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RcsB DNA-binding transcriptional dual regulator

Synonyms: RcsB-Pasp56
Summary:
RcsB protein for "Regulator capsule synthesis B," is a response regulator that belongs to the multicomponent RcsF/RcsC/RcsD/RcsA-RcsB phosphorelay system [5, 14, 15, 16, 17, 18] and is involved in the regulation of the synthesis of colanic acid capsule, cell division, periplasmic proteins, motility, biofilm formation, and a small RNA [3, 15, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32]. The response regulator RcsB is the principal regulator of this system and is capable of forming complexes with the RcsA [15, 18, 20, 23, 28, 29, 33, 34, 35] and MatA, DctR, and BglJ proteins (forming a heterodimer) [35], while RcsB activates the others genes independently (in the form of a homodimer) [2, 3, 9, 10, 12, 15, 35, 36]. 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
RcsB-Pasp56 Functional Covalent Holo [GEA], [SM] [1]
Evolutionary Family: LuxR/UhpA
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
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) bdm, ftsA, ftsZ, gadA, gadB, gadC, gadX, gadY, hdeA, hdeB, hdeD, lolA, osmB, osmC, rarA, rpoE, rprA, rseA, rseB, rseC, rseD, safA, sra, ydeO, ydeP, yhiD
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
pH (6)
Transcription related (6)
membrane (4)
sigma factors, anti-sigmafactors (4)
other (mechanical, nutritional, oxidative stress) (4)
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Regulated operon(s) bdm-sra, gadAXW, gadBC, gadY, hdeAB-yhiD, hdeD, lolA-rarA, mraZ-rsmH-ftsLI-murEF-mraY-murD-ftsW-murGC-ddlB-ftsQAZ-lpxC, osmB, osmC, rprA, rseD-rpoE-rseABC, safA-ydeO, ydeP
First gene in the operon(s) bdm, ftsA, gadA, gadB, gadY, hdeA, hdeD, osmB, osmC, rseD, rprA, safA, ydeP, lolA
Simple and complex regulons AcrR,CRP,FliZ,Fur,H-NS,HdfR,IHF,LrhA,MatA,OmpR,QseB,RcsB,YjjQ
AdiY,ArcA,CRP,FNR,Fis,GadE,GadW,GadX,H-NS,RcsB,TorR,ppGpp
AdiY,CRP,Fis,FliZ,GadE,GadW,GadX,RcsB
BasR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsB,RstA,ppGpp
CRP,Fis,H-NS,LeuO,RcsB,StpA
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[RcsB,+](28)
[RcsB,-](3)


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
  RcsB-Pasp56 activator bdmp nd -41.5 -101.5 bdm, sra
aatcatcaacCAGGACTAATCTTAacaacgaagc
1556375 1556388 [BPP], [GEA] [2]
  RcsB-Pasp56 activator ftsAp1 Sigma70 -43.5 -464.5 ftsA, ftsZ
ctgatgaattGAAGATTCATCTGGttgaatatgt
103511 103524 [GEA], [HIBSCS], [SM] [3]
  RcsB-Pasp56 repressor gadAp Sigma38, Sigma70, Sigma38, Sigma70 -18.5 -45.5 gadA, gadX
tgcttccattGCGGATAAATCCTActtttttatt
3667619 3667632 [BPP], [GEA], [IHBCE], [SM] [4], [5], [6]
  RcsB-Pasp56 activator gadBp Sigma38, Sigma70, Sigma38, Sigma70 -64.5 -92.0 gadB, gadC
ataaataacaTTAGGATTTTGTTATttaaacacga
1572130 1572144 [GEA], [HIBSCS] [5], [7]
  RcsB-Pasp56 activator gadYp Sigma38 nd nd gadY nd nd [GEA] [7]
  RcsB-Pasp56 activator hdeAp Sigma38, Sigma70, Sigma70, Sigma38 nd nd hdeA, hdeB, yhiD nd nd [GEA] [7]
  RcsB-Pasp56 activator hdeDp Sigma38, Sigma70 nd nd hdeD nd nd [GEA] [7]
  RcsB-Pasp56 activator lolAp Sigma70 -43.5 -87.5 lolA, rarA
aactgaaaatTCAGTATTTTCTTCtttcctcaag
937278 937291 [GEA], [HIBSCS] [8]
  RcsB-Pasp56 activator osmBp1 Sigma38 -41.5 -189.5 osmB
ggttgataatTAAGACTATTTACCtgttattaac
1343511 1343524 [GEA], [HIBSCS] [9]
  RcsB-Pasp56 activator osmCp1 Sigma70 -41.5 -70.5 osmC
cggattttatTCGGAATATCCTGCttatcctcgt
1556548 1556561 [BPP], [GEA], [SM] [2], [10]
  RcsB-Pasp56 activator rpoEp2b Sigma70, Sigma54 -52.5 -227.5 rseD, rpoE, rseA, rseB, rseC
aatttactaaACATGGTTTGGTCAgcatagcatc
2710385 2710398 [BPP], [HIBSCS], [SM] [11]
  RcsB-Pasp56 activator rprAp nd -42.5 -42.5 rprA
tttaaactaaTGAGACGAATCTGAtcgacgcaaa
1770323 1770336 [GEA], [HIBSCS], [SM] [12]
  RcsB-Pasp56 activator safAp Sigma70 nd nd safA, ydeO nd nd [GEA] [7]
  RcsB-Pasp56 activator ydePp Sigma70 nd nd ydeP nd nd [BPP], [GEA] [7], [13]


Alignment and PSSM for RcsB TFBSs    

Aligned TFBS of RcsB   
  Sequence
  CTAAATGTATTCTGAAA
  CTTGATATATTCTGAAT
  ATAAATATTTTCTGAAA
  CTTTATATATTCTGAAT
  CTAAGGATTATCCGAAA
  CTAAGATTTTTCCTAAA
  CTTTATAAATTCCTAAA
  CTTTATAAATTCCTAAA
  ATAAATGATTTCTGAAA
  CTTTATGTTTTCCGAAT
  AGCAGGATATTCCGAAT
  CTAAAGAAACTCCTAAA
  CGAGTCATATTCTGAAA
  GTGAGGTTAATCCTAAA
  AGAAGAAAATACTGAAT
  GTAGGATTTATCCGCAA
  AATAACAAAATCCTAAT
  CCAGGACTAATCTTAAC
  AAAGGATATTTCAGAAA
  AGGTAAATAGTCTTAAT
  GCAGTCAGATTCTTAAA
  ACCAGATGAATCTTCAA
  ATTGAATGACACTTAAT
  ATGAGACGAATCTGATC
  CATGGTTTGGTCAGCAT
  ATTAGTGAATTGCCATT

Position weight matrix (PWM). RcsB matrix-quality result   
A	11	3	12	13	12	9	13	8	18	7	2	0	2	0	23	24	14
C	12	3	2	0	0	3	2	0	0	2	0	25	11	1	3	0	2
G	3	4	3	8	12	4	4	4	1	2	0	1	0	14	0	0	0
T	0	16	9	5	2	10	7	14	7	15	24	0	13	11	0	2	10

Consensus   
;	consensus.strict             	ctaagtatatTCcgAAa
;	consensus.strict.rc          	TTTCGGAATATACTTAG
;	consensus.IUPAC              	mtwrrwawatTCykAAw
;	consensus.IUPAC.rc           	WTTMRGAATWTWYYWAK
;	consensus.regexp             	[ac]t[at][ag][ag][at]a[at]atTC[ct][gt]AA[at]
;	consensus.regexp.rc          	[AT]TT[AC][AG]GAAT[AT]T[AT][CT][CT][AT]A[GT]

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    

 [GEA] Gene expression analysis

 [SM] Site mutation

 [BPP] Binding of purified proteins

 [HIBSCS] Human inference based on similarity to consensus sequences

 [IHBCE] Inferred by a human based on computational evidence



Reference(s)    

 [1] 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

 [2] 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

 [3] 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

 [4] Castanie-Cornet MP., Cam K., Bastiat B., Cros A., Bordes P., Gutierrez C., 2010, Acid stress response in Escherichia coli: mechanism of regulation of gadA transcription by RcsB and GadE., Nucleic Acids Res 38(11):3546-54

 [5] 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

 [6] Krin E., Danchin A., Soutourina O., 2010, RcsB plays a central role in H-NS-dependent regulation of motility and acid stress resistance in Escherichia coli., Res Microbiol 161(5):363-371

 [7] Johnson MD., Burton NA., Gutierrez B., Painter K., Lund PA., 2011, RcsB Is Required for Inducible Acid Resistance in Escherichia coli and Acts at gadE-Dependent and -Independent Promoters., J Bacteriol 193(14):3653-6

 [8] Tao K., Narita S., Tokuda H., 2012, Defective lipoprotein sorting induces lolA expression through the Rcs stress response phosphorelay system., J Bacteriol 194(14):3643-50

 [9] 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

 [10] 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

 [11] Klein G., Stupak A., Biernacka D., Wojtkiewicz P., Lindner B., Raina S., 2016, Multiple Transcriptional Factors Regulate Transcription of the rpoE Gene in Escherichia coli under Different Growth Conditions and When the Lipopolysaccharide Biosynthesis Is Defective., J Biol Chem 291(44):22999-23019

 [12] 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

 [13] Yoshida M., Ishihama A., Yamamoto K., 2015, Cross talk in promoter recognition between six NarL-family response regulators of Escherichia coli two-component system., Genes Cells 20(7):601-12

 [14] 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

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

 [16] 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

 [17] 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

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

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

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

 [21] 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

 [22] 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

 [23] 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

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

 [25] 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

 [26] 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

 [27] 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

 [28] 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

 [29] 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

 [30] 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

 [31] 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, 2006 Aug

 [32] Corbett D, Roberts IS, 2008, Capsular polysaccharides in Escherichia coli., Adv Appl Microbiol, 2008

 [33] 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

 [34] 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

 [35] Pannen D, Fabisch M, Gausling L, Schnetz K, 2016, Interaction of the RcsB Response Regulator with Auxiliary Transcription Regulators in Escherichia coli., J Biol Chem, 2016 Jan 29

 [36] 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

 [37] 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

 [38] Schmöe K, Rogov VV, Rogova NY, Löhr F, Güntert P, Bernhard F, Dötsch V, 2011, Structural insights into Rcs phosphotransfer: the newly identified RcsD-ABL domain enhances interaction with the response regulator RcsB., Structure, 2011 Apr 13

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

 [40] 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

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

 [42] 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

 [43] Ren G., Wang Z., Li Y., Hu X., Wang X., 2016, Effects of Lipopolysaccharide Core Sugar Deficiency on Colanic Acid Biosynthesis in Escherichia coli., J Bacteriol 198(11):1576-84

 [44] 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)

 [45] 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



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