Difference between revisions of "Sandbox"

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* '''Description:''' trigger enzyme: catabolic glutamate dehydrogenase induced by arginine, ornithine or proline, subject to carbon catabolite repression  <br/><br/>
+
* '''Description:''' threonyl-tRNA synthetase (minor) <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'''
−
|''rocG''
+
|''thrZ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''thrS2 ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glutamate dehydrogenase (major)  
+
|style="background:#ABCDEF;" align="center"| '''Product''' || threonyl-tRNA synthetase (minor)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || arginine utilization, controls the activity of [[GltC]]
+
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 46.2 kDa, 6.28
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 73 kDa, 5.753 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1272 bp, 424 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1914 bp, 638 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yweA]]'', ''[[rocA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ywhA]]'', ''[[mmr]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15806&#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:CAB15783&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rocG_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:thrZ_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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<br/><br/>
 
<br/><br/>
−
 
  
 
=The gene=
 
=The gene=
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=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 3879765 - 3881036
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
Poor growth on complex media such as SP (sporulation medium). No growth in minimal media with arginine as the only carbon source. Rapid accumulation of suppressor mutants ([[gudB |''gudB1'']])
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocG.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/thrZ-ywhA.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10621]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10421]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
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=== Basic information/ Evolution ===
 
=== 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 [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' Glu/Leu/Phe/Val dehydrogenases family
+
* '''Protein family:'''
  
−
* '''Paralogous protein(s):''' [[GudB]]
+
* '''Paralogous protein(s):''' [[ThrS]], one of the two proteins has to be present for viability [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' RocG-[[GltC]], this interaction prevents transcription activation of the ''[[gltA]]-[[gltB]]'' operon by GltC [http://www.ncbi.nlm.nih.gov/sites/entrez/17608797 PubMed]
+
* '''Interactions:'''
  
 
* '''Localization:'''
 
* '''Localization:'''
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P39633]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37790]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU37560]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.4.1.2 1.4.1.2]
+
* '''E.C. number:'''
  
 
=== 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:''' ''rocG''
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigL]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+10468601 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' induced by arginine ([[RocR]], [[AhrC]]), ornithine or proline, subject to carbon catabolite repression ([[CcpA]])
+
* '''Regulation:'''  
  
−
* '''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
+
* '''Regulatory mechanism:'''  
  
−
* '''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]  
−
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]
 
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP747 (spc), GP726 (aphA3), GP810 (tet) available in [[Stülke]] lab
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP902 (in [[pGP172]], N-terminal Strep-tag), a series of ''rocG'' variants is also available in [[pGP172]], 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=
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=References=
 
=References=
  
−
'''Enzymatic activity of RocG'''
+
# 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]
−
# 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]
+
# Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 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]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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]
 
−
 
 
−
'''Function in the control of [[GltC]] activity'''
 
−
# 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]  
 
−
# 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 (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]
 
−
 
 
−
'''Expression of ''rocG'''''
 
−
# 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/sites/entrez/12634342 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]
 

Revision as of 23:54, 16 April 2009

  • Description: threonyl-tRNA synthetase (minor)

Gene name thrZ
Synonyms thrS2
Essential no
Product threonyl-tRNA synthetase (minor)
Function translation
MW, pI 73 kDa, 5.753
Gene length, protein length 1914 bp, 638 aa
Immediate neighbours ywhA, mmr
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ThrZ context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s): ThrS, one of the two proteins has to be present for viability PubMed

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization:

Database entries

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

Additional information

  • subject to Clp-dependent proteolysis upon glucose starvation PubMed

Expression and regulation

  • Operon:
  • Regulation:
  • Regulatory mechanism:
  • Additional information: subject to Clp-dependent proteolysis upon glucose starvation PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

Your additional remarks

References

  1. Gerth et al. (2008) Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis. J Bacteriol 190:321-331 PubMed
  2. Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. PubMed
  3. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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