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| * '''Description:''' regulation of a large regulon (more than 100 genes and operons) 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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| |-
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| |style="background:#ABCDEF;" align="center"| '''Essential''' || no
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| |-
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| |style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional pleiotropic repressor
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| |-
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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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| |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16170 codY]
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| |colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=CodY CodY]
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| |colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/subtipathways/search.php?enzyme=codY codY]'''
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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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| |style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16170 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16170 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16170 DNA_with_flanks]
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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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| |colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=codY_1690119_1690898_1 Expression at a glance]'''   {{PubMed|22383849}}<br/>[[Image:codY_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16170]]
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| |-
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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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| <br/><br/><br/><br/>
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| <br/><br/><br/><br/>
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| <br/><br/>
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|
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| = [[Categories]] containing this gene/protein =
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| {{SubtiWiki category|[[transcription factors and their control]]}},
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| {{SubtiWiki category|[[regulators of core metabolism]]}},
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| {{SubtiWiki category|[[phosphoproteins]]}}
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|
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| = This gene is a member of the following [[regulons]] =
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| {{SubtiWiki regulon|[[CodY regulon]]}}
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| =The [[CodY regulon]]=
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| =The gene=
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| === Basic information ===
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| * '''Locus tag:''' BSU16170
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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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| * the mutation suppresses the mucoid phenotype of ''[[motA]]'' or ''[[motB]]'' mutants due to loss of [[DegU]] phosphorylation and concomitant reduced expression of the ''[[capB]]-[[capC]]-[[capA]]-[[capE]]'' operon {{PubMed|24296669}}
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| * inactivation of ''[[codY]]'' suppresses the requirement of a ''[[relA]] [[sasA]] [[sasB]]'' triple mutant for branched chain amino acids, methionine and threonine {{PubMed|24163341}}
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| === Database entries ===
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| * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16170&redirect=T BSU16170]
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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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|
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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:''' codY family (according to Swiss-Prot)
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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]]:''' contains a GAF domain (ligand binding domain)
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| * '''Modification:''' phosphorylation on Ser-215 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
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| * '''[[Cofactors]]:'''
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| * '''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}}
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| * '''[[SubtInteract|Interactions]]:'''
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| ** active as dimer (according to {{PubMed|20408793}})
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| ** [[CcpA]]-[[CodY]] {{PubMed|22512862}}
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| ** [[RpoA]]-[[CodY]] {{PubMed|22512862}}
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| * '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)
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|
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| === Database entries ===
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| * '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16170&redirect=T BSU16170]
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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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| * '''UniProt:''' [http://www.uniprot.org/uniprot/P39779 P39779]
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| * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu: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:''' ''[[codV]]-[[clpQ]]-[[clpY]]-[[codY]]'' {{PubMed|7783641}}
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| * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=codY_1690119_1690898_1 codY] {{PubMed|22383849}}
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| * '''[[Sigma factor]]:''' [[SigA]] {{PubMed|7783641}}
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| * '''Regulation:'''
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| ** repressed during growth in the presence of branched chain amino acids ([[CodY]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/11331605 PubMed]
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| * '''Regulatory mechanism:'''
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| ** [[CodY]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/11331605 PubMed]
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| * '''Additional information:'''
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| ** the intracellular concentration of CodY is about 2.5 myM (according to {{PubMed|20408793}})
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| ** number of protein molecules per cell (minimal medium with glucose and ammonium): 955 {{PubMed|24696501}}
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| ** number of protein molecules per cell (complex medium with amino acids, without glucose): 3409 {{PubMed|24696501}}
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| ** number of protein molecules per cell (minimal medium with glucose and ammonium, exponential phase): 350 {{PubMed|21395229}}
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| ** number of protein molecules per cell (minimal medium with glucose and ammonium, early stationary phase after glucose exhaustion): 351 {{PubMed|21395229}}
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| ** number of protein molecules per cell (minimal medium with glucose and ammonium, late stationary phase after glucose exhaustion): 272 {{PubMed|21395229}}
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| =Biological materials =
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| * '''Mutant:'''
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| ** GP566, available in [[Jörg Stülke]]'s lab
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| ** a ''[[codY]]::erm'' mutant is available in [[Linc Sonenshein]]'s lab
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| ** a ''[[codY]]::spc'' (BB1043) mutant is available in [[Linc Sonenshein]]'s, [[Fabian Commichau]]'s and [[Jörg Stülke]]'s labs
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| * '''Expression vector:'''
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| ** for expression, purification in ''E. coli'' with N-terminal His-tag, in [[pWH844]]: pGP245, available in [[Jörg Stülke]]'s lab
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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, [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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| ==Reviews==
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| <pubmed>15802253, 17982469,20408793 24462007 </pubmed>
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|
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| ==The [[CodY regulon]]==
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| <pubmed>18083814,12618455, 23569278 24843172 </pubmed>
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| ==Original Publications==
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| <pubmed>19542274,17493123,18641142,19202088,16995897,17993518,9287005,11331605,17218307,19500589,12591885,19202088,11331605,15228537,8793880, 15937175,15916605,15916606,11331605,15228537 19749041 7783641 20935095 21097623 21699902 21764931 22981860 22512862,21856856 23911932 24296669 24163341 25157083 25645558 24682323 25666135</pubmed>
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| [[Category:Protein-coding genes]]
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