Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''Description:''' extracellular alkaline serine protease (subtilisin E) <br/><br/>
+
* '''Description:''' competence transcription factor (CTF) <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'''
−
|''aprE''
+
|''comK''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''sprE ''
+
|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''' || extracellular alkaline serine protease (subtilisin E))
+
|style="background:#ABCDEF;" align="center"| '''Product''' || competence transcription factor (CTF)
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || protein degradation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || regulation of competence and DNA uptake
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 39 kDa, 9.342  
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 22 kDa, 7.669  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 1143 bp, 381 aa  
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 576 bp, 192 aa  
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhfN]]'', ''[[yhfO]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yhzC]]'', ''[[yhxD]]''
 
|-
 
|-
−
|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB12870&#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:CAB12882&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
 
|-
 
|-
−
|-
+
|colspan="2" | '''Genetic context''' <br/> [[Image:comK_context.gif]]
−
|-
 
−
|colspan="2" | '''Genetic context''' <br/> [[Image:aprE_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 31: Line 29:
 
__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/>
  
 
=The gene=
 
=The gene=
Line 37: Line 35:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Locus tag:''' BSU10300
+
* '''Locus tag:''' BSU10420
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
Line 43: Line 41:
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/aprE.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/comK.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10190]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11059]
  
 
=== Additional information===
 
=== Additional information===
Line 54: Line 52:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:''' Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1 (according to Swiss-Prot)
+
* '''Catalyzed reaction/ biological activity:'''  
  
−
* '''Protein family:''' peptidase S8 family (according to Swiss-Prot)
+
* '''Protein family:'''
  
 
* '''Paralogous protein(s):'''
 
* '''Paralogous protein(s):'''
Line 72: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[AprE]]-[[PaiA]]
+
* '''Interactions:''' [[MecA]]-[[ComK]] [http://www.ncbi.nlm.nih.gov/sites/entrez/10447896 PubMed]
  
−
* '''Localization:''' secreted (according to Swiss-Prot),  extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''Structure:''' [http://www.rcsb.org/pdb/explore.do?structureId=1SBC 1SBC]
+
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P04189 P04189]
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P40396 P40396]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10300]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU10420]
  
 
* '''E.C. number:'''
 
* '''E.C. number:'''
Line 94: Line 92:
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:''' repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584,  PubMed]  
+
* '''Regulation:''' repressed during logrithmic growth ([[AbrB]]) [http://www.ncbi.nlm.nih.gov/sites/entrez/12586407,  PubMed] repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] 
  
−
* '''Regulatory mechanism:''' [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/2504584,  PubMed]  
+
* '''Regulatory mechanism:''' [[AbrB]]:  transcription repression [http://www.ncbi.nlm.nih.gov/sites/entrez/12586407,  PubMed]  
  
−
* '''Additional information:''' the mRNA is extremely stable (more than 25 min) [http://www.ncbi.nlm.nih.gov/sites/entrez/11101663 PubMed]
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
Line 115: Line 113:
  
 
=Labs working on this gene/protein=
 
=Labs working on this gene/protein=
 +
 +
[[Oscar Kuipers]], University of Groningen, The Netherlands
 +
[http://molgen.biol.rug.nl/molgen/index.php Homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 121:
 
=References=
 
=References=
  
−
<pubmed>18957862 11101663 12055299, </pubmed>
+
<pubmed> 10447896, 12028382, 8016067, 10361283, 11703662, 12107147, 17581123, 17493123,16391071,16436435 </pubmed>
−
# Voigt et al. (2009) Cell physiology and protein secretion of ''Bacillus licheniformis'' compared to ''Bacillus subtilis''. ''J Mol Microbiol Biotechnol.'' '''16:''' 53-68 [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
 
−
# Hambraeus, G., Persson, M. & Rutberg, B. (2000). The ''aprE'' leader is a determinant of extreme mRNA stability in ''Bacillus subtilis''. Microbiology 146, 3051-3059. [http://www.ncbi.nlm.nih.gov/sites/entrez/11101663 PubMed]
 
−
# Hambraeus, G., Karhumaa, K. & Rutberg, B. (2002). A 5' stem-loop and ribosome binding but not translation are important for the stability of ''Bacillus subtilis aprE'' leader mRNA. Microbiology 148, 1795-1803. [http://www.ncbi.nlm.nih.gov/sites/entrez/12055299 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 20:57, 10 June 2009

  • Description: competence transcription factor (CTF)

Gene name comK
Synonyms
Essential no
Product competence transcription factor (CTF)
Function regulation of competence and DNA uptake
MW, pI 22 kDa, 7.669
Gene length, protein length 576 bp, 192 aa
Immediate neighbours yhzC, yhxD
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
ComK context.gif
This image was kindly provided by SubtiList




The gene

Basic information

  • Locus tag: BSU10420

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:
  • Localization:

Database entries

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

Additional information

Expression and regulation

  • Operon:
  • Regulation: repressed during logrithmic growth (AbrB) PubMed repressed by casamino acids PubMed
  • Regulatory mechanism: AbrB: transcription repression PubMed
  • Additional information:

Biological materials

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

Labs working on this gene/protein

Oscar Kuipers, University of Groningen, The Netherlands Homepage

Your additional remarks

References

Wiep Klaas Smits, Cristina Bongiorni, Jan-Willem Veening, Leendert W Hamoen, Oscar P Kuipers, Marta Perego
Temporal separation of distinct differentiation pathways by a dual specificity Rap-Phr system in Bacillus subtilis.
Mol Microbiol: 2007, 65(1);103-20
[PubMed:17581123] [WorldCat.org] [DOI] (P p)

Wiep Klaas Smits, Tran Thu Hoa, Leendert W Hamoen, Oscar P Kuipers, David Dubnau
Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein.
Mol Microbiol: 2007, 64(2);368-81
[PubMed:17493123] [WorldCat.org] [DOI] (P p)

Kim A Susanna, Fabrizia Fusetti, Andy-Mark W H Thunnissen, Leendert W Hamoen, Oscar P Kuipers
Functional analysis of the competence transcription factor ComK of Bacillus subtilis by characterization of truncation variants.
Microbiology (Reading): 2006, 152(Pt 2);473-483
[PubMed:16436435] [WorldCat.org] [DOI] (P p)

Kim A Susanna, Chris D den Hengst, Leendert W Hamoen, Oscar P Kuipers
Expression of transcription activator ComK of Bacillus subtilis in the heterologous host Lactococcus lactis leads to a genome-wide repression pattern: a case study of horizontal gene transfer.
Appl Environ Microbiol: 2006, 72(1);404-11
[PubMed:16391071] [WorldCat.org] [DOI] (P p)

Ulrike Mäder, Georg Homuth, Christian Scharf, Knut Büttner, Rüdiger Bode, Michael Hecker
Transcriptome and proteome analysis of Bacillus subtilis gene expression modulated by amino acid availability.
J Bacteriol: 2002, 184(15);4288-95
[PubMed:12107147] [WorldCat.org] [DOI] (P p)

Michiko M Nakano, Shunji Nakano, Peter Zuber
Spx (YjbD), a negative effector of competence in Bacillus subtilis, enhances ClpC-MecA-ComK interaction.
Mol Microbiol: 2002, 44(5);1341-9
[PubMed:12028382] [WorldCat.org] [DOI] (P p)

M M Nakano, F Hajarizadeh, Y Zhu, P Zuber
Loss-of-function mutations in yjbD result in ClpX- and ClpP-independent competence development of Bacillus subtilis.
Mol Microbiol: 2001, 42(2);383-94
[PubMed:11703662] [WorldCat.org] [DOI] (P p)

M Persuh, K Turgay, I Mandic-Mulec, D Dubnau
The N- and C-terminal domains of MecA recognize different partners in the competence molecular switch.
Mol Microbiol: 1999, 33(4);886-94
[PubMed:10447896] [WorldCat.org] [DOI] (P p)

M Ogura, L Liu, M Lacelle, M M Nakano, P Zuber
Mutational analysis of ComS: evidence for the interaction of ComS and MecA in the regulation of competence development in Bacillus subtilis.
Mol Microbiol: 1999, 32(4);799-812
[PubMed:10361283] [WorldCat.org] [DOI] (P p)

L Kong, D Dubnau
Regulation of competence-specific gene expression by Mec-mediated protein-protein interaction in Bacillus subtilis.
Proc Natl Acad Sci U S A: 1994, 91(13);5793-7
[PubMed:8016067] [WorldCat.org] [DOI] (P p)


  1. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
Retrieved from "http://subtiwiki-test.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=90296"