Team:Imperial College London/M2/genes

From 2009.igem.org

(Difference between revisions)
(→YbaY)
Line 274: Line 274:
Predicted outer membrane lipoprotein
Predicted outer membrane lipoprotein
 +
 +
 +
{{Imperial/09/Division}}
 +
 +
 +
==Repression:==
 +
 +
<html>
 +
 +
 +
 +
<p class="ecoparagraph">
 +
<map name="MAP91787">
 +
<area coords="1,128,32,145" onmouseover="return overlib('CRP-cAMP transcriptional dual regulator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -170.5 (ranging from -160 to -181)<br><b>Evidence:</b> Gene expression analysis [Zheng04], Automated inference based on similarity to consensus sequences [Zheng04]');" onmouseout="return nd();">
 +
<area coords="39,128,70,145"  onmouseover="return overlib('CpxR-Phosphorylated represses transcription from associated promoter<br><b>Distance to transcription start site:</b> -100.5 (ranging from -93 to -107)<br><b>Evidence:</b> Binding of purified proteins [Jubelin05], Gene expression analysis [Jubelin05], Human inference based on similarity to consensus sequences [Jubelin05]');" onmouseout="return nd();">
 +
<area coords="135,128,166,145"  onmouseover="return overlib('CpxR-Phosphorylated represses transcription from associated promoter<br><b>Distance to transcription start site:</b> -20.5 (ranging from -13 to -27)<br><b>Evidence:</b> Binding of purified proteins [Jubelin05], Gene expression analysis [Jubelin05], Human inference based on similarity to consensus sequences [Jubelin05]');" onmouseout="return nd();">
 +
<area coords="166,128,197,145"  onmouseover="return overlib('CpxR-Phosphorylated represses transcription from associated promoter<br><b>Distance to transcription start site:</b> 2.5 (ranging from 10 to -5)<br><b>Evidence:</b> Binding of purified proteins [Jubelin05], Gene expression analysis [Jubelin05], Human inference based on similarity to consensus sequences [Jubelin05]');" onmouseout="return nd();">
 +
<area coords="79,74,110,91"  onmouseover="return overlib('RstA-Phosphorylated transcriptional regulator represses transcription from associated promoter<br><b>Distance to transcription start site:</b> -50.5 (ranging from -44 to -57)<br><b>Evidence:</b> Binding of purified proteins [Ogasawara07a], Gene expression analysis [Ogasawara07a], Human inference based on similarity to consensus sequences [Ogasawara07a]');" onmouseout="return nd();">
 +
<area coords="74,128,109,145"  onmouseover="return overlib('CpxR-Phosphorylated represses transcription from associated promoter<br><b>Distance to transcription start site:</b> -52 (ranging from -45 to -59)<br><b>Evidence:</b> Binding of purified proteins [PrigentCom01], Gene expression analysis [PrigentCom01], Human inference based on similarity to consensus sequences [PrigentCom01]');" onmouseout="return nd();">
 +
<area coords="76,110,111,127" onmouseover="return overlib('CpxR-Phosphorylated represses transcription from associated promoter<br><b>Distance to transcription start site:</b> -51 (ranging from -44 to -58)<br><b>Evidence:</b> Binding of purified proteins [Jubelin05], Gene expression analysis [Jubelin05], Human inference based on similarity to consensus sequences [Jubelin05]');" onmouseout="return nd();">
 +
<area coords="81,56,116,73"  onmouseover="return overlib('CpxR-Phosphorylated represses transcription from associated promoter<br><b>Distance to transcription start site:</b> -48.5 (ranging from -41 to -55)<br><b>Evidence:</b> Binding of purified proteins [Jubelin05], Gene expression analysis [Jubelin05], Human inference based on similarity to consensus sequences [Jubelin05]');" onmouseout="return nd();">
 +
<area coords="238,0,276,17" onmouseover="return overlib('CsgD transcriptional dual regulator activates transcription from associated promoter<br>The exact location of this binding site is unknown or not specified.');" onmouseout="return nd();">
 +
<area coords="238,18,280,35"  onmouseover="return overlib('RcsAB 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 [Vianney05]');" onmouseout="return nd();">
 +
<area coords="79,92,123,109" onmouseover="return overlib('OmpR-Phosphorylated transcriptional dual regulator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -47.5 (ranging from -38 to -57)<br><b>Evidence:</b> Binding of purified proteins [Jubelin05], Gene expression analysis [Jubelin05], Human inference based on similarity to consensus sequences [Jubelin05]');" onmouseout="return nd();">
 +
<area coords="87,38,135,55" onmouseover="return overlib('CRP-cAMP transcriptional dual regulator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -42.5 (ranging from -32 to -53)<br><b>Evidence:</b> Gene expression analysis [Zheng04], Automated inference based on similarity to consensus sequences [Zheng04]');" onmouseout="return nd();">
 +
<area coords="218,114,279,145" onmouseover="return overlib(' <b>Gene:</b>  csgD    G6546    b1040    ECK1026<br><b>Location:</b> 1,101,769 <- 1,102,419  <br> <b>Product:</b> CsgD transcriptional dual regulator');" onmouseout="return nd();">
 +
<area coords="279,114,340,145" onmouseover="return overlib(' <b>Gene:</b>  csgE    G6545    b1039    ECK1025<br><b>Location:</b> 1,101,375 <- 1,101,764  <br> <b>Product:</b> curli production assembly/transport component, subunit of Curli Secretion and Assembly Complex');" onmouseout="return nd();">
 +
<area coords="343,114,404,145" onmouseover="return overlib(' <b>Gene:</b>  csgF    G6544    b1038    ECK1024<br><b>Location:</b> 1,100,934 <- 1,101,350  <br> <b>Product:</b> curli assembly component, subunit of Curli Secretion and Assembly Complex');" onmouseout="return nd();">
 +
 +
<area coords="407,114,476,145" onmouseover="return overlib(' <b>Gene:</b>  csgG    G6543    b1037    ECK1023<br><b>Location:</b> 1,100,074 <- 1,100,907  <br> <b>Product:</b> curli production component, subunit of Curli Secretion and Assembly Complex');" onmouseout="return nd();">
 +
<area coords="121,0,280,162" onmouseover="return overlib('<b>Operon:</b> csgDp1 (Experim. ev.)  <BR><b>Tr.Activators:</b> (OmpR-P<SUP>asp</SUP> CsgD CRP-cAMP) <BR><b>Tr.Inhibitors:</b> (RstA-P<SUP>asp</SUP> RcsAB CpxR-P<SUP>asp</SUP>)');" onmouseout="return nd();">
 +
<area coords="0,0,478,162" onmouseover="return overlib('<b>Operon</b>: csgDEFG');" onmouseout="return nd();">
 +
</map>
 +
<img src="https://static.igem.org/mediawiki/2009/a/aa/Op6.gif" usemap="#MAP91787" border="0">
 +
</p>
 +
 +
</html>
 +
Line 316: Line 354:
-
<html>
 
-
 
-
 
-
 
-
<p class="ecoparagraph">
 
-
<map name="MAP91787">
 
-
<area coords="1,128,32,145" onmouseover="return overlib('CRP-cAMP transcriptional dual regulator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -170.5 (ranging from -160 to -181)<br><b>Evidence:</b> Gene expression analysis [Zheng04], Automated inference based on similarity to consensus sequences [Zheng04]');" onmouseout="return nd();">
 
-
<area coords="39,128,70,145"  onmouseover="return overlib('CpxR-Phosphorylated represses transcription from associated promoter<br><b>Distance to transcription start site:</b> -100.5 (ranging from -93 to -107)<br><b>Evidence:</b> Binding of purified proteins [Jubelin05], Gene expression analysis [Jubelin05], Human inference based on similarity to consensus sequences [Jubelin05]');" onmouseout="return nd();">
 
-
<area coords="135,128,166,145"  onmouseover="return overlib('CpxR-Phosphorylated represses transcription from associated promoter<br><b>Distance to transcription start site:</b> -20.5 (ranging from -13 to -27)<br><b>Evidence:</b> Binding of purified proteins [Jubelin05], Gene expression analysis [Jubelin05], Human inference based on similarity to consensus sequences [Jubelin05]');" onmouseout="return nd();">
 
-
<area coords="166,128,197,145"  onmouseover="return overlib('CpxR-Phosphorylated represses transcription from associated promoter<br><b>Distance to transcription start site:</b> 2.5 (ranging from 10 to -5)<br><b>Evidence:</b> Binding of purified proteins [Jubelin05], Gene expression analysis [Jubelin05], Human inference based on similarity to consensus sequences [Jubelin05]');" onmouseout="return nd();">
 
-
<area coords="79,74,110,91"  onmouseover="return overlib('RstA-Phosphorylated transcriptional regulator represses transcription from associated promoter<br><b>Distance to transcription start site:</b> -50.5 (ranging from -44 to -57)<br><b>Evidence:</b> Binding of purified proteins [Ogasawara07a], Gene expression analysis [Ogasawara07a], Human inference based on similarity to consensus sequences [Ogasawara07a]');" onmouseout="return nd();">
 
-
<area coords="74,128,109,145"  onmouseover="return overlib('CpxR-Phosphorylated represses transcription from associated promoter<br><b>Distance to transcription start site:</b> -52 (ranging from -45 to -59)<br><b>Evidence:</b> Binding of purified proteins [PrigentCom01], Gene expression analysis [PrigentCom01], Human inference based on similarity to consensus sequences [PrigentCom01]');" onmouseout="return nd();">
 
-
<area coords="76,110,111,127" onmouseover="return overlib('CpxR-Phosphorylated represses transcription from associated promoter<br><b>Distance to transcription start site:</b> -51 (ranging from -44 to -58)<br><b>Evidence:</b> Binding of purified proteins [Jubelin05], Gene expression analysis [Jubelin05], Human inference based on similarity to consensus sequences [Jubelin05]');" onmouseout="return nd();">
 
-
<area coords="81,56,116,73"  onmouseover="return overlib('CpxR-Phosphorylated represses transcription from associated promoter<br><b>Distance to transcription start site:</b> -48.5 (ranging from -41 to -55)<br><b>Evidence:</b> Binding of purified proteins [Jubelin05], Gene expression analysis [Jubelin05], Human inference based on similarity to consensus sequences [Jubelin05]');" onmouseout="return nd();">
 
-
<area coords="238,0,276,17" onmouseover="return overlib('CsgD transcriptional dual regulator activates transcription from associated promoter<br>The exact location of this binding site is unknown or not specified.');" onmouseout="return nd();">
 
-
<area coords="238,18,280,35"  onmouseover="return overlib('RcsAB 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 [Vianney05]');" onmouseout="return nd();">
 
-
<area coords="79,92,123,109" onmouseover="return overlib('OmpR-Phosphorylated transcriptional dual regulator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -47.5 (ranging from -38 to -57)<br><b>Evidence:</b> Binding of purified proteins [Jubelin05], Gene expression analysis [Jubelin05], Human inference based on similarity to consensus sequences [Jubelin05]');" onmouseout="return nd();">
 
-
<area coords="87,38,135,55" onmouseover="return overlib('CRP-cAMP transcriptional dual regulator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -42.5 (ranging from -32 to -53)<br><b>Evidence:</b> Gene expression analysis [Zheng04], Automated inference based on similarity to consensus sequences [Zheng04]');" onmouseout="return nd();">
 
-
<area coords="218,114,279,145" onmouseover="return overlib(' <b>Gene:</b>  csgD    G6546    b1040    ECK1026<br><b>Location:</b> 1,101,769 <- 1,102,419  <br> <b>Product:</b> CsgD transcriptional dual regulator');" onmouseout="return nd();">
 
-
<area coords="279,114,340,145" onmouseover="return overlib(' <b>Gene:</b>  csgE    G6545    b1039    ECK1025<br><b>Location:</b> 1,101,375 <- 1,101,764  <br> <b>Product:</b> curli production assembly/transport component, subunit of Curli Secretion and Assembly Complex');" onmouseout="return nd();">
 
-
<area coords="343,114,404,145" onmouseover="return overlib(' <b>Gene:</b>  csgF    G6544    b1038    ECK1024<br><b>Location:</b> 1,100,934 <- 1,101,350  <br> <b>Product:</b> curli assembly component, subunit of Curli Secretion and Assembly Complex');" onmouseout="return nd();">
 
-
 
-
<area coords="407,114,476,145" onmouseover="return overlib(' <b>Gene:</b>  csgG    G6543    b1037    ECK1023<br><b>Location:</b> 1,100,074 <- 1,100,907  <br> <b>Product:</b> curli production component, subunit of Curli Secretion and Assembly Complex');" onmouseout="return nd();">
 
-
<area coords="121,0,280,162" onmouseover="return overlib('<b>Operon:</b> csgDp1 (Experim. ev.)  <BR><b>Tr.Activators:</b> (OmpR-P<SUP>asp</SUP> CsgD CRP-cAMP) <BR><b>Tr.Inhibitors:</b> (RstA-P<SUP>asp</SUP> RcsAB CpxR-P<SUP>asp</SUP>)');" onmouseout="return nd();">
 
-
<area coords="0,0,478,162" onmouseover="return overlib('<b>Operon</b>: csgDEFG');" onmouseout="return nd();">
 
-
</map>
 
-
<img src="https://static.igem.org/mediawiki/2009/a/aa/Op6.gif" usemap="#MAP91787" border="0">
 
-
</p>
 
-
 
-
</html>
 

Revision as of 19:33, 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




Repression:




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"