Difference between revisions of "Sandbox"

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|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
−
|''codY''
+
|''cysS''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''snpA ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || cysteinyl-tRNA synthetase (EC 6.1.1.16)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || controls gene expression in response
+
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
−
 
 
−
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''' || 53 kDa, 5.07  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 777 bp, 259 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1398 bp, 466 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[clpY]]'', ''[[flgB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[cysE]]'', ''[[mrnC]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/codY_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/cysS_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/codY_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/cysS_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:codY_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:cysS_context.gif]]
 
|-
 
|-
 
|}
 
|}
Line 41: Line 39:
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
−
No swarming motility on B medium. [http://www.ncbi.nlm.nih.gov/sites/entrez/19202088 PubMed]
+
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 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/gltX-cysES-yazC-yacOP.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10968]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10156]
  
 
=== Additional information===
 
=== Additional information===
Line 61: Line 59:
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
−
 
−
=== Genes/ operons controlled by CodY ===
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 70: Line 66:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on Ser-215 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
+
* '''Modification:''' phosphorylation on Ser-270 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
Line 119: Line 115:
  
 
=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]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 127: Line 121:
  
 
# 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]
 
# 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]
+
# Gagnon Y., Breton R., Putzer H., Pelchat M., Grunberg-Manago M., Lapointe J. (1994) Clustering and co-transcription of the Bacillus subtilis genes encoding the aminoacyl-tRNA synthetases specific for glutamate and for cysteine and the first enzyme for cysteine biosynthesis. ''J. Biol. Chem.'' '''269:''' 7473-7482. [http://www.ncbi.nlm.nih.gov/sites/entrez/7510287 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 09:34, 16 March 2009

  • Description: write here

Gene name cysS
Synonyms snpA
Essential yes PubMed
Product cysteinyl-tRNA synthetase (EC 6.1.1.16)
Function
MW, pI 53 kDa, 5.07
Gene length, protein length 1398 bp, 466 aa
Immediate neighbours cysE, mrnC
Gene sequence (+200bp) Protein sequence
Genetic context
CysS context.gif



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

essential PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification: phosphorylation on Ser-270 PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry:
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • 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

  1. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  2. Gagnon Y., Breton R., Putzer H., Pelchat M., Grunberg-Manago M., Lapointe J. (1994) Clustering and co-transcription of the Bacillus subtilis genes encoding the aminoacyl-tRNA synthetases specific for glutamate and for cysteine and the first enzyme for cysteine biosynthesis. J. Biol. Chem. 269: 7473-7482. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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