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codY [Thu Oct 01 2015 13:51:44 GMT+0200 (CEST)]
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codY [Thu Oct 01 2015 13:51:44 GMT+0200 (CEST)]

regulation of a large regulon (more than 100 genes and operons) in response to branched-chain amino acid limitation
locus
BSU16170
pI
4.00
mw
28.00 kDa
function
regulation of a large regulon in response to branched-chain amino acid limitation
product
transcriptional pleiotropic repressor
essential
no
synonyms
Outlinks
KEGGBsubCycSubtiListUniProtExpression Browser

Genomic Context

      

categories

  • [category|SW 3|Information processing] → [category|SW 3.4|Regulation of gene expression] → [category|SW 3.4.2|Transcription factors and their control] → [category|SW 3.4.2.5|Transcription factors/ other]
  • [category|SW 3|Information processing] → [category|SW 3.4|Regulation of gene expression] → [category|SW 3.4.5|Regulators of core metabolism]
  • [category|SW 6|Groups of genes] → [category|SW 6.4|Phosphoproteins] → [category|SW 6.4.5|Phosphorylation on a Ser residue]

    • [SW|Categories] containing this gene/protein

  • [SW|transcription factors and their control], [SW|regulators of core metabolism], [SW|phosphoproteins]

    • This gene is a member of the following [SW|regulons]

  • [SW|CodY regulon]

    • Gene

    Coordinates on the chromosome (coding sequence)
    1,690,119 -> 1,690,898

    Phenotypes of a mutant

  • no swarming motility on B medium. [Pubmed|19202088]
  • the mutation suppresses the mucoid phenotype of ''[protein|search|motA]'' or ''[protein|search|motB]'' mutants due to loss of [protein|search|DegU] phosphorylation and concomitant reduced expression of the ''[protein|search|capB]-[protein|search|capC]-[protein|search|capA]-[protein|search|capE]'' operon [Pubmed|24296669]
  • inactivation of ''[protein|search|codY]'' suppresses the requirement of a ''[protein|search|relA] [protein|search|sasA] [protein|search|sasB]'' triple mutant for branched chain amino acids, methionine and threonine [Pubmed|24163341]

    • The protein

    Protein family

  • codY family (according to Swiss-Prot)

    • [SW|Domains]

  • contains a GAF domain (ligand binding domain)

    • Modification

  • phosphorylation on Ser-215 [Pubmed|17218307]

    • Effectors of protein activity

  • GTP and branched chained amino acids (BCAA) increase the affinity of CodY for its DNA target sequences [Pubmed|11331605,15228537,21856856]

    • Structure

  • [PDB|2B0L] (C-terminal DNA-binding domain), [PDB|2GX5] (N-terminal Gaf domain)

    • [SW|Localization]

  • cytoplasm (according to Swiss-Prot)

    • [SW|Interactions]

  • active as dimer (according to [Pubmed|20408793])
  • [protein|search|CcpA]-[protein|search|CodY] [Pubmed|22512862]
  • [protein|search|RpoA]-[protein|search|CodY] [Pubmed|22512862]

    • Expression and Regulation

    Operon

  • ''[protein|search|codV]-[protein|search|clpQ]-[protein|search|clpY]-[protein|search|codY]'' [Pubmed|7783641]

    • [SW|Sigma factor]

  • [protein|search|SigA] [Pubmed|7783641]

    • Regulation

  • repressed during growth in the presence of branched chain amino acids ([protein|search|CodY]) [Pubmed|11331605]

    • Regulatory mechanism

  • [protein|search|CodY]: transcription repression [Pubmed|11331605]

    • Additional information

  • the intracellular concentration of CodY is about 2.5 myM (according to [PubMed|20408793])

    • Biological materials

    Mutant

  • GP566, available in [SW|Jörg Stülke]'s lab
  • a ''[protein|search|codY]::erm'' mutant is available in [SW|Linc Sonenshein]'s lab
  • a ''[protein|search|codY]::spc'' (BB1043) mutant is available in [SW|Linc Sonenshein]'s, [SW|Fabian Commichau]'s and [SW|Jörg Stülke]'s labs
  • BKE16170 (''codY''::''erm trpC2'') is available from the [http://bgsc.org Bacillus Genetic Stock Center]

    • Expression vector

  • for expression, purification in ''E. coli'' with N-terminal His-tag, in [SW|pWH844]: pGP245, available in [SW|Jörg Stülke]'s lab

    • two-hybrid system

  • ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([SW|BACTH]), available in [SW|Fabian Commichau]'s lab

    • Labs working on this gene/protein

  • [SW|Linc Sonenshein], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
  • [SW|Tony Wilkinson], York University, U.K. [http://www.york.ac.uk/depts/chem/staff/ajw.html Homepage]
  • [SW|Oscar Kuipers], University of Groningen, The Netherlands, [http://molgen.biol.rug.nl/molgen/index.php Homepage]

    • References

    Reviews

  • 15802253,17982469,20408793,24462007

    • The [SW|CodY regulon]

  • 18083814,12618455,23569278,24843172

    • Original Publications

  • 19542274,17493123,18641142,19202088,16995897,17993518,9287005,11331605,17218307,19500589,12591885,19202088,11331605,15228537,8793880,26170408,15937175,15916605,15916606,11331605,15228537,19749041,7783641,20935095,21097623,21699902,21764931,22981860,22512862,21856856,23911932,24296669,24163341,25157083,25645558,24682323,25666135,25966844,26220295,26473603,26728191