Escherichia coli K-12 substr. MG1655 Polypeptide: positive DNA-binding transcriptional regulator of capsular polysaccharide synthesis, activates its own expression

Gene: rcsA Accession Numbers: EG10820 (EcoCyc), b1951, ECK1949

Synonyms: cpsR, positive regulator of capsular polysaccharide synthesis

Regulation Summary Diagram: ?

Regulation summary diagram for rcsA

Component of: RcsAB DNA-binding transcriptional dual regulator (extended summary available)

The binding site length comes from a single reference [Ebel99]. The amount of RcsA protein is limited both by its rapid degradation by Lon, an ATP-dependent protease, and by its low level of synthesis. RcsA is degraded in a Lon-dependent fashion. RcsA belongs to the LuxR/UhpA protein family.

Citations: [Stout90, Gottesman91, Sledjeski96]

Locations: cytosol

Map Position: [2,021,992 -> 2,022,615] (43.58 centisomes, 157°)
Length: 624 bp / 207 aa

Molecular Weight of Polypeptide: 23.516 kD (from nucleotide sequence)

pI: 9.21

Unification Links: ASAP:ABE-0006482 , CGSC:17980 , DIP:DIP-48090N , EchoBASE:EB0813 , EcoGene:EG10820 , EcoliWiki:b1951 , ModBase:P69405 , OU-Microarray:b1951 , PortEco:rcsA , PR:PRO_000023689 , Protein Model Portal:P0DMC9 , RefSeq:NP_416461 , RegulonDB:EG10820 , SMR:P69405 , String:511145.b1951 , UniProt:P0DMC9

Relationship Links: InterPro:IN-FAMILY:IPR000792 , InterPro:IN-FAMILY:IPR011991 , InterPro:IN-FAMILY:IPR016032 , Pfam:IN-FAMILY:PF00196 , Prints:IN-FAMILY:PR00038 , Prosite:IN-FAMILY:PS00622 , Prosite:IN-FAMILY:PS50043 , Smart:IN-FAMILY:SM00421

Reactions known to consume the compound:

RcsCDB Two-Component Signal Transduction System :
RcsA + RcsB → RcsAB

Gene-Reaction Schematic: ?

Gene-Reaction Schematic

Genetic Regulation Schematic: ?

Genetic regulation schematic for rcsA

GO Terms:

Biological Process: GO:0006351 - transcription, DNA-templated Inferred from experiment Inferred by computational analysis [UniProtGOA11a, Stout91, FrancezCharlot03, Wehland00, Vianney05, Ebel99]
GO:0006355 - regulation of transcription, DNA-templated Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0007165 - signal transduction Inferred by computational analysis [GOA06]
GO:0050896 - response to stimulus Inferred by computational analysis [UniProtGOA11a]
Molecular Function: GO:0003677 - DNA binding Inferred by computational analysis [UniProtGOA11a, GOA06, GOA01a]
GO:0003700 - sequence-specific DNA binding transcription factor activity Inferred by computational analysis [GOA01a]
GO:0004871 - signal transducer activity Inferred by computational analysis [GOA06]
Cellular Component: GO:0005829 - cytosol Inferred by computational analysis [DiazMejia09]

MultiFun Terms: cell structure surface antigens (ECA, O antigen of LPS)
information transfer RNA related Transcription related
metabolism biosynthesis of macromolecules (cellular constituents) colanic acid (M antigen)
metabolism biosynthesis of macromolecules (cellular constituents) K antigen
regulation genetic unit regulated operon
regulation type of regulation transcriptional level activator
regulation type of regulation transcriptional level repressor

Essentiality data for rcsA knockouts: ?

Growth Medium Growth? T (°C) O2 pH Osm/L Growth Observations
LB enriched Yes 37 Aerobic 6.95   Yes [Gerdes03, Comment 1]
LB Lennox Yes 37 Aerobic 7   Yes [Baba06, Comment 2]
M9 medium with 1% glycerol Yes 37 Aerobic 7.2 0.35 Yes [Joyce06, Comment 3]
MOPS medium with 0.4% glucose Yes 37 Aerobic 7.2 0.22 Yes [Baba06, Comment 2]

Subunit of: RcsAB DNA-binding transcriptional dual regulator

Synonyms: RcsAB

Subunit composition of RcsAB DNA-binding transcriptional dual regulator = [RcsB][RcsA]
         positive DNA-binding transcriptional regulator of capsular polysaccharide synthesis, activates its own expression = RcsA (summary available)

RcsB protein for "Regulator capsule synthesis B," is a response regulator that belongs to the multicomponent RcsF/RcsC/RcsD/RcsA-RcsB phosphorelay system [Chen01c, CastanieCornet07, Majdalani05, Majdalani05a, CastanieCornet06, Gottesman91] and is involved in the regulation of the synthesis of colanic acid capsule, cell division, periplasmic proteins, motility, and a small RNA [Huang06a, Majdalani05, Stout94, Jayaratne93, Brill88, Wehland00, Sledjeski96, Carballes99, Gottesman85, Stout91, Sledjeski95, Stout96, FrancezCharlot03, Vianney05, Fredericks06, Corbett08].

The response regulator RcsB is the principal regulator of this system and it may form complexes with the RcsA auxiliary protein (forming a heterodimer) [Gottesman91, Stout94, Wehland00, Stout96, Majdalani05, Ogasawara07a, FrancezCharlot03, Ferrieres07], while RcsB activates the others genes independently (in the form of a homodimer) [Majdalani05, DavalosGarcia01, FrancezCharlot05, Boulanger05, Carballes99, Majdalani02, Gervais92].

RcsC is a sensor histidine kinase and is known to be a transmembrane protein composed of three domains: the external sensory domain (amino terminal), a cytoplasmic transmitter domain (carboxyl terminal), and a transmembrane hydrophobic central domain (unknown function). RcsC is a membrane-bound protein that is able to sense extracellular changes in temperature, overexpression of membrane protein, and osmolarity [Mouslim03, Majdalani05, Sledjeski96]. RcsC is a hybrid kinase, contains both an H1 and D1 domain, and is able to transfer phosphoryl groups to the conserved Hpt domain of RcsD [Majdalani05, Huang06a, Majdalani05]. RcsC and RcsD are inner membrane proteins that are involved in the phosphorylation of RcsB in response to environmental signals [Majdalani05, Gupte97]. Once phosphorylated, the RcsB protein is a positive regulator and it increases the affinity for the specific DNA-binding sites and controls the transcriptional expression of operons [Wehland00, Stout94, Sledjeski96, Brill88, Carballes99, Majdalani05]. It is believed that RcsF protein may also be capable of phosphorylating RcsB.

Lys180 is a residue that is located within the predicted DNA-binding motif for RcsB transcriptional regulation. Nε-Lysine modulates through this residue the RcsB-dependent repression of the flhDC operon [Thao10].

The RcsB/RcsA complex has major affinity for binding sites of which RcsB is only one. The homodimers of RcsB activate transcription, interacting with the RNA polymerase, by overlapping the -35 box of the core promoter; the central position of the binding site is located near bp -41.5 [Majdalani05, DavalosGarcia01, FrancezCharlot05, Boulanger05, Carballes99, Majdalani02]. The formation of heterodimers between RcsB and the RcsA auxiliary protein stabilizes interactions with the distant binding sites [Wehland00, Stout96, Majdalani05, Ogasawara07a, FrancezCharlot03, Ferrieres07].

The amount of RcsA protein is limited both by its rapid degradation by two proteases, Lon and ClpYQ, and by its low level of synthesis [Majdalani05, Sledjeski95, Gottesman85, TorresCabassa87, Stout91, Dierksen96, Gottesman91, Kuo04, Lee03].

RcsB, which belongs to the two-component family, shows a helix-turn-helix motif for interaction with DNA in the C-terminal domain, while the the N-terminal domain is typical of the response regulator [Majdalani05].

Reviews:[Majdalani05, Huang06a].

Citations: [Stout90]

Reactions known to produce the compound:

RcsCDB Two-Component Signal Transduction System :
RcsA + RcsB → RcsAB

DNA binding site length: 15 base-pairs

Symmetry: Inverted Repeat

Consensus DNA Binding Sequence: TaaGGATaATCCTTA

Regulated Transcription Units (6 total): ?


Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Transcription-unit diagram

Sequence Features

Protein sequence of positive DNA-binding transcriptional regulator of capsular polysaccharide synthesis, activates its own expression with features indicated

Feature Class Location Citations Comment
Conserved-Region 131 -> 196
UniProt: HTH luxR-type;
Mutagenesis-Variant 145
[Stout91, UniProt15]
UniProt: In rcsA*; increases stability and capsule synthesis.
DNA-Binding-Region 155 -> 174
UniProt: H-T-H motif; Non-Experimental Qualifier: by similarity;

Gene Local Context (not to scale): ?

Gene local context diagram

Transcription Unit:

Transcription-unit diagram


10/20/97 Gene b1951 from Blattner lab Genbank (v. M52) entry merged into EcoCyc gene EG10820; confirmed by SwissProt match.


Baba06: Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko KA, Tomita M, Wanner BL, Mori H (2006). "Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection." Mol Syst Biol 2;2006.0008. PMID: 16738554

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

CastanieCornet06: 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

CastanieCornet07: 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

DavalosGarcia01: 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

DiazMejia09: Diaz-Mejia JJ, Babu M, Emili A (2009). "Computational and experimental approaches to chart the Escherichia coli cell-envelope-associated proteome and interactome." FEMS Microbiol Rev 33(1);66-97. PMID: 19054114

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

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

FrancezCharlot03: 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

FrancezCharlot05: 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

Gerdes03: Gerdes SY, Scholle MD, Campbell JW, Balazsi G, Ravasz E, Daugherty MD, Somera AL, Kyrpides NC, Anderson I, Gelfand MS, Bhattacharya A, Kapatral V, D'Souza M, Baev MV, Grechkin Y, Mseeh F, Fonstein MY, Overbeek R, Barabasi AL, Oltvai ZN, Osterman AL (2003). "Experimental determination and system level analysis of essential genes in Escherichia coli MG1655." J Bacteriol 185(19);5673-84. PMID: 13129938

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

GOA01a: GOA, DDB, FB, MGI, ZFIN (2001). "Gene Ontology annotation through association of InterPro records with GO terms."

GOA06: GOA, SIB (2006). "Electronic Gene Ontology annotations created by transferring manual GO annotations between orthologous microbial proteins."

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

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

Joyce06: Joyce AR, Reed JL, White A, Edwards R, Osterman A, Baba T, Mori H, Lesely SA, Palsson BO, Agarwalla S (2006). "Experimental and computational assessment of conditionally essential genes in Escherichia coli." J Bacteriol 188(23);8259-71. PMID: 17012394

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

Lee03: 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

Majdalani05a: 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

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 178(4);1204-6. PMID: 8576059

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

Thao10: Thao S, Chen CS, Zhu H, Escalante-Semerena JC (2010). "Nε-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity." PLoS One 5(12);e15123. PMID: 21217812

TorresCabassa87: 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

UniProt09: UniProt Consortium (2009). "UniProt version 15.8 released on 2009-10-01 00:00:00." Database.

UniProt10a: UniProt Consortium (2010). "UniProt version 2010-07 released on 2010-06-15 00:00:00." Database.

UniProt15: UniProt Consortium (2015). "UniProt version 2015-01 released on 2015-01-16 00:00:00." Database.

UniProtGOA11a: UniProt-GOA (2011). "Gene Ontology annotation based on manual assignment of UniProtKB keywords in UniProtKB/Swiss-Prot entries."

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

Other References Related to Gene Regulation

Ghosh09: Ghosh D, Roy K, Williamson KE, Srinivasiah S, Wommack KE, Radosevich M (2009). "Acyl-homoserine lactones can induce virus production in lysogenic bacteria: an alternative paradigm for prophage induction." Appl Environ Microbiol 75(22);7142-52. PMID: 19783745

Hommais04: Hommais F, Krin E, Coppee JY, Lacroix C, Yeramian E, Danchin A, Bertin P (2004). "GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli." Microbiology 150(Pt 1);61-72. PMID: 14702398

Kamenšek13: Kamenšek S, Žgur-Bertok D (2013). "Global transcriptional responses to the bacteriocin colicin M in Escherichia coli." BMC Microbiol 13;42. PMID: 23421615

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Please cite the following article in publications resulting from the use of EcoCyc: Nucleic Acids Research 41:D605-12 2013
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