Difference between revisions of "Sandbox"

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−
* '''Description:''' forespore-specific protein, inhibitor of [[SigG]] <br/><br/>
+
* '''Description:''' DEAD-box RNA helicase<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'''
−
|''csfB''
+
|''cshB ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yaaM ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqfR''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || inhibitor of [[SigG]]
+
|style="background:#ABCDEF;" align="center"| '''Product''' || DEAD-box RNA helicase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || control of [[SigG]] activity
+
|style="background:#ABCDEF;" align="center"|'''Function''' || RNA helicase
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 7 kDa, 7.671  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 49 kDa, 9.89  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 192 bp, 64 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1314 bp, 438 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rrnA-5S]]'', ''[[xpaC]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[nfo]]'', ''[[yqfQ]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11800&#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:CAB14444&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:csfB_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yqfR_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:''' BSU00240
+
* '''Locus tag:''' BSU25140
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
  
−
premature activation of [[SigG]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17921305 PubMed]
 
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/csfB.html]
+
* '''DBTBS entry:''' no entry
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10088]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11664]
  
 
=== Additional information===
 
=== Additional information===
Line 53: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' inhibitor of [[SigG]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17921305 PubMed1] [http://www.ncbi.nlm.nih.gov/sites/entrez/19497328 PubMed2]
+
* '''Catalyzed reaction/ biological activity:''' RNA helicase
  
 +
* '''Protein family:''' DEAD box helicase family (according to Swiss-Prot) DEAD-box RNA helicase
  
−
* '''Protein family:'''
+
* '''Paralogous protein(s):''' [[CshA]], [[DeaD]], [[YfmL]]
−
 
 
−
* '''Paralogous protein(s):'''
 
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
Line 72: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[CsfB]]-[[SigG]] [http://www.ncbi.nlm.nih.gov/sites/entrez/19497328 PubMed]
+
* '''Interactions:''' [[CshB]]-[[CspB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]
  
−
* '''Localization:''' forespore
+
* '''Localization:''' cytoplasma, colocalizes with the ribosomes [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]
  
 
=== Database entries ===
 
=== Database entries ===
Line 80: Line 78:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37534 P37534]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P54475 P54475]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU00240]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25140]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 90: Line 88:
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''csfB''
+
* '''Operon:'''  
  
−
* '''[[Sigma factor]]:''' [[SigF]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16497325 PubMed]
+
* '''Sigma factor:'''  
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
Line 98: Line 96:
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 110: Line 108:
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:'''  
+
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
  
 
* '''Antibody:'''
 
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Mohamed Marahiel]], Marburg University, Germany [http://www.uni-marburg.de/fb15/fachgebiete/bio/marahiel?language_sync=1 homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 120:
 
=References=
 
=References=
  
−
<pubmed>16497325 17921305, </pubmed>
+
<pubmed>16352840, </pubmed>
−
# Wang et al. (2006) The forespore line of gene expression in ''Bacillus subtilis''. ''J. Mol. Biol.'' '''358:''' 16-37. [http://www.ncbi.nlm.nih.gov/sites/entrez/16497325 PubMed]
+
# Hunger, K., Beckering, C. L., Wiegeshoff, F., Graumann, P. L. & Marahiel, M. A. (2006). Cold-induced putative DEAD box RNA helicases CshA and CshB are essential for cold adaptation and interact with cold shock protein B in ''Bacillus subtilis''. J Bacteriol. 188:240-248. [http://www.ncbi.nlm.nih.gov/sites/entrez/16352840 PubMed]
−
# Chary et al. (2007) Expression of the sigmaF-directed ''csfB'' locus prevents premature appearance of sigmaG activity during sporulation of ''Bacillus subtilis''.''J. Bacteriol.'' '''189:''' 8754-8757. [http://www.ncbi.nlm.nih.gov/sites/entrez/17921305 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 13:13, 8 June 2009

  • Description: DEAD-box RNA helicase

Gene name cshB
Synonyms yqfR
Essential no
Product DEAD-box RNA helicase
Function RNA helicase
MW, pI 49 kDa, 9.89
Gene length, protein length 1314 bp, 438 aa
Immediate neighbours nfo, yqfQ
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
YqfR context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU25140

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: RNA helicase
  • Protein family: DEAD box helicase family (according to Swiss-Prot) DEAD-box RNA helicase

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
  • Localization: cytoplasma, colocalizes with the ribosomes PubMed

Database entries

  • Structure:
  • KEGG entry: [2]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • GFP fusion:
  • two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab
  • Antibody:

Labs working on this gene/protein

Mohamed Marahiel, Marburg University, Germany homepage

Your additional remarks

References

Karen Hunger, Carsten L Beckering, Frank Wiegeshoff, Peter L Graumann, Mohamed A Marahiel
Cold-induced putative DEAD box RNA helicases CshA and CshB are essential for cold adaptation and interact with cold shock protein B in Bacillus subtilis.
J Bacteriol: 2006, 188(1);240-8
[PubMed:16352840] [WorldCat.org] [DOI] (P p)

  1. Hunger, K., Beckering, C. L., Wiegeshoff, F., Graumann, P. L. & Marahiel, M. A. (2006). Cold-induced putative DEAD box RNA helicases CshA and CshB are essential for cold adaptation and interact with cold shock protein B in Bacillus subtilis. J Bacteriol. 188:240-248. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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