Difference between revisions of "Sandbox"

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* '''Description:''' transcriptional activator of arginine utilization operons <br/><br/>
+
* '''Description:''' membrane protein translocase, essential for sigma-G activity at stage III <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'''
−
|''rocR''
+
|''spoIIIJ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spo0J87 ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
+
|style="background:#ABCDEF;" align="center"| '''Product''' || membrane protein translocase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || transcriptional activator of arginine utilization operons
+
|style="background:#ABCDEF;" align="center"|'''Function''' || control of SigG activity
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52.6 kDa, 6.08
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 9.992 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1383 bp, 461 amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 783 bp, 261 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rocD]]'', ''[[yyxA]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[jag]]'', ''[[rnpA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16072&#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:CAB16141&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rocR_context.gif]]
+
|-
 +
|-
 +
|colspan="2" | '''Genetic context''' <br/> [[Image:ThdF_jag_spoIIIJ_rnpA_rpmH_context.png]]
 
  <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/>
−
 
 
  
 
=The gene=
 
=The gene=
Line 36: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:''' 4144771 - 4146153
+
* '''Coordinates:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
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=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocR.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/spoIIIJ-jag.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10723]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10062]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
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=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' transcription activation at [[SigL]]-dependent promoters of ''[[rocA|rocABC]]'', ''[[rocD|rocDEF]]'', and ''[[rocG]]''
+
* '''Catalyzed reaction/ biological activity:'''  
 +
 
 +
* '''Protein family:'''
  
−
* '''Protein family:''' [[SigL | Sigma-54]] interacting transcription activator
+
* '''Paralogous protein(s):''' [[YqjG]], one of the two proteins has to be present for viability [http://www.ncbi.nlm.nih.gov/sites/entrez/17114254 PubMed]
  
−
* '''Paralogous protein(s):'''
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Domains:'''  
 
* '''Domains:'''  
−
**[[SigL | Sigma-54]] factor interaction domain (143–372)
 
−
**2x nucleotid-binding domain (171–178),(233–242)
 
−
**HTH motif (434–453)
 
  
 
* '''Modification:'''
 
* '''Modification:'''
  
−
* '''Cofactor(s):''' ornithine or citrulline are required for RocR-dependent transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/9194709  PubMed]
+
* '''Cofactor(s):'''
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[RocR]]-[[SigL]], RocR-[[SigL]]
+
* '''Interactions:''' [[SpoIIIAE]]-[[SpoIIIJ]],  
  
−
* '''Localization:'''
+
* '''Localization:''' membrane [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P38022]
+
* '''Swiss prot entry:'''
 +
 
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU41040]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40350]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''rocR''
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]
+
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' autoregulation by [[RocR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]
+
* '''Regulation:'''  
  
−
* '''Regulatory mechanism:''' autorepression
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' QB5533 (aphA3), from [[Michel Debarbouille]], available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
+
       
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
 +
 +
* '''two-hybrid system:'''
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Michel Debarbouille]], Pasteur Institute, Paris, France [http://www.pasteur.fr/ip/easysite/go/03b-00000m-0ob/recherche/departements-scientifiques/microbiologie/unites-et-groupes/unite-de-biologie-des-bacteries-pathogenes-a-gram-positif/les-membres-de-l-equipe Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
# 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/sites/entrez/9829940  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 BR, Sonenshein, AL: (1999) An enhancer element located downstream of the major glutamate dehydrogenase gene of Bacillus subtilis. Proc Natl Acad Sci USA , 96:10290-10295. [http://www.ncbi.nlm.nih.gov/sites/entrez/10468601  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]
−
# Gardan R, Rapoport G, Débarbouillé M:(1997) Role of the transcriptional activator RocR in the arginine-degradation pathway of Bacillus subtilis. Mol Microbiol , 24:825-837. [http://www.ncbi.nlm.nih.gov/sites/entrez/9194709  PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Gardan R, Rapoport G, Débarbouillé M: (1995) Expression of the rocDEF operon involved in arginine catabolism in Bacillus subtilis. J Mol Biol , 249:843-856. [http://www.ncbi.nlm.nih.gov/sites/entrez/7540694  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/sites/entrez/12634342 PubMed]
 
−
# Calogero S, Gardan R, Glaser P, Schweizer J, Rapoport G, Debarbouille M. (1994) RocR, a novel regulatory protein controlling arginine utilization in ''Bacillus subtilis'', belongs to the NtrC/NifA family of transcriptional activators. ''J. Bacteriol.'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/8113162 PubMed]
 
−
# Author1, Author2 & Author3 (year) Title # Author1, Author2 & Author3 (year) Title ''Journal'' '''176:''' 1234-1241. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 

Revision as of 00:26, 28 April 2009

  • Description: membrane protein translocase, essential for sigma-G activity at stage III

Gene name spoIIIJ
Synonyms spo0J87
Essential no
Product membrane protein translocase
Function control of SigG activity
MW, pI 29 kDa, 9.992
Gene length, protein length 783 bp, 261 aa
Immediate neighbours jag, rnpA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ThdF jag spoIIIJ rnpA rpmH context.png
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): YqjG, 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:
  • Localization: membrane PubMed

Database entries

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