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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 [3]. 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 [4] 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 [3]. 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 [3]. Based on wide-scale analyses, the conservation of the TetR-family transcriptional regulators (TFTRs) across two genera, Escherichia and Salmonella, were analyzed and compared on three levels: genus, species, and strain.
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
CecR Functional   nd nd nd
Evolutionary Family: TetR/AcrR
TFBs symmetry: inverted-repeat
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
cecR-ybhGFSR
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 Confidence level (C: Confirmed, S: Strong, W: Weak) References
  CecR repressor cecRp Sigma70 2.5 -24.5 cecR, ybhG, ybhF, ybhS, ybhR
gagtcataatCTTAATCAATCATTTGATTAAgaatggactg
 830658 830678 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [1], [2], [2]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  CecR activator rhlE Transcription-Unit nd
cagtccattcTTAATCAAATGATTGATTAAGattatgactc
830658 830678 830667.5 nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-GSELEX], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [1], [2]


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


Evidence    

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins


Reference(s)    

 [1] 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

 [2] 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

 [3] 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

 [4] 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, 69(2):326 10.1128/MMBR.69.2.326-356.2005

 [5] Colclough AL, Scadden J, Blair JMA, 2019, TetR-family transcription factors in Gram-negative bacteria: conservation, variation and implications for efflux-mediated antimicrobial resistance., BMC Genomics, 20(1):731 10.1186/s12864-019-6075-5


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