Difference between revisions of "Sandbox"

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−
* '''Description:''' xylan beta-1,4-xylosidase <br/><br/>
+
* '''Description:''' general stress protein, survival of ethanol  stress, spore coat protein <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'''
−
|''xynB''
+
|''yaaH''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''ynaK ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || xylan beta-1,4-xylosidase
+
|style="background:#ABCDEF;" align="center"| '''Product''' || spore coat protein
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || xylan degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || survival of ethanol  stress
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 61 kDa, 5.326  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 48 kDa, 5.618  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1599 bp, 533 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1281 bp, 427 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[xynP]]'', ''[[xylR]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dgk]]'', ''[[yaaI]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB13642&#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:CAB11792&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yaaH_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:xynB_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 37: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU17580
+
* '''Locus tag:''' BSU00160
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/xynPB.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/yaaH.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11987]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10080]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Hydrolysis of (1->4)-beta-D-xylans, to remove successive D-xylose residues from the non-reducing termini (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' glycosyl hydrolase 43 family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
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* '''Interactions:'''
 
* '''Interactions:'''
  
−
* '''Localization:''' cell membrane (according to Swiss-Prot)
+
* '''Localization:''' spore wall (according to Swiss-Prot),  spore coat [http://www.ncbi.nlm.nih.gov/sites/entrez/11964120 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1YIF 1YIF]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P94489 P94489]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37531 P37531]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU17580]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00160]
  
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/3.2.1.37 3.2.1.37]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
 +
 +
required for survival of ethanol stress [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[xynP]]-[[xynB]]''
+
* '''Operon:''' ''yaaH'' [http://www.ncbi.nlm.nih.gov/sites/entrez/10419957 PubMed]
  
−
* '''[[Sigma factor]]:''' [[SigA]]
+
* '''[[Sigma factor]]:''' [[SigE]] [http://www.ncbi.nlm.nih.gov/sites/entrez/10419957 PubMed], [[SigB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
  
−
* '''Regulation:''' repressed by glucose ([[CcpA]]) ,  carbon catabolite repression ([[CcpA]]), induction by xylose ([[XylR]])
+
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed], expressed during sporulation [http://www.ncbi.nlm.nih.gov/sites/entrez/10419957 PubMed]
  
−
* '''Regulatory mechanism:''' [[CcpA]]: transcription repression,  [[CcpA]]: transcription repression, [[XylR]]: transcription repression
+
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:''' the mRNA is very stable (half-life > 15 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/12884008 PubMed]
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>8012596, </pubmed>
+
<pubmed>15805528 10419957 15805528 11964120, </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]
−
# Lindner, C., Stülke, J. & Hecker, M. (1994) Regulation of xylanolytic enzymes in Bacillus subtilis. Microbiology 140: 753-757. [http://www.ncbi.nlm.nih.gov/sites/entrez/8012596 PubMed]
+
# Kodama et al. (1999) The ''Bacillus subtilis yaaH'' gene is transcribed by SigE RNA polymerase during sporulation, and its product is involved in germination of spores.''J. Bacteriol.'' '''181:''' 4584-4591. [http://www.ncbi.nlm.nih.gov/sites/entrez/10419957 PubMed]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
# Höper et al. (2005) Comprehensive characterization of the contribution of individual SigB-dependent general stress genes to stress resistance of ''Bacillus subtilis''.''J.Bacteriol.'' '''187:''' 2810-2826. [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
 +
# Aronson (2002) Sporulation and delta-endotoxin synthesis by ''Bacillus thuringiensis''.''Cell. Mol. Life Sci.'' '''59:''' 417-425. [http://www.ncbi.nlm.nih.gov/sites/entrez/11964120 PubMed]

Revision as of 13:42, 8 June 2009

  • Description: general stress protein, survival of ethanol stress, spore coat protein

Gene name yaaH
Synonyms
Essential no
Product spore coat protein
Function survival of ethanol stress
MW, pI 48 kDa, 5.618
Gene length, protein length 1281 bp, 427 aa
Immediate neighbours dgk, yaaI
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YaaH context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU00160

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):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Interactions:
  • Localization: spore wall (according to Swiss-Prot), spore coat PubMed

Database entries

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

Additional information

required for survival of ethanol stress PubMed

Expression and regulation

  • Regulation: induced by stress (SigB) PubMed, expressed during sporulation PubMed
  • Regulatory mechanism:
  • Additional information: the mRNA is very stable (half-life > 15 min) PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/protein

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 Aronson
Sporulation and delta-endotoxin synthesis by Bacillus thuringiensis.
Cell Mol Life Sci: 2002, 59(3);417-25
[PubMed:11964120] [WorldCat.org] [DOI] (P p)

T Kodama, H Takamatsu, K Asai, K Kobayashi, N Ogasawara, K Watabe
The Bacillus subtilis yaaH gene is transcribed by SigE RNA polymerase during sporulation, and its product is involved in germination of spores.
J Bacteriol: 1999, 181(15);4584-91
[PubMed:10419957] [WorldCat.org] [DOI] (P p)

  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. Kodama et al. (1999) The Bacillus subtilis yaaH gene is transcribed by SigE RNA polymerase during sporulation, and its product is involved in germination of spores.J. Bacteriol. 181: 4584-4591. PubMed
  3. Höper et al. (2005) Comprehensive characterization of the contribution of individual SigB-dependent general stress genes to stress resistance of Bacillus subtilis.J.Bacteriol. 187: 2810-2826. PubMed
  4. Aronson (2002) Sporulation and delta-endotoxin synthesis by Bacillus thuringiensis.Cell. Mol. Life Sci. 59: 417-425. PubMed
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