RegulonDB RegulonDB 11.1: Operon Form
   

chbBCARFG operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: chbBCARFG
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: chbBCARFG
Gene(s): chbG, chbF, chbR, chbA, chbC, chbB   Genome Browser M3D Gene expression COLOMBOS
Note(s): chbBCARFG is a cryptic operon Parker LL,1990involved in the catabolism of N,N'-diacetylchitobiose Keyhani NO,1997 A Cel+ phenotype was conferred by mutations which acted concertedly to alter the regulation of this operon Kachroo AH,2007
Plumbridge and Pelligrini (2004) proposed a model for chbBCARFG expression in which they mentioned that when the operon is repressed, NagC and ChbR sites are occupied, probably forming a complex structure involving an interaction between the two NagC proteins and formation of a DNA loop. It could be that cAMP/CRP is present in the complex. When the cell is grown on chitobiose, it generates the inducing signals for both ChbR and NagC. Transport of chitobiose produces chitobiose-6P. Its subsequent metabolism generates GlcNAc-6P, the inducer for NagC, which displaces NagC from its sites. The unidentified inducer for ChbR converts ChbR into an activator in the presence of cAMP/CAP and allows RNA polymerase to bind and transcribe the chb operon Plumbridge J,2004
Based on cells with plasmids and three inducible promoters of genes (matA, safA, and chbB), three novel fluorescent biosensors sensitive to terahertz (THz) radiation were developed, and they controlled the expression of a fluorescent protein Serdyukov DS, Goryachkovskaya TN, Mescheryakova IA, Bannikova SV, Kuznetsov SA, Cherkasova OP, Popik VM, Peltek SE,2020 The induction of these biosensors was manifested as fluorescent luminosity and reflected the activity of transcription units matA, safA-ydeO, and chbBCARFG, which contain the transcription factors MatA, YdeO, and ChbR, respectively Serdyukov DS, Goryachkovskaya TN, Mescheryakova IA, Bannikova SV, Kuznetsov SA, Cherkasova OP, Popik VM, Peltek SE,2020
Reference(s): [1] Keyhani NO., et al., 1997
[2] Reizer J., et al., 1990
Promoter
Name: chbBp
+1: 1821726
Distance from start of the gene: 107
Sequence: gaaacaatttataaggtcaaagaaatactattgctcaggtctataccgtatactcctttcAgccacaaaaaaagtcatgtt
Evidence: [EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [3] Plumbridge J., et al., 2004
TF binding sites (TFBSs)
[CRP,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CRP-cyclic-AMP activator chbBp 1821799 1821820 -83.5 tatttgcccgAAATGTGAAGAGGGTCATAACCacaggtcaag nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3], [4]
[ChbR,+] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ChbR-6-phospho-β-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine activator chbBp 1821755 1821773 -38.0 acaatttataAGGTCAAAGAAATACTATTgctcaggtct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
proximal ChbR-6-phospho-β-D-glucosaminyl-(1->4)-N-acetyl-D-glucosamine activator chbBp 1821778 1821796 -61.0 tcataaccacAGGTCAAGGAGAAACAATTtataaggtca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
[ChbR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal ChbR repressor chbBp 1821755 1821773 -38.0 acaatttataAGGTCAAAGAAATACTATTgctcaggtct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
proximal ChbR repressor chbBp 1821778 1821796 -61.0 tcataaccacAGGTCAAGGAGAAACAATTtataaggtca nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
[NagC,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal NagC repressor chbBp 1821715 1821737 1.0 tctataccgtATACTCCTTTCAGCCACAAAAAAagtcatgttg nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [3]
remote NagC repressor chbBp 1821827 1821849 -112.0 ggcctgagttCTTAATTATCTTCGCGAATTATTtgcccgaaat nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Translational
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -16.9 1819826 1819851 ttttaatcgaTGCCGGTACGGGTAATCGTGCCGGTaagaaaagag
  terminator -10.0 1821233 1821254 ataaatcaatACCGCAATATTTAAATTGCGGtttttaaggg
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

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

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

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

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Keyhani NO., Roseman S., 1997, Wild-type Escherichia coli grows on the chitin disaccharide, N,N'-diacetylchitobiose, by expressing the cel operon., Proc Natl Acad Sci U S A 94(26):14367-71

 [2] Reizer J., Reizer A., Saier MH., 1990, The cellobiose permease of Escherichia coli consists of three proteins and is homologous to the lactose permease of Staphylococcus aureus., Res Microbiol 141(9):1061-7

 [3] 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

 [4] Zheng D., Constantinidou C., Hobman JL., Minchin SD., 2004, Identification of the CRP regulon using in vitro and in vivo transcriptional profiling., Nucleic Acids Res 32(19):5874-93

 [5] Overgaard M., Johansen J., Moller-Jensen J., Valentin-Hansen P., 2009, Switching off small RNA regulation with trap-mRNA., Mol Microbiol 73(5):790-800

 [6] Plumbridge J., Bossi L., Oberto J., Wade JT., Figueroa-Bossi N., 2014, Interplay of transcriptional and small RNA-dependent control mechanisms regulates chitosugar uptake in Escherichia coli and Salmonella., Mol Microbiol 92(4):648-58

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