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:''' large subunit of glutamate synthase  <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''
+
|''gltA''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|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 regulator (LysR family)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate synthase (large subunit)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || positive regulation <br/>of the glutamate synthase operon (''gltAB'')
+
|style="background:#ABCDEF;" align="center"|'''Function''' || glutamate biosynthesis
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33.9 kDa, 5.62
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 168 kDa, 5.47
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 900 bp, 300 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 4560 bp, 1520 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltA]]'', ''[[proJ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[gltC]]'', ''[[gltB]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
Line 24: Line 24:
 
|-
 
|-
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:gltC_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:gltA_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 31: Line 31:
 
__TOC__
 
__TOC__
  
−
<br/><br/><br/><br/><br/>
+
<br/><br/>
 +
 
  
 
=The gene=
 
=The gene=
Line 37: Line 38:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 2013989 - 2014888
+
* '''Coordinates:''' 2009283 - 2013842
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
''gltC'' mutants  are auxotrophic for glutamate.
+
 
 +
auxotrophic for glutamate
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gltC.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/gltAB.html]
  
−
* '''SubtiList entry:'''[http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10810]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10811]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 54: Line 57:
 
=== 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:''' 2 L-glutamate + NADP(+) <=> L-glutamine + 2-oxoglutarate + NADPH
  
−
* '''Protein family:''' LysR-type transcription regulator [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
+
* '''Protein family:''' glutamate synthase family
  
−
* '''Paralogous protein(s):''' none, but there are 19 members of the LysR family in ''B. subtilis''
+
* '''Paralogous protein(s):''' [[YerD]]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 64: Line 67:
 
* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:''' DNA-binding helix-turn-helix motif: AA 18 ... 37
+
* '''Domains:'''  
 +
** Glutamine amidotransferase type-2 domain (22-415)
 +
** Nucleotide binding domain (1060-1112)
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):'''
+
* '''Cofactor(s):''' 3Fe-4S, FAD, FMN
  
−
* '''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:''' membrane associated [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18763711 PubMed], cytoplasm
  
 
=== Database entries ===
 
=== Database entries ===
Line 81: Line 85:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P20668 P20668]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39812]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18460]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU18450]
 +
 
 +
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.13 1.4.1.13]
  
 
=== Additional information===
 
=== Additional information===
 +
 +
subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[gltC]]''
+
* '''Operon:''' ''[[gltA]]-[[gltB]]''
−
 
 
−
* '''Sigma factor:''' [[SigA]]
 
  
−
* '''Regulation:''' autoregulation by GltC
+
* '''[[Sigma factor]]:''' [[SigA]]
  
−
* '''Regulatory mechanism:''' autorepression
+
* '''Regulation:''' expression activated by glucose (11 fold) [http://www.ncbi.nlm.nih.gov/pubmed/12850135 PubMed],  induced by sugar [http://www.ncbi.nlm.nih.gov/sites/entrez/14523131 PubMed], repressed by arginine [http://www.ncbi.nlm.nih.gov/sites/entrez/15150225 PubMed], ammonium required [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11029411 PubMed]
  
−
* '''Database entries:''' [http://dbtbs.hgc.jp/COG/prom/gltC.html DBTBS]
+
* '''Regulatory mechanism:''' Activator: [[GltC]] [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]; Repressor: [[TnrA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11029411 PubMed], pos. regulated by a mutant form of [[GltR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+9023181 PubMed]
  
−
* ''' Additional information:'''
+
* '''Additional information:''' subject to Clp-dependent proteolysis upon glucose starvation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 PubMed]
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP344 (erm), GP738 (spc) (available in [[Stülke]] lab)
+
* '''Mutant:''' GP807 (del ''gltAB''::''tet''), GP222 (''gltA'' under the control of p-xyl), available in [[Stülke]] lab
  
−
* '''Expression vector:''' pGP903 (in [[pWH844]], N-terminal His-tag), pGP951 (C-terminal Strep-tag) (available in [[Stülke]] lab)
+
* '''Expression vector:'''
 
 
−
* '''lacZ fusion:'''
+
* '''lacZ fusion:''' pGP526 (in [[pAC7]]), pGP919 (in [[pAC5]]), available in [[Stülke]] lab
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
+
* '''Antibody:'''
 +
 
 +
=Labs working on this gene/protein=
 +
 
  
−
* '''Antibody:''' available in Stülke lab
 
  
−
=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]
 
[[Linc Sonenshein|Linc Sonenshein]], Tufts University, Boston, MA, USA [http://www.tufts.edu/sackler/microbiology/faculty/sonenshein/index.html Homepage]
Line 126: Line 133:
 
=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]
 
# 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]
 
# 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]
 
# 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. (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]
Line 134: Line 142:
 
# 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]
 
# 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]
 
# 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]
+
# Belitsky BR, Sonenshein AL (1997) Altered transcription activation specificity of a mutant form of Bacillus subtilis GltR, a LysR family member. J Bacteriol 179:1035-1043 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11029411 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]
+
# Belitsky, B. R., Wray, L. V., Jr., Fisher, S. H., Bohannon, D. E. & Sonenshein, A. L. (2000). Role of TnrA in nitrogen source-dependent repression of Bacillus subtilis glutamate synthase gene expression. J Bacteriol 182, 5939-5947. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+11029411 PubMed]
 +
# Commichau, F. M., Gunka, K., Landmann, J. J. & Stülke, J. (2008) Glutamate metabolism in Bacillus subtilis: Gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations in the system. J. Bacteriol. 190: 3557-3564. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18326565 PubMed]
 +
# Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+17981983 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/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+18763711 PubMed]

Revision as of 15:19, 15 April 2009

  • Description: large subunit of glutamate synthase

Gene name gltA
Synonyms
Essential no
Product glutamate synthase (large subunit)
Function glutamate biosynthesis
MW, pI 168 kDa, 5.47
Gene length, protein length 4560 bp, 1520 amino acids
Immediate neighbours gltC, gltB
Hier soll was neues rein
Genetic context
GltA context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Coordinates: 2009283 - 2013842

Phenotypes of a mutant

auxotrophic for glutamate

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: 2 L-glutamate + NADP(+) <=> L-glutamine + 2-oxoglutarate + NADPH
  • Protein family: glutamate synthase family
  • Paralogous protein(s): YerD

Extended information on the protein

  • Kinetic information:
  • Domains:
    • Glutamine amidotransferase type-2 domain (22-415)
    • Nucleotide binding domain (1060-1112)
  • Modification:
  • Cofactor(s): 3Fe-4S, FAD, FMN
  • Effectors of protein activity:
  • Interactions:
  • Localization: membrane associated PubMed, cytoplasm

Database entries

  • Structure:
  • Swiss prot entry: [3]
  • KEGG entry: [4]

Additional information

subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Regulation: expression activated by glucose (11 fold) PubMed, induced by sugar PubMed, repressed by arginine PubMed, ammonium required PubMed
  • Additional information: subject to Clp-dependent proteolysis upon glucose starvation PubMed

Biological materials

  • Mutant: GP807 (del gltAB::tet), GP222 (gltA under the control of p-xyl), available in Stülke lab
  • Expression vector:
  • GFP fusion:
  • 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. 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
  3. Belitsky, B. R., and Sonenshein, A. L. (1995) Mutations in GltC that increase Bacillus subtilis gltA expression. J Bacteriol 177: 5696-5700.PubMed
  4. 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
  5. Bohannon, D. E., and Sonenshein, A. L. (1989) Positive regulation of glutamate biosynthesis in Bacillus subtilis. J Bacteriol 171: 4718-4727.PubMed
  6. 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
  7. 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
  8. 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
  9. 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
  10. Belitsky BR, Sonenshein AL (1997) Altered transcription activation specificity of a mutant form of Bacillus subtilis GltR, a LysR family member. J Bacteriol 179:1035-1043 PubMed
  11. Belitsky, B. R., Wray, L. V., Jr., Fisher, S. H., Bohannon, D. E. & Sonenshein, A. L. (2000). Role of TnrA in nitrogen source-dependent repression of Bacillus subtilis glutamate synthase gene expression. J Bacteriol 182, 5939-5947. PubMed
  12. Commichau, F. M., Gunka, K., Landmann, J. J. & Stülke, J. (2008) Glutamate metabolism in Bacillus subtilis: Gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations in the system. J. Bacteriol. 190: 3557-3564. PubMed
  13. Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 PubMed
  14. Hahne et al. (2008) From complementarity to comprehensiveness--targeting the membrane proteome of growing Bacillus subtilis by divergent approaches. Proteomics 8:4123-4136 PubMed
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