Difference between revisions of "Sandbox"

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* '''Description:''' Trigger enzyme: aconitase and RNA binding protein<br/><br/>
+
* '''Description:''' secondary transporter of divalent metal ions/citrate complexes <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''
+
|''citH''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yxiQ ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || aconitate hydratase (aconitase)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || secondary transporter of divalent metal ions/citrate complexes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || citrate  uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 99 kDa, 4.903  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 9.278  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2727 bp, 909 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1278 bp, 426 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[sspO]], [[yneN]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[katE]]'', ''[[bglS]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13684&#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:CAB15932&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:citB_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:citH_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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=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU18000
+
* '''Locus tag:''' BSU39060
  
 
===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:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10478]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11146]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Citrate = isocitrate (according to Swiss-Prot) : 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 65: Line 66:
 
* '''Domains:'''  
 
* '''Domains:'''  
  
−
* '''Modification:'''
+
* '''Modification:''' phosphorylation on Ser-149 [http://www.ncbi.nlm.nih.gov/sites/entrez/17218307 PubMed]
  
−
* '''Cofactor(s):''' FeS cluster
+
* '''Cofactor(s):'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
Line 73: Line 74:
 
* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1L5J 1L5J] (''E. coli'')
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P09339 P09339]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P42308 P42308]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18000]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU39060]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/4.2.1.3 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:'''  
 
* '''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]
 
−
** less expressed under conditions of extreme iron limitation ([[FsrA]]) [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
 
  
 
* '''Regulatory mechanism:'''  
 
* '''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]
 
−
** [[FsrA]]: translational repression [http://www.ncbi.nlm.nih.gov/pubmed/18697947 PubMed]
 
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP683 (erm), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 119: Line 112:
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
  
−
* '''Antibody:''' available in [[Linc Sonenshein]] lab
+
* '''Antibody:'''
  
 
=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 132: Line 120:
 
=References=
 
=References=
  
−
<pubmed>12850135 2413006 10656796 10468622 6143742 12591885 16395550 16923907 9642180 9393699 12591885 2105305, </pubmed>
+
<pubmed>17218307, </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]
+
# 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]
−
# 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 13:11, 8 June 2009

  • Description: secondary transporter of divalent metal ions/citrate complexes

Gene name citH
Synonyms yxiQ
Essential no
Product secondary transporter of divalent metal ions/citrate complexes
Function citrate uptake
MW, pI 45 kDa, 9.278
Gene length, protein length 1278 bp, 426 aa
Immediate neighbours katE, bglS
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CitH context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU39060

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

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-149 PubMed
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: cell membrane (according to Swiss-Prot)

Database entries

  • Structure:
  • KEGG entry: [2]
  • 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

Boris Macek, Ivan Mijakovic, Jesper V Olsen, Florian Gnad, Chanchal Kumar, Peter R Jensen, Matthias Mann
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis.
Mol Cell Proteomics: 2007, 6(4);697-707
[PubMed:17218307] [WorldCat.org] [DOI] (P p)

  1. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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