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CsqR DNA-binding transcriptional repressor

Synonyms: CsqR-6-sulfo-D-quinovose, CsqR
Summary:
CsqR, formerly known as YihW and hypothesized to be a transcriptional regulator [5], functions as a repressor for genes of catabolism of sulfoquinovose (SQ), a hydrolysis product of sulfoquinovosyl diacylglycerol (SQDG) [4]. CsqR belongs to the DeoR family of transcription factors. It acts as a carbon source-dependent dual regulator involved in sustaining baseline growth in the absence of the lac operon [1]. CsqR is likely involved in regulation of lactose metabolism and functions either in a complementary or opposite manner to a global regulator of carbohydrate metabolism, cAMP-CRP, and functions as a sugar-dependent dual regulator [1]. CsqR is part of a cluster of genes involved in degradation of sulfoquinovose (SQ); see the |FRAME: PWY-7446| pathway. The activity of the CsqR transcriptional regulator is controlled by SQ and sulfoquinovosyl glycerol (SQG) during the exponential growth phase. Both SQ and SQG act as inducers for the yihUTS operon and yihV gene, and also for csqR expression [4]. Read more >


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
CsqR Functional   Apo [APPHINH], [HIFS], [IEP] [1], [2], [3], [4]
CsqR-6-sulfo-D-quinovose Non-Functional   Holo nd nd
Connectivity class: Local Regulator
Gene name: csqR
  Genome position: 4074669-4075454
  Length: 786 bp / 261 aa
Operon name: yihV-csqR
TU(s) encoding the TF:
Transcription unit        Promoter
yihW
csqRp
 
yihVp1


Regulon       
Regulated gene(s) csqR, yihS, yihT, yihU, yihV
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (4)
Transcription related (1)
repressor (1)
regulon (1)
detoxification (1)
Regulated operon(s) yihUTS, yihV-csqR
First gene in the operon(s) csqR, yihV, yihU
Simple and complex regulons CRP,CsqR
CsqR
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[CsqR,-](3)


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
  CsqR repressor csqRp Sigma70 nd nd csqR nd nd [BPP], [CV(GEA/GS)], [GEA], [GS] [4]
  CsqR repressor yihUp5 Sigma70 -11.0 -103.0 yihU, yihT, yihS
caccaattgtTTAAAAAGTGACGGCTGTCAATTTTTtgacgataaa
4073662 4073687 [BPP], [CV(GEA/GS)], [GEA], [GS] [4]
  CsqR repressor yihVp1 Sigma70 -38.0 -65.0 yihV, csqR
tttatcgtcaAAAAATTGACAGCCGTCACTTTTTAAacaattggtg
4073662 4073687 [BPP], [CV(GEA/GS)], [GEA], [GS] [4]


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


Evidence    

 [APPHINH] Assay of protein purified to homogeneity from its native host

 [HIFS] Human inference of function from sequence

 [IEP] Inferred from expression pattern

 [BPP] Binding of purified proteins

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

 [GEA] Gene expression analysis

 [GS] genomic SELEX



Reference(s)    

 [1] Kaznadzey A., Shelyakin P., Belousova E., Eremina A., Shvyreva U., Bykova D., Emelianenko V., Korosteleva A., Tutukina M., Gelfand MS., 2018, The genes of the sulphoquinovose catabolism in Escherichia coli are also associated with a previously unknown pathway of lactose degradation., Sci Rep 8(1):3177

 [2] 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

 [3] 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

 [4] Shimada T., Yamamoto K., Nakano M., Watanabe H., Schleheck D., Ishihama A., 2019, Regulatory role of CsqR (YihW) in transcription of the genes for catabolism of the anionic sugar sulfoquinovose (SQ) in Escherichia coli K-12., Microbiology 165(1):78-89

 [5] Denger K., Weiss M., Felux AK., Schneider A., Mayer C., Spiteller D., Huhn T., Cook AM., Schleheck D., 2014, Sulphoglycolysis in Escherichia coli K-12 closes a gap in the biogeochemical sulphur cycle., Nature 507(7490):114-7



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