Difference between revisions of "Sandbox"

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* '''Description:''' write here <br/><br/>
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* '''Description:''' catabolic glutamate dehydrogenase induced by arginine, ornithine or proline, subject to carbon catabolite repression  <br/><br/>
  
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    {| align="right" border="1" cellpadding="2"  
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{| align="right" border="1" cellpadding="2"  
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    |-
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|-
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    |style="background:#ABCDEF;" align="center"|'''Gene name'''
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|style="background:#ABCDEF;" align="center"|'''Gene name'''
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    |''ccpC''
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|''rocG''
−
    |-
+
|-
−
    |style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykuM ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
−
    |-
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|-
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    |style="background:#ABCDEF;" align="center"| '''Essential''' ||  
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no
−
    |-
+
|-
−
    |style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator (LysR family)
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|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate dehydrogenase (major)  
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    |-
+
|-
−
    |style="background:#ABCDEF;" align="center"|'''Function''' || carbon catabolite and anaerobic repression of citB and citZ
+
|style="background:#ABCDEF;" align="center"|'''Function''' || arginine utilization, controls the activity of GltC
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    |-
+
|-
−
    |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 5.932 
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46.2 kDa, 6.28
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    |-
+
|-
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    |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 879 bp, 293 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1272 bp, 424 amino acids
−
    |-
+
|-
−
    |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' ||  
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yweA]]'', ''[[rocA]]''
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    |-
+
|-
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    |style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ccpC_nucleotide.txt    Gene sequence      (+200bp)   ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rocG_nucleotide.txt    Gene sequence      (+200bp) corrected  ]'''  
−
    |style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ccpC_protein.txt Protein sequence]'''
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rocG_protein.txt Protein sequence]'''
−
    |-
+
|-
−
    |colspan="2" | '''Genetic context''' <br/> [[Image:ccpC_context.gif]]
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|colspan="2" | '''Genetic context''' <br/> [[Image:rocG_context.gif]]
−
    |-
+
|-
−
    |}
+
|}
  
−
    __TOC__
+
__TOC__
  
−
    <br/><br/>
+
<br/><br/>
  
−
    =The gene=
 
  
−
    === Basic information ===
+
=The gene=
  
−
    * '''Coordinates:'''
+
=== Basic information ===
  
−
    ===Phenotypes of a mutant ===
+
* '''Coordinates:''' 3879765 - 3881036
  
−
    === Database entries ===
+
===Phenotypes of a mutant ===
  
−
    * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpC.html]
+
Poor growth on complex media such as LB. No growth in minimal media with arginine as the only carbon source. Rapid accumulation of suppressor mutants ([[gudB |''gudB1'']])
  
−
    * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13297]
+
=== Database entries ===
  
−
    === Additional information===
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocG.html]
  
 +
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10621]
  
−
    =The protein=
+
=== Additional information===
  
−
    === Basic information/ Evolution ===
+
=The protein=
  
−
    * '''Catalyzed reaction/ biological activity:'''
+
=== Basic information/ Evolution ===
  
−
    * '''Protein family:'''
+
* '''Catalyzed reaction/ biological activity:''' L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH, controls the activity of the [[GltC]] transcription activator [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
  
−
    * '''Paralogous protein(s):'''
+
* '''Protein family:''' Glu/Leu/Phe/Val dehydrogenases family
  
−
    === Extended information on the protein ===
+
* '''Paralogous protein(s):''' [[GudB]]
  
−
    * '''Kinetic information:'''
+
=== Extended information on the protein ===
  
−
    * '''Domains:'''  
+
* '''Kinetic information:'''
  
−
    * '''Modification:'''
+
* '''Domains:'''  
  
−
    * '''Cofactor(s):'''
+
* '''Modification:'''
  
−
    * '''Effectors of protein activity:'''
+
* '''Cofactor(s):'''
  
−
    * '''Interactions:'''
+
* '''Effectors of protein activity:'''
  
−
    * '''Localization:'''
+
* '''Interactions:''' RocG-[[GltC]], this interaction prevents transcription activation of the ''gltAB'' operon by GltC [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
  
−
    === Database entries ===
+
* '''Localization:'''
  
−
    * '''Structure:'''
+
=== Database entries ===
  
−
    * '''Swiss prot entry:'''
+
* '''Structure:'''
  
−
    * '''KEGG entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39633]
  
−
    * '''E.C. number:'''
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU37790]
  
−
    === Additional information===
+
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.2]
  
−
    =Expression and regulation=
+
=== Additional information===
  
−
    * '''Operon:'''
 
  
−
    * '''Sigma factor:'''
+
=Expression and regulation=
  
−
    * '''Regulation:'''  
+
* '''Operon:''' ''rocG''
  
−
    * '''Regulatory mechanism:'''  
+
* '''Sigma factor:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]
  
−
    * '''Additional information:'''  
+
* '''Regulation:''' induced by arginine ([[RocR]], [[AhrC]]), ornithine or proline, subject to carbon catabolite repression ([[CcpA]])
  
−
    =Biological materials =
+
* '''Regulatory mechanism:''' [[RocR]]: transcription activation [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed][http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]; [[AhrC]]: transcription activation ; [[CcpA]]: transcription repression
  
−
    * '''Mutant:'''
+
* '''Additional information:'''
 +
Activation by RocR requires binding of RocG to a downstream element [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed]
  
−
    * '''Expression vector:'''
+
=Biological materials =
−
           
 
−
    * '''lacZ fusion:'''
 
  
−
    * '''GFP fusion:'''
+
* '''Mutant:''' GP747 (spc), GP726 (aphA3), available in [[Stülke]] lab
  
−
    * '''two-hybrid system:'''  
+
* '''Expression vector:''' pGP902 (in [[pGP172]], N-terminal Strep-tag), a series of ''rocG'' variants is also available in [[pGP172]], available in [[Stülke]] lab
 +
 +
* '''lacZ fusion:'''
  
−
    * '''Antibody:'''
+
* '''GFP fusion:'''
  
−
    =Labs working on this gene/protein=
+
* '''two-hybrid system:''' ''B. pertussis'' adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
  
−
    =Your additional remarks=
+
* '''Antibody:''' available in [[Stülke]] lab
  
−
    =References=
+
=Labs working on this gene/protein=
  
−
    # Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
[[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=
 +
 
 +
=References=
 +
 
 +
# 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] 
 +
# 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]
 +
# 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]
 +
# Ali, N. O., J. Jeusset, E. Larquet, E. le Cam, B. Belitsky, A. L. Sonenshein, T. Msadek, and M. Débarbouillé. 2003. Specificity of the interaction of RocR with the rocG-rocA intergenic region in Bacillus subtilis. Microbiology 149: 739-750. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+12634342 PubMed]
 +
# Belitsky BR, Sonenshein AL (1998) Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J Bacteriol 180:6298-6305 [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+9829940 PubMed]
 +
# Belitsky BR, Sonenshein, AL: An enhancer element located downstream of the major glutamate dehydrogenase gene of Bacillus subtilis. Proc Natl Acad Sci USA 1999, 96:10290-10295. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]
 +
# Belitsky BR, Sonenshein, AL: CcpA-dependent regulation of Bacillus subtilis glutamate dehydrogenase gene expression. J Bacteriol 2004, 186:3392-3398. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15150224 PubMed]
 +
# Belitsky BR, Sonenshein AL (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/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+15150225 PubMed]
 +
# Khan, M. I., K. Ito, H. Kim, H. Ashida, T. Ishikawa, H. Shibata, and Y. Sawa. 2005. Molecular properties and enhancement of thermostability by random mutagenesis of glutamate dehydrogenase from Bacillus subtilis. Biosci. Biotechnol. Biochem. 69: 1861-1870. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+16244435 PubMed]
 +
# Stillman TJ, Baker PJ, Britton KL, Rice DW Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis. J Mol Biol 1993, 234:1131-1139. [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+8263917 PubMed]

Revision as of 14:21, 2 February 2009

  • Description: catabolic glutamate dehydrogenase induced by arginine, ornithine or proline, subject to carbon catabolite repression

Gene name rocG
Synonyms
Essential no
Product glutamate dehydrogenase (major)
Function arginine utilization, controls the activity of GltC
MW, pI 46.2 kDa, 6.28
Gene length, protein length 1272 bp, 424 amino acids
Immediate neighbours yweA, rocA
Gene sequence (+200bp) corrected Protein sequence
Genetic context
RocG context.gif




The gene

Basic information

  • Coordinates: 3879765 - 3881036

Phenotypes of a mutant

Poor growth on complex media such as LB. No growth in minimal media with arginine as the only carbon source. Rapid accumulation of suppressor mutants (gudB1)

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH, controls the activity of the GltC transcription activator PubMed
  • Protein family: Glu/Leu/Phe/Val dehydrogenases family
  • Paralogous protein(s): GudB

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions: RocG-GltC, this interaction prevents transcription activation of the gltAB operon by GltC PubMed
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry: [3]
  • KEGG entry: [4]
  • E.C. number: [5]

Additional information

Expression and regulation

  • Operon: rocG
  • Regulation: induced by arginine (RocR, AhrC), ornithine or proline, subject to carbon catabolite repression (CcpA)
  • Regulatory mechanism: RocR: transcription activation PubMedPubMed; AhrC: transcription activation ; CcpA: transcription repression
  • Additional information:

Activation by RocR requires binding of RocG to a downstream element PubMed

Biological materials

  • Mutant: GP747 (spc), GP726 (aphA3), available in Stülke lab
  • Expression vector: pGP902 (in pGP172, N-terminal Strep-tag), a series of rocG variants is also available in pGP172, 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

  1. 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
  2. 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
  3. 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
  4. 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
  5. Ali, N. O., J. Jeusset, E. Larquet, E. le Cam, B. Belitsky, A. L. Sonenshein, T. Msadek, and M. Débarbouillé. 2003. Specificity of the interaction of RocR with the rocG-rocA intergenic region in Bacillus subtilis. Microbiology 149: 739-750. PubMed
  6. Belitsky BR, Sonenshein AL (1998) Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J Bacteriol 180:6298-6305 PubMed
  7. Belitsky BR, Sonenshein, AL: An enhancer element located downstream of the major glutamate dehydrogenase gene of Bacillus subtilis. Proc Natl Acad Sci USA 1999, 96:10290-10295. PubMed
  8. Belitsky BR, Sonenshein, AL: CcpA-dependent regulation of Bacillus subtilis glutamate dehydrogenase gene expression. J Bacteriol 2004, 186:3392-3398. PubMed
  9. Belitsky BR, Sonenshein AL (2004) Modulation of activity of Bacillus subtilis regulatory proteins GltC and TnrA by glutamate dehydrogenase. J Bacteriol 186:3399-3407 PubMed
  10. Khan, M. I., K. Ito, H. Kim, H. Ashida, T. Ishikawa, H. Shibata, and Y. Sawa. 2005. Molecular properties and enhancement of thermostability by random mutagenesis of glutamate dehydrogenase from Bacillus subtilis. Biosci. Biotechnol. Biochem. 69: 1861-1870. PubMed
  11. Stillman TJ, Baker PJ, Britton KL, Rice DW Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis. J Mol Biol 1993, 234:1131-1139. PubMed
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