Difference between revisions of "Sandbox"

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−
* '''Description:''' transcriptional activator of the  malA-glvR-malP operon <br/><br/>
+
* '''Description:''' aconitate hydratase (aconitase)<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'''
−
|''acoR''
+
|''citB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yfjG, yzcB ''
+
|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''' || transcriptional activator (for SigL-dependent promoter)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || aconitate hydratase (aconitase)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of acetoin utilization
+
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 66 kDa, 7.884  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 99 kDa, 4.903  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1815 bp, 605 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2727 bp, 909 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[acoL]]'', ''[[sspH]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sspO]], [[yneN]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/acoR_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/citB_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/acoR_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/citB_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:acoR_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:citB_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 39: Line 39:
  
 
===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/acoR-sspH.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/citB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11790]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10478]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''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]
  
 
* '''Protein family:'''
 
* '''Protein family:'''
Line 67: Line 68:
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' FeS cluster
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
Line 77: Line 78:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1L5J 1L5J] (''E. coli'')
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08100]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18000]
  
−
* '''E.C. number:'''
+
* '''E.C. number:''' 4.2.1.3
  
 
=== 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:'''  
+
* '''Operon:''' ''[[citB]]''
  
−
* '''Sigma factor:'''  
+
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:''' repressed by glucose (3.7-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed]   
+
* '''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]
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression  
+
* '''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]
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP683 (erm), available in [[Stülke]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 115: Line 117:
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
  
−
[[Michel Debarbouille]], Pasteur Institute, Paris, France [http://www.pasteur.fr/ip/easysite/go/03b-00000m-0ob/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-des-bacteries-pathogenes-a-gram-positif/les-membres-de-l-equipe Homepage]
+
[[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 122: Line 127:
  
 
# 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]
 
# 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]
−
# Ali, N. O., Bignon, J., Rapoport, G., and Débarbouillé, M. (2001) Regulation of the acetoin catabolic pathway is controlled by sigma L in ''Bacillus subtilis''. J. Bacteriol. 183, 2497-2504. [http://www.ncbi.nlm.nih.gov/sites/entrez/11274109  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 10:02, 6 April 2009

  • Description: aconitate hydratase (aconitase)

Gene name citB
Synonyms
Essential no
Product aconitate hydratase (aconitase)
Function TCA cycle
MW, pI 99 kDa, 4.903
Gene length, protein length 2727 bp, 909 aa
Immediate neighbours sspO, yneN
Gene sequence (+200bp) Protein sequence
Genetic context
CitB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

glutamate auxotrophy and a defect in sporulation PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: : Citrate <---> Isocitrate, binding to iron responsive elements (IRE RNA) in the absence of the FeS cluster PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

  • Structure: 1L5J (E. coli)
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number: 4.2.1.3

Additional information

B. subtilis aconitase is both an enzyme and an RNA binding protein PubMed

Expression and regulation

  • Regulation: repressed by glucose (3.7-fold) (CcpA) PubMed, repression by glucose + arginine (CcpC) PubMed
  • Regulatory mechanism: CcpA: transcription repression, CcpC: transcription repression PubMed, AbrB: transcription activation PubMed
  • Additional information:

Biological materials

  • Mutant: GP683 (erm), 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

Jörg Stülke, University of Göttingen, Germany Homepage

Your additional remarks

References

  1. 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 PubMed
  2. Rosenkrantz MS, Dingman DW, Sonenshein AL (1985) Bacillus subtilis citB gene is regulated synergistically by glucose and glutamine. J Bacteriol 164:155-164. PubMed
  3. 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. PubMed
  4. Alén C, Sonenshein AL (1999) Bacillus subtilis aconitase is an RNA-binding protein. Proc Natl Acad Sci USA 96:10412-10417. PubMed
  5. Fisher SH, Magasanik B (1984) 2-Ketoglutarate and the regulation of aconitase and histidase formation Bacillus subtilis. J Bacteriol 158:379-382. PubMed
  6. 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
  7. 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. PubMed
  8. 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. PubMed
  9. Nakano MM, Zuber P, Sonenshein AL (1998) Anaerobic regulation of Bacillus subtilis Krebs cycle genes. J Bacteriol. 180:3304-3311. PubMed
  10. 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. PubMed
  11. 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. PubMed
  12. 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. PubMed
  13. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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