Difference between revisions of "Sandbox"

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−
* '''Description:''' 2-oxoglutarate dehydrogenase (E1 subunit) <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'''
−
|''odhA''
+
|''sigB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''citK ''
+
|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''' || 2-oxoglutarate dehydrogenase (E1 subunit)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase [[sigma factor]] SigB
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || TCA cycle
+
|style="background:#ABCDEF;" align="center"|'''Function''' || general stress response
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/carbon_flow.html Central C-metabolism]'''
+
|colspan="2" style="background:#FAF8CC;" align="center"| '''Metabolic function and regulation of this protein in [[SubtiPathways|''Subti''Pathways]]: <br/>[http://subtiwiki.uni-goettingen.de/pathways/stress_response.html Stress]'''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 105 kDa, 5.871  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.418  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 2823 bp, 941 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yojO]], [[odhB]]''
+
|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:CAB13829&#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:sigB_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:odhA_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 39: Line 37:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU19370
+
* '''Locus tag:''' BSU04730
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 45: Line 43:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/odhAB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rsbRSTUVW-sigB-rsbX.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10272]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10735]
  
 
=== Additional information===
 
=== Additional information===
Line 56: Line 54:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' 2-oxoglutarate + [dihydrolipoyllysine-residue succinyltransferase] lipoyllysine = [dihydrolipoyllysine-residue succinyltransferase] S-succinyldihydrolipoyllysine + CO<sub>2</sub> (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' 2-oxoacid dehydrogenase family (according to Swiss-Prot)
+
* '''Protein family:''' SigB subfamily (according to Swiss-Prot)
  
 
* '''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 74: Line 76:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[OdhA]]-[[OdhB]]-[[PdhD]]
+
* '''Interactions:''' [[SigB]]-[[RsbW]]
  
 
* '''Localization:'''
 
* '''Localization:'''
Line 82: Line 84:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P23129 P23129]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P06574 P06574]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU19370]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU04730]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/1.2.4.2 1.2.4.2]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[odhA]]''-''[[odhB]]''
+
* '''Operon:'''  
 +
** ''[[rsbR]]-[[rsbS]]-[[rsbT]]-[[rsbU]]-[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
 +
** ''[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/2170324 PubMed]
 +
 +
* '''[[Sigma factor]]:'''
 +
** ''[[rsbR]]'': [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
 +
** ''[[rsbV]]:'' [[SigB]] [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
  
−
* '''Sigma factor:''' [[SigA]]
+
* '''Regulation:''' 
−
 
+
** ''[[rsbV]]:'' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
−
* '''Regulation:''' constitutive
 
−
 
 
−
* '''Regulatory mechanism:'''
 
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 104: Line 109:
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP671 (spc), GP665 (aphA3), GP684 (cat), available in [[Stülke]] lab
+
* '''Mutant:'''
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
Line 117: Line 122:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
* [[Bill Haldenwang]], San Antonio, USA
 +
* [[Chet Price]], Davis, USA [http://foodscience.ucdavis.edu/price_lab/pricelab.html homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 130:
 
=References=
 
=References=
  
−
<pubmed>2500417,,1508153, </pubmed>
+
<pubmed>8655572,18035607,3123466,8682769,11717291,8460143,10369900,3112122,8468294,8458834,13129942,6784117,12867438,3100810,8253681,12270815,12486038,8764398,3027048,7601843,15342585,17575448,15342582,10482513,8002610,11591687,10220166,17586624,9767581,3016731,11902719,14651641,10503549,15205443,6405278,10383961,15312768,17498739,11377871,15805528 10482513 11544224 11532142 6790515 116131, </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]
 +
# 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]
 +
# 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 15:47, 13 June 2009

Gene name sigB
Synonyms rpoF
Essential no
Product RNA polymerase sigma factor SigB
Function general stress response
Metabolic function and regulation of this protein in SubtiPathways:
Stress
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

  • Locus tag: BSU04730

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: SigB subfamily (according to Swiss-Prot)
  • 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:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • 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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