Difference between revisions of "Sandbox"

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−
* '''Description:''' "Catabolite repression HPr-like protein", Cofactor of the [[CcpA]] transcription factor<br/><br/>
+
* '''Description:''' general stress 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'''
−
|''crh''
+
|''csbB''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yvcM''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yfhN ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || catabolite repression HPr-like protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || unknown
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || catabolite repression
+
|style="background:#ABCDEF;" align="center"|'''Function''' || survival of ethanol and salt stress
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 9,2 kDa, 4.70
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 37 kDa, 9.199 
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 255 bp, 85  amino acids
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 987 bp, 329 aa
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yvcL]]'', ''[[yvcN]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yfhM]]'', ''[[yfhO]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB15479&#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:CAB12688&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:crh_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:csbB_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:''' BSU34740
+
* '''Locus tag:''' BSU08600
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 41: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' no entry
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/csbB.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG12403]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11834]
  
 
=== Additional information===
 
=== Additional information===
 +
  
 
=The protein=
 
=The protein=
Line 53: Line 54:
 
* '''Catalyzed reaction/ biological activity:'''  
 
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' HPr family (according to Swiss-Prot) [[PtsH]],HPr family
+
* '''Protein family:''' GtrB subfamily (according to Swiss-Prot)
  
−
* '''Paralogous protein(s):''' [[PtsH |HPr]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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* '''Kinetic information:'''
 
* '''Kinetic information:'''
  
−
* '''Domains:''' HPr domain (1–85)
+
* '''Domains:'''  
  
−
* '''Modification:''' phosphorylation on Ser46 by [[HprK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed]
+
* '''Modification:'''
  
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
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* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' Crh-[[GapA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed], Crh-[[CcpA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/12972249 PubMed], [[HprK]]-Crh [http://www.ncbi.nlm.nih.gov/sites/entrez/12009882 PubMed]
+
* '''Interactions:'''
  
−
* '''Localization:'''
+
* '''Localization:''' cell membrane (according to Swiss-Prot)
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=2AK7 2AK7] (dimeric Crh-Ser46-P),  [http://www.rcsb.org/pdb/explore.do?structureId=1ZVV 1ZVV] (CcpA-Crh-DNA complex),  [http://www.rcsb.org/pdb/explore.do?structureId=2RLZ 2RLZ] (dimer),  [http://www.rcsb.org/pdb/explore.do?structureId=1MU4 1MU4],  [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=24634 NCBI], dimer [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=64943  NCBI], CcpA-Crh-DNA complex [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=52326  NCBI], dimeric phosphor-Crh [http://www.ncbi.nlm.nih.gov/Structure/mmdb/mmdbsrv.cgi?Dopt=s&uid=39567 NCBI]
+
* '''Structure:'''
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O06976 O06976]
+
 
 +
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/Q45539 Q45539]
 +
 
 +
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU08600]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU34740]
+
* '''E.C. number:'''
  
 
=== Additional information===
 
=== Additional information===
−
 
−
Crh does not possess the phosphorylation site used for PTS phosphotransfer (His-15 in [[PtsH]]), it can only be phosphorylated on Ser-46
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:''' ''[[yvcI]]-[[yvcJ]]-[[yvcK]]-[[yvcL]]-[[crh]]-[[yvcN]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed]
+
* '''Operon:''' ''[[csbB]]''
  
−
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]
+
* '''[[Sigma factor]]:''' [[SigB]], [[SigX]]
  
−
* '''Regulation:''' very weak stimuation of expression by citrate and succinate [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]
+
* '''Regulation:''' induced by stress ([[SigB]]) [http://www.ncbi.nlm.nih.gov/pubmed/15805528 PubMed]
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' Crh is weakly expressed. This results in part from a poorly conserved ribosomal binding site of the mRNA. [http://www.ncbi.nlm.nih.gov/sites/entrez/15126459 PubMed]
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:''' GP860 (aphA3), QB7097 (spc), available in [[Stülke]] lab
+
* '''Mutant:'''
  
−
* '''Expression vector:''' pGP41 (N-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP380]]), pGP734 (C-terminal Strep-tag, purification from ''B. subtilis'', for [[SPINE]], in [[pGP382]]), available in [[Stülke]] lab
+
* '''Expression vector:'''
−
+
       
−
* '''lacZ fusion:''' see ''[[yvcI]]''
+
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Boris Görke| Görke]] lab
+
* '''two-hybrid system:'''  
  
−
* '''Antibody:''' available in [[Stülke]] lab (not very good)
+
* '''Antibody:'''
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
−
 
−
[[Boris Görke]], University of Göttingen, Germany
 
−
[http://wwwuser.gwdg.de/~genmibio/goerke.html Homepage]
 
−
 
−
[[Anne Galinier]], University of Marseille, France
 
−
 
−
[[Wolfgang Hillen]], Erlangen University, Germany [http://www.biologie.uni-erlangen.de/mibi/index2.html Homepage]
 
−
 
−
[[Richard Brennan]], Houston, Texas, USA [http://www.mdanderson.org/departments/biochem/display.cfm?id=556ef368-6c81-4043-b74f350d41dd06cb&method=displayfull&pn=a8427ebd-d0ff-11d4-80fd00508b603a14 Homepage]
 
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 125: Line 118:
 
=References=
 
=References=
  
−
<pubmed>12972249 9973552 9237995 16272399 15126459 10217795 17142398 16316990, </pubmed>
+
<pubmed>15805528, </pubmed>
−
# Juy M, Penin F, Favier A (2003) Dimerization of Crh by reversible 3D domain swapping induces structural adjustments to its monomeric homologue Hpr. ''J Mol Biol.'' '''332(4):'''767-76. [http://www.ncbi.nlm.nih.gov/sites/entrez/12972249 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]
−
# Galinier A, Deutscher J, Martin-Verstraete I: Phosphorylation of either Crh or HPr mediates binding of CcpA to the ''Bacillus subtilis xyn cre'' and catabolite repression of the ''xyn'' operon. J Mol Biol 1999, 286:307-314. [http://www.ncbi.nlm.nih.gov/sites/entrez/9973552 PubMed]
+
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
−
# Galinier, A., Haiech, J., Kilhoffer, M.-C., Jaquinod, M., Stülke, J., Deutscher, J., & Martin-Verstraete, I. (1997) The ''Bacillus subtilis crh'' gene encodes a HPr-like protein involved in carbon catabolite repression. Proc. Natl. Acad. Sci. USA 94: 8439-8444. [http://www.ncbi.nlm.nih.gov/sites/entrez/9237995 PubMed]
 
−
# Görke et al. (2005) YvcK of ''Bacillus subtilis'' is required for a normal cell shape and for growth on Krebs cycle intermediates and substrates of the pentose phosphate pathway. Microbiology 151: 3777-3791. [http://www.ncbi.nlm.nih.gov/sites/entrez/16272399 PubMed]
 
−
# Görke, B., Fraysse, L. & Galinier, A. Drastic differences in Crh and HPr synthesis levels reflect their different impacts on catabolite repression in ''Bacillus subtilis''. J. Bacteriol. 186, 2992-2995 (2004). [http://www.ncbi.nlm.nih.gov/sites/entrez/15126459 PubMed]
 
−
# Martin-Verstraete, I., Deutscher, J., and Galinier, A. (1999) Phosphorylation of HPr and Crh by HprK, early steps in the catabolite repression signalling pathway for the ''Bacillus subtilis'' levanase operon. J Bacteriol 181: 2966-2969. [http://www.ncbi.nlm.nih.gov/sites/entrez/10217795 PubMed]
 
−
# Pompeo ''et al.'' (2007) Interaction of GapA with HPr and its homologue, Crh: Novel levels of regulation of a key step of glycolysis in ''Bacillus subtilis''? J Bacteriol 189, 1154-1157.[http://www.ncbi.nlm.nih.gov/sites/entrez/17142398 PubMed]
 
−
# Schumacher, M. A., Seidel, G., Hillen, W. & Brennan, R. G. Phosphoprotein Crh-Ser46-P displays altered binding to CcpA to effect carbon catabolite regulation. J. Biol. Chem. 281, 6793-6800 (2006). [http://www.ncbi.nlm.nih.gov/sites/entrez/16316990 PubMed]
 

Revision as of 13:13, 8 June 2009

  • Description: general stress protein

Gene name csbB
Synonyms yfhN
Essential no
Product unknown
Function survival of ethanol and salt stress
MW, pI 37 kDa, 9.199
Gene length, protein length 987 bp, 329 aa
Immediate neighbours yfhM, yfhO
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CsbB context.gif
This image was kindly provided by SubtiList



The gene

Basic information

  • Locus tag: BSU08600

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: GtrB subfamily (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

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

Database entries

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

Additional information

Expression and regulation

  • 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

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)

  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. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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