Difference between revisions of "Sandbox"
Line 1: | Line 1: | ||
− | * '''Description:''' | + | * '''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''' | ||
− | |'' | + | |''sigB'' |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' '' | + | |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''' || | + | |style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase [[sigma factor]] SigB |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"|'''Function''' || | + | |style="background:#ABCDEF;" align="center"|'''Function''' || general stress response |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || | + | |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.418 |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || | + | |style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 aa |
|- | |- | ||
− | |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ | + | |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+[EMBLCDS: | + | |colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBLCDS:CAB12280]+-newId sequences] <br/> (Barbe ''et al.'', 2009)''' |
|- | |- | ||
− | |colspan="2" | '''Genetic context''' <br/> [[Image: | + | |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 35: | Line 35: | ||
=== Basic information === | === Basic information === | ||
− | * '''Locus tag:''' | + | * '''Locus tag:''' BSU04730 |
===Phenotypes of a mutant === | ===Phenotypes of a mutant === | ||
Line 41: | Line 41: | ||
=== Database entries === | === Database entries === | ||
− | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ | + | * '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rsbRSTUVW-sigB-rsbX.html] |
− | * '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+ | + | * '''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 === | ||
− | * '''Catalyzed reaction/ biological activity:''' | + | * '''Catalyzed reaction/ biological activity:''' |
− | * '''Protein family:''' | + | * '''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 64: | Line 68: | ||
* '''Domains:''' | * '''Domains:''' | ||
− | * '''Modification:''' | + | * '''Modification:''' |
* '''Cofactor(s):''' | * '''Cofactor(s):''' | ||
Line 70: | Line 74: | ||
* '''Effectors of protein activity:''' | * '''Effectors of protein activity:''' | ||
− | * '''Interactions:''' | + | * '''Interactions:''' [[SigB]]-[[RsbW]] |
− | * '''Localization:''' | + | * '''Localization:''' |
=== Database entries === | === Database entries === | ||
Line 78: | Line 82: | ||
* '''Structure:''' | * '''Structure:''' | ||
− | * '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/ | + | * '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P06574 P06574] |
− | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+ | + | * '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU04730] |
− | * '''E.C. number:''' | + | * '''E.C. number:''' |
=== Additional information=== | === Additional information=== | ||
Line 88: | Line 92: | ||
=Expression and regulation= | =Expression and regulation= | ||
− | * '''Operon:''' '' | + | * '''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]]:''' | * '''[[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] | ||
− | * '''Regulation:''' | + | * '''Regulation:''' |
− | + | ** ''[[rsbV]]:'' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed] | |
− | * '' | ||
* '''Additional information:''' | * '''Additional information:''' | ||
Line 113: | Line 120: | ||
=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 118: | Line 128: | ||
=References= | =References= | ||
− | <pubmed> | + | <pubmed>15805528 10482513 11544224 11532142 6790515 116131, </pubmed> |
− | # | + | # 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 [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 13:36, 8 June 2009
- Description: RNA polymerase sigma factor SigB
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 ![]() This image was kindly provided by SubtiList
|
Contents
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:
- Swiss prot entry: P06574
- 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
- Bill Haldenwang, San Antonio, USA
- Chet Price, Davis, USA homepage
Your additional remarks
References
Dirk Höper, Uwe Völker, Michael Hecker
Comprehensive characterization of the contribution of individual SigB-dependent general stress genes to stress resistance of Bacillus subtilis.
J Bacteriol: 2005, 187(8);2810-26
[PubMed:15805528]
[WorldCat.org]
[DOI]
(P p)
A Petersohn, M Brigulla, S Haas, J D Hoheisel, U Völker, M Hecker
Global analysis of the general stress response of Bacillus subtilis.
J Bacteriol: 2001, 183(19);5617-31
[PubMed:11544224]
[WorldCat.org]
[DOI]
(P p)
C W Price, P Fawcett, H Cérémonie, N Su, C K Murphy, P Youngman
Genome-wide analysis of the general stress response in Bacillus subtilis.
Mol Microbiol: 2001, 41(4);757-74
[PubMed:11532142]
[WorldCat.org]
[DOI]
(P p)
A Petersohn, J Bernhardt, U Gerth, D Höper, T Koburger, U Völker, M Hecker
Identification of sigma(B)-dependent genes in Bacillus subtilis using a promoter consensus-directed search and oligonucleotide hybridization.
J Bacteriol: 1999, 181(18);5718-24
[PubMed:10482513]
[WorldCat.org]
[DOI]
(P p)
J F Ollington, W G Haldenwang, T V Huynh, R Losick
Developmentally regulated transcription in a cloned segment of the Bacillus subtilis chromosome.
J Bacteriol: 1981, 147(2);432-42
[PubMed:6790515]
[WorldCat.org]
[DOI]
(P p)
W G Haldenwang, R Losick
A modified RNA polymerase transcribes a cloned gene under sporulation control in Bacillus subtilis.
Nature: 1979, 282(5736);256-60
[PubMed:116131]
[WorldCat.org]
[DOI]
(P p)
- 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
- 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
- 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
- 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
- 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
- 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
- Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed