Team:Imperial College London/M2/genes

From 2009.igem.org

(Difference between revisions)

Revision as of 20:08, 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:

RcsB is able to heterodimerise with a second protein: RcsA. This complex is able to bind to and induce a number of operons. One of these operons codes for RcsA, this initiates a positive feedback loop.

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.]

References

Arifuzzama06: "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699

Boulanger05: Boulanger A, Francez-Charlot A, Conter A, Castanie-Cornet MP, Cam K, Gutierrez C (2005). "Multistress regulation in Escherichia coli: expression of osmB involves two independent promoters responding either to sigmaS or to the RcsCDB His-Asp phosphorelay." J Bacteriol 187(9);3282-6. PMID: 15838058

Brill88: Brill JA, Quinlan-Walshe C, Gottesman S (1988). "Fine-structure mapping and identification of two regulators of capsule synthesis in Escherichia coli K-12." J Bacteriol 1988;170(6);2599-611. PMID: 2836365

Carballes99: Carballes F, Bertrand C, Bouche JP, Cam K (1999). "Regulation of Escherichia coli cell division genes ftsA and ftsZ by the two-component system rcsC-rcsB." Mol Microbiol 1999;34(3);442-50. PMID: 10564486

CastanieCo06: Castanie-Cornet MP, Cam K, Jacq A (2006). "RcsF is an outer membrane lipoprotein involved in the RcsCDB phosphorelay signaling pathway in Escherichia coli." J Bacteriol 188(12);4264-70. PMID: 16740933

CastanieCo07: Castanie-Cornet MP, Treffandier H, Francez-Charlot A, Gutierrez C, Cam K (2007). "The glutamate-dependent acid resistance system in Escherichia coli: essential and dual role of the His-Asp phosphorelay RcsCDB/AF." Microbiology 153(Pt 1);238-46. PMID: 17185552

Chen01c: Chen MH, Takeda S, Yamada H, Ishii Y, Yamashino T, Mizuno T (2001). "Characterization of the RcsC-->YojN-->RcsB phosphorelay signaling pathway involved in capsular synthesis in Escherichia coli." Biosci Biotechnol Biochem 65(10);2364-7. PMID: 11758943

Corbett08: Corbett D, Roberts IS (2008). "Capsular polysaccharides in Escherichia coli." Adv Appl Microbiol 65;1-26. PMID: 19026860

DavalosGar01: Davalos-Garcia M, Conter A, Toesca I, Gutierrez C, Cam K (2001). "Regulation of osmC gene expression by the two-component system rcsB-rcsC in Escherichia coli." J Bacteriol 183(20);5870-6. PMID: 11566985

Dierksen96: Dierksen KP, Trempy JE (1996). "Identification of a second RcsA protein, a positive regulator of colanic acid capsular polysaccharide genes, in Escherichia coli." J Bacteriol 178(16);5053-6. PMID: 8759878

Dominguez01: Dominguez M, Torano A (2001). "Leishmania immune adherence reaction in vertebrates." Parasite Immunol 23(5);259-65. PMID: 11309136

Ebel99: Ebel W, Trempy JE (1999). "Escherichia coli RcsA, a positive activator of colanic acid capsular polysaccharide synthesis, functions to activate its own expression." J Bacteriol 1999;181(2);577-84. PMID: 9882673

Ferrieres07: Ferrieres L, Aslam SN, Cooper RM, Clarke DJ (2007). "The yjbEFGH locus in Escherichia coli K-12 is an operon encoding proteins involved in exopolysaccharide production." Microbiology 153(Pt 4);1070-80. PMID: 17379715

FrancezCha03: Francez-Charlot A, Laugel B, Van Gemert A, Dubarry N, Wiorowski F, Castani?-Cornet MP, Gutierrez C, Cam K (2003). "RcsCDB His-Asp phosphorelay system negatively regulates the flhDC operon in Escherichia coli." Mol Microbiol 49(3);823-32. PMID: 12864862

FrancezCha05: Francez-Charlot A, Castanie-Cornet MP, Gutierrez C, Cam K (2005). "Osmotic Regulation of the Escherichia coli bdm (Biofilm-Dependent Modulation) Gene by the RcsCDB His-Asp Phosphorelay." J Bacteriol 187(11);3873-7. PMID: 15901715

Fredericks06: Fredericks CE, Shibata S, Aizawa S, Reimann SA, Wolfe AJ (2006). "Acetyl phosphate-sensitive regulation of flagellar biogenesis and capsular biosynthesis depends on the Rcs phosphorelay." Mol Microbiol 61(3);734-47. PMID: 16776655

Gervais92: Gervais FG, Phoenix P, Drapeau GR (1992). "The rcsB gene, a positive regulator of colanic acid biosynthesis in Escherichia coli, is also an activator of ftsZ expression." J Bacteriol 1992;174(12);3964-71. PMID: 1597415

GOA00: GOA (2000). "Gene Ontology annotation based on Swiss-Prot keyword mapping."

GOA01: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

Gottesman85: Gottesman S, Trisler P, Torres-Cabassa A (1985). "Regulation of capsular polysaccharide synthesis in Escherichia coli K-12: characterization of three regulatory genes." J Bacteriol 162(3);1111-9. PMID: 3888955

Gottesman91: Gottesman S, Stout V (1991). "Regulation of capsular polysaccharide synthesis in Escherichia coli K12." Mol Microbiol 1991;5(7);1599-606. PMID: 1943696

Gupte97: Gupte G, Woodward C, Stout V (1997). "Isolation and characterization of rcsB mutations that affect colanic acid capsule synthesis in Escherichia coli K-12." J Bacteriol 1997;179(13);4328-35. PMID: 9209051

Hirakawa03: Hirakawa H, Nishino K, Hirata T, Yamaguchi A (2003). "Comprehensive studies of drug resistance mediated by overexpression of response regulators of two-component signal transduction systems in Escherichia coli." J Bacteriol 185(6);1851-6. PMID: 12618449

Huang06a: Huang YH, Ferrieres L, Clarke DJ (2006). "The role of the Rcs phosphorelay in Enterobacteriaceae." Res Microbiol 157(3);206-12. PMID: 16427772

Jayaratne93: Jayaratne P, Keenleyside WJ, MacLachlan PR, Dodgson C, Whitfield C (1993). "Characterization of rcsB and rcsC from Escherichia coli O9:K30:H12 and examination of the role of the rcs regulatory system in expression of group I capsular polysaccharides." J Bacteriol 1993;175(17);5384-94. PMID: 8366025

Kuo04: Kuo MS, Chen KP, Wu WF (2004). "Regulation of RcsA by the ClpYQ (HslUV) protease in Escherichia coli." Microbiology 150(Pt 2);437-46. PMID: 14766922

Lee03b: Lee YY, Chang CF, Kuo CL, Chen MC, Yu CH, Lin PI, Wu WF (2003). "Subunit oligomerization and substrate recognition of the Escherichia coli ClpYQ (HslUV) protease implicated by in vivo protein-protein interactions in the yeast two-hybrid system." J Bacteriol 185(8);2393-401. PMID: 12670962

Majdalani02: Majdalani N, Hernandez D, Gottesman S (2002). "Regulation and mode of action of the second small RNA activator of RpoS translation, RprA." Mol Microbiol 46(3);813-26. PMID: 12410838

Majdalani05: Majdalani N, Gottesman S (2005). "The Rcs phosphorelay: a complex signal transduction system." Annu Rev Microbiol 59;379-405. PMID: 16153174

Majdalani05b: Majdalani N, Heck M, Stout V, Gottesman S (2005). "Role of RcsF in signaling to the Rcs phosphorelay pathway in Escherichia coli." J Bacteriol 187(19);6770-8. PMID: 16166540

Mouslim03: Mouslim C, Latifi T, Groisman EA (2003). "Signal-dependent requirement for the co-activator protein RcsA in transcription of the RcsB-regulated ugd gene." J Biol Chem 278(50);50588-95. PMID: 14514676

Ogasawara07a: Ogasawara H, Hasegawa A, Kanda E, Miki T, Yamamoto K, Ishihama A (2007). "Genomic SELEX search for target promoters under the control of the PhoQP-RstBA signal relay cascade." J Bacteriol 189(13);4791-9. PMID: 17468243

Pao95: Pao GM, Saier MH (1995). "Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution." J Mol Evol 1995;40(2);136-54. PMID: 7699720

Parkinson92: Parkinson JS, Kofoid EC (1992). "Communication modules in bacterial signaling proteins." Annu Rev Genet 1992;26;71-112. PMID: 1482126

Parkinson93: Parkinson JS (1993). "Signal transduction schemes of bacteria." Cell 1993;73(5);857-71. PMID: 8098993

Sledjeski95: Sledjeski D, Gottesman S (1995). "A small RNA acts as an antisilencer of the H-NS-silenced rcsA gene of Escherichia coli." Proc Natl Acad Sci U S A 1995;92(6);2003-7. PMID: 7534408

Sledjeski96: Sledjeski DD, Gottesman S (1996). "Osmotic shock induction of capsule synthesis in Escherichia coli K-12." J Bacteriol 1996;178(4);1204-6. PMID: 8576059

Stock90: Stock JB, Stock AM, Mottonen JM (1990). "Signal transduction in bacteria." Nature 1990;344(6265);395-400. PMID: 2157156

Stout90: Stout V, Gottesman S (1990). "RcsB and RcsC: a two-component regulator of capsule synthesis in Escherichia coli." J Bacteriol 1990;172(2);659-69. PMID: 2404948

Stout91: Stout V, Torres-Cabassa A, Maurizi MR, Gutnick D, Gottesman S (1991). "RcsA, an unstable positive regulator of capsular polysaccharide synthesis." J Bacteriol 173(5);1738-47. PMID: 1999391

Stout94: Stout V "Regulation of capsule synthesis includes interactions of the RcsC/RcsB regulatory pair." Res Microbiol 1994;145(5-6);389-92. PMID: 7855424

Stout96: Stout V (1996). "Identification of the promoter region for the colanic acid polysaccharide biosynthetic genes in Escherichia coli K-12." J Bacteriol 178(14);4273-80. PMID: 8763957

TorresCaba87: Torres-Cabassa AS, Gottesman S (1987). "Capsule synthesis in Escherichia coli K-12 is regulated by proteolysis." J Bacteriol 169(3);981-9. PMID: 3029041

UniProt08: UniProt Consortium (2008). "UniProt version 14.6 released on 2008-12-16." Database.

Vianney05: Vianney A, Jubelin G, Renault S, Dorel C, Lejeune P, Lazzaroni JC (2005). "Escherichia coli tol and rcs genes participate in the complex network affecting curli synthesis." Microbiology 151(Pt 7);2487-97. PMID: 16000739

Wehland00: Wehland M, Bernhard F (2000). "The RcsAB box. Characterization of a new operator essential for the regulation of exopolysaccharide biosynthesis in enteric bacteria." J Biol Chem 2000;275(10);7013-20. PMID: 10702265

Report Errors or Provide Feedback
Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 37:D464-70 2009

@@ Line 386: / Line 386: @@
 {{Imperial/09/Division}}
-<html>
 <b>References</b>
@@ Line 398: / Line 397: @@
+<html>
 <hr>  <h3> <b>References</b>
 </h3>  <p class="ecoparagraph"> <a name="16606699"></a>
-  <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=16606699&amp;dopt=Abstract" class="CITATION-FRAME" onmouseover="return overlib('16606699');" onmouseout="return nd();">  <b>Arifuzzama06</b>:  Arifuzzaman M, Maeda M, Itoh A, Nishikata K, Takita C, Saito R, Ara T, Nakahigashi K, Huang HC, Hirai A, Tsuzuki K, Nakamura S, Altaf-Ul-Amin M, Oshima T, Baba T, Yamamoto N, Kawamura T, Ioka-Nakamichi T, Kitagawa M, Tomita M, Kanaya S, Wada C, Mori H (2006). "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699
+  <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=16606699&amp;dopt=Abstract" class="CITATION-FRAME" onmouseover="return overlib('16606699');" onmouseout="return nd();">  <b>Arifuzzama06</b>: "Large-scale identification of protein-protein interaction of Escherichia coli K-12." Genome Res 16(5);686-91. PMID: 16606699
 </a>  </p><p class="ecoparagraph"> <a name="15838058"></a>
   <a href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;db=PubMed&amp;list_uids=15838058&amp;dopt=Abstract" class="CITATION-FRAME" onmouseover="return overlib('15838058');" onmouseout="return nd();">  <b>Boulanger05</b>:  Boulanger A, Francez-Charlot A, Conter A, Castanie-Cornet MP, Cam K, Gutierrez C (2005). "Multistress regulation in Escherichia coli: expression of osmB involves two independent promoters responding either to sigmaS or to the RcsCDB His-Asp phosphorelay." J Bacteriol 187(9);3282-6. PMID: 15838058