Difference between revisions of "Sandbox"

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−
* '''Description:''' glycerol-3-phosphate permease <br/><br/>
+
* '''Description:''' Transcriptional activator of the ''gltAB'' operon. Activates expression of the operon in the absence of arginine. <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'''
−
|''glpT''
+
|''gltC''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ybeE ''
+
|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''' || glycerol-3-phosphate permease
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator (LysR family)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || glycerol-3-phosphate uptake
+
|style="background:#ABCDEF;" align="center"|'''Function''' || positive regulation <br/>of the glutamate synthase operon (''gltAB'')
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 9.366 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33.9 kDa, 5.62
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1332 bp, 444 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 900 bp, 300 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glpQ]]'', ''[[ybeF]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltA]]'', ''[[proJ]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12008&#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:CAB13729&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:glpT_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>
 
|-
 
|-
Line 29: Line 31:
 
__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU02140
+
* '''Locus tag:''' BSU18460
  
 
===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/glpTQ.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gltC.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10645]
+
* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10810]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 52: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' transcription activation of the ''[[gltA]]-[[gltB]]'' operon [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
  
−
* '''Protein family:''' SLC37A family (according to Swiss-Prot)
+
* '''Protein family:''' glutamate synthase family (according to Swiss-Prot) LysR-type transcription regulator [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
  
−
* '''Paralogous protein(s):'''
+
* '''Paralogous protein(s):''' none, but there are 19 members of the LysR family in ''B. subtilis''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 62: Line 64:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:'''  
+
* '''Domains:''' DNA-binding helix-turn-helix motif: AA 18 ... 37
  
 
* '''Modification:'''
 
* '''Modification:'''
Line 68: Line 70:
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:''' 2-oxoglutarate stimulates transcription activation, glutamate inhibits transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/17134717 PubMed]
  
 
* '''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:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
Line 78: Line 81:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37948 P37948]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P20668 P20668]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU02140]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18460]
−
 
 
−
* '''E.C. number:'''
 
  
 
=== Additional information===
 
=== Additional information===
Line 88: Line 89:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[gltC]]''
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:''' [[SigA]]
  
−
* '''Regulation:''' repressed by glucose (6.2-fold) ([[CcpA]]) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed] 
+
* '''Regulation:''' autoregulation by GltC
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression
+
* '''Regulatory mechanism:''' autorepression
  
−
* '''Additional information:'''  
+
* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/gltC.html DBTBS]
 +
 
 +
* ''' Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' GP344 (erm), GP738 (spc) (available in [[Stülke]] lab)
  
−
* '''Expression vector:'''
+
* '''Expression vector:''' pGP903 (in [[pWH844]], N-terminal His-tag), pGP951 (C-terminal Strep-tag) (available in [[Stülke]] lab)
−
       
+
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:'''  
+
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
  
−
* '''Antibody:'''
+
* '''Antibody:''' available in Stülke lab
  
 
=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 118: Line 126:
 
=References=
 
=References=
  
−
<pubmed>12850135, </pubmed>
+
<pubmed>7559360 15150225 2548995 17183217 17608797 17134717 14523131, </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]
+
# 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]
−
# 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. (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]
 +
# 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: Transcriptional activator of the gltAB operon. Activates expression of the operon in the absence of arginine.

Gene name gltC
Synonyms
Essential No
Product transcriptional regulator (LysR family)
Function positive regulation
of the glutamate synthase operon (gltAB)
MW, pI 33.9 kDa, 5.62
Gene length, protein length 900 bp, 300 amino acids
Immediate neighbours gltA, proJ
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
GltC context.gif
This image was kindly provided by SubtiList






The gene

Basic information

  • Locus tag: BSU18460

Phenotypes of a mutant

gltC mutants are auxotrophic for glutamate.

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: transcription activation of the gltA-gltB operon PubMed
  • Protein family: glutamate synthase family (according to Swiss-Prot) LysR-type transcription regulator PubMed
  • Paralogous protein(s): none, but there are 19 members of the LysR family in B. subtilis

Extended information on the protein

  • Kinetic information:
  • Domains: DNA-binding helix-turn-helix motif: AA 18 ... 37
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity: 2-oxoglutarate stimulates transcription activation, glutamate inhibits transcription activation PubMed
  • 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. PubMed
  • Localization:

Database entries

  • Structure:
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation: autoregulation by GltC
  • Regulatory mechanism: autorepression
  • Additional information:

Biological materials

  • Mutant: GP344 (erm), GP738 (spc) (available in Stülke lab)
  • Expression vector: pGP903 (in pWH844, N-terminal His-tag), pGP951 (C-terminal Strep-tag) (available in Stülke lab)
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
  • Antibody: available in Stülke lab

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

Fabian M Commichau, Christina Herzberg, Philipp Tripal, Oliver Valerius, Jörg Stülke
A regulatory protein-protein interaction governs glutamate biosynthesis in Bacillus subtilis: the glutamate dehydrogenase RocG moonlights in controlling the transcription factor GltC.
Mol Microbiol: 2007, 65(3);642-54
[PubMed:17608797] [WorldCat.org] [DOI] (P p)

Fabian M Commichau, Ingrid Wacker, Jan Schleider, Hans-Matti Blencke, Irene Reif, Philipp Tripal, Jörg Stülke
Characterization of Bacillus subtilis mutants with carbon source-independent glutamate biosynthesis.
J Mol Microbiol Biotechnol: 2007, 12(1-2);106-13
[PubMed:17183217] [WorldCat.org] [DOI] (P p)

Silvia Picossi, Boris R Belitsky, Abraham L Sonenshein
Molecular mechanism of the regulation of Bacillus subtilis gltAB expression by GltC.
J Mol Biol: 2007, 365(5);1298-313
[PubMed:17134717] [WorldCat.org] [DOI] (P p)

Boris R Belitsky, Abraham L Sonenshein
Modulation of activity of Bacillus subtilis regulatory proteins GltC and TnrA by glutamate dehydrogenase.
J Bacteriol: 2004, 186(11);3399-407
[PubMed:15150225] [WorldCat.org] [DOI] (P p)

Ingrid Wacker, Holger Ludwig, Irene Reif, Hans-Matti Blencke, Christian Detsch, Jörg Stülke
The regulatory link between carbon and nitrogen metabolism in Bacillus subtilis: regulation of the gltAB operon by the catabolite control protein CcpA.
Microbiology (Reading): 2003, 149(Pt 10);3001-3009
[PubMed:14523131] [WorldCat.org] [DOI] (P p)

B R Belitsky, A L Sonenshein
Mutations in GltC that increase Bacillus subtilis gltA expression.
J Bacteriol: 1995, 177(19);5696-700
[PubMed:7559360] [WorldCat.org] [DOI] (P p)

D E Bohannon, A L Sonenshein
Positive regulation of glutamate biosynthesis in Bacillus subtilis.
J Bacteriol: 1989, 171(9);4718-27
[PubMed:2548995] [WorldCat.org] [DOI] (P p)

  1. 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. PubMed
  2. Belitsky, B. R., and Sonenshein, A. L. (1995) Mutations in GltC that increase Bacillus subtilis gltA expression. J Bacteriol 177: 5696-5700.PubMed
  3. 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.PubMed
  4. Bohannon, D. E., and Sonenshein, A. L. (1989) Positive regulation of glutamate biosynthesis in Bacillus subtilis. J Bacteriol 171: 4718-4727.PubMed
  5. 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. PubMed
  6. 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. PubMed
  7. 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. PubMed
  8. 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.PubMed
  9. 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. PubMed
  10. Schell, M. A. (1993). Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol 47, 597-626. PubMed
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