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RcsAB DNA-binding transcriptional dual regulator

Synonyms: RcsAB
Summary:
RcsB protein for "Regulator capsule synthesis B," is a response regulator that belongs to the multicomponent RcsF/RcsC/RcsD/RcsA-RcsB phosphorelay system [3, 12, 13, 14, 15, 16] and is involved in the regulation of the synthesis of colanic acid capsule, cell division, periplasmic proteins, motility, and a small RNA [4, 8, 14, 17, 18, 19, 20, 21, 22][1999391][7534408][8763957][12864862][16000739][16776655][19026860]|. The response regulator RcsB is the principal regulator of this system and it may form complexes with the RcsA auxiliary protein (forming a heterodimer) [2, 3, 8, 10, 11, 14, 18, 23], while RcsB activates the others genes independently (in the form of a homodimer) [14, 21, 24, 25, 26, 27, 28]. 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).
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
RcsAB Functional   [APPH], [GEA], [IGI] [1], [2], [3], [4], [5], [6], [7], [8]
Connectivity class: Local Regulator
Gene name: rcsA
  Genome position: 2023968-2024591
  Length: 624 bp / 207 aa
Operon name: rcsA
TU(s) encoding the TF:
Transcription unit        Promoter
rcsA
rcsAp
Gene name: rcsB
  Genome position: 2316177-2316827
  Length: 651 bp / 216 aa
Operon name: rcsDB
TU(s) encoding the TF:
Transcription unit        Promoter
rcsB
rcsBp1
rcsB
rcsBp2
rcsDB
rcsDp


Regulon       
Regulated gene(s) csgD, csgE, csgF, csgG, flhC, flhD, rcsA, wcaA, wcaB, wza, wzb, wzc, yjbE, yjbF, yjbG, yjbH
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
colanic acid (M antigen) (6)
Transcription related (4)
activator (4)
repressor (4)
biosynthesis of macromolecules (cellular constituents) (4)
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Regulated operon(s) csgDEFG, flhDC, rcsA, wza-wzb-wzc-wcaAB, yjbEFGH
First gene in the operon(s) csgD, flhD, rcsA, wza, yjbE, yjbE
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence LeftPos RightPos Evidence (Confirmed, Strong, Weak) References
  RcsAB repressor csgDp1 Sigma38, Sigma70 nd nd csgD, csgE, csgF, csgG nd nd [GEA] [7]
  RcsAB repressor flhDp Sigma70 11.0 -188.0 flhD, flhC
ttgcgtcgatTTAGGAAAAATCTTAgataagtgta
1978378 1978392 [BPP], [GEA], [SM] [2], [9]
  RcsAB activator rcsAp Sigma70 -172.0 -304.0 rcsA
ctgatattatTAGTGAATTGCCATTaatataattc
2023657 2023671 [AIBSCS], [GEA] [1]
  RcsAB activator rcsAp Sigma70 -125.0 -257.0 rcsA
catgttatccTAAGGATTATCCGAAaaataatacc
2023704 2023718 [BCE], [BPP], [SM] [8]
  RcsAB activator wzap Sigma70 -105.0 -445.0 wza, wzb, wzc, wcaA, wcaB
attgtcaaccTAAAGAAACTCCTAAaaaccatatt
2137681 2137695 [BPP], [SM] [3], [8], [10]
  RcsAB activator wzap Sigma70 -83.0 -423.0 wza, wzb, wzc, wcaA, wcaB
taaaaaccatATTGAATGACACTTAatataattct
2137659 2137673 [AIBSCS], [GEA] [1]
  RcsAB activator yjbEp1 Sigma70 -209.0 -257.0 yjbE, yjbF, yjbG, yjbH
aatcataccgTGAGGTTAATCCTAAaatagatttt
4235642 4235656 [GEA], [HIBSCS] [11]


Alignment and PSSM for RcsAB TFBSs    

Aligned TFBS of RcsAB   
  Sequence
  CTAAGGATTATCCGAAAA
  GTGAGGTTAATCCTAAAA
  CTAAAGAAACTCCTAAAA
  CTAAGATTTTTCCTAAAT
  TTAAGTGTCATTCAATAT
  TTAATGGCAATTCACTAA

Position weight matrix (PWM). RcsAB matrix-quality result   
A	0	0	5	6	1	1	2	1	3	4	0	0	0	2	5	4	6	4
C	3	0	0	0	0	0	0	1	1	1	0	4	6	0	1	0	0	0
G	1	0	1	0	4	4	2	0	0	0	0	0	0	1	0	0	0	0
T	2	6	0	0	1	1	2	4	2	1	6	2	0	3	0	2	0	2

Consensus   
;	consensus.strict             	cTaAGGgtaaTCCtaaAa
;	consensus.strict.rc          	TTTTAGGATTACCCTTAG
;	consensus.IUPAC              	yTaAGGdtwaTYCwawAw
;	consensus.IUPAC.rc           	WTWTWGRATWAHCCTTAR
;	consensus.regexp             	[ct]TaAGG[agt]t[at]aT[CT]C[at]a[at]A[at]
;	consensus.regexp.rc          	[AT]T[AT]T[AT]G[AG]AT[AT]A[ACT]CCTTA[AG]

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


Evidence    

 [APPH] Assay of protein purified to homogeneity

 [GEA] Gene expression analysis

 [IGI] Inferred from genetic interaction

 [BPP] Binding of purified proteins

 [SM] Site mutation

 [AIBSCS] Automated inference based on similarity to consensus sequences

 [BCE] Binding of cellular extracts

 [HIBSCS] Human inference based on similarity to consensus sequences



Reference(s)    

 [1] 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 181(2):577-84

 [2] 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

 [3] Gottesman S., Stout V., 1991, Regulation of capsular polysaccharide synthesis in Escherichia coli K12., Mol Microbiol 5(7):1599-606

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

 [5] Stout V., Gottesman S., 1990, RcsB and RcsC: a two-component regulator of capsule synthesis in Escherichia coli., J Bacteriol 172(2):659-69

 [6] 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

 [7] 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

 [8] 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 275(10):7013-20

 [9] Filippova EV., Zemaitaitis B., Aung T., Wolfe AJ., Anderson WF., 2018, Structural Basis for DNA Recognition by the Two-Component Response Regulator RcsB., MBio 9(1)

 [10] 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

 [11] 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

 [12] 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, 2001 Oct

 [13] 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

 [14] Majdalani N., Gottesman S., 2005, The Rcs phosphorelay: a complex signal transduction system., Annu Rev Microbiol 59:379-405

 [15] 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

 [16] Castanié-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, 2006 Jun

 [17] Huang YH., Ferrieres L., Clarke DJ., 2006, The role of the Rcs phosphorelay in Enterobacteriaceae., Res Microbiol 157(3):206-12

 [18] Stout V, 1994, Regulation of capsule synthesis includes interactions of the RcsC/RcsB regulatory pair., Res Microbiol, 1994 Jun-Aug

 [19] 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 175(17):5384-94

 [20] 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 Jun

 [21] 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 34(3):442-50

 [22] 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, 1985 Jun

 [23] 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

 [24] 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

 [25] 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

 [26] 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

 [27] 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

 [28] 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 Jun

 [29] 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

 [30] 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 179(13):4328-35

 [31] Thao S, Chen CS, Zhu H, Escalante-Semerena JC, 2010, N?-lysine acetylation of a bacterial transcription factor inhibits Its DNA-binding activity., PLoS One, 2010 Dec 31

 [32] 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 92(6):2003-7

 [33] Torres-Cabassa AS, Gottesman S, 1987, Capsule synthesis in Escherichia coli K-12 is regulated by proteolysis., J Bacteriol, 1987 Mar

 [34] 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, 1996 Aug

 [35] Kuo MS, Chen KP, Wu WF, 2004, Regulation of RcsA by the ClpYQ (HslUV) protease in Escherichia coli., Microbiology, 2004 Feb

 [36] 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



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