Difference between revisions of "Sandbox"

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* '''Description:''' aconitate hydratase (aconitase)<br/><br/>
+
* '''Description:''' small acid-soluble spore protein (minor) <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'''
−
|''citB''
+
|''sspO''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''cotK ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || aconitate hydratase (aconitase)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || small acid-soluble spore protein (minor)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || protection of spore DNA
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 99 kDa, 4.903  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 5 kDa, 10.47  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2727 bp, 909 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 144 bp, 48 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sspO]], [[yneN]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sspP]]'', ''[[citB]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:citB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sspO_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 38: Line 38:
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
glutamate auxotrophy and a defect in sporulation [http://www.ncbi.nlm.nih.gov/pubmed/9393699 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sspOP.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10478]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11920]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' : Citrate <---> Isocitrate, binding to iron responsive elements (IRE RNA) in the absence of the FeS cluster [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]
+
* '''Catalyzed reaction/ biological activity:'''  
  
 
* '''Protein family:'''
 
* '''Protein family:'''
Line 67: Line 66:
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):''' FeS cluster
+
* '''Cofactor(s):'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
Line 77: Line 76:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1L5J 1L5J] (''E. coli'')
+
* '''Structure:'''
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18000]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17990]
  
−
* '''E.C. number:''' 4.2.1.3
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
''B. subtilis'' aconitase is both an enzyme and an RNA binding protein [http://www.ncbi.nlm.nih.gov/pubmed/10468622 PubMed]
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[citB]]''
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed by glucose (3.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  repression by glucose + arginine ([[CcpC]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/16395550 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpC]]: transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12100558 PubMed], [[AbrB]]: transcription activation [http://www.ncbi.nlm.nih.gov/pubmed/12591885 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP683 (erm), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 115: Line 113:
  
 
=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]
 
−
 
−
[[Stülke|Jörg Stülke]], University of Göttingen, Germany
 
−
[http://wwwuser.gwdg.de/~genmibio/stuelke.html Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 125: Line 118:
 
=References=
 
=References=
  
−
# Blencke et al. (2003) Transcriptional profiling of gene expression in response to glucose in ''Bacillus subtilis'': regulation of the central metabolic pathways. ''Metab Eng.'' '''5:''' 133-149 [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]
 
−
# Rosenkrantz MS, Dingman DW, Sonenshein AL (1985) Bacillus subtilis citB gene is regulated synergistically by glucose and glutamine. J Bacteriol 164:155-164. [http://www.ncbi.nlm.nih.gov/sites/entrez/2413006 PubMed]
 
−
# Jourlin-Castelli C, Mani N, Nakano MM, Sonenshein AL (2000) CcpC, a novel regulator of the LysR family required for glucose repression of the citB gene in Bacillus subtilis. J Mol Biol 295:865-878. [http://www.ncbi.nlm.nih.gov/sites/entrez/10656796 PubMed]
 
−
# Alén C, Sonenshein AL (1999) Bacillus subtilis aconitase is an RNA-binding protein. Proc Natl Acad Sci USA 96:10412-10417. [http://www.ncbi.nlm.nih.gov/sites/entrez/10468622 PubMed]
 
−
# Fisher SH, Magasanik B (1984) 2-Ketoglutarate and the regulation of aconitase and histidase formation Bacillus subtilis. J Bacteriol 158:379-382. [http://www.ncbi.nlm.nih.gov/sites/entrez/6143742 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]
 
−
# Blencke, H.-M., Reif, I., Commichau, F. M., Detsch, C., Wacker, I., Ludwig, H. & Stülke, J. (2006) Regulation of citB expression in Bacillus subtilis: Integration of multiple metabolic signals in the citrate pool and by the general nitrogen regulatory system. Arch. Microbiol. 185: 136-146. [http://www.ncbi.nlm.nih.gov/sites/entrez/16395550 PubMed]
 
−
# Serio, A. W., Pechter, K. B., and Sonenshein, A. L. (2006) Bacillus subtilis aconitase is required for efficient late-sporulation gene expression. J Bacteriol 188: 6396-6405. [http://www.ncbi.nlm.nih.gov/sites/entrez/16923907 PubMed]
 
−
# Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of ''Bacillus subtilis'' Krebs cycle genes. J Bacteriol. 180:3304-3311. [http://www.ncbi.nlm.nih.gov/pubmed/9642180 PubMed]
 
−
# Craig JE, Ford MJ, Blaydon DC, Sonenshein AL (1997) A null mutation in the ''Bacillus subtilis'' aconitase gene causes a block in Spo0A-phosphate-dependent gene expression. J Bacteriol 197:7351-7359. [http://www.ncbi.nlm.nih.gov/pubmed/9393699 PubMed]
 
−
# Kim HJ, Kim SI, Ratnayake-Lecamwasam M, Tachikawa K, Sonenshein AL, Strauch M (2003) Complex regulation of the ''Bacillus subtilis'' aconitase gene. J Bacteriol. 185:1672-1680. [http://www.ncbi.nlm.nih.gov/pubmed/12591885 PubMed]
 
−
# Fouet, A., and Sonenshein, A. L. (1990) A target for carbon source-dependent negative regulation of the ''citB'' promoter of ''Bacillus subtilis''. J Bacteriol 172: 835-844. [http://www.ncbi.nlm.nih.gov/sites/entrez/2105305 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 19:38, 15 April 2009

  • Description: small acid-soluble spore protein (minor)

Gene name sspO
Synonyms cotK
Essential no
Product small acid-soluble spore protein (minor)
Function protection of spore DNA
MW, pI 5 kDa, 10.47
Gene length, protein length 144 bp, 48 aa
Immediate neighbours sspP, citB
Hier soll was neues rein
Genetic context
SspO 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:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry:
  • KEGG entry: [3]
  • 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

  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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