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RcdA DNA-binding transcriptional dual regulator

Synonyms: RcdA
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 [] 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 [] The R32 residue of RcdA plays an important role in the recognition of and binding to DNA [] 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

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)
posttranscriptional (2)
pH (1)
Transcription related (1)
activator (1)
repressor (1)
Read more >
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,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)

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
1671254 1671264 [BPP], [GEA], [IC] [2]
  RcdA activator asrp Sigma38, Sigma70 -58.5 -107.0 asr
1671264 1671274 [BPP], [GEA], [IC] [2]
  RcdA activator bluFp Sigma70 -222.5 -254.0 bluF
1215724 1215734 [BPP], [GEA], [HIBSCS] [2]
  RcdA activator bluFp Sigma70 -211.5 -243.0 bluF
1215713 1215723 [BPP], [GEA], [HIBSCS] [2]
  RcdA activator csgDp1 Sigma38, Sigma70 -298.5 -447.0 csgD, csgE, csgF, csgG
1103638 1103648 [BPP], [GEA], [IC] [2]
  RcdA repressor sulAp Sigma70 33.5 4.0 sulA
1020910 1020920 [BPP], [GEA], [HIBSCS] [2]
  RcdA repressor sulAp Sigma70 47.5 18.0 sulA
1020896 1020906 [BPP], [GEA], [HIBSCS] [2]
  RcdA repressor yagKp6 Sigma70 3.5 -168.0 yagK
293111 293121 [BPP] [2]
  RcdA activator ydeIp5 Sigma70 nd 1624497.0 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 Evidence (Confirmed, Strong, Weak) References
  RcdA activator rcdA nd nd 887393 887403 [AISGDTU] nd
  RcdA activator rcdA nd nd 887383 887393 [AISGDTU] nd
  RcdA repressor ybjJI nd nd 887393 887403 [ICWHO] nd
  RcdA repressor ybjJI nd nd 887383 887393 [ICWHO] nd
Other High-throughput regulatory interactions with weak evidence

Alignment and PSSM for RcdA TFBSs    

Aligned TFBS of RcdA   

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


 [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

 [AISGDTU] Automated inference that a single-gene directon is a transcription unit

 [ICWHO] Inferred computationally without human oversight


 [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