Difference between revisions of "Sandbox"

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* '''Description:''' RNA polymerase forespore-specific (early) [[sigma factor]] SigF <br/><br/>
+
* '''Description:''' RNA polymerase sigma factor SigI <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'''
−
|''sigF''
+
|''sigI''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''spoIIAC ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ykoZ ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase forespore-specific <br/>(early) [[sigma factor]] SigF
+
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase sigma factor SigI
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || transcription of sporulation genes (late mother cell)
+
|style="background:#ABCDEF;" align="center"|'''Function''' || control of a class of heat shock genes
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 5.078  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 29 kDa, 8.306  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 765 bp, 255 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 753 bp, 251 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[spoVAA]]'', ''[[spoIIAB]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[ykoY]]'', ''[[rsgI]]''
 
|-
 
|-
−
|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" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13218&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:sigF_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:sigI_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:''' BSU23450
+
* '''Locus tag:''' BSU13450
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
 +
 +
temperature-sensitive growth on agar plates [http://www.ncbi.nlm.nih.gov/sites/entrez/11157964 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/dacF-spoIIAAB-sigF.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/sigI-rsgI.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10298]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13269]
  
 
=== Additional information===
 
=== Additional information===
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* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' sigma-70 factor family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
  
−
=== Genes controlled by SigF ===
+
=== Members of the SigI regulon ===
  
−
''[[dacF]]-[[spoIIAA]]-[[spoIIAB]]-[[sigF]]'', ''[[sigG]]'','' [[pbpF]]'', ''[[yphA]]-[[seaA]]''
+
''[[gsiB]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/11157964 PubMed], ''[[mreBH]], [[bcrC]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/18156261 PubMed]
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 74: Line 76:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[SigF]]-[[SpoIIAB]]
+
* '''Interactions:''' [[RsgI]]-[[SigI]],  [[RsgI]]-[[SigI]], the interaction inhibits SigI activity [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 PubMed]
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1L0O 1L0O] (complex with SpoIIAB, Geobacillus stearothermophilus)
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P07860 P07860]
+
* '''Swiss prot entry:'''
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU23450]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU13450]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
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=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[dacF]]-[[spoIIAA]]-[[spoIIAB]]-[[sigF]]''
+
* '''Operon:'''
−
''[[spoIIAA]]-[[spoIIAB]]-[[sigF]]''
+
* '''Operon:''' ''[[sigI]]-[[rsgI]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 PubMed]
  
−
* '''[[Sigma factor]]:''' ''[[dacF]]'': [[SigF]], [[SigG]]
+
* '''Sigma factor:''' [[SigI]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 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
+
* '''Regulation:''' induced by heat [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 PubMed]
  
−
* '''Regulatory mechanism:''' ''[[spoIIAA]]'': activated by [[Spo0A]] and repressed by [[SinR]]
+
* '''Regulatory mechanism:'''  
  
 
* '''Additional information:'''
 
* '''Additional information:'''
Line 119: Line 120:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
* [[Charles Moran]], Emory University, NC, USA [http://www.microbiology.emory.edu/moran_c.html homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 126: Line 125:
 
=References=
 
=References=
  
−
<pubmed>12107147, </pubmed>
+
<pubmed>17185538 11157964 18156261, </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]
+
# Asai K, Ootsuji T, Obata K, Matsumoto T, Fujita Y, Sadaie Y. (2007) Regulatory role of RsgI in ''sigI'' expression in ''Bacillus subtilis''. ''Microbiology'' '''153:''' 92-101. [http://www.ncbi.nlm.nih.gov/sites/entrez/17185538 PubMed]
 +
# Zuber, U., K. Drzewiecki, and M. Hecker (2001) Putative sigma factor SigI (YkoZ) of ''Bacillus subtilis'' is induced by heat shock ''J. Bacteriol.'' '''183:''' 1472-1475. [http://www.ncbi.nlm.nih.gov/sites/entrez/11157964 PubMed]
 +
# Tseng, C. L., and Shaw, G. C. (2008) Genetic evidence for the actin homolog gene ''mreBH'' and the bacitracin resistance gene ''bcrC'' as targets of the alternative sigma factor SigI of ''Bacillus subtilis''. ''J. Bacteriol.'' '''190:''' 1561-1567. [http://www.ncbi.nlm.nih.gov/sites/entrez/18156261 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 SigI

Gene name sigI
Synonyms ykoZ
Essential no
Product RNA polymerase sigma factor SigI
Function control of a class of heat shock genes
MW, pI 29 kDa, 8.306
Gene length, protein length 753 bp, 251 aa
Immediate neighbours ykoY, rsgI
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
SigI context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU13450

Phenotypes of a mutant

temperature-sensitive growth on agar plates PubMed

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity:
  • Protein family:
  • Paralogous protein(s):

Members of the SigI regulon

gsiB PubMed, mreBH, bcrC PubMed

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

  • Regulation: induced by heat PubMed
  • 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

Chi-Ling Tseng, Gwo-Chyuan Shaw
Genetic evidence for the actin homolog gene mreBH and the bacitracin resistance gene bcrC as targets of the alternative sigma factor SigI of Bacillus subtilis.
J Bacteriol: 2008, 190(5);1561-7
[PubMed:18156261] [WorldCat.org] [DOI] (I p)

Kei Asai, Takafumi Ootsuji, Kazue Obata, Takashi Matsumoto, Yasutaro Fujita, Yoshito Sadaie
Regulatory role of RsgI in sigI expression in Bacillus subtilis.
Microbiology (Reading): 2007, 153(Pt 1);92-101
[PubMed:17185538] [WorldCat.org] [DOI] (P p)

U Zuber, K Drzewiecki, M Hecker
Putative sigma factor SigI (YkoZ) of Bacillus subtilis is induced by heat shock.
J Bacteriol: 2001, 183(4);1472-5
[PubMed:11157964] [WorldCat.org] [DOI] (P p)

  1. Asai K, Ootsuji T, Obata K, Matsumoto T, Fujita Y, Sadaie Y. (2007) Regulatory role of RsgI in sigI expression in Bacillus subtilis. Microbiology 153: 92-101. PubMed
  2. Zuber, U., K. Drzewiecki, and M. Hecker (2001) Putative sigma factor SigI (YkoZ) of Bacillus subtilis is induced by heat shock J. Bacteriol. 183: 1472-1475. PubMed
  3. Tseng, C. L., and Shaw, G. C. (2008) Genetic evidence for the actin homolog gene mreBH and the bacitracin resistance gene bcrC as targets of the alternative sigma factor SigI of Bacillus subtilis. J. Bacteriol. 190: 1561-1567. PubMed
  4. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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