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RcdA DNA-binding transcriptional dual regulator

Synonyms: RcdA
Summary:
RcdA, also known as YbjK, belongs to the TetR family and is involved in the regulation of a number of stress response genes, biofilm formation, and transcription regulator genes [1]
Genomic SELEX analysis showed that RcdA can bind to the upstream regions of 27 genes. Among these predicted targets of RcdA, six genes correspond to transcription regulators (AppY, CsgD, FimB, RcdA, Sxy, and YcgF). This indicates that a large number of genes must be regulated indirectly by these regulators. Another group of target genes includes membrane-associated stress response proteins (CsgB, NanC, OmpA, PgaA, YbjJ, YehA, and YoeA) and stress response cytoplasmic proteins (Asr and YdeI), among others [1]
RcdA exhibits strong cooperative DNA binding and produces aggregates of RcdA-DNA complexes. In a specific way and with high binding affinity, this regulator recognizes and binds to sites that have closely related sequences. Furthermore, a consensus sequence has been proposed for RcdA sites. This consensus sequence shows a core binding site of 9 bp, TTGTgtACA, with inverted repeat symmetry [1] According to the analysis performed by the curator, the consensus sequence has a length of 10 bp (TTGTgtACAa).
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
RcdA     nd nd
Evolutionary Family: TetR/AcrR
Connectivity class: Local Regulator
Gene name: rcdA
  Genome position: 887423-887959
  Length: 537 bp / 178 aa
Operon name: rcdA
TU(s) encoding the TF:
Transcription unit        Promoter
rcdA
null


Regulon       
Regulated gene(s) asr, bluF, csgD, csgE, csgF, csgG, sulA, yagK, ydeI
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
pH (1)
posttranscriptional (1)
Transcription related (1)
activator (1)
repressor (1)
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Regulated operon(s) asr, bluF, csgDEFG, sulA, yagK, ydeI
First gene in the operon(s) asr, bluF, csgD, sulA, yagK, ydeI
Simple and complex regulons BasR,CRP,CpxR,Cra,CsgD,FliZ,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA
H-NS,PhoB,RcdA,RstA
LexA,RcdA
RcdA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[RcdA,-](2)
[RcdA,+](3)


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
  RcdA activator asrp Sigma38 -68.5 -117.5 asr
tttattcagcGTTTGTACATatcgttacac
1671254 1671263 [BPP], [GEA], [IC] [1]
  RcdA activator asrp Sigma38 -58.5 -107.5 asr
gtttgtacatATCGTTACACgctgaaacca
1671264 1671273 [BPP], [GEA], [IC] [1]
  RcdA activator bluFp Sigma70 -222.5 -253.5 bluF
aatagcaaacTTGTACGAAAtatgtgtaca
1215724 1215733 [BPP], [GEA], [HIBSCS] [1]
  RcdA activator bluFp Sigma70 -211.5 -242.5 bluF
tgtacgaaatATGTGTACAGaatgataaat
1215713 1215722 [BPP], [GEA], [HIBSCS] [1]
  RcdA activator csgDp1 Sigma38 -298.5 -446.5 csgD, csgE, csgF, csgG
gcgatatgtcTTGCGCACAAgccgtgacaa
1103638 1103647 [BPP], [GEA], [IC] [1]
  RcdA repressor sulAp Sigma70 33.5 4.5 sulA
tggattgattATGTACACTTcaggctatgc
1020910 1020919 [BPP], [GEA], [HIBSCS] [1]
  RcdA repressor sulAp Sigma70 47.5 18.5 sulA
acacttcaggCTATGCACATcgttcttcgt
1020896 1020905 [BPP], [GEA], [HIBSCS] [1]
  RcdA repressor yagKp6 Sigma70 3.5 -167.5 yagK
tataatggcaTTGTGTACTCttactacctg
293111 293120 [BPP] [1]
  RcdA activator ydeIp5 Sigma70 nd nd ydeI nd nd [BPP], [GEA] [1]


Alignment and PSSM for RcdA TFBSs    

Aligned TFBS of RcdA   
  Sequence
  AAGAGTACACAA
  GGCTATGCACAT
  AAGTGTACATAA
  GCTTGTGCGCAA
  ATGTGTACAGAA
  ACTTGTACGAAA
  GTTTGTACATAT
  GCGTGTAACGAT

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

PWM logo   


 


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


Evidence    

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IC] Inferred by curator

 [HIBSCS] Human inference based on similarity to consensus sequences



Reference(s)    

 [1] Shimada T., Katayama Y., Kawakita S., Ogasawara H., Nakano M., Yamamoto K., Ishihama A., 2012, A novel regulator RcdA of the csgD gene encoding the master regulator of biofilm formation in Escherichia coli., Microbiologyopen. 1(4):381-94



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