Difference between revisions of "CggR"

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(→‎Extended information on the protein)
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** The intracellular concentration of CggR is about 230 nM  (according to {{PubMed|20408793}}).
 
** The intracellular concentration of CggR is about 230 nM  (according to {{PubMed|20408793}}).
 
**  The accumulation of the ''[[cggR]]-[[gapA]]'' mRNA is strongly dependent on the presence of the [[YkzW]] peptide, due to stabilization of the mRNA {{PubMed|20444087}}.
 
**  The accumulation of the ''[[cggR]]-[[gapA]]'' mRNA is strongly dependent on the presence of the [[YkzW]] peptide, due to stabilization of the mRNA {{PubMed|20444087}}.
 +
** the mRNA is substantially stabilized upon depletion of [[Rny|RNase Y]] {{PubMed|21815947}}
  
 
=Biological materials =
 
=Biological materials =
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==Original Publications==
 
==Original Publications==
 +
<big>''Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J''  </big>
 +
<big>'''RNA processing in ''Bacillus subtilis'': identification of targets of the essential RNase Y.''' </big>
 +
<big>Mol Microbiol. 2011 81(6): 1459-1473. </big>
 +
[http://www.ncbi.nlm.nih.gov/pubmed/21815947 PubMed:21815947]
 
<pubmed>19193632,12850135,12622823,18186488,10799476,11489127,12123463,12634343,18052209 , 17293407 20361740 20444087 18554327,</pubmed>
 
<pubmed>19193632,12850135,12622823,18186488,10799476,11489127,12123463,12634343,18052209 , 17293407 20361740 20444087 18554327,</pubmed>
 
'''Additional publications:''' {{PubMed|20462860}}  
 
'''Additional publications:''' {{PubMed|20462860}}  
 
[[Category:Protein-coding genes]]
 
[[Category:Protein-coding genes]]

Revision as of 19:47, 19 November 2011

Gene name cggR
Synonyms yvbQ
Essential no
Product central glycolytic genes regulator
Function transcriptional regulator
Metabolic function and regulation of this protein in SubtiPathways:
Central C-metabolism
MW, pI 37,2 kDa,5.68
Gene length, protein length 1020 bp, 340 amino acids
Immediate neighbours gapA, araE
Get the DNA and protein sequences
(Barbe et al., 2009)
Genetic context
CggR context.gif
This image was kindly provided by SubtiList








Categories containing this gene/protein

carbon core metabolism, transcription factors and their control, regulators of core metabolism

This gene is a member of the following regulons

CggR regulon

The CggR regulon:

The gene

Basic information

  • Locus tag: BSU33950

Phenotypes of a mutant

Database entries

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

Additional information

The protein

Basic information/ Evolution

  • Catalyzed reaction/ biological activity: transcription repression of the glycolytic gapA operon
  • Protein family: sorC transcriptional regulatory family (according to Swiss-Prot)
  • Paralogous protein(s):

Extended information on the protein

  • Kinetic information:
  • Domains:
    • DNA binding domain (H-T-H motif) (37–56)
  • Modification:
  • Cofactor(s):
  • Effectors of protein activity: fructose 1.6-bisphosphate PubMed and dihydroxyacetone phosphate, glucose-6-phosphate and fructose-6-phosphate PubMed act as inducer and result in release of CggR from the DNA

Database entries

  • Structure: 2OKG ( effector binding domain), 3BXH (in complex with fructose-6-phosphate), complex with Fructose-6-Phosphate NCBI, effector binding domain NCBI
  • KEGG entry: [3]

Additional information

Expression and regulation

  • Regulation:
    • expression activated by glucose (77-fold) (CggR) PubMed
  • Regulatory mechanism:
  • Additional information:
    • The primary mRNAs of the operon are highly unstable. The primary mRNA is subject to processing at the very end of the cggR open reading frame. This results in stable mature gapA and gapA-pgk-tpiA-pgm-eno mRNAs. PubMed The processing event requires the RNase Y PubMed.
    • The intracellular concentration of CggR is about 230 nM (according to PubMed).
    • The accumulation of the cggR-gapA mRNA is strongly dependent on the presence of the YkzW peptide, due to stabilization of the mRNA PubMed.
    • the mRNA is substantially stabilized upon depletion of RNase Y PubMed

Biological materials

  • Expression vector: pGP705 (N-terminal His-tag, in pWH844), available in Stülke lab
  • GFP fusion:
  • Antibody: available in Stülke lab

Labs working on this gene/protein

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

Your additional remarks

References

Reviews

Sabine Brantl, Andreas Licht
Characterisation of Bacillus subtilis transcriptional regulators involved in metabolic processes.
Curr Protein Pept Sci: 2010, 11(4);274-91
[PubMed:20408793] [WorldCat.org] [DOI] (I p)


Original Publications

Lehnik-Habrink M, Schaffer M, Mäder U, Diethmaier C, Herzberg C, Stülke J  
RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y. 
Mol Microbiol. 2011 81(6): 1459-1473. 
PubMed:21815947

Matthias Gimpel, Nadja Heidrich, Ulrike Mäder, Hans Krügel, Sabine Brantl
A dual-function sRNA from B. subtilis: SR1 acts as a peptide encoding mRNA on the gapA operon.
Mol Microbiol: 2010, 76(4);990-1009
[PubMed:20444087] [WorldCat.org] [DOI] (I p)

Cédric Atmanene, Denix Chaix, Yannick Bessin, Nathalie Declerck, Alain Van Dorsselaer, Sarah Sanglier-Cianferani
Combination of noncovalent mass spectrometry and traveling wave ion mobility spectrometry reveals sugar-induced conformational changes of central glycolytic genes repressor/DNA complex.
Anal Chem: 2010, 82(9);3597-605
[PubMed:20361740] [WorldCat.org] [DOI] (I p)

Fabian M Commichau, Fabian M Rothe, Christina Herzberg, Eva Wagner, Daniel Hellwig, Martin Lehnik-Habrink, Elke Hammer, Uwe Völker, Jörg Stülke
Novel activities of glycolytic enzymes in Bacillus subtilis: interactions with essential proteins involved in mRNA processing.
Mol Cell Proteomics: 2009, 8(6);1350-60
[PubMed:19193632] [WorldCat.org] [DOI] (I p)

Pavlína Rezácová, Milan Kozísek, Shiu F Moy, Irena Sieglová, Andrzej Joachimiak, Mischa Machius, Zbyszek Otwinowski
Crystal structures of the effector-binding domain of repressor Central glycolytic gene Regulator from Bacillus subtilis reveal ligand-induced structural changes upon binding of several glycolytic intermediates.
Mol Microbiol: 2008, 69(4);895-910
[PubMed:18554327] [WorldCat.org] [DOI] (I p)

Thierry Doan, Laetitia Martin, Silvia Zorrilla, Denis Chaix, Stéphane Aymerich, Gilles Labesse, Nathalie Declerck
A phospho-sugar binding domain homologous to NagB enzymes regulates the activity of the central glycolytic genes repressor.
Proteins: 2008, 71(4);2038-50
[PubMed:18186488] [WorldCat.org] [DOI] (I p)

Silvia Zorrilla, Denis Chaix, Alvaro Ortega, Carlos Alfonso, Thierry Doan, Emmanuel Margeat, Germán Rivas, Stephan Aymerich, Nathalie Declerck, Catherine A Royer
Fructose-1,6-bisphosphate acts both as an inducer and as a structural cofactor of the central glycolytic genes repressor (CggR).
Biochemistry: 2007, 46(51);14996-5008
[PubMed:18052209] [WorldCat.org] [DOI] (P p)

Silvia Zorrilla, Thierry Doan, Carlos Alfonso, Emmanuel Margeat, Alvaro Ortega, Germán Rivas, Stéphane Aymerich, Catherine A Royer, Nathalie Declerck
Inducer-modulated cooperative binding of the tetrameric CggR repressor to operator DNA.
Biophys J: 2007, 92(9);3215-27
[PubMed:17293407] [WorldCat.org] [DOI] (P p)

Hans-Matti Blencke, Georg Homuth, Holger Ludwig, Ulrike Mäder, Michael Hecker, Jörg Stülke
Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways.
Metab Eng: 2003, 5(2);133-49
[PubMed:12850135] [WorldCat.org] [DOI] (P p)

Christoph Meinken, Hans-Matti Blencke, Holger Ludwig, Jörg Stülke
Expression of the glycolytic gapA operon in Bacillus subtilis: differential syntheses of proteins encoded by the operon.
Microbiology (Reading): 2003, 149(Pt 3);751-761
[PubMed:12634343] [WorldCat.org] [DOI] (P p)

Thierry Doan, Stéphane Aymerich
Regulation of the central glycolytic genes in Bacillus subtilis: binding of the repressor CggR to its single DNA target sequence is modulated by fructose-1,6-bisphosphate.
Mol Microbiol: 2003, 47(6);1709-21
[PubMed:12622823] [WorldCat.org] [DOI] (P p)

Holger Ludwig, Nicole Rebhan, Hans-Matti Blencke, Matthias Merzbacher, Jörg Stülke
Control of the glycolytic gapA operon by the catabolite control protein A in Bacillus subtilis: a novel mechanism of CcpA-mediated regulation.
Mol Microbiol: 2002, 45(2);543-53
[PubMed:12123463] [WorldCat.org] [DOI] (P p)

H Ludwig, G Homuth, M Schmalisch, F M Dyka, M Hecker, J Stülke
Transcription of glycolytic genes and operons in Bacillus subtilis: evidence for the presence of multiple levels of control of the gapA operon.
Mol Microbiol: 2001, 41(2);409-22
[PubMed:11489127] [WorldCat.org] [DOI] (P p)

S Fillinger, S Boschi-Muller, S Azza, E Dervyn, G Branlant, S Aymerich
Two glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium.
J Biol Chem: 2000, 275(19);14031-7
[PubMed:10799476] [WorldCat.org] [DOI] (P p)

Additional publications: PubMed

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