Difference between revisions of "CggR"
| Line 114: | Line 114: | ||
* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cggR_3482752_3483774_-1 cggR] {{PubMed|22383849}} | * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=cggR_3482752_3483774_-1 cggR] {{PubMed|22383849}} | ||
| − | * '''Sigma factor:''' [[SigA]] {{PubMed|11489127}} | + | * '''[[Sigma factor]]:''' [[SigA]] {{PubMed|11489127}} |
* '''Regulation:''' | * '''Regulation:''' | ||
| Line 133: | Line 133: | ||
* '''Mutant:''' | * '''Mutant:''' | ||
| − | ** GP311 (in frame deletion), available in [[Stülke]] lab | + | ** GP311 (in frame deletion), available in [[Jörg Stülke]]'s lab |
** SM-NB7 (cggR-spc), available in [[Anne Galinier]]'s and [[Boris Görke]]'s labs | ** SM-NB7 (cggR-spc), available in [[Anne Galinier]]'s and [[Boris Görke]]'s labs | ||
| − | * '''Expression vector:''' pGP705 (N-terminal His-tag, in [[pWH844]]), available in [[Stülke]] lab | + | * '''Expression vector:''' pGP705 (N-terminal His-tag, in [[pWH844]]), available in [[Jörg Stülke]]'s lab |
| − | * '''lacZ fusion:''' pGP504 (in [[pAC7]]), pGP509 (in [[pAC6]]), available in [[Stülke]] lab | + | * '''lacZ fusion:''' pGP504 (in [[pAC7]]), pGP509 (in [[pAC6]]), available in [[Jörg Stülke]]'s lab |
* '''GFP fusion:''' | * '''GFP fusion:''' | ||
| − | * '''Antibody:''' available in [[Stülke]] lab | + | * '''Antibody:''' available in [[Jörg Stülke]]'s lab |
=Labs working on this gene/protein= | =Labs working on this gene/protein= | ||
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==Original Publications== | ==Original Publications== | ||
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| − | <pubmed> 22190493 23280112 | + | <pubmed>20462860 22190493 23280112 21815947 19193632,12850135, 12622823,18186488,10799476,11489127, 12123463,12634343, 18052209 , 17293407 20361740 20444087 18554327,</pubmed> |
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[[Category:Protein-coding genes]] | [[Category:Protein-coding genes]] | ||
Revision as of 15:25, 13 July 2013
- Description: repressor of the glycolytic gapA operon, DeoR family
| Gene name | cggR |
| Synonyms | yvbQ |
| Essential | no |
| Product | central glycolytic genes regulator |
| Function | transcriptional regulator |
| Gene expression levels in SubtiExpress: cggR | |
| 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 |
| Sequences | Protein DNA DNA_with_flanks |
Genetic context 
This image was kindly provided by SubtiList
| |
Expression at a glance PubMed
| |
Contents
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
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
- Interactions:
- active as dimer (according to PubMed)
- Localization: cytoplasma PubMed
Database entries
- Structure: 2OKG ( effector binding domain), 3BXH (in complex with fructose-6-phosphate), complex with Fructose-6-Phosphate NCBI, effector binding domain NCBI
- UniProt: O32253
- KEGG entry: [3]
Additional information
Expression and regulation
- Database entries: DBTBS
- 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
- Mutant:
- GP311 (in frame deletion), available in Jörg Stülke's lab
- SM-NB7 (cggR-spc), available in Anne Galinier's and Boris Görke's labs
- Expression vector: pGP705 (N-terminal His-tag, in pWH844), available in Jörg Stülke's lab
- lacZ fusion: pGP504 (in pAC7), pGP509 (in pAC6), available in Jörg Stülke's lab
- GFP fusion:
- Antibody: available in Jörg Stülke's lab
Labs working on this gene/protein
Stephane Aymerich, Microbiology and Molecular Genetics, INRA Paris-Grignon, France
Your additional remarks
References
Reviews
Original Publications
Nathalie Declerck, Catherine A Royer
Interactions in gene expression networks studied by two-photon fluorescence fluctuation spectroscopy.
Methods Enzymol: 2013, 519;203-30
[PubMed:23280112]
[WorldCat.org]
[DOI]
(I p)
Matthew L Ferguson, Dominique Le Coq, Matthieu Jules, Stéphane Aymerich, Ovidiu Radulescu, Nathalie Declerck, Catherine A Royer
Reconciling molecular regulatory mechanisms with noise patterns of bacterial metabolic promoters in induced and repressed states.
Proc Natl Acad Sci U S A: 2012, 109(1);155-60
[PubMed:22190493]
[WorldCat.org]
[DOI]
(I p)
Martin Lehnik-Habrink, Marc Schaffer, Ulrike Mäder, Christine Diethmaier, Christina Herzberg, Jörg Stülke
RNA processing in Bacillus subtilis: identification of targets of the essential RNase Y.
Mol Microbiol: 2011, 81(6);1459-73
[PubMed:21815947]
[WorldCat.org]
[DOI]
(I p)
Denis Chaix, Matthew L Ferguson, Cedric Atmanene, Alain Van Dorsselaer, Sarah Sanglier-Cianférani, Catherine A Royer, Nathalie Declerck
Physical basis of the inducer-dependent cooperativity of the Central glycolytic genes Repressor/DNA complex.
Nucleic Acids Res: 2010, 38(17);5944-57
[PubMed:20462860]
[WorldCat.org]
[DOI]
(I p)
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)
