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RacR DNA-binding transcriptional dual regulator

Synonyms: RacR
RacR is an essential transcriptional repressor for toxin genes ydaS and ydaT, and is thus critical for cell survival; these genes are adjacent to and encode proteins divergent from RacR [1, 2]. RacR's essentiality is based on keeping these toxins transcriptionally silent [1, 2]. RacR comprises a helix-turn-helix (HTH) motif and, based on the genomic context, racR and ydaS cooccur, suggesting a functional interaction between RacR and YdaST [2]. Deletion of the racR gene is lethal [2]. When RacR is overexpressed, growth is inhibited in E. coli strains JM83 or DH5 but not in strains BL21(DE3) or MG1655 [].

Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
RacR Functional   [AIFS], [APPHINH], [IEP], [IHBCE] [1], [2], [3], [4]
Connectivity class: Local Regulator
Gene name: racR
  Genome position: 1419765-1420241
  Length: 477 bp / 158 aa
Operon name: racR
TU(s) encoding the TF:
Transcription unit        Promoter

Regulated gene(s)
Regulated operon(s)
First gene in the operon(s)
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

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
  RacR repressor nd nd nd 1420295 1420310 nd [BPP], [GEA], [IHBCE] [1], [2]
  RacR repressor nd nd nd 1420270 1420281 nd [BPP], [GEA], [IHBCE] [1], [2]
  RacR repressor nd nd nd 1420321 1420336 nd [BPP], [GEA], [IHBCE] [1], [2]
  RacR repressor nd nd nd 1420218 1420224 nd [BPP], [GEA], [IHBCE] [1], [2]

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



 [1] Bindal G., Krishnamurthi R., Seshasayee ASN., Rath D., 2017, CRISPR-Cas-Mediated Gene Silencing Reveals RacR To Be a Negative Regulator of YdaS and YdaT Toxins in Escherichia coli K-12., mSphere 2(6)

 [2] Krishnamurthi R., Ghosh S., Khedkar S., Seshasayee ASN., 2017, Repression of YdaS Toxin Is Mediated by Transcriptional Repressor RacR in the Cryptic rac Prophage of Escherichia coli K-12., mSphere 2(6)

 [3] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [4] 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