Team:Imperial College London/M2/genes

From 2009.igem.org

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(Colanic Acid Biosynthesis:)
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===<b>Signal Amplification:</b>===
===<b>Signal Amplification:</b>===
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<area coords="0,74,32,91" onmouseover="return overlib('RcsAB transcriptional dual regulator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -166.5 (ranging from -173 to -160)<br><b>Evidence:</b> Gene expression analysis [Ebel99], Automated inference based on similarity to consensus sequences [Ebel99]');" onmouseout="return nd();">
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<area coords="34,74,66,91" onmouseover="return overlib('RcsAB transcriptional dual regulator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -125.5 (ranging from -132 to -119)<br><b>Evidence:</b> Binding of cellular extracts, Site mutation [Wehland00], Binding of purified proteins [Wehland00]');" onmouseout="return nd();">
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<area coords="147,0,184,17" onmouseover="return overlib('GadE transcriptional activator activates transcription from associated promoter<br>The exact location of this binding site is unknown or not specified.<br><b>Evidence:</b> Binding of purified proteins [Hommais04], Gene expression analysis [Hommais04]');" onmouseout="return nd();">
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<area coords="104,60,165,91" onmouseover="return overlib(' <b>Gene:</b>  rcsA    EG10820    b1951    ECK1949<br><b>Synonyms:</b> cpsR<br><b>Location:</b> 2,021,992 -> 2,022,615  <br> <b>Product:</b> positive DNA-binding transcriptional regulator of capsular polysaccharide synthesis, activates its own expression, subunit of RcsAB transcriptional dual regulator');" onmouseout="return nd();">
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<area coords="24,0,184,108" onmouseover="return overlib('<b>Operon:</b> rcsAp (Experim. ev.)  <BR><b>Tr.Activators:</b> (GadE RcsAB) <BR><b>Tr.Inhibitors:</b> (Hns)');" onmouseout="return nd();">
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<img src="https://static.igem.org/mediawiki/2009/8/89/Op1.gif" usemap="#MAP79413" border="0">
<img src="https://static.igem.org/mediawiki/2009/8/89/Op1.gif" usemap="#MAP79413" border="0">
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<area coords="41,55,72,72" onmouseover="return overlib('IHF transcriptional dual regulator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -71 (ranging from -77 to -65)<br><b>Evidence:</b> Binding of purified proteins [Murtin98], Human inference based on similarity to consensus sequences [Murtin98]');" onmouseout="return nd();">
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<area coords="0,55,32,72" onmouseover="return overlib('RcsAB transcriptional dual regulator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -147.5 (ranging from -154 to -141)<br><b>Evidence:</b> Gene expression analysis [Ferrieres07], Human inference based on similarity to consensus sequences [Ferrieres07]');" onmouseout="return nd();">
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<area coords="98,41,137,72" onmouseover="return overlib(' <b>Gene:</b>  yjbE    EG11923    b4026    ECK4018<br><b>Location:</b> 4,233,929 -> 4,234,171  <br> <b>Product:</b> predicted protein');" onmouseout="return nd();">
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<area coords="154,41,247,72" onmouseover="return overlib(' <b>Gene:</b>  yjbF    EG11924    b4027    ECK4019<br><b>Location:</b> 4,234,285 -> 4,234,923  <br> <b>Product:</b> predicted lipoprotein');" onmouseout="return nd();">
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<area coords="246,41,353,72" onmouseover="return overlib(' <b>Gene:</b>  yjbG    EG11925    b4028    ECK4020<br><b>Location:</b> 4,234,920 -> 4,235,657  <br> <b>Product:</b> conserved protein');" onmouseout="return nd();">
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<area coords="352,41,640,72"  onmouseover="return overlib(' <b>Gene:</b>  yjbH    EG11926    b4029    ECK4021<br><b>Location:</b> 4,235,657 -> 4,237,753  <br> <b>Product:</b> predicted porin');" onmouseout="return nd();">
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<area coords="22,0,143,89" onmouseover="return overlib('<b>Operon:</b> yjbEp (No experim. ev.)  <BR><b>Tr.Activators:</b> (RcsAB IHF)');" onmouseout="return nd();">
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<area coords="0,0,642,89" onmouseover="return overlib('<b>Operon</b>: yjbEFGH');" onmouseout="return nd();">
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{{Imperial/09/Division}}
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<html>
 
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<p class="ecoparagraph">
 
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<map name="MAP91791">
 
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<area coords="147,18,177,35" 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<br>The nature of binding of this protein is not well known.');" onmouseout="return nd();">
 
-
<area coords="0,74,32,91" onmouseover="return overlib('RcsAB transcriptional dual regulator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -166.5 (ranging from -173 to -160)<br><b>Evidence:</b> Gene expression analysis [Ebel99], Automated inference based on similarity to consensus sequences [Ebel99]');" onmouseout="return nd();">
 
-
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-
<area coords="147,0,184,17" onmouseover="return overlib('GadE transcriptional activator activates transcription from associated promoter<br>The exact location of this binding site is unknown or not specified.<br><b>Evidence:</b> Binding of purified proteins [Hommais04], Gene expression analysis [Hommais04]');" onmouseout="return nd();">
 
-
<area coords="104,60,165,91" onmouseover="return overlib(' <b>Gene:</b>  rcsA    EG10820    b1951    ECK1949<br><b>Synonyms:</b> cpsR<br><b>Location:</b> 2,021,992 -> 2,022,615  <br> <b>Product:</b> positive DNA-binding transcriptional regulator of capsular polysaccharide synthesis, activates its own expression, subunit of RcsAB transcriptional dual regulator');" onmouseout="return nd();">
 
-
<area coords="24,0,184,108" onmouseover="return overlib('<b>Operon:</b> rcsAp (Experim. ev.)  <BR><b>Tr.Activators:</b> (GadE RcsAB) <BR><b>Tr.Inhibitors:</b> (Hns)');" onmouseout="return nd();">
 
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</p>
 
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{{Imperial/09/Division}}
{{Imperial/09/Division}}
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<html>
 
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</p><p class="ecoparagraph">
 
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<area coords="41,55,72,72" onmouseover="return overlib('IHF transcriptional dual regulator activates transcription from associated promoter<br><b>Distance to transcription start site:</b> -71 (ranging from -77 to -65)<br><b>Evidence:</b> Binding of purified proteins [Murtin98], Human inference based on similarity to consensus sequences [Murtin98]');" onmouseout="return nd();">
 
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<area coords="98,41,137,72" onmouseover="return overlib(' <b>Gene:</b>  yjbE    EG11923    b4026    ECK4018<br><b>Location:</b> 4,233,929 -> 4,234,171  <br> <b>Product:</b> predicted protein');" onmouseout="return nd();">
 
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<area coords="154,41,247,72" onmouseover="return overlib(' <b>Gene:</b>  yjbF    EG11924    b4027    ECK4019<br><b>Location:</b> 4,234,285 -> 4,234,923  <br> <b>Product:</b> predicted lipoprotein');" onmouseout="return nd();">
 
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<area coords="246,41,353,72" onmouseover="return overlib(' <b>Gene:</b>  yjbG    EG11925    b4028    ECK4020<br><b>Location:</b> 4,234,920 -> 4,235,657  <br> <b>Product:</b> conserved protein');" onmouseout="return nd();">
 
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<area coords="352,41,640,72"  onmouseover="return overlib(' <b>Gene:</b>  yjbH    EG11926    b4029    ECK4021<br><b>Location:</b> 4,235,657 -> 4,237,753  <br> <b>Product:</b> predicted porin');" onmouseout="return nd();">
 
-
<area coords="22,0,143,89" onmouseover="return overlib('<b>Operon:</b> yjbEp (No experim. ev.)  <BR><b>Tr.Activators:</b> (RcsAB IHF)');" onmouseout="return nd();">
 
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<area coords="0,0,642,89" onmouseover="return overlib('<b>Operon</b>: yjbEFGH');" onmouseout="return nd();">
 
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{{Imperial/09/Division}}
{{Imperial/09/Division}}

Revision as of 19:39, 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:



Signal Amplification:



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.]


























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