RocG

• Description: trigger enzyme: catabolic glutamate dehydrogenase induced by arginine, ornithine or proline, subject to carbon catabolite repression
  
  

Gene name	rocG
Synonyms
Essential	no
Product	trigger enzyme: glutamate dehydrogenase (major)
Function	arginine utilization, controls the activity of GltC
Interactions involving this protein in SubtInteract: RocG
Metabolic function and regulation of this protein in SubtiPathways: Ammonium/ glutamate
MW, pI	46.2 kDa, 6.28
Gene length, protein length	1272 bp, 424 amino acids
Immediate neighbours	rocA, yweA
Get the DNA and protein sequences (Barbe et al., 2009)
Genetic context This image was kindly provided by SubtiList

Categories containing this gene/protein

utilization of amino acids, transcription factors and their control, trigger enzyme

This gene is a member of the following regulons

AbrB regulon, AhrC regulon, CcpA regulon, RocR regulon, SigL regulon

The gene

Basic information

• Locus tag: BSU37790

Phenotypes of a mutant

Poor growth on complex media such as SP (sporulation medium). No growth in minimal media with arginine as the only carbon source. Rapid accumulation of suppressor mutants (gudB1)

Database entries

• DBTBS entry: [1]

• SubtiList entry: [2]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity: L-glutamate + H₂O + NAD⁺ = 2-oxoglutarate + NH₃ + NADH (according to Swiss-Prot) L-glutamate + H(2)O + NAD(+) = 2-oxoglutarate + NH(3) + NADH, controls the activity of the GltC transcription activator PubMed

• Protein family: Glu/Leu/Phe/Val dehydrogenases family (according to Swiss-Prot) Glu/Leu/Phe/Val dehydrogenases family

• Paralogous protein(s): GudB

Extended information on the protein

• Kinetic information:

• Domains:

• Modification:

• Cofactor(s):

• Effectors of protein activity:

• Interactions:
  • RocG-GltC, this interaction prevents transcription activation of the gltA-gltB operon by GltC PubMed

• Localization:

Database entries

• Structure: 3K92 (super-repressor mutant that is capable of constitutive inactivation of GltC, E93K mutation) PubMed

• UniProt: P39633

• KEGG entry: [3]

• E.C. number: 1.4.1.2

Expression and regulation

• Operon: rocG PubMed

• Sigma factor: SigL PubMed

• Regulation:
  • induced by arginine (RocR, AhrC), ornithine or proline PubMed
  • subject to carbon catabolite repression (CcpA) PubMed

• Regulatory mechanism:
  • RocR: transcription activation PubMed
  • AhrC: transcription activation PubMed
  • CcpA: transcription repression PubMed
  • AbrB: transcription repression PubMed

• Additional information:

Activation by RocR requires binding of RocR to a downstream element PubMed

Biological materials

• Mutant: GP747 (spc), GP726 (aphA3), GP810 (del tet), GP1157 (cat) all available in Stülke lab

• Expression vector:
  • expression of native rocG in B. subtilis: pGP529 (in pBQ200), available in Stülke lab
  • for purification of RocG from E. coli carrying an N-terminal Strep-tag: pGP902 (in pGP172), a series of rocG variants is also available in pGP172, available in Stülke lab
  • for expression/ purification from E. coli with N-terminal His-tag and thrombin cleavage site, in pWH844: pGP860, available in Stülke lab
  • purification from B. subtilis with an N-terminal Strep-tag, for SPINE, (in pGP380): pGP1709, available in Stülke lab

• lacZ fusion:

• GFP fusion:

• two-hybrid system: B. pertussis adenylate cyclase-based bacterial two hybrid system (BACTH), available in Stülke lab

• Antibody: available in Stülke lab

Labs working on this gene/protein

Linc Sonenshein, Tufts University, Boston, MA, USA Homepage

Jörg Stülke, University of Göttingen, Germany Homepage

References

Enzymatic activity of RocG

Kenji Manabe, Yasushi Kageyama, Takuya Morimoto, Tadahiro Ozawa, Kazuhisa Sawada, Keiji Endo, Masatoshi Tohata, Katsutoshi Ara, Katsuya Ozaki, Naotake Ogasawara
Combined effect of improved cell yield and increased specific productivity enhances recombinant enzyme production in genome-reduced Bacillus subtilis strain MGB874.
Appl Environ Microbiol: 2011, 77(23);8370-81
[PubMed:21965396] [WorldCat.org] [DOI] (I p)

Katrin Gunka, Joseph A Newman, Fabian M Commichau, Christina Herzberg, Cecilia Rodrigues, Lorraine Hewitt, Richard J Lewis, Jörg Stülke
Functional dissection of a trigger enzyme: mutations of the bacillus subtilis glutamate dehydrogenase RocG that affect differentially its catalytic activity and regulatory properties.
J Mol Biol: 2010, 400(4);815-27
[PubMed:20630473] [WorldCat.org] [DOI] (I p)

Shigeki Kada, Masahiro Yabusaki, Takayuki Kaga, Hitoshi Ashida, Ken-ichi Yoshida
Identification of two major ammonia-releasing reactions involved in secondary natto fermentation.
Biosci Biotechnol Biochem: 2008, 72(7);1869-76
[PubMed:18603778] [WorldCat.org] [DOI] (I p)

Fabian M Commichau, Katrin Gunka, Jens J Landmann, Jörg Stülke
Glutamate metabolism in Bacillus subtilis: gene expression and enzyme activities evolved to avoid futile cycles and to allow rapid responses to perturbations of the system.
J Bacteriol: 2008, 190(10);3557-64
[PubMed:18326565] [WorldCat.org] [DOI] (I p)

Md Iqbal Hassan Khan, Kousuke Ito, Hyeung Kim, Hiroyuki Ashida, Takahiro Ishikawa, Hitoshi Shibata, Yoshihiro Sawa
Molecular properties and enhancement of thermostability by random mutagenesis of glutamate dehydrogenase from Bacillus subtilis.
Biosci Biotechnol Biochem: 2005, 69(10);1861-70
[PubMed:16244435] [WorldCat.org] [DOI] (P p)

Iqbal Hassan Khan, Hyeung Kim, Hiroyuki Ashida, Takahiro Ishikawa, Hitoshi Shibata, Yoshihiro Sawa
Altering the substrate specificity of glutamate dehydrogenase from Bacillus subtilis by site-directed mutagenesis.
Biosci Biotechnol Biochem: 2005, 69(9);1802-5
[PubMed:16195607] [WorldCat.org] [DOI] (P p)

B R Belitsky, A L Sonenshein
Role and regulation of Bacillus subtilis glutamate dehydrogenase genes.
J Bacteriol: 1998, 180(23);6298-305
[PubMed:9829940] [WorldCat.org] [DOI] (P p)

Expression of rocG

Additional publications: PubMed

Boris R Belitsky, Hyun-Jin Kim, Abraham L Sonenshein
CcpA-dependent regulation of Bacillus subtilis glutamate dehydrogenase gene expression.
J Bacteriol: 2004, 186(11);3392-8
[PubMed:15150224] [WorldCat.org] [DOI] (P p)

Naima Ould Ali, Josette Jeusset, Eric Larquet, Eric Le Cam, Boris Belitsky, Abraham L Sonenshein, Tarek Msadek, Michel Débarbouillé
Specificity of the interaction of RocR with the rocG-rocA intergenic region in Bacillus subtilis.
Microbiology (Reading): 2003, 149(Pt 3);739-750
[PubMed:12634342] [WorldCat.org] [DOI] (P p)

B R Belitsky, A L Sonenshein
An enhancer element located downstream of the major glutamate dehydrogenase gene of Bacillus subtilis.
Proc Natl Acad Sci U S A: 1999, 96(18);10290-5
[PubMed:10468601] [WorldCat.org] [DOI] (P p)

B R Belitsky, A L Sonenshein
Role and regulation of Bacillus subtilis glutamate dehydrogenase genes.
J Bacteriol: 1998, 180(23);6298-305
[PubMed:9829940] [WorldCat.org] [DOI] (P p)

Structural analysis of glutamate dehydrogenase

Katrin Gunka, Joseph A Newman, Fabian M Commichau, Christina Herzberg, Cecilia Rodrigues, Lorraine Hewitt, Richard J Lewis, Jörg Stülke
Functional dissection of a trigger enzyme: mutations of the bacillus subtilis glutamate dehydrogenase RocG that affect differentially its catalytic activity and regulatory properties.
J Mol Biol: 2010, 400(4);815-27
[PubMed:20630473] [WorldCat.org] [DOI] (I p)

T J Stillman, P J Baker, K L Britton, D W Rice
Conformational flexibility in glutamate dehydrogenase. Role of water in substrate recognition and catalysis.
J Mol Biol: 1993, 234(4);1131-9
[PubMed:8263917] [WorldCat.org] [DOI] (P p)

Bypass of rocG mutations

Lope A Flórez, Katrin Gunka, Rafael Polanía, Stefan Tholen, Jörg Stülke
SPABBATS: A pathway-discovery method based on Boolean satisfiability that facilitates the characterization of suppressor mutants.
BMC Syst Biol: 2011, 5;5
[PubMed:21219666] [WorldCat.org] [DOI] (I e)