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DecR DNA-binding transcriptional dual regulator

Synonyms: DecR
Summary:
DecR 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 [2]. DecR is a regulator with an important role in cysteine detoxification. The absence of decR increases the inhibitory effect on bacterial growth caused by cysteine [5]. The presence of cysteine improves the interaction between DecR and the promoter region of the operon yhaOM, thereby causing activation [5]. Compared to known global TFs, DecR 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 [2]. DecR (YbaO) may have a role in Rob-mediated regulation [1].
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Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence (Confirmed, Strong, Weak) References
DecR Functional   [APPINH], [HIFS], [IEP], [IPI] [1], [2], [3], [4], [5]
Evolutionary Family: AsnC
Connectivity class: Local Regulator
Gene name: decR
  Genome position: 468383-468841
  Length: 459 bp / 152 aa
Operon name: decR
TU(s) encoding the TF:
Transcription unit        Promoter
decR
decRp


Regulon       
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 Center Position Growth Condition Evidence (Confirmed, Strong, Weak) References
  DecR activator nd tu nd
nd
nd nd nd nd [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    


Reference(s)    

 [1] Bennik MH., Pomposiello PJ., Thorne DF., Demple B., 2000, Defining a rob regulon in Escherichia coli by using transposon mutagenesis., J Bacteriol 182(13):3794-801

 [2] 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

 [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] Shimada T., Tanaka K., Ishihama A., 2016, Transcription factor DecR (YbaO) controls detoxification of L-cysteine in Escherichia coli., Microbiology 162(9):1698-1707

 [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] Loddeke M., Schneider B., Oguri T., Mehta I., Xuan Z., Reitzer L., 2017, Anaerobic Cysteine Degradation and Potential Metabolic Coordination in Salmonella enterica and Escherichia coli., J Bacteriol 199(16)



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