Difference between revisions of "Sandbox"

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−
* '''Description:''' glycyl-tRNA synthetase (alpha subunit) <br/><br/>
+
* '''Description:''' transcriptional repressor of gluconeogenetic genes and of [[sr1]]. repression in the presence of glucose <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'''
−
|''glyQ''
+
|''ccpN''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqfJ ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqzB ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || glycyl-tRNA synthetase (alpha subunit)
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
+
|style="background:#ABCDEF;" align="center"|'''Function''' || repressor of genes involved in <br/>gluconeogenesis (''[[gapB]]'','' [[pckA]]'') and of ''[[sr1]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 33 kDa, 4.8 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23.4 kDa, 7.22
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 885 bp, 295 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[glyS]]'', ''[[recO]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfL]]'', ''[[glyS]]''
 
|-
 
|-
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|colspan="2" style="background:#FAF8CC;" align="center"|'''Hier soll was neues rein'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:glyQ_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yqzB_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 29: Line 29:
 
__TOC__
 
__TOC__
  
−
<br/><br/>
+
<br/><br/><br/>
 +
 
  
 
=The gene=
 
=The gene=
Line 35: Line 36:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''Coordinates:'''
+
* '''Coordinates:''' 2604195 - 2604830
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
+
Impaired growth on glucose due to re-routing of carbon from glycolysis to the pentose phosphate pathway [http://www.ncbi.nlm.nih.gov/sites/entrez/18586936 PubMed]
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/glyQS.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpN-yqfL.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG11657]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13768]
  
 
=== Additional information===
 
=== Additional information===
−
 
  
 
=The protein=
 
=The protein=
Line 54: Line 53:
 
=== Basic information/ Evolution ===
 
=== Basic information/ Evolution ===
  
−
* '''Catalyzed reaction/ biological activity:'''  
+
* '''Catalyzed reaction/ biological activity:''' transcription repression of the ''[[gapB]]'', ''[[pckA]]'', and ''[[sr1]]'' genes in the presence of glucose [http://www.ncbi.nlm.nih.gov/sites/entrez/2548995 PubMed]
  
 
* '''Protein family:'''
 
* '''Protein family:'''
Line 70: Line 69:
 
* '''Cofactor(s):'''
 
* '''Cofactor(s):'''
  
−
* '''Effectors of protein activity:'''
+
* '''Effectors of protein activity:'''  
 +
** [[YqfL]] (negative effector of CcpN activity) [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
 +
** ATP enhances CcpN-dependent repression, ADP counteracts the repressing activity of CcpN [http://www.ncbi.nlm.nih.gov/sites/entrez/18511073 PubMed]
  
 
* '''Interactions:'''
 
* '''Interactions:'''
Line 80: Line 81:
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34994]
  
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25270]
+
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU25250]
  
−
* '''E.C. number:'''
+
=== Additional information===
  
−
=== Additional information===
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
−
* '''Operon:'''  
+
* '''Operon:''' ''[[ccpN]]''-''[[yqfL]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
  
 
* '''[[Sigma factor]]:'''  
 
* '''[[Sigma factor]]:'''  
  
−
* '''Regulation:'''  
+
* '''Regulation:''' constitutively expressed [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
  
−
* '''Regulatory mechanism:'''
+
* '''Additional information:'''
−
 
 
−
* '''Additional information:'''  
 
  
 
=Biological materials =
 
=Biological materials =
  
−
* '''Mutant:'''
+
* '''Mutant:''' DB104 ''ccpN''::[[cat]], available in [[Sabine Brantl]] lab
  
 
* '''Expression vector:'''
 
* '''Expression vector:'''
−
       
+
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
 
* '''GFP fusion:'''
 
* '''GFP fusion:'''
  
−
* '''two-hybrid system:'''  
+
* '''Antibody:''' available in [[Sabine Brantl]] lab
  
−
* '''Antibody:'''
+
=Labs working on this gene/protein=
  
−
=Labs working on this gene/protein=
+
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
 +
 
 +
[[Sabine Brantl |Sabine Brantl]], Bacterial Genetics, Friedrich-Schiller-University of Jena, Germany [http://www.uni-jena.de/AG_Bakteriengenetik_(_Doz__Dr__Sabine_Brantl_).html homepage]
 +
 
 +
[[Uwe Sauer]], ETH Zürich, Switzerland [http://www.imsb.ethz.ch/researchgroup/sauer homepage]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 120: Line 122:
 
=References=
 
=References=
  
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
+
 
 +
# Servant et al. (2005) CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of ''Bacillus subtilis'' gluconeogenic genes. Mol. Microbiol. 55: 1435-1451. [http://www.ncbi.nlm.nih.gov/sites/entrez/15720552 PubMed]
 +
# Licht et al. (2005) Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in ''Bacillus subtilis''. Mol. Microbiol. 58: 189-206. [http://www.ncbi.nlm.nih.gov/sites/entrez/16164558 PubMed]
 +
# Licht & Brantl (2006) Transcriptional repressor CcpN from ''Bacillus subtilis'' compensates asymmetric contact distribution by cooperative binding. J. Mol. Biol. 364: 434-448. [http://www.ncbi.nlm.nih.gov/sites/entrez/17011578 PubMed]
 +
# Licht et al. (2008) Identification of ligands affecting the activity of the transcriptional repressor CcpN from ''Bacillus subtilis''. J. Mol. Biol. 380: 17-30. [http://www.ncbi.nlm.nih.gov/sites/entrez/18511073 PubMed]
 +
# Tännler et al. (2008) CcpN controls central carbon fluxes in ''Bacillus subtilis''. J. Bacteriol. 190: 6178-6187. [http://www.ncbi.nlm.nih.gov/sites/entrez/18586936 PubMed]

Revision as of 18:45, 15 April 2009

  • Description: transcriptional repressor of gluconeogenetic genes and of sr1. repression in the presence of glucose

Gene name ccpN
Synonyms yqzB
Essential no
Product transcriptional regulator
Function repressor of genes involved in
gluconeogenesis (gapB, pckA) and of sr1
MW, pI 23.4 kDa, 7.22
Gene length, protein length 636 bp, 212 amino acids
Immediate neighbours yqfL, glyS
Hier soll was neues rein
Genetic context
YqzB context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Coordinates: 2604195 - 2604830

Phenotypes of a mutant

Impaired growth on glucose due to re-routing of carbon from glycolysis to the pentose phosphate pathway PubMed

Database entries

  • DBTBS entry: [1]
  • SubtiList entry: [2]

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: transcription repression of the gapB, pckA, and sr1 genes in the presence of glucose PubMed
  • Protein family:
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity:
    • YqfL (negative effector of CcpN activity) PubMed
    • ATP enhances CcpN-dependent repression, ADP counteracts the repressing activity of CcpN PubMed
  • Interactions:
  • Localization:

Database entries

  • Structure:
  • Swiss prot entry: [3]
  • KEGG entry: [4]

Additional information

Expression and regulation

  • Regulation: constitutively expressed PubMed
  • Additional information:

Biological materials

  • Expression vector:
  • lacZ fusion:
  • GFP fusion:

Labs working on this gene/protein

Stephane Aymerich, Microbiology and Molecular Genetics, INRA Paris-Grignon, France

Sabine Brantl, Bacterial Genetics, Friedrich-Schiller-University of Jena, Germany homepage

Uwe Sauer, ETH Zürich, Switzerland homepage

Your additional remarks

References

  1. Servant et al. (2005) CcpN (YqzB), a novel regulator for CcpA-independent catabolite repression of Bacillus subtilis gluconeogenic genes. Mol. Microbiol. 55: 1435-1451. PubMed
  2. Licht et al. (2005) Implication of CcpN in the regulation of a novel untranslated RNA (SR1) in Bacillus subtilis. Mol. Microbiol. 58: 189-206. PubMed
  3. Licht & Brantl (2006) Transcriptional repressor CcpN from Bacillus subtilis compensates asymmetric contact distribution by cooperative binding. J. Mol. Biol. 364: 434-448. PubMed
  4. Licht et al. (2008) Identification of ligands affecting the activity of the transcriptional repressor CcpN from Bacillus subtilis. J. Mol. Biol. 380: 17-30. PubMed
  5. Tännler et al. (2008) CcpN controls central carbon fluxes in Bacillus subtilis. J. Bacteriol. 190: 6178-6187. PubMed
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