Team:Imperial College London/M2/genes

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Revision as of 19:39, 11 October 2009

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) The Rcs two-component system regulates expression of lysozyme inhibitors and is induced by exposure to lysozyme

2) Gene Expression Induced in Escherichia coli O157:H7 upon Exposure to Model Apple Juice

3) Structural and functional features of the Escherichia coli hydroperoxide resistance protein OsmC.

4) The Rcs phosphorelay: a complex signal transduction system.

@@ Line 21: / Line 21: @@
 ===<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();">
+<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="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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@@ Line 45: / Line 65: @@
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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();">
+<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();">
+<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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@@ Line 393: / Line 432: @@
 {{Imperial/09/Division}}
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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();">
-<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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 {{Imperial/09/Division}}
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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();">
-<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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 {{Imperial/09/Division}}