 <- 1,341,352  <br> <b>Product:</b> OsmB osmotically inducible lipoprotein');" onmouseout="return nd();">
 +
<area coords="0,0,115,89" onmouseover="return overlib('<b>Operon:</b> osmBp1 (Experim. ev.)  <BR><b>Tr.Activators:</b> (phospho-RcsB)');" onmouseout="return nd();">
 +
<area coords="0,0,164,89" onmouseover="return overlib('<b>Operon</b>: osmB');" onmouseout="return nd();">
 +
</map>
 +
<img src="https://static.igem.org/mediawiki/2009/9/9f/Op5.gif" usemap="#MAP91783" border="0">
 +
</p>
 +
 +
 +
 +
 +
</html>
Line 86: Line 105:
<area coords="25,20,61,37"  onmouseover="return overlib('RcsB-Pasp trancriptional activator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -41.5 (ranging from -48 to -35)<br><b>Evidence:</b> Site mutation [DavalosGar01], Gene expression analysis [DavalosGar01], Binding of purified proteins [FrancezCha05]');" onmouseout="return nd();">
<area coords="25,20,61,37"  onmouseover="return overlib('RcsB-Pasp trancriptional activator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -41.5 (ranging from -48 to -35)<br><b>Evidence:</b> Site mutation [DavalosGar01], Gene expression analysis [DavalosGar01], Binding of purified proteins [FrancezCha05]');" onmouseout="return nd();">
<area coords="19,38,70,55"  onmouseover="return overlib('NhaR-Na+ transcriptional activator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -41 (ranging from -50 to -32)<br><b>Evidence:</b> Gene expression analysis [Toesca01], Binding of cellular extracts [Sturny03], Site mutation [Toesca01]');" onmouseout="return nd();">
<area coords="19,38,70,55"  onmouseover="return overlib('NhaR-Na+ transcriptional activator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -41 (ranging from -50 to -32)<br><b>Evidence:</b> Gene expression analysis [Toesca01], Binding of cellular extracts [Sturny03], Site mutation [Toesca01]');" onmouseout="return nd();">
-
<area coords="87,42,177,73" onmouseover="return overlib(' <b>Gene:</b>  osmC   EG10680    b1482    ECK1476<br><b>Location:</b> 1,554,649 -> 1,555,080  <br> <b>Product:</b> osmotically inducible peroxidase OsmC');" onmouseout="return nd();">
+
<area coords="87,42,177,73" onmouseover="return overlib(' <b>Gene:</b>   
 +
 
 +
 
 +
C   EG10680    b1482    ECK1476<br><b>Location:</b> 1,554,649 -> 1,555,080  <br> <b>Product:</b> osmotically inducible peroxidase OsmC');" onmouseout="return nd();">
<area coords="19,0,172,90" onmouseover="return overlib('<b>Operon:</b> osmCp1 (Experim. ev.)  <BR><b>Tr.Activators:</b> (NhaR-Na<SUP>+</SUP> phospho-RcsB) <BR><b>Tr.Inhibitors:</b> (Lrp Hns)');" onmouseout="return nd();">
<area coords="19,0,172,90" onmouseover="return overlib('<b>Operon:</b> osmCp1 (Experim. ev.)  <BR><b>Tr.Activators:</b> (NhaR-Na<SUP>+</SUP> phospho-RcsB) <BR><b>Tr.Inhibitors:</b> (Lrp Hns)');" onmouseout="return nd();">
<area coords="0,0,179,90" onmouseover="return overlib('<b>Operon</b>: osmC');" onmouseout="return nd();">
<area coords="0,0,179,90" onmouseover="return overlib('<b>Operon</b>: osmC');" onmouseout="return nd();">
Line 142: Line 164:
<img src="https://static.igem.org/mediawiki/2009/1/1c/Op2.gif" usemap="#MAP80844" border="0">
<img src="https://static.igem.org/mediawiki/2009/1/1c/Op2.gif" usemap="#MAP80844" border="0">
  </p>
  </p>
 +
 +
</html>
 +
 +
 +
 +
 +
<html>
 +
 +
<p class="ecoparagraph">
 +
<map name="MAP91781">
 +
<area coords="17,55,48,72" onmouseover="return overlib('RcsB-Pasp trancriptional activator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -41.5 (ranging from -35 to -48)<br><b>Evidence:</b> Binding of purified proteins [FrancezCha05], Gene expression analysis [FrancezCha05]');" onmouseout="return nd();">
 +
<area coords="165,41,207,72"  onmouseover="return overlib(' <b>Gene:</b>  sra    EG11508    b1480    ECK1474<br><b>Synonyms:</b> rpsV<br><b>Location:</b> 1,553,850 <- 1,553,987  <br> <b>Product:</b> 30S ribosomal subunit protein S22, subunit of ribosome');" onmouseout="return nd();">
 +
<area coords="75,41,136,72" onmouseover="return overlib(' <b>Gene:</b>  bdm    G6776    b1481    ECK1475<br><b>Synonyms:</b> yddX<br><b>Location:</b> 1,554,089 <- 1,554,304  <br> <b>Product:</b> biofilm-dependent modulation protein');" onmouseout="return nd();">
 +
<area coords="0,0,103,89" onmouseover="return overlib('<b>Operon:</b> bdmp (Experim. ev.)  <BR><b>Tr.Activators:</b> (phospho-RcsB)');" onmouseout="return nd();">
 +
<area coords="0,0,209,89" onmouseover="return overlib('<b>Operon</b>: bdm-sra');" onmouseout="return nd();">
 +
</map>
 +
<img src="https://static.igem.org/mediawiki/2009/a/ae/Op4.gif" usemap="#MAP91781" border="0">
 +
</p>
 +
 +
 +
 +
</html>
 +
 +
 +
 +
<html>
 +
 +
 +
 +
<p class="ecoparagraph">
 +
<map name="MAP91785">
 +
<area coords="12,55,43,72" onmouseover="return overlib('RcsB-Pasp trancriptional activator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -45 (ranging from -51 to -39)<br><b>Evidence:</b> Gene expression analysis, Human inference based on similarity to consensus sequences, Site mutation');" onmouseout="return nd();">
 +
<area coords="0,0,99,89" onmouseover="return overlib('<b>Operon:</b> ftsAp1 (Experim. ev.)  <BR><b>Tr.Activators:</b> (phospho-RcsB)');" onmouseout="return nd();">
 +
<area coords="521,41,829,72" onmouseover="return overlib(' <b>Gene:</b>  ftsZ    EG10347    b0095    ECK0096<br><b>Synonyms:</b> sfiB, sulB<br><b>Location:</b> 105,305 -> 106,456  <br> <b>Product:</b> essential cell division protein FtsZ');" onmouseout="return nd();">
 +
<area coords="167,41,505,72" onmouseover="return overlib(' <b>Gene:</b>  ftsA    EG10339    b0094    ECK0095<br><b>Synonyms:</b> divA<br><b>Location:</b> 103,982 -> 105,244  <br> <b>Product:</b> essential cell division protein FtsA');" onmouseout="return nd();">
 +
<area coords="0,0,831,89" onmouseover="return overlib('<b>Operon</b>: ftsAZ');" onmouseout="return nd();">
 +
</map>
 +
<img src="https://static.igem.org/mediawiki/2009/e/e8/FtsA.gif" usemap="#MAP91785" border="0">
 +
</p>
 +
</html>
</html>
Line 235: Line 297:
{{Imperial/09/Division}}
{{Imperial/09/Division}}
-
 
-
<html>
 
-
 
-
<p class="ecoparagraph">
 
-
<map name="MAP91779">
 
-
<area coords="142,0,172,17" onmouseover="return overlib('H-NS transcriptional dual regulator represses transcription from associated promoter<br>The exact location of this binding site is unknown or not specified.<br><b>Evidence:</b> Gene expression analysis [Bouvier98]<br>The nature of binding of this protein is not well known.');" onmouseout="return nd();">
 
-
<area coords="1,56,32,73" onmouseover="return overlib('Lrp transcriptional dual regulator represses transcription from associated promoter<br><b>Distance to transcription start site:</b> -52 (ranging from -58 to -46)<br><b>Evidence:</b> Gene expression analysis, Binding of purified proteins, Human inference based on similarity to consensus sequences, Site mutation');" onmouseout="return nd();">
 
-
<area coords="25,20,61,37"  onmouseover="return overlib('RcsB-Pasp trancriptional activator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -41.5 (ranging from -48 to -35)<br><b>Evidence:</b> Site mutation [DavalosGar01], Gene expression analysis [DavalosGar01], Binding of purified proteins [FrancezCha05]');" onmouseout="return nd();">
 
-
<area coords="19,38,70,55"  onmouseover="return overlib('NhaR-Na+ transcriptional activator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -41 (ranging from -50 to -32)<br><b>Evidence:</b> Gene expression analysis [Toesca01], Binding of cellular extracts [Sturny03], Site mutation [Toesca01]');" onmouseout="return nd();">
 
-
<area coords="87,42,177,73" onmouseover="return overlib(' <b>Gene:</b>  osmC    EG10680    b1482    ECK1476<br><b>Location:</b> 1,554,649 -> 1,555,080  <br> <b>Product:</b> osmotically inducible peroxidase OsmC');" onmouseout="return nd();">
 
-
<area coords="19,0,172,90" onmouseover="return overlib('<b>Operon:</b> osmCp1 (Experim. ev.)  <BR><b>Tr.Activators:</b> (NhaR-Na<SUP>+</SUP> phospho-RcsB) <BR><b>Tr.Inhibitors:</b> (Lrp Hns)');" onmouseout="return nd();">
 
-
<area coords="0,0,179,90" onmouseover="return overlib('<b>Operon</b>: osmC');" onmouseout="return nd();">
 
-
</map>
 
-
<img src="https://static.igem.org/mediawiki/2009/1/10/Op3.gif" usemap="#MAP91779" border="0">
 
-
</p>
 
-
 
-
</html>
 
{{Imperial/09/Division}}
{{Imperial/09/Division}}
-
 
-
 
-
<html>
 
-
 
-
<p class="ecoparagraph">
 
-
<map name="MAP91781">
 
-
<area coords="17,55,48,72" onmouseover="return overlib('RcsB-Pasp trancriptional activator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -41.5 (ranging from -35 to -48)<br><b>Evidence:</b> Binding of purified proteins [FrancezCha05], Gene expression analysis [FrancezCha05]');" onmouseout="return nd();">
 
-
<area coords="165,41,207,72"  onmouseover="return overlib(' <b>Gene:</b>  sra    EG11508    b1480    ECK1474<br><b>Synonyms:</b> rpsV<br><b>Location:</b> 1,553,850 <- 1,553,987  <br> <b>Product:</b> 30S ribosomal subunit protein S22, subunit of ribosome');" onmouseout="return nd();">
 
-
<area coords="75,41,136,72" onmouseover="return overlib(' <b>Gene:</b>  bdm    G6776    b1481    ECK1475<br><b>Synonyms:</b> yddX<br><b>Location:</b> 1,554,089 <- 1,554,304  <br> <b>Product:</b> biofilm-dependent modulation protein');" onmouseout="return nd();">
 
-
<area coords="0,0,103,89" onmouseover="return overlib('<b>Operon:</b> bdmp (Experim. ev.)  <BR><b>Tr.Activators:</b> (phospho-RcsB)');" onmouseout="return nd();">
 
-
<area coords="0,0,209,89" onmouseover="return overlib('<b>Operon</b>: bdm-sra');" onmouseout="return nd();">
 
-
</map>
 
-
<img src="https://static.igem.org/mediawiki/2009/a/ae/Op4.gif" usemap="#MAP91781" border="0">
 
-
</p>
 
-
 
-
 
-
 
-
</html>
 
Line 279: Line 306:
-
 
-
<html>
 
-
 
-
<p class="ecoparagraph">
 
-
<map name="MAP91783">
 
-
<area coords="17,55,48,72" onmouseover="return overlib('RcsB-Pasp trancriptional activator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -41.5 (ranging from -35 to -48)<br><b>Evidence:</b> Gene expression analysis [Boulanger05], Human inference based on similarity to consensus sequences [Boulanger05]');" onmouseout="return nd();">
 
-
<area coords="101,41,162,72" onmouseover="return overlib(' <b>Gene:</b>  osmB    EG10679    b1283    ECK1278<br><b>Location:</b> 1,341,134 <- 1,341,352  <br> <b>Product:</b> OsmB osmotically inducible lipoprotein');" onmouseout="return nd();">
 
-
<area coords="0,0,115,89" onmouseover="return overlib('<b>Operon:</b> osmBp1 (Experim. ev.)  <BR><b>Tr.Activators:</b> (phospho-RcsB)');" onmouseout="return nd();">
 
-
<area coords="0,0,164,89" onmouseover="return overlib('<b>Operon</b>: osmB');" onmouseout="return nd();">
 
-
</map>
 
-
<img src="https://static.igem.org/mediawiki/2009/9/9f/Op5.gif" usemap="#MAP91783" border="0">
 
-
</p>
 
-
 
-
 
-
 
-
 
-
</html>
 
-
 
-
{{Imperial/09/Division}}
 
-
 
-
 
-
 
-
 
-
<html>
 
-
 
-
 
-
 
-
<p class="ecoparagraph">
 
-
<map name="MAP91785">
 
-
<area coords="12,55,43,72" onmouseover="return overlib('RcsB-Pasp trancriptional activator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -45 (ranging from -51 to -39)<br><b>Evidence:</b> Gene expression analysis, Human inference based on similarity to consensus sequences, Site mutation');" onmouseout="return nd();">
 
-
<area coords="0,0,99,89" onmouseover="return overlib('<b>Operon:</b> ftsAp1 (Experim. ev.)  <BR><b>Tr.Activators:</b> (phospho-RcsB)');" onmouseout="return nd();">
 
-
<area coords="521,41,829,72" onmouseover="return overlib(' <b>Gene:</b>  ftsZ    EG10347    b0095    ECK0096<br><b>Synonyms:</b> sfiB, sulB<br><b>Location:</b> 105,305 -> 106,456  <br> <b>Product:</b> essential cell division protein FtsZ');" onmouseout="return nd();">
 
-
<area coords="167,41,505,72" onmouseover="return overlib(' <b>Gene:</b>  ftsA    EG10339    b0094    ECK0095<br><b>Synonyms:</b> divA<br><b>Location:</b> 103,982 -> 105,244  <br> <b>Product:</b> essential cell division protein FtsA');" onmouseout="return nd();">
 
-
<area coords="0,0,831,89" onmouseover="return overlib('<b>Operon</b>: ftsAZ');" onmouseout="return nd();">
 
-
</map>
 
-
<img src="https://static.igem.org/mediawiki/2009/e/e8/FtsA.gif" usemap="#MAP91785" border="0">
 
-
</p>
 
-
 
-
 
-
</html>
 

Revision as of 19:32, 11 October 2009

Contents

RcsB

Background:

RcsB is a transcription factor that forms part of a phosphorelay system. In response to membrane stress, RcsB is phosphorylated into its DNA binding form. In this state, it is able to regulate ~5% of the E.coli genome 4.


The Rcs Phosphorelay System:

In this system, RcsC encodes a membrane bound sensor kinase, while RcsB functions as the response regulator. The protein RcsA is an auxiliary activator protein that heterodimerises with RcsB to induce a mucoid phenotype. Levels of RcsA are controlled by the ATP dependent protease Lon.


RcsB upregulates the following genes:


Colanic Acid Biosynthesis:




wcaF
  • Putative colanic acid biosynthesis acetyltransferase 2
gmd

Codes for GDP-mannose 4,6-dehydratase which is a subunit of GDP-mannose 4,6-dehydratase. This enzyme is involved in colanic acid biosynthesis.

wcaD
  • Predicted colanic acid polymerase
wza
  • This codes for a lipoprotein that is required for colanic acid translocation through the outer membrane. The lipoprotein is a subunit of the capsular polysaccharide export apparatus.
fcl
  • Codes for a subunit of GDP-fucose synthase. This enzyme is involved in colanic acid biosynthesis.




General Protective:



ivy (Inhibitor of Vertebrate lysozyme)
  • Discovered in 2001 as the first bacterial lysozyme inhibitor. This Type-C lysozyme inhibitor resides in the periplasm.1
MilC (Membrane-bound lysozyme inhibitor of Type C lysozyme)
  • This is a lipoprotein that resides in the membrane. 1



OsmC (Osmotically-inducible protein C)
  • This protein provides defense against oxidative stress caused by exposure to organic hydroperoxides. 2 3


KatE
  • Codes for a subunit of heme d synthase / hydroperoxidase. This bacterial catalase protects against osmotic stress.




Global Regulators:





Sra (stationary-phase-induced ribosome-associated)

Sra is a sub-stoichiometric component of the 30S ribosomal subunit that is more abundant at stationary phase than during log phase growth.

rprA

rprA is a gene encoding a small RNA molecule that is involved in the post-transcriptional control of the alternative sigma factor, ("sigma S").


FtsA

FtsA is an essential cell division protein which colocalizes with FtsZ to the septal ring structure.

FtsZ
  • Essential cell division protein.
yfbR
  • dCMP phosphohydrolase


Membrane Proteins:

bdm (biofilm-dependent modulation protein)
OsmB
  • OsmB encodes an outer membrane lipoprotein.
OsmY

Hyperosmotically inducible periplasmic protein

PhnQ
ycfJ
  • Uncharacterized putative inner membrane protein.
ygaC
spy
ymgD
  • Putative periplasmic protein.
ypeC
  • Unknown function


ymgG
YbaY

Predicted outer membrane lipoprotein




References

1) [http://www.ncbi.nlm.nih.gov/pubmed/19136591 The Rcs two-component system regulates expression of lysozyme inhibitors and is induced by exposure to lysozyme]

2) [http://www.ncbi.nlm.nih.gov/pubmed/19346340 Gene Expression Induced in Escherichia coli O157:H7 upon Exposure to Model Apple Juice]

3) [http://www.ncbi.nlm.nih.gov/pubmed/14627744 Structural and functional features of the Escherichia coli hydroperoxide resistance protein OsmC.]

4) [http://www.ncbi.nlm.nih.gov/pubmed/16153174?ordinalpos=5&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum The Rcs phosphorelay: a complex signal transduction system.]


























Mr. Gene   Geneart   Clontech   Giant Microbes

Retrieved from "http://2009.igem.org/Team:Imperial_College_London/M2/genes"