Difference between revisions of "Sandbox"

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* '''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>
 
|-
 
|-
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__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/>
  
 
=The gene=
 
=The gene=
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 72: Line 70:
 
* '''Effectors of protein activity:'''
 
* '''Effectors of protein activity:'''
  
−
* '''Interactions:''' [[AprE]]-[[PaiA]],  
+
* '''Interactions:''' [[MecA]]-[[ComK]],  
  
−
* '''Localization:''' extracellular (signal peptide) [http://www.ncbi.nlm.nih.gov/pubmed/18957862 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Swiss prot entry:'''
 
* '''Swiss prot entry:'''
  
−
* '''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:'''
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* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' repressed by casamino acids [http://www.ncbi.nlm.nih.gov/pubmed/12107147 PubMed] 
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''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=
  
−
# 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]
+
# 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]
−
# 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]
+
# Smits, W.K., Bongiorni, C., Veening, J.W., Hamoen, L.W.,  Kuipers, O.P. & Perego, M. (2007) Temporal separation of distinct differentiation pathways by a dual specificity Rap-Phr system in Bacillus subtilis. Mol. Microbiol. 65, 103-120. [http://www.ncbi.nlm.nih.gov/sites/entrez/17581123 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]
+
# Smits, W.K., Hoa, T.T.,  Hamoen, L.W., Kuipers, O.P. & Dubnau, D. (2007) Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein. Mol. Microbiol. 64, 368-381. [http://www.ncbi.nlm.nih.gov/sites/entrez/17493123 PubMed]
 +
# Smits, W.K., Kuipers, O.P. & Veening, J.W. (2006) Phenotypic variation in bacteria: the role of feedback regulation. Nat. Rev. Microbiol. 4, 259-271. [http://www.ncbi.nlm.nih.gov/sites/entrez/16541134 PubMed]
 +
# Susanna, K.A., den Hengst, C.D., Hamoen, L.W. & Kuipers, O.P. (2006) 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. 72, 404-411. [http://www.ncbi.nlm.nih.gov/sites/entrez/16391071 PubMed]
 +
# Susanna, K.A., Fusetti, F., Thunnissen, A.M., Hamoen, L.W. & Kuipers, O.P. (2006) Functional analysis of the competence transcription factor ComK of Bacillus subtilis by characterization of truncation variants. Microbiology 152, 473-483. [http://www.ncbi.nlm.nih.gov/sites/entrez/16436435 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 23:53, 27 April 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

  • Coordinates:

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:
  • Swiss prot entry:
  • KEGG entry: [3]
  • E.C. number:

Additional information

Expression and regulation

  • Operon:
  • Regulation: repressed by casamino acids PubMed
  • Regulatory mechanism:
  • 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

  1. Mäder et al. (2002) Transcriptome and Proteome Analysis of Bacillus subtilis Gene Expression Modulated by Amino Acid Availability. J. Bacteriol 184: 1844288-4295 PubMed
  2. Smits, W.K., Bongiorni, C., Veening, J.W., Hamoen, L.W., Kuipers, O.P. & Perego, M. (2007) Temporal separation of distinct differentiation pathways by a dual specificity Rap-Phr system in Bacillus subtilis. Mol. Microbiol. 65, 103-120. PubMed
  3. Smits, W.K., Hoa, T.T., Hamoen, L.W., Kuipers, O.P. & Dubnau, D. (2007) Antirepression as a second mechanism of transcriptional activation by a minor groove binding protein. Mol. Microbiol. 64, 368-381. PubMed
  4. Smits, W.K., Kuipers, O.P. & Veening, J.W. (2006) Phenotypic variation in bacteria: the role of feedback regulation. Nat. Rev. Microbiol. 4, 259-271. PubMed
  5. Susanna, K.A., den Hengst, C.D., Hamoen, L.W. & Kuipers, O.P. (2006) 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. 72, 404-411. PubMed
  6. Susanna, K.A., Fusetti, F., Thunnissen, A.M., Hamoen, L.W. & Kuipers, O.P. (2006) Functional analysis of the competence transcription factor ComK of Bacillus subtilis by characterization of truncation variants. Microbiology 152, 473-483. PubMed
  7. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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