Difference between revisions of "Sandbox"

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−
* '''Description:''' RNA polymerase [[sigma factor]] SigB <br/><br/>
+
* '''Description:''' RNA polymerase forespore-specific (early) [[sigma factor]] SigF <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''
+
|''sigF''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''rpoF ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spoIIAC ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase [[sigma factor]] SigB
+
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase forespore-specific <br/>(early) [[sigma factor]] SigF
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || general stress response
+
|style="background:#ABCDEF;" align="center"|'''Function''' || transcription of sporulation genes (late mother cell)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.418  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.078  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 792 bp, 264 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 765 bp, 255 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rsbW]]'', ''[[rsbX]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spoVAA]]'', ''[[spoIIAB]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB14277&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:sigB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sigF_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>
 
|-
 
|-
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__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 35: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU04730
+
* '''Locus tag:''' BSU23450
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/rsbRSTUVW-sigB-rsbX.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dacF-spoIIAAB-sigF.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10735]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10298]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' SigB subfamily (according to Swiss-Prot)
+
* '''Protein family:''' sigma-70 factor family (according to Swiss-Prot)
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
  
−
=== Genes/ operons controlled by SigB ===
+
=== Genes controlled by SigF ===
  
−
''[[csbB]]'', ''[[ctc]]'', ''[[gsiB]]'', ''[[katE]], [[lexA]],[[licR]], [[sfA]], [[xpf]], [[yaaH]], [[ydeC]], [[ytzE]], [[yvaN]], [[ywhH]]'',
+
''[[dacF]]-[[spoIIAA]]-[[spoIIAB]]-[[sigF]]'', ''[[sigG]]'','' [[pbpF]]'', ''[[yphA]]-[[seaA]]''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 74: Line 74:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[SigB]]-[[RsbW]]
+
* '''Interactions:''' [[SigF]]-[[SpoIIAB]]
  
−
* '''Localization:'''
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:'''
+
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1L0O 1L0O] (complex with SpoIIAB, Geobacillus stearothermophilus)
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P06574 P06574]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P07860 P07860]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU04730]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23450]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 92: Line 92:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[dacF]]-[[spoIIAA]]-[[spoIIAB]]-[[sigF]]''
−
** ''[[rsbR]]-[[rsbS]]-[[rsbT]]-[[rsbU]]-[[rsbV]]-[[rsbW]]-[[sigB]]-[[rsbX]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/8002610 PubMed]
+
''[[spoIIAA]]-[[spoIIAB]]-[[sigF]]''
−
** ''[[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]
 
  
−
* '''Regulation:'''
+
* '''[[Sigma factor]]:''' ''[[dacF]]'': [[SigF]], [[SigG]]
−
** ''[[rsbV]]:'' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/11544224 PubMed]
+
''[[spoIIAA]]'': [[SigH]]
 +
 
 +
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] ,  ''[[dacF]]'': expressed during sporulation, ''[[spoIIAA]]'': expressed early during sporulation
 +
 
 +
* '''Regulatory mechanism:''' ''[[spoIIAA]]'': activated by [[Spo0A]] and repressed by [[SinR]]
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 121: Line 120:
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
  
−
* [[Bill Haldenwang]], San Antonio, USA
+
* [[Charles Moran]], Emory University, NC, USA [http://www.microbiology.emory.edu/moran_c.html homepage]
−
* [[Chet Price]], Davis, USA [http://foodscience.ucdavis.edu/price_lab/pricelab.html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 128: Line 126:
 
=References=
 
=References=
  
−
<pubmed>15805528 10482513 11544224 11532142 6790515 116131, </pubmed>
+
<pubmed>12107147, </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]
+
# M&#228;der et al. (2002) Transcriptome and Proteome Analysis of ''Bacillus subtilis'' Gene Expression Modulated by Amino Acid Availability. ''J. Bacteriol'' '''184:''' 1844288-4295 [http://www.ncbi.nlm.nih.gov/pubmed/12107147 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 forespore-specific (early) sigma factor SigF

Gene name sigF
Synonyms spoIIAC
Essential no
Product RNA polymerase forespore-specific
(early) sigma factor SigF
Function transcription of sporulation genes (late mother cell)
MW, pI 29 kDa, 5.078
Gene length, protein length 765 bp, 255 aa
Immediate neighbours spoVAA, spoIIAB
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SigF context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Locus tag: BSU23450

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: sigma-70 factor family (according to Swiss-Prot)
  • Paralogous protein(s):

Genes controlled by SigF

dacF-spoIIAA-spoIIAB-sigF, sigG, pbpF, yphA-seaA

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: cell membrane (according to Swiss-Prot)

Database entries

  • Structure: 1L0O (complex with SpoIIAB, Geobacillus stearothermophilus)
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

spoIIAA-spoIIAB-sigF

spoIIAA: SigH

  • Regulation: repressed by casamino acids PubMed , dacF: expressed during sporulation, spoIIAA: expressed early during sporulation
  • 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. Mäder et al. (2002) Transcriptome and Proteome Analysis of Bacillus subtilis Gene Expression Modulated by Amino Acid Availability. J. Bacteriol 184: 1844288-4295 PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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