Difference between revisions of "Sandbox"

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* '''Description:''' two-component ATP-dependent protease <br/><br/>
+
* '''Description:''' regulation of a large regulon in response to branched-chain amino acid limitation <br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
|''clpY''
+
|''codY''
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''hslU, codX ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Product''' || two-component ATP-dependent protease
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional pleiotropic repressor
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of a large regulon in response to
 +
branched-chain amino acid limitation
 +
 
 +
to the presence of branched-chain amino acids
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52 kDa, 5.31  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 4.75  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1401 bp, 467 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 777 bp, 259 aa  
 
|-
 
|-
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[clpQ]]'', ''[[codY]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[clpY]]'', ''[[flgB]]''
 
|-
 
|-
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13489&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13490&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
|colspan="2" | '''Genetic context''' <br/> [[Image:clpY_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:codY_context.gif]]
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
Line 29: Line 32:
 
__TOC__
 
__TOC__
  
<br/><br/>
+
<br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 38: Line 41:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 43: Line 48:
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/codV-clpQY-codY.html]
 
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/codV-clpQY-codY.html]
  
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10967]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10968]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 59:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
* '''Protein family:''' HslU subfamily (according to Swiss-Prot)
+
* '''Protein family:''' codY family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
=== Genes/ operons controlled by CodY ===
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 64: Line 71:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Ser-215 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 72: Line 79:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
* '''Localization:'''
+
* '''Localization:''' cytoplasm (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
* '''Structure:'''
+
* '''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)
  
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39779 P39779]
  
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16160 BSU16160]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16170 BSU16170]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 113: Line 120:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
 +
 +
[[Tony Wilkinson]], York University, U.K. [http://www.york.ac.uk/depts/chem/staff/ajw.html homepage]
 +
 +
[[Oscar Kuipers]], University of Groningen, The Netherlands
 +
[http://molgen.biol.rug.nl/molgen/index.php Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 118: Line 132:
 
=References=
 
=References=
  
 +
# 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]
 +
# 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]
 +
# 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]
 +
# 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]
 +
# 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]
 +
# 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]
 +
# 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]
 +
# 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]
 +
# 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]
 +
# 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]
 +
# 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]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 12:19, 20 May 2009

  • Description: regulation of a large regulon 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

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
CodY context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Coordinates:

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:
  • Modification: phosphorylation on Ser-215 PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

  • Structure: 2B0L (C-terminal DNA-binding domain), 2GX5 (N-terminal Gaf domain)
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • 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

  1. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  2. 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. PubMed
  3. 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. PubMed
  4. 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. PubMed
  5. Sonenshein AL: CodY, a global regulator of stationary phase and virulence in Gram-positive bacteria. Curr Opin Microbiol 2005, 8:203-207. PubMed
  6. 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.PubMed
  7. 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. PubMed
  8. 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. PubMed
  9. 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. PubMed
  10. Shivers RP, Sonenshein AL: Bacillus subtilis ilvB operon: an intersection of global regulons. Mol Microbiol 2005, 56:1549-1559. PubMed
  11. 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. PubMed
  12. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed