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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 [2] 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 [2] 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 [2] According to the analysis performed by the curator, the consensus sequence has a length of 10 bp (TTGTgtACAa). The X-ray structure of RcdA was determined at 2.55 A resolution [4] Atomic force microscopic observations of several aggregates of RcdA-DNA-forming filaments showed that the T46 residue of RcdA is apparently involved in this oligomerization mode [4] The R32 residue of RcdA plays an important role in the recognition of and binding to DNA [4] Read more >


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
RcdA Functional   [AIFS], [APPH], [IEP], [IMP] [1], [2]
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
ybjK
null


Regulon       
Regulated gene(s) asr, bluF, csgD, csgE, csgF, csgG, rmf, rsd, sulA, yagK, ydeI
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
posttranscriptional (2)
Transcription related (2)
pH (1)
activator (1)
repressor (1)
Read more >
Regulated operon(s) asr, bluF, csgDEFG, rmf, rsd, sulA, yagK, ydeI
First gene in the operon(s) asr, bluF, csgD, rmf, rsd, sulA, yagK, ydeI
Simple and complex regulons ArcA,CRP,McbR,RcdA,SdiA,SlyA,ppGpp
ArcA,McbR,RcdA,SdiA,SlyA
BasR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsB,RstA,ppGpp
H-NS,PhoB,RcdA,RstA
LexA,RcdA
Read more >
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[RcdA,-](2)
[RcdA,+](6)


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
  RcdA activator asrp Sigma38, Sigma70 -68.5 -117.0 asr
tttattcagcGTTTGTACATAtcgttacacg
1671254 1671264 [BPP], [GEA], [IC] [2]
  RcdA activator asrp Sigma38, Sigma70 -58.5 -107.0 asr
gtttgtacatATCGTTACACGctgaaaccaa
1671264 1671274 [BPP], [GEA], [IC] [2]
  RcdA activator bluFp Sigma70 -222.5 -254.0 bluF
caatagcaaaCTTGTACGAAAtatgtgtaca
1215724 1215734 [BPP], [GEA], [HIBSCS] [2]
  RcdA activator bluFp Sigma70 -211.5 -243.0 bluF
ttgtacgaaaTATGTGTACAGaatgataaat
1215713 1215723 [BPP], [GEA], [HIBSCS] [2]
  RcdA activator csgDp1 Sigma38, Sigma70 -298.5 -447.0 csgD, csgE, csgF, csgG
tgcgatatgtCTTGCGCACAAgccgtgacaa
1103638 1103648 [BPP], [GEA], [IC] [2]
  RcdA activator rmfp nd nd nd rmf nd nd [BPP], [GEA], [3]
  RcdA activator rsdp2 Sigma70 nd nd rsd nd nd [BPP], [GEA], [3]
  RcdA repressor sulAp Sigma70 33.5 4.0 sulA
ctggattgatTATGTACACTTcaggctatgc
1020910 1020920 [BPP], [GEA], [HIBSCS] [2]
  RcdA repressor sulAp Sigma70 47.5 18.0 sulA
tacacttcagGCTATGCACATcgttcttcgt
1020896 1020906 [BPP], [GEA], [HIBSCS] [2]
  RcdA repressor yagKp6 Sigma70 3.5 -168.0 yagK
atataatggcATTGTGTACTCttactacctg
293111 293121 [BPP] [2]
  RcdA activator ydeIp5 Sigma70 nd nd ydeI nd nd [BPP], [GEA] [2]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Growth Condition Evidence (Confirmed, Strong, Weak) References
  RcdA activator ybjK nd nd 887393 887403 nd [BPP], [GEA], [HIBSCS] [2]
  RcdA activator ybjK nd nd 887383 887393 nd [BPP], [GEA], [HIBSCS] [2]
  RcdA repressor nd nd nd 887393 887403 nd [BPP], [GEA], [HIBSCS] [2]
  RcdA repressor nd nd nd 887383 887393 nd [BPP], [GEA], [HIBSCS] [2]
Other High-throughput regulatory interactions with weak evidence


Alignment and PSSM for RcdA TFBSs    

Aligned TFBS of RcdA   
  Sequence
  ATGTGTACAGAATG
  ATGTACAAACGCTG
  ATGTGCATAGCCTG
  AAGAGTACACAATG
  TTGCGCACAAGCCG
  ATCGTTACACGCTG
  AAGTGTACATAATC
  TTGTACGAAATATG

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

Consensus   
;	consensus.strict             	atGtGcACAcgcTG
;	consensus.strict.rc          	CAGCGTGTGCACAT
;	consensus.IUPAC              	atGtGyACAsrmTG
;	consensus.IUPAC.rc           	CAKYSTGTRCACAT
;	consensus.regexp             	atGtG[ct]ACA[cg][ag][ac]TG
;	consensus.regexp.rc          	CA[GT][CT][CG]TGT[AG]CACAT

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    

 [AIFS] Automated inference of function from sequence

 [APPH] Assay of protein purified to homogeneity

 [IEP] Inferred from expression pattern

 [IMP] Inferred from mutant phenotype

 [BPP] Binding of purified proteins

 [GEA] Gene expression analysis

 [IC] Inferred by curator

 [HIBSCS] Human inference based on similarity to consensus sequences

 [GS] genomic SELEX



Reference(s)    

 [1] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [2] 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

 [3] Yoshida H., Shimada T., Ishihama A., null, Coordinated Hibernation of Transcriptional and Translational Apparatus during Growth Transition of Escherichia coli to Stationary Phase., mSystems 3(5)

 [4] Sugino H, Usui T, Shimada T, Nakano M, Ogasawara H, Ishihama A, Hirata A, 2017, A structural sketch of RcdA, a transcription factor controlling the master regulator of biofilm formation., FEBS Lett, 2017 Jul



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