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ChbR DNA-binding transcriptional dual regulator

Synonyms: ChbR-6-phospho-β-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine, ChbR
Summary:
"Chitobiose regulator," ChbR, is a dual transcriptional factor that regulates an operon (chb) involved in transport and degradation of the β-glucoside N,N'-diacetylchitobiose (chitobiose) [4, 5, 6]. ChbR is encoded within the chb operon itself. In the presence of chitobiose, ChbR binds to two direct repeats located between two NagC binding sites and activates the transcription of the chb operon by overlapping the -35 box of chbBp [1, 5]. In the absence of chitobiose, ChbR acts as a repressor of the chb operon [1, 5]. Monoacetylchitobiose-6-P has been experimentally determined to be the inducer for ChbR [7]. Parker et al. defined in 1990 the chb operon for a cellobiose degradation system as cryptic, because it requires a mutation in chbR for its activation [4, 5, 8].
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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
ChbR Functional   Apo nd nd nd
ChbR-6-phospho-β-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine Functional Allosteric Holo nd nd nd
Evolutionary Family: AraC/XylS
TFBs length: 19
TFBs symmetry: asymmetric
Sensing class: External sensing using transported metabolites
Connectivity class: Local Regulator
Gene name: chbR
  Genome position: 1818605-1819447
  Length: 843 bp / 280 aa
Operon name: chbBCARFG
TU(s) encoding the TF:
Transcription unit        Promoter
chbBCARFG
chbBp


Regulon       
Regulated gene(s) chbA, chbB, chbC, chbF, chbG, chbR
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
carbon compounds (5)
Phosphotransferase Systems (PEP-dependent PTS) (3)
membrane (1)
polysaccharides (1)
Transcription related (1)
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Regulated operon(s) chbBCARFG
First gene in the operon(s) chbB
Simple and complex regulons CRP,ChbR,NagC
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[ChbR,-](1)
[ChbR,+](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
  ChbR repressor chbBp nd -61.0 -168.0 chbB, chbC, chbA, chbR, chbF, chbG
tcataaccacAGGTCAAGGAGAAACAATTtataaggtca
 1821778 1821796 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [3]
  ChbR-6-phospho-β-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine activator chbBp nd -61.0 -168.0 chbB, chbC, chbA, chbR, chbF, chbG
tcataaccacAGGTCAAGGAGAAACAATTtataaggtca
 1821778 1821796 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [3]
  ChbR repressor chbBp nd -38.0 -145.0 chbB, chbC, chbA, chbR, chbF, chbG
acaatttataAGGTCAAAGAAATACTATTgctcaggtct
 1821755 1821773 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [3]
  ChbR-6-phospho-β-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine activator chbBp nd -38.0 -145.0 chbB, chbC, chbA, chbR, chbF, chbG
acaatttataAGGTCAAAGAAATACTATTgctcaggtct
 1821755 1821773 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1], [2], [3]


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

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

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


Reference(s)    

 [1] Plumbridge J., Pellegrini O., 2004, Expression of the chitobiose operon of Escherichia coli is regulated by three transcription factors: NagC, ChbR and CAP., Mol Microbiol 52(2):437-49

 [2] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [3] Kachroo AH., Kancherla AK., Singh NS., Varshney U., Mahadevan S., 2007, Mutations that alter the regulation of the chb operon of Escherichia coli allow utilization of cellobiose., Mol Microbiol 66(6):1382-95

 [4] Parker LL, Hall BG, 1990, Mechanisms of activation of the cryptic cel operon of Escherichia coli K12., Genetics, 124(3):473 10.1093/genetics/124.3.473

 [5] Parker LL., Hall BG., 1990, Characterization and nucleotide sequence of the cryptic cel operon of Escherichia coli K12., Genetics 124(3):455-71

 [6] Keyhani NO, Bacia K, Roseman S, 2000, The transport/phosphorylation of N,N'-diacetylchitobiose in Escherichia coli. Characterization of phospho-IIB(Chb) and of a potential transition state analogue in the phosphotransfer reaction between the proteins IIA(Chb) AND IIB(Chb)., J Biol Chem, 275(42):33102 10.1074/jbc.M001045200

 [7] Verma SC., Mahadevan S., 2012, The chbG Gene of the Chitobiose (chb) Operon of Escherichia coli Encodes a Chitooligosaccharide Deacetylase., J Bacteriol 194(18):4959-71

 [8] Gallegos MT., Schleif R., Bairoch A., Hofmann K., Ramos JL., 1997, Arac/XylS family of transcriptional regulators., Microbiol Mol Biol Rev 61(4):393-410


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