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RcsB DNA-binding transcriptional dual regulator

Synonyms: RcsB-Pasp56


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
RcsB-Pasp56     nd nd
Evolutionary Family: LuxR/UhpA
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: gadE
  Genome position: 3658366-3658893
  Length: 528 bp / 175 aa
Operon name: gadE-mdtEF
TU(s) encoding the TF:
Transcription unit        Promoter
gadE
gadEp1
gadE
gadEp3
gadE-mdtEF
gadEp
gadE-mdtEF
gadEp4
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) bdm, ftsA, ftsZ, gadA, gadB, gadC, gadX, gadY, hdeA, hdeB, hdeD, lolA, osmB, osmC, rarA, rprA, safA, sra, ydeO, ydeP, yhiD
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
pH (6)
membrane (3)
antisense RNA (3)
cell division (2)
Transcription related (2)
Read more >
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, safA-ydeO, ydeP
First gene in the operon(s) bdm, ftsA, gadA, gadB, gadY, hdeA, hdeD, lolA, osmB, osmC, rprA, safA, ydeP
Simple and complex regulons AdiY,ArcA,CRP,FNR,Fis,GadE-RcsB,GadW,GadX,H-NS,RcsB,TorR
AdiY,CRP,Fis,FliZ,GadE,GadW,GadX,RcsB
CpxR,RcsB
EvgA,H-NS,NagC,NarL,NarP,PhoP,RcsB,UvrY
EvgA,PhoP,RcsB,YdeO
Read more >
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[RcsB,-](2)
[RcsB-BglJ,+](23)


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] [1]
  RcsB-Pasp56 activator ftsAp1 Sigma70 -43.5 -464.5 ftsA, ftsZ
ctgatgaattGAAGATTCATCTGGttgaatatgt
103511 103524 [GEA], [HIBSCS], [SM] [2]
  RcsB-Pasp56 repressor gadAp Sigma38 -18.5 -45.5 gadA, gadX
tgcttccattGCGGATAAATCCTActtttttatt
3667619 3667632 [BPP], [GEA], [IHBCE], [SM] [3], [4], [5]
  RcsB-Pasp56 activator gadBp Sigma38 -64.5 -91.5 gadB, gadC
taaataacatTAGGATTTTGTTATttaaacacga
1572130 1572143 [GEA], [HIBSCS] [4], [6]
  RcsB-Pasp56 activator gadYp Sigma38 nd nd gadY nd nd [GEA] [6]
  RcsB-Pasp56 activator hdeAp Sigma38 nd nd hdeA, hdeB, yhiD nd nd [GEA] [6]
  RcsB-Pasp56 activator hdeDp Sigma70 nd nd hdeD nd nd [GEA] [6]
  RcsB-Pasp56 activator lolAp Sigma70 -43.5 -87.5 lolA, rarA
aactgaaaatTCAGTATTTTCTTCtttcctcaag
937278 937291 [GEA], [HIBSCS] [7]
  RcsB-Pasp56 activator osmBp1 Sigma38 -41.5 -189.5 osmB
ggttgataatTAAGACTATTTACCtgttattaac
1343511 1343524 [GEA], [HIBSCS] [8]
  RcsB-Pasp56 activator osmCp1 Sigma70 -41.5 -70.5 osmC
cggattttatTCGGAATATCCTGCttatcctcgt
1556548 1556561 [BPP], [GEA], [SM] [1], [9]
  RcsB-Pasp56 activator rprAp nd -42.5 -42.5 rprA
tttaaactaaTGAGACGAATCTGAtcgacgcaaa
1770323 1770336 [GEA], [HIBSCS], [SM] [10]
  RcsB-Pasp56 activator safAp Sigma70 nd nd safA, ydeO nd nd [GEA] [6]
  RcsB-Pasp56 activator ydePp Sigma70 nd nd ydeP nd nd [BPP], [GEA] [6], [11]


Alignment and PSSM for RcsB TFBSs    

Aligned TFBS of RcsB   
  Sequence
  AACCAGATGAATCT
  ATTCAGTATTTTCT
  ATTAAGACTATTTA
  ACCAGGACTAATCT
  ATTCGGAATATCCT
  ATTAGGATTTTGTT
  AATGAGACGAATCT
  AGTAGGATTTATCC

Position weight matrix (PWM).   
A	8	2	0	4	4	0	7	2	0	5	4	0	0	1
C	0	1	2	3	0	0	0	3	0	0	0	1	6	1
G	0	1	0	1	4	8	0	0	2	0	0	1	0	0
T	0	4	6	0	0	0	1	3	6	3	4	6	2	6

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    

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [HIBSCS] Human inference based on similarity to consensus sequences

 [SM] Site mutation

 [IHBCE] Inferred by a human based on computational evidence



Reference(s)    

 [1] 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

 [2] 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

 [3] 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

 [4] 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

 [5] 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

 [6] 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

 [7] 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

 [8] 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

 [9] 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

 [10] 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

 [11] 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



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