Difference between revisions of "Sandbox"

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* '''Description:''' write here <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'''
−
|''mbl''
+
|''ccpN''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
+
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || ''yqzB ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || MreB-like protein
+
|style="background:#ABCDEF;" align="center"| '''Product''' || transcriptional regulator
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' ||  
+
|style="background:#ABCDEF;" align="center"|'''Function''' || repressor of genes involved in gluconeogenesis (''[[gapB]]'','' [[pckA]]'') and of ''[[sr1]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 35 kDa, 5.669 
+
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 23.4 kDa, 7.22
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 999 bp, 333 aa
+
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 636 bp, 212 amino acids
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[flhO]]'', ''[[spoIIID]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yqfL]]'', ''[[glyS]]''
 
|-
 
|-
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/mbl_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ccpN_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
−
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/mbl_protein.txt Protein sequence]'''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/ccpN_protein.txt Protein sequence]'''
 
|-
 
|-
−
|colspan="2" | '''Genetic context''' <br/> [[Image:mbl_context.gif]]
+
|colspan="2" | '''Genetic context''' <br/> [[Image:yqzB_context.gif]]
 
|-
 
|-
 
|}
 
|}
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<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]
−
non-viable in the presence of low Mg(2+), readily accumulate ''[[rsgI]]'' suppressor mutants [http://www.ncbi.nlm.nih.gov/sites/entrez/19114499 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
  
−
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/usd-spoIIID-mbl-flhOP.html]
+
* '''DBTBS entry:''' [http://dbtbs.hgc.jp/COG/prom/ccpN-yqfL.html]
  
−
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10916]
+
* '''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:'''
  
−
* '''Paralogous protein(s):''' [[MreB]], [[MreBH]]
+
* '''Paralogous protein(s):'''
  
 
=== Extended information on the protein ===
 
=== Extended information on the protein ===
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:''' [[MreB]]-[[Mbl]], [[Mbl]]-[[MreBH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17064365 PubMed]
+
* '''Interactions:'''
  
−
* '''Localization:''' forms helical structures close to the inner surface of the cytoplasmic membrane [http://www.ncbi.nlm.nih.gov/sites/entrez/16950129 PubMed]
+
* '''Localization:'''
  
 
=== Database entries ===
 
=== Database entries ===
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* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:'''
+
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/O34994]
  
−
* '''KEGG entry:'''
+
* '''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 Fips riecht nach faulen Eiern '''
−
 
 
−
* '''Additional Fips riecht nach faulen Eiern '''  
 
  
 
=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:''' available in the [[Jeff Errington]] and [[Peter Graumann]] labs
+
=Labs working on this gene/protein=
  
−
=Labs working on this gene/protein=
+
[[Stephane Aymerich |Stephane Aymerich]], Microbiology and Molecular Genetics, INRA Paris-Grignon, France
  
−
[[Peter Graumann]], Freiburg University, Germany [http://www.biologie.uni-freiburg.de/data/bio2/graumann/index.htm homepage]
+
[[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]
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 120:
 
=References=
 
=References=
  
−
# Carballido-Lopez, R., Formstone, A., Li, Y., Ehrlich, S. D., and Errington, J. (2006) Actin homolog MreBH governs cell morphogenesis by localization of the cell wall hydrolase LytE. Dev. Cell 11: 399-409. [http://www.ncbi.nlm.nih.gov/sites/entrez/16950129 PubMed]
+
 
−
# Defeu Soufo, H. J., and P. Graumann. 2006. Dynamic localization and interaction with other Bacillus subtilis actin-like proteins are important for the funtion of MreB. Mol. Microbiol. 62: 1340-1356. [http://www.ncbi.nlm.nih.gov/sites/entrez/17064365 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]
−
# Schirner K, Errington J. (2009) Cell wall regulator {sigma}I specifically suppresses the lethal phenotype of mbl mutants in ''Bacillus subtilis''. ''J. Bacteriol.'' '''191:''' 1404-1413. [http://www.ncbi.nlm.nih.gov/sites/entrez/19114499 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]
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID 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 15:33, 18 March 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
Gene sequence (+200bp) Protein sequence
Genetic context
YqzB context.gif




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 Fips riecht nach faulen Eiern
  • 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

  • Sigma factor:
  • Regulation: constitutively expressed PubMed
  • Additional Fips riecht nach faulen Eiern

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

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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