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| * '''Description:''' regulation of a large regulon in response to branched-chain amino acid limitation <br/><br/>
| | {{#bank: CodY}} |
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| {| align="right" border="1" cellpadding="2"
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| |style="background:#ABCDEF;" align="center"|'''Gene name'''
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| |''codY''
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| |-
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| |style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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| |style="background:#ABCDEF;" align="center"| '''Essential''' || no
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| |style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional pleiotropic repressor
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| |style="background:#ABCDEF;" align="center"|'''Function''' || regulation of a large regulon in response to
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| branched-chain amino acid limitation
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| to the presence of branched-chain amino acids
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| |-
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| |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 4.75
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| |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 777 bp, 259 aa
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| |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[clpY]]'', ''[[flgB]]''
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| |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB13490]+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
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| |colspan="2" | '''Genetic context''' <br/> [[Image:codY_context.gif]]
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| <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
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| |-
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| |}
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| __TOC__
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| <br/><br/><br/><br/>
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| =The gene=
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| === Basic information ===
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| * '''Coordinates:'''
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| ===Phenotypes of a mutant ===
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| No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
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| === Database entries ===
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| * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/codV-clpQY-codY.html]
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| * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10968]
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| === Additional information===
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| =The protein=
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| === Basic information/ Evolution ===
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| * '''Catalyzed reaction/ biological activity:'''
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| * '''Protein family:'''
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| * '''Paralogous protein(s):'''
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| === Genes/ operons controlled by CodY ===
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| === Extended information on the protein ===
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| * '''Kinetic information:'''
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| * '''Domains:'''
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| * '''Modification:''' phosphorylation on Ser-215 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
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| * '''Cofactor(s):'''
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| * '''Effectors of protein activity:'''
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| * '''Interactions:'''
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| * '''Localization:''' cytoplasm (according to Swiss-Prot)
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| === Database entries ===
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| * '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2B0L 2B0L] (C-terminal DNA-binding domain), [http://www.rcsb.org/pdb/explore.do?structureId=2GX5 2GX5] (N-terminal Gaf domain)
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| * '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39779 P39779]
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| * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16170 BSU16170]
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| * '''E.C. number:'''
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| === Additional information===
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| =Expression and regulation=
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| * '''Operon:'''
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| * '''[[Sigma factor]]:'''
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| * '''Regulation:'''
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| * '''Regulatory mechanism:'''
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| * '''Additional information:'''
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| =Biological materials =
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| * '''Mutant:'''
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| * '''Expression vector:'''
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| * '''lacZ fusion:'''
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| * '''GFP fusion:'''
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| * '''two-hybrid system:'''
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| * '''Antibody:'''
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| =Labs working on this gene/protein=
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| [[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
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| [[Tony Wilkinson]], York University, U.K. [http://www.york.ac.uk/depts/chem/staff/ajw.html homepage]
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| [[Oscar Kuipers]], University of Groningen, The Netherlands
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| [http://molgen.biol.rug.nl/molgen/index.php Homepage]
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| =Your additional remarks=
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| =References=
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| # Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium ''Bacillus subtilis''. Mol. Cell. Proteomics 6: 697-707 [http://www.ncbi.nlm.nih.gov/pubmed/17218307 PubMed]
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| # Kim, H. J., S. I. Kim, M. Ratnayake-Lecamwasam, K. Tachikawa, A. L. Sonenshein, and M. Strauch. (2003) Complex regulation of the Bacillus subtilis aconitase gene. J. Bacteriol. 185:1672-1680. [http://www.ncbi.nlm.nih.gov/sites/entrez/12591885 PubMed]
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| # Hamze et al. (2009) Identification of genes required for different stages of dendritic swarming in ''Bacillus subtilis'', with a novel role for ''phrC''. ''Microbiology'' '''155:''' 398-412. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
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| # Molle V, Nakura Y, Shivers RP, Yamaguchi H, Losick R, Fujita Y, Sonenshein AL: Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis. J Bacteriol 2003, 185:1911-1922. [http://www.ncbi.nlm.nih.gov/sites/entrez/12618455 PubMed]
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| # Sonenshein AL: CodY, a global regulator of stationary phase and virulence in Gram-positive bacteria. Curr Opin Microbiol 2005, 8:203-207. [http://www.ncbi.nlm.nih.gov/sites/entrez/15802253 PubMed]
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| # Ratnayake-Lecamwasam M, Serror P, Wong KW, Sonenshein AL: Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels. Genes Dev 2001, 15:1093-1103.[http://www.ncbi.nlm.nih.gov/sites/entrez/11331605 PubMed]
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| # Shivers RP, Sonenshein AL: Activation of the Bacillus subtilis global regulator CodY by direct interaction with branched-chain amino acids. Mol Microbiol 2004, 53:599-611. [http://www.ncbi.nlm.nih.gov/sites/entrez/15228537 PubMed]
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| # Serror P, Sonenshein AL: Interaction of CodY, the novel Bacillus subtilis DNA-binding protein, with the dpp promoter region. Mol Microbiol 1996, 20:843-852. [http://www.ncbi.nlm.nih.gov/sites/entrez/8793880 PubMed]
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| # Joseph P, Ratnayake-Lecamwasam M, Sonenshein AL: A region of Bacillus subtilis CodY protein required for interaction with DNA. J Bacteriol 2005, 187:4127-4139. [http://www.ncbi.nlm.nih.gov/sites/entrez/15937175 PubMed]
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| # Shivers RP, Sonenshein AL: Bacillus subtilis ilvB operon: an intersection of global regulons. Mol Microbiol 2005, 56:1549-1559. [http://www.ncbi.nlm.nih.gov/sites/entrez/15916605 PubMed]
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| # Tojo S, Satomura T, Morisaki K, Deutscher J, Hirooka K, Fujita Y: Elaborate transcription regulation of the Bacillus subtilis ilv-leu operon involved in the biosynthesis of branched-chain amino acids through global regulators of CcpA, CodY and TnrA. Mol Microbiol 2005, 56:1560-1573. [http://www.ncbi.nlm.nih.gov/sites/entrez/15916606 PubMed]
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| # Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
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