Difference between revisions of "Sandbox"

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−
* '''Description:''' Transcriptional activator of the ''gltAB'' operon. Activates expression of the operon in the absence of arginine. <br/><br/>
+
* '''Description:''' H+/Na+-glutamate symport protein <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'''
−
|''gltC''
+
|''gltT''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yhfG ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || No
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator (LysR family)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || H+/Na+-glutamate symport protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || positive regulation <br/>of the glutamate synthase operon (''gltAB'')
+
|style="background:#ABCDEF;" align="center"|'''Function''' || glutamate and aspartate uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33.9 kDa, 5.62
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 45 kDa, 9.029 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 900 bp, 300 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1287 bp, 429 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltA]]'', ''[[proJ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhfF]]'', ''[[yhfH]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13729&#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:CAB12862&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:gltT_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gltC_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/><br/>
  
 
=The gene=
 
=The gene=
Line 37: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU18460
+
* '''Locus tag:''' BSU10220
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
''gltC'' mutants  are auxotrophic for glutamate.
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gltC.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10810]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12595]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' transcription activation of the ''[[gltA]]-[[gltB]]'' operon [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' glutamate synthase family (according to Swiss-Prot) LysR-type transcription regulator [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
+
* '''Protein family:''' View classification (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' none, but there are 19 members of the LysR family in ''B. subtilis''
+
* '''Paralogous protein(s):''' [[GltP]], [[DctP]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 64: Line 62:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:''' DNA-binding helix-turn-helix motif: AA 18 ... 37
+
* '''Domains:'''  
  
 
* '''Modification:'''
 
* '''Modification:'''
Line 70: Line 68:
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' 2-oxoglutarate stimulates transcription activation, glutamate inhibits transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/17134717 PubMed]
+
* '''Effectors of protein activity:'''
  
 
* '''Interactions:'''
 
* '''Interactions:'''
−
** GltC-[[RocG]], This interaction takes place in the presence of glutamate. It prevents the transcription activation of the ''[[gltA]]-[[gltB]]'' operon. Note that [[RocG]] expression is strongly regulated by carbon and nitrogen sources, respectively. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
 
  
−
* '''Localization:'''
+
* '''Localization:''' cell membrane (according to Swiss-Prot),  membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 81: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P20668 P20668]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O07605 O07605]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18460]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10220]
 +
 
 +
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[gltC]]''
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' autoregulation by GltC
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' autorepression
+
* '''Regulatory mechanism:'''  
  
−
* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/gltC.html DBTBS]
+
* '''Additional information:'''  
−
 
 
−
* ''' Additional information:'''
 
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP344 (erm), GP738 (spc) (available in [[Stülke]] lab)
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP903 (in [[pWH844]], N-terminal His-tag), pGP951 (C-terminal Strep-tag) (available in [[Stülke]] lab)
+
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''two-hybrid system:'''  
  
−
* '''Antibody:''' available in Stülke 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 126: Line 118:
 
=References=
 
=References=
  
−
<pubmed>7559360 15150225 2548995 17183217 17608797 17134717 14523131, </pubmed>
+
<pubmed>18763711, </pubmed>
−
# Yoshida K, et al. (2003) Identification of additional TnrA-regulated genes of Bacillus subtilis associated with a TnrA box. ''Mol Microbiol'' '''49(1):''' 157-65. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12823818 PubMed]
+
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
−
# Belitsky, B. R., and Sonenshein, A. L. (1995) Mutations in GltC that increase ''Bacillus subtilis gltA'' expression. J Bacteriol 177: 5696-5700.[http://www.ncbi.nlm.nih.gov/sites/entrez/7559360 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Belitsky, B. R., and Sonenshein, A. L. (2004) Modulation of activity of ''Bacillus subtilis'' regulatory proteins GltC and TnrA by glutamate dehydrogenase. J Bacteriol 186: 3399-3407.[http://www.ncbi.nlm.nih.gov/sites/entrez/15150225 PubMed]
 
−
# Bohannon, D. E., and Sonenshein, A. L. (1989) Positive regulation of glutamate biosynthesis in ''Bacillus subtilis''. J Bacteriol 171: 4718-4727.[http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
 
−
# Commichau, F. M., Wacker, I., Schleider, J., Blencke, H.-M., Reif, I., Tripal, P., and Stülke, J. (2007) Characterization of ''Bacillus subtilis'' mutants with carbon source-independent glutamate biosynthesis. J Mol Microbiol Biotechnol 12: 106-113. [http://www.ncbi.nlm.nih.gov/sites/entrez/17183217 PubMed]
 
−
# Commichau, F. M., Herzberg, C., Tripal, P., Valerius, O., and Stülke, J. (2007) A regulatory protein-protein interaction governs glutamate biosynthesis in ''Bacillus subtilis'': The glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC. Mol Microbiol 65: 642-654. [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed] 
 
−
# Picossi, S., Belitsky, B. R., and Sonenshein, A. L. (2007) Molecular mechanism of the regulation of ''Bacillus subtilis gltAB'' expression by GltC. J Mol Biol 365: 1298-1313. [http://www.ncbi.nlm.nih.gov/sites/entrez/17134717 PubMed]
 
−
# Wacker, I., Ludwig, H., Reif, I., Blencke, H. M., Detsch, C., and Stülke, J. (2003) The regulatory link between carbon and nitrogen metabolism in ''Bacillus subtilis'': regulation of the ''gltAB'' operon by the catabolite control protein CcpA. Microbiology 149: 3001-3009.[http://www.ncbi.nlm.nih.gov/sites/entrez/14523131 PubMed]
 
−
# Herzberg, C., Flórez Weidinger, L. A., Dörrbecker, B., Hübner, S., Stülke, J. & Commichau, F. M. (2007) SPINE: A method for the rapid detection and analysis of protein-protein interactions in vivo. Proteomics 7: 4032-4035. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17994626 PubMed]
 
−
# Schell, M. A. (1993). Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 47, 597-626. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+8257110 PubMed]
 

Revision as of 13:19, 8 June 2009

  • Description: H+/Na+-glutamate symport protein

Gene name gltT
Synonyms yhfG
Essential no
Product H+/Na+-glutamate symport protein
Function glutamate and aspartate uptake
MW, pI 45 kDa, 9.029
Gene length, protein length 1287 bp, 429 aa
Immediate neighbours yhfF, yhfH
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GltT context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU10220

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: View classification (according to Swiss-Prot)

Extended information on the protein

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

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

  1. Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8: 4123-4136 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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