Difference between revisions of "CodY"
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| − | * '''Description:''' regulation of a large regulon in response to branched-chain amino acid limitation <br/><br/> | + | * '''Description:''' regulation of a large regulon (more than 100 genes and operons) in response to branched-chain amino acid limitation <br/><br/> |
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=== Additional information=== | === Additional information=== | ||
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=The protein= | =The protein= | ||
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<pubmed>18083814,12618455, </pubmed> | <pubmed>18083814,12618455, </pubmed> | ||
==Original Publications== | ==Original Publications== | ||
| − | <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 </pubmed> | + | <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 </pubmed> |
[[Category:Protein-coding genes]] | [[Category:Protein-coding genes]] | ||
Revision as of 10:28, 28 June 2011
- Description: regulation of a large regulon (more than 100 genes and operons) in response to branched-chain amino acid limitation
| Gene name | codY |
| Synonyms | |
| Essential | no |
| Product | transcriptional pleiotropic repressor |
| Function | regulation of a large regulon in response to
branched-chain amino acid limitation to the presence of branched-chain amino acids |
| Metabolic function and regulation of this protein in SubtiPathways: Alternative nitrogen sources, Lipid synthesis, Protein secretion | |
| MW, pI | 28 kDa, 4.75 |
| Gene length, protein length | 777 bp, 259 aa |
| Immediate neighbours | clpY, flgB |
| Get the DNA and protein sequences (Barbe et al., 2009) | |
Genetic context 
This image was kindly provided by SubtiList
| |
Contents
Categories containing this gene/protein
transcription factors and their control, regulators of core metabolism, phosphoproteins
This gene is a member of the following regulons
The CodY regulon
The gene
Basic information
- Locus tag: BSU16170
Phenotypes of a mutant
No swarming motility on B medium. PubMed
Database entries
- DBTBS entry: [1]
- SubtiList entry: [2]
Additional information
The protein
Basic information/ Evolution
- Catalyzed reaction/ biological activity:
- Protein family: codY family (according to Swiss-Prot)
- Paralogous protein(s):
Genes/ operons controlled by CodY
Extended information on the protein
- Kinetic information:
- Domains: contains a GAF domain (ligand binding domain)
- Modification: phosphorylation on Ser-215 PubMed
- Cofactor(s):
- Effectors of protein activity: GTP and branched chained amino acids (BCAA) increase the affinity of CodY for its DNA target sequences PubMed
- Interactions: active as dimer (according to PubMed)
- Localization: cytoplasm (according to Swiss-Prot)
Database entries
- UniProt: P39779
- KEGG entry: [3]
- E.C. number:
Additional information
Expression and regulation
- Additional information:
- the intracellular concentration of CodY is about 2.5 myM (according to PubMed)
Biological materials
- Mutant: GP566, available in Stülke lab
- Expression vector:
- lacZ fusion:
- GFP fusion:
- two-hybrid system:
- Antibody:
Labs working on this gene/protein
Linc Sonenshein, Tufts University, Boston, MA, USA Homepage
Tony Wilkinson, York University, U.K. homepage
Oscar Kuipers, University of Groningen, The Netherlands Homepage
Your additional remarks
References
Reviews
The CodY regulon
Boris R Belitsky, Abraham L Sonenshein
Genetic and biochemical analysis of CodY-binding sites in Bacillus subtilis.
J Bacteriol: 2008, 190(4);1224-36
[PubMed:18083814]
[WorldCat.org]
[DOI]
(I p)
Virginie Molle, Yoshiko Nakaura, Robert P Shivers, Hirotake Yamaguchi, Richard Losick, Yasutaro Fujita, Abraham L Sonenshein
Additional targets of the Bacillus subtilis global regulator CodY identified by chromatin immunoprecipitation and genome-wide transcript analysis.
J Bacteriol: 2003, 185(6);1911-22
[PubMed:12618455]
[WorldCat.org]
[DOI]
(P p)
Original Publications
Boris R Belitsky, Abraham L Sonenshein
Roadblock repression of transcription by Bacillus subtilis CodY.
J Mol Biol: 2011, 411(4);729-43
[PubMed:21699902]
[WorldCat.org]
[DOI]
(I p)
Boris R Belitsky, Abraham L Sonenshein
Contributions of multiple binding sites and effector-independent binding to CodY-mediated regulation in Bacillus subtilis.
J Bacteriol: 2011, 193(2);473-84
[PubMed:21097623]
[WorldCat.org]
[DOI]
(I p)
Shaun R Brinsmade, Roelco J Kleijn, Uwe Sauer, Abraham L Sonenshein
Regulation of CodY activity through modulation of intracellular branched-chain amino acid pools.
J Bacteriol: 2010, 192(24);6357-68
[PubMed:20935095]
[WorldCat.org]
[DOI]
(I p)
Anuradha C Villapakkam, Luke D Handke, Boris R Belitsky, Vladimir M Levdikov, Anthony J Wilkinson, Abraham L Sonenshein
Genetic and biochemical analysis of the interaction of Bacillus subtilis CodY with branched-chain amino acids.
J Bacteriol: 2009, 191(22);6865-76
[PubMed:19749041]
[WorldCat.org]
[DOI]
(I p)
Heike Preis, Rita A Eckart, Rajani K Gudipati, Nadja Heidrich, Sabine Brantl
CodY activates transcription of a small RNA in Bacillus subtilis.
J Bacteriol: 2009, 191(17);5446-57
[PubMed:19542274]
[WorldCat.org]
[DOI]
(I p)
Vladimir M Levdikov, Elena Blagova, Vicki L Colledge, Andrey A Lebedev, David C Williamson, Abraham L Sonenshein, Anthony J Wilkinson
Structural rearrangement accompanying ligand binding in the GAF domain of CodY from Bacillus subtilis.
J Mol Biol: 2009, 390(5);1007-18
[PubMed:19500589]
[WorldCat.org]
[DOI]
(I p)
Kassem Hamze, Daria Julkowska, Sabine Autret, Krzysztof Hinc, Krzysztofa Nagorska, Agnieszka Sekowska, I Barry Holland, Simone J Séror
Identification of genes required for different stages of dendritic swarming in Bacillus subtilis, with a novel role for phrC.
Microbiology (Reading): 2009, 155(Pt 2);398-412
[PubMed:19202088]
[WorldCat.org]
[DOI]
(P p)
Shigeo Tojo, Takenori Satomura, Kanako Kumamoto, Kazutake Hirooka, Yasutaro Fujita
Molecular mechanisms underlying the positive stringent response of the Bacillus subtilis ilv-leu operon, involved in the biosynthesis of branched-chain amino acids.
J Bacteriol: 2008, 190(18);6134-47
[PubMed:18641142]
[WorldCat.org]
[DOI]
(I p)
Luke D Handke, Robert P Shivers, Abraham L Sonenshein
Interaction of Bacillus subtilis CodY with GTP.
J Bacteriol: 2008, 190(3);798-806
[PubMed:17993518]
[WorldCat.org]
[DOI]
(I p)
Wiep Klaas Smits, Tran Thu Hoa, Leendert W Hamoen, Oscar P Kuipers, David Dubnau
Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein.
Mol Microbiol: 2007, 64(2);368-81
[PubMed:17493123]
[WorldCat.org]
[DOI]
(P p)
Boris Macek, Ivan Mijakovic, Jesper V Olsen, Florian Gnad, Chanchal Kumar, Peter R Jensen, Matthias Mann
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis.
Mol Cell Proteomics: 2007, 6(4);697-707
[PubMed:17218307]
[WorldCat.org]
[DOI]
(P p)
Robert P Shivers, Sean S Dineen, Abraham L Sonenshein
Positive regulation of Bacillus subtilis ackA by CodY and CcpA: establishing a potential hierarchy in carbon flow.
Mol Microbiol: 2006, 62(3);811-22
[PubMed:16995897]
[WorldCat.org]
[DOI]
(P p)
Pascale Joseph, Manoja Ratnayake-Lecamwasam, Abraham L Sonenshein
A region of Bacillus subtilis CodY protein required for interaction with DNA.
J Bacteriol: 2005, 187(12);4127-39
[PubMed:15937175]
[WorldCat.org]
[DOI]
(P p)
Shigeo Tojo, Takenori Satomura, Kaori Morisaki, Josef Deutscher, Kazutake Hirooka, Yasutaro Fujita
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(6);1560-73
[PubMed:15916606]
[WorldCat.org]
[DOI]
(P p)
Robert P Shivers, Abraham L Sonenshein
Bacillus subtilis ilvB operon: an intersection of global regulons.
Mol Microbiol: 2005, 56(6);1549-59
[PubMed:15916605]
[WorldCat.org]
[DOI]
(P p)
Robert P Shivers, Abraham L Sonenshein
Activation of the Bacillus subtilis global regulator CodY by direct interaction with branched-chain amino acids.
Mol Microbiol: 2004, 53(2);599-611
[PubMed:15228537]
[WorldCat.org]
[DOI]
(P p)
Hyun-Jin Kim, Sam-In Kim, Manoja Ratnayake-Lecamwasam, Kiyoshi Tachikawa, Abraham L Sonenshein, Mark Strauch
Complex regulation of the Bacillus subtilis aconitase gene.
J Bacteriol: 2003, 185(5);1672-80
[PubMed:12591885]
[WorldCat.org]
[DOI]
(P p)
M Ratnayake-Lecamwasam, P Serror, K W Wong, A L Sonenshein
Bacillus subtilis CodY represses early-stationary-phase genes by sensing GTP levels.
Genes Dev: 2001, 15(9);1093-103
[PubMed:11331605]
[WorldCat.org]
[DOI]
(P p)
L V Wray, A E Ferson, S H Fisher
Expression of the Bacillus subtilis ureABC operon is controlled by multiple regulatory factors including CodY, GlnR, TnrA, and Spo0H.
J Bacteriol: 1997, 179(17);5494-501
[PubMed:9287005]
[WorldCat.org]
[DOI]
(P p)
P Serror, A L Sonenshein
Interaction of CodY, a novel Bacillus subtilis DNA-binding protein, with the dpp promoter region.
Mol Microbiol: 1996, 20(4);843-52
[PubMed:8793880]
[WorldCat.org]
[DOI]
(P p)
F J Slack, P Serror, E Joyce, A L Sonenshein
A gene required for nutritional repression of the Bacillus subtilis dipeptide permease operon.
Mol Microbiol: 1995, 15(4);689-702
[PubMed:7783641]
[WorldCat.org]
[DOI]
(P p)
