Difference between revisions of "Sandbox"

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−
* '''Description:''' response regulator aspartate phosphatase <br/><br/>
+
* '''Description:''' transcriptional activator of arginine utilization operons <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'''
−
|''rapG''
+
|''rocR''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yycM ''
+
|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''' || response regulator aspartate phosphatase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of sporulation initiation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || transcriptional activator of arginine utilization operons
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 42 kDa, 4.807 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 52.6 kDa, 6.08
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1095 bp, 365 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1383 bp, 461 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yycN]]'', ''[[phrG]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rocD]]'', ''[[yyxA]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB16067&#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:CAB16072&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:rapG_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rocR_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 30: Line 30:
  
 
<br/><br/>
 
<br/><br/>
 +
  
 
=The gene=
 
=The gene=
Line 35: Line 36:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Coordinates:''' 4144771 - 4146153
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 42:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rapG-phrG.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rocR.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11466]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10723]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' transcription activation at [[SigL]]-dependent promoters of ''[[rocA|rocABC]]'', ''[[rocD|rocDEF]]'', and ''[[rocG]]''
  
−
* '''Protein family:'''
+
* '''Protein family:''' [[SigL | Sigma-54]] interacting transcription activator
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 63: Line 63:
  
 
* '''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):'''
+
* '''Cofactor(s):''' ornithine or citrulline are required for RocR-dependent transcription activation [http://www.ncbi.nlm.nih.gov/sites/entrez/9194709  PubMed]
  
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[DegU]]-[[RapG]],  
+
* '''Interactions:''' [[RocR]]-[[SigL]], RocR-[[SigL]]
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 78: Line 81:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.expasy.ch/cgi-bin/sprot-search-ac?P38022]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40300]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU40350]
−
 
 
−
* '''E.C. number:'''
 
  
 
=== Additional information===
 
=== Additional information===
Line 88: Line 89:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''rocR''
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]
  
−
* '''Regulation:'''  
+
* '''Regulation:''' autoregulation by [[RocR]] [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=+7540694 PubMed]
  
−
* '''Regulatory mechanism:'''  
+
* '''Regulatory mechanism:''' autorepression
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' QB5533 (aphA3), from [[Michel Debarbouille]], available in [[Stülke]] lab
  
 
* '''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=
Line 118: Line 119:
 
=References=
 
=References=
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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/sites/entrez/9829940  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]
 +
# 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]
 +
# 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: transcriptional activator of arginine utilization operons

Gene name rocR
Synonyms
Essential no
Product transcriptional regulator
Function transcriptional activator of arginine utilization operons
MW, pI 52.6 kDa, 6.08
Gene length, protein length 1383 bp, 461 amino acids
Immediate neighbours rocD, yyxA
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
RocR context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Coordinates: 4144771 - 4146153

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: transcription activation at SigL-dependent promoters of rocABC, rocDEF, and rocG
  • Protein family: Sigma-54 interacting transcription activator
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
    • Sigma-54 factor interaction domain (143–372)
    • 2x nucleotid-binding domain (171–178),(233–242)
    • HTH motif (434–453)
  • Modification:
  • Cofactor(s): ornithine or citrulline are required for RocR-dependent transcription activation PubMed
  • Effectors of protein activity:
  • Localization:

Database entries

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

Additional information

Expression and regulation

  • Operon: rocR
  • Regulatory mechanism: autorepression
  • Additional information:

Biological materials

  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • Antibody:

Labs working on this gene/protein

Michel Debarbouille, Pasteur Institute, Paris, France Homepage

Your additional remarks

References

  1. Belitsky BR, Sonenshein AL (1998) Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. J Bacteriol 180:6298-6305. PubMed
  2. 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. PubMed
  3. 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. PubMed
  4. 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. 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. 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. PubMed
  7. Author1, Author2 & Author3 (year) Title # Author1, Author2 & Author3 (year) Title Journal 176: 1234-1241. PubMed
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