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CecR DNA-binding transcriptional repressor

Synonyms: CecR
Summary:
CecR was confirmed as a TF through an integrated workflow comprised of computational prediction, knowledge-based classification, and experimental validation of candidate TFs at the genome scale [1]. CecR belongs to the TetR family of transcription factors, and because this family forms dimers under physiological conditions, it is proposed that the CecR transcription factor must have a dimeric form [7] The transcriptional factor binding sites (TFBSs) of CecR enclose AT-rich inverted repeats separated by 7 nt. This finding is consistent with structural predictions that this TF likely forms homodimers or tetramers which facilitate tight binding to DNA molecules in the cell [1]. Compared to known global TFs, CecR exhibits some interesting regulatory features. First, it has more intragenic binding peaks and fewer peaks located within putative regulatory regions. Second, it has fewer binding peaks than global TFs, such as CRP, Lrp, Fnr, and ArcA. Third, it binds to more genes with putative functions. Finally, its expression level is lower relative to that of the majority of global TFs [1]. CecR controls genes involved in the control of sensitivity to cefoperazone and chloramphenicol [5] CecR (Cefoperazone and chloramphenicol Regulator of sensitivity) [5] Read more >


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
CecR Functional   [AUPEINH], [HIFS], [IEP], [IPI] [1], [2], [3], [4], [5]
Evolutionary Family: TetR/AcrR
Connectivity class: Local Regulator
Gene name: cecR
  Genome position: 829972-830643
  Length: 672 bp / 223 aa
Operon name: cecR-ybhGFSR
TU(s) encoding the TF:
Transcription unit        Promoter
 
cecRp


Regulon       
Regulated gene(s) cecR, ybhF, ybhG, ybhR, ybhS
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
ABC superfamily, membrane component (2)
membrane (2)
Transcription related (1)
transcriptional level (1)
ABC superfamily ATP binding cytoplasmic component (1)
Regulated operon(s) cecR-ybhGFSR
First gene in the operon(s) cecR
Simple and complex regulons CecR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[CecR,-](1)


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
  CecR repressor cecRp Sigma70 2.5 -24.5 cecR, ybhG, ybhF, ybhS, ybhR
gagtcataatCTTAATCAATCATTTGATTAAgaatggactg
830658 830678 [APIORCISFBSCS], [BPP], [CV(GEA/GS)], [GEA], [GS] [5], [6]



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
  CecR activator rhlE nd nd 830658 830678 nd [APIORCISFBSCS], [BPP], [GEA], [GS] [5], [6]


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


Evidence    

 [AUPEINH] Assay of unpurified protein expressed in its native host

 [HIFS] Human inference of function from sequence

 [IEP] Inferred from expression pattern

 [IPI] Inferred from physical interaction

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [BPP] Binding of purified proteins

 [CV(GEA/GS)] cross validation(GEA/GS)

 [GEA] Gene expression analysis

 [GS] genomic SELEX



Reference(s)    

 [1] Gao Y., Yurkovich JT., Seo SW., Kabimoldayev I., Drager A., Chen K., Sastry AV., Fang X., Mih N., Yang L., Eichner J., Cho BK., Kim D., Palsson BO., 2018, Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655., Nucleic Acids Res 46(20):10682-10696

 [2] Griffith JM., Basting PJ., Bischof KM., Wrona EP., Kunka KS., Tancredi AC., Moore JP., Hyman MRL., Slonczewski JL., 2019, Experimental Evolution of Escherichia coli K-12 in the Presence of Proton Motive Force (PMF) Uncoupler Carbonyl Cyanide m -Chlorophenylhydrazone Selects for Mutations Affecting PMF-Driven Drug Efflux Pumps., Appl Environ Microbiol 85(5)

 [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

 [5] Yamanaka Y., Shimada T., Yamamoto K., Ishihama A., 2016, Transcription factor CecR (YbiH) regulates a set of genes affecting the sensitivity of Escherichia coli against cefoperazone and chloramphenicol., Microbiology 162(7):1253-64

 [6] Shimada T., Ogasawara H., Ishihama A., 2018, Single-target regulators form a minor group of transcription factors in Escherichia coli K-12., Nucleic Acids Res 46(8):3921-3936

 [7] Ramos JL, Martínez-Bueno M, Molina-Henares AJ, Terán W, Watanabe K, Zhang X, Gallegos MT, Brennan R, Tobes R, 2005, The TetR family of transcriptional repressors., Microbiol Mol Biol Rev, 2005 Jun



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