Difference between revisions of "Sandbox"

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−
* '''Description:''' transcription repressor of the pur operon <br/><br/>
+
* '''Description:''' RNA polymerase [[sigma factor]] SigB <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'''
−
|''purR''
+
|''sigB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yabI ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rpoF ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || transcription repressor of the pur operon
+
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase [[sigma factor]] SigB
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of purine biosynthesis
+
|style="background:#ABCDEF;" align="center"|'''Function''' || general stress response
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 31 kDa, 5.771  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.418  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 855 bp, 285 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ispE]]'', ''[[yabJ]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbW]]'', ''[[rsbX]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11823&#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:CAB12280&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:purR_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sigB_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 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/purR-yabJ.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rsbRSTUVW-sigB-rsbX.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10110]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10735]
  
 
=== Additional information===
 
=== Additional information===
Line 52: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Biological activity:''' transcriptional repressor of purine biosynthetic operons
+
* '''Catalyzed reaction/ biological activity:'''  
  
 
* '''Protein family:'''
 
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
 +
 +
=== Genes/ operons controlled by SigB ===
 +
 +
''[[csbB]]'', ''[[ctc]]'', ''[[gsiB]]'', ''[[katE]], [[lexA]],[[licR]], [[sfA]], [[xpf]], [[yaaH]], [[ydeC]], [[ytzE]], [[yvaN]], [[ywhH]]'',
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 68: Line 72:
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:''' PRPP acts as inducer, binding results in release of PurR from the operator [http://www.ncbi.nlm.nih.gov/sites/entrez/10919400 PubMed]
+
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[PurR]]-[[Prs]],
+
* '''Interactions:''' [[SigB]]-[[RsbW]],  
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 76: Line 80:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' 1P4A (complex with PRPP) [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?uid=25670 NCBI] [http://www.ncbi.nlm.nih.gov/sites/entrez/12837783 PubMed]
+
* '''Structure:'''
  
 
* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00470]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU04730]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
−
requires [[YabJ]] for ''in vivo'' activity
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[purR]]-[[yabJ]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed]
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:'''  
+
* '''[[Sigma factor]]:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
  
−
* '''Regulation:''' negative autoregulation [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed]
+
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
  
−
* '''Regulatory mechanism:''' repression by [[PurR]] [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed]
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 120: Line 122:
 
=References=
 
=References=
  
−
# Weng et al. (1995) Identification of the ''Bacillus subtilis pur'' operon repressor. ''Proc. Natl. Acad. Sci. USA'' '''92:''' 7455-7459. [http://www.ncbi.nlm.nih.gov/sites/entrez/7638212 PubMed]
+
# H&ouml;per et al. (2005) Comprehensive Characterization of the Contribution of Individual [[SigB]]-Dependent General Stress Genes to Stress Resistance of ''Bacillus subtilis''. J. Bact. '''187:''' 2810-2826  [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
−
# Weng & Zalkin (2000) Mutations in the ''Bacillus subtilis'' purine repressor that perturb PRPP effector function ''in vitro'' and ''in vivo''.''Currr. Microbiol.'' '''41:''' 56-59. [http://www.ncbi.nlm.nih.gov/sites/entrez/10919400 PubMed]
+
# Petersohn, A., Bernhardt, J., Gerth, U., Höper, D., Koburger, T., Völker, U. and Hecker, M. 1999. Identification of sigma(B)-dependent genes in Bacillus subtilis using a promoter consensus-directed search and oligonucleotide hybridization. J. Bacteriol. 181: 5718-5724. [http://www.ncbi.nlm.nih.gov/sites/entrez/10482513 PubMed]
−
# Sinha et al. (2003) The purine repressor of ''Bacillus subtilis'': a novel combination of domains adapted for transcription regulation.''J. Bacteriol.'' '''185:''' 4087-4098. [http://www.ncbi.nlm.nih.gov/sites/entrez/12837783 PubMed]
+
# Petersohn, A., Brigulla, M., Haas, S., Hoheisel, J. D., Völker, U. and Hecker, M. 2001. Global analysis of the general stress reponse of Bacillus subtilis. J. Bacteriol. 183: 5617-5631. [http://www.ncbi.nlm.nih.gov/sites/entrez/11544224 PubMed]
 +
# Price, C. W., Fawcett, P., Cérémonie, H., Su, N., Murphy, C. K. and Youngman, P. 2001. Genome-wide analysis of the general stress response in Bacillus subtilis. Mol. Microbiol. 41: 757-774. [http://www.ncbi.nlm.nih.gov/sites/entrez/11532142 PubMed]
 +
# Ollington, J. F., Haldenwang, W. G., Huynh, T. V. and Losick, R. 1981. Developmentally regulated transcription in a cloned segment of the Bacillus subtilis chromosome. J. Bacteriol. 147: 432-442. [http://www.ncbi.nlm.nih.gov/sites/entrez/6790515 PubMed]
 +
# Haldenwang, W. G. & Losick, R. (1979). A modified RNA polymerase transcribes a cloned gene under sporulation control in Bacillus subtilis. Nature 282, 256-260 [http://www.ncbi.nlm.nih.gov/pubmed/116131 PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 23:50, 27 April 2009

Gene name sigB
Synonyms rpoF
Essential no
Product RNA polymerase sigma factor SigB
Function general stress response
MW, pI 29 kDa, 5.418
Gene length, protein length 792 bp, 264 aa
Immediate neighbours rsbW, rsbX
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SigB 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):

Genes/ operons controlled by SigB

csbB, ctc, gsiB, katE, lexA,licR, sfA, xpf, yaaH, ydeC, ytzE, yvaN, ywhH,

Extended information on the protein

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

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • 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. Höper et al. (2005) Comprehensive Characterization of the Contribution of Individual SigB-Dependent General Stress Genes to Stress Resistance of Bacillus subtilis. J. Bact. 187: 2810-2826 PubMed
  2. Petersohn, A., Bernhardt, J., Gerth, U., Höper, D., Koburger, T., Völker, U. and Hecker, M. 1999. Identification of sigma(B)-dependent genes in Bacillus subtilis using a promoter consensus-directed search and oligonucleotide hybridization. J. Bacteriol. 181: 5718-5724. PubMed
  3. Petersohn, A., Brigulla, M., Haas, S., Hoheisel, J. D., Völker, U. and Hecker, M. 2001. Global analysis of the general stress reponse of Bacillus subtilis. J. Bacteriol. 183: 5617-5631. PubMed
  4. Price, C. W., Fawcett, P., Cérémonie, H., Su, N., Murphy, C. K. and Youngman, P. 2001. Genome-wide analysis of the general stress response in Bacillus subtilis. Mol. Microbiol. 41: 757-774. PubMed
  5. Ollington, J. F., Haldenwang, W. G., Huynh, T. V. and Losick, R. 1981. Developmentally regulated transcription in a cloned segment of the Bacillus subtilis chromosome. J. Bacteriol. 147: 432-442. PubMed
  6. Haldenwang, W. G. & Losick, R. (1979). A modified RNA polymerase transcribes a cloned gene under sporulation control in Bacillus subtilis. Nature 282, 256-260 PubMed
  7. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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