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RcsAB DNA-binding transcriptional dual regulator

Synonyms: RcsAB


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
RcsAB     nd nd
Evolutionary Family: LuxR/UhpA
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)
Read more >
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 regulons BasR,CRP,CpxR,Cra,CsgD,FliZ,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA
CRP,FliZ,Fur,H-NS,HdfR,IHF,LrhA,MatA,OmpR,QseB,RcsAB,YjjQ
GadE,H-NS,RcsAB
IHF,RcsAB
RcsAB
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)


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 nd nd csgD, csgE, csgF, csgG nd nd [GEA] [1]
  RcsAB repressor flhDp Sigma70 11.0 -188.0 flhD, flhC
ttgcgtcgatTTAGGAAAAATCTTAgataagtgta
1978378 1978392 [BPP], [GEA], [SM] [2]
  RcsAB activator rcsAp Sigma70 -172.0 -304.0 rcsA
ctgatattatTAGTGAATTGCCATTaatataattc
2023657 2023671 [AIBSCS], [GEA] [3]
  RcsAB activator rcsAp Sigma70 -125.0 -257.0 rcsA
catgttatccTAAGGATTATCCGAAaaataatacc
2023704 2023718 [BCE], [BPP], [SM] [4]
  RcsAB activator wzap Sigma70 -105.0 -445.0 wza, wzb, wzc, wcaA, wcaB
attgtcaaccTAAAGAAACTCCTAAaaaccatatt
2137681 2137695 [BPP], [SM] [4], [5], [6]
  RcsAB activator wzap Sigma70 -83.0 -423.0 wza, wzb, wzc, wcaA, wcaB
taaaaaccatATTGAATGACACTTAatataattct
2137659 2137673 [AIBSCS], [GEA] [3]
  RcsAB activator yjbEp1 Sigma70 -209.0 -257.0 yjbE, yjbF, yjbG, yjbH
aatcataccgTGAGGTTAATCCTAAaatagatttt
4235642 4235656 [GEA], [HIBSCS] [7]


Alignment and PSSM for RcsAB TFBSs    

Aligned TFBS of RcsAB   
  Sequence
  AGATTTTTCCTAAAT
  TGAATTGCCATTAAT
  AGGATTATCCGAAAA
  TGAATGACACTTAAT
  AAGAAACTCCTAAAA
  AGGTTAATCCTAAAA

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

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

 [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] 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

 [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] 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

 [4] 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

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

 [6] 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

 [7] 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



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