Difference between revisions of "Sandbox"

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* '''Description:''' regulation of a large regulon in response to branched-chain amino acid limitation <br/><br/>
+
* '''Description:''' two-component response regulator, control of cellular responses to protein secretion stress <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'''
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|''codY''
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|''cssR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvqA ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|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"| '''Product''' || two-component response regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of a large regulon in response to
+
|style="background:#ABCDEF;" align="center"|'''Function''' || control of cellular responses to protein secretion stress
−
branched-chain amino acid limitation
 
−
 
 
−
to the presence of branched-chain amino acids
 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 28 kDa, 4.75  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 26 kDa, 5.071  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 777 bp, 259 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 675 bp, 225 aa  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[clpY]]'', ''[[flgB]]''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[htrB]]'', ''[[cssS]]''
 
|-
 
|-
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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+&#91;EMBLCDS:CAB13490&#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:CAB15291&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:codY_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:cssR_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>
 
|-
 
|-
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__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/>
+
<br/><br/>
  
 
=The gene=
 
=The gene=
Line 41: Line 38:
  
 
===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 ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/codV-clpQY-codY.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/cssRS.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10968]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG14131]
  
 
=== Additional information===
 
=== Additional information===
Line 59: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' codY family (according to Swiss-Prot)
+
* '''Protein family:''' OmpR family of two-component response regulators
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
−
 
−
=== Genes/ operons controlled by CodY ===
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on Ser-215 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 83: Line 76:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''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)
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39779 P39779]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O32192 O32192]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU16170 BSU16170]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU33010 BSU33010]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=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=
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=References=
 
=References=
  
−
<pubmed> Bacillus codY </pubmed>
+
Test.
−
 
+
<pubmed> 19136592</pubmed>
  
−
# 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]
 
  
−
[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=subtilis+codY&log$=activity search PubMed]
+
# Darmon E, Noone D, Masson A, Bron S, Kuipers OP, Devine KM, van Dijl JM. (2002) A novel class of heat and secretion stress-responsive genes is controlled by the autoregulated CssRS two-component system of Bacillus subtilis. ''J Bacteriol. '' '''184(20):''' 5661-71. [http://www.ncbi.nlm.nih.gov/sites/entrez/12270824 PubMed]
 +
# Hyyryläinen HL, Bolhuis A, Darmon E, Muukkonen L, Koski P, Vitikainen M, Sarvas M, Prágai Z, Bron S, van Dijl JM, Kontinen VP. (2001) A novel two-component regulatory system in Bacillus subtilis for the survival of severe secretion stress. ''Mol Microbiol. '' '''41(5):''' 1159-72. [http://www.ncbi.nlm.nih.gov/sites/entrez/11555295 PubMed]

Revision as of 01:37, 23 May 2009

  • Description: two-component response regulator, control of cellular responses to protein secretion stress

Gene name cssR
Synonyms yvqA
Essential no
Product two-component response regulator
Function control of cellular responses to protein secretion stress
MW, pI 26 kDa, 5.071
Gene length, protein length 675 bp, 225 aa
Immediate neighbours htrB, cssS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CssR context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family: OmpR family of two-component response regulators
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cytoplasm (according to Swiss-Prot)

Database entries

  • Structure:
  • 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

Your additional remarks

References

Test.

Jeffrey G Gardner, Jorge C Escalante-Semerena
In Bacillus subtilis, the sirtuin protein deacetylase, encoded by the srtN gene (formerly yhdZ), and functions encoded by the acuABC genes control the activity of acetyl coenzyme A synthetase.
J Bacteriol: 2009, 191(6);1749-55
[PubMed:19136592] [WorldCat.org] [DOI] (I p)


  1. Darmon E, Noone D, Masson A, Bron S, Kuipers OP, Devine KM, van Dijl JM. (2002) A novel class of heat and secretion stress-responsive genes is controlled by the autoregulated CssRS two-component system of Bacillus subtilis. J Bacteriol. 184(20): 5661-71. PubMed
  2. Hyyryläinen HL, Bolhuis A, Darmon E, Muukkonen L, Koski P, Vitikainen M, Sarvas M, Prágai Z, Bron S, van Dijl JM, Kontinen VP. (2001) A novel two-component regulatory system in Bacillus subtilis for the survival of severe secretion stress. Mol Microbiol. 41(5): 1159-72. PubMed
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