GapA

• Description: Glyceraldehyde 3-phosphate dehydrogenase, NAD-dependent, glycolytic enzyme, forms a transhydrogenation cycle with GapB for balancing of NADPH
  
  

Gene name	gapA
Synonyms
Essential	Yes (PubMed)
Product	glyceraldehyde 3-phosphate dehydrogenase
Function	catabolic enzyme in glycolysis
Gene expression levels in SubtiExpress: gapA
Interactions involving this protein in SubtInteract: GapA
Metabolic function and regulation of this protein in SubtiPathways: gapA
MW, pI	35.7 kDa, 5.03
Gene length, protein length	1005 bp, 335 amino acids
Immediate neighbours	pgk, cggR
Sequences	Protein DNA DNA_with_flanks
Genetic context This image was kindly provided by SubtiList
Expression at a glance   PubMed

Categories containing this gene/protein

carbon core metabolism, essential genes, membrane proteins, phosphoproteins

This gene is a member of the following regulons

CggR regulon

The gene

Basic information

• Locus tag: BSU33940

Phenotypes of a mutant

• Essential PubMed

Database entries

• DBTBS entry: [1]

• SubtiList entry:[2]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity: D-glyceraldehyde 3-phosphate + phosphate + NAD⁺ = 3-phospho-D-glyceroyl phosphate + NADH (according to Swiss-Prot)
  • This reaction is part of the glycolysis.

• Protein family: glyceraldehyde-3-phosphate dehydrogenase family (according to Swiss-Prot)

• Paralogous protein(s): GapB

Extended information on the protein

• Kinetic information: Michaelis-Menten PubMed

• Domains:

• Modification:
  • phosphorylated on Arg-199 PubMed
  • Phosphorylation on (Ser-148 OR Ser-151 OR Thr-153 OR Thr-154) PubMed1, PubMed2
  • Reversible thiol modifications after exposure to toxic quinones PubMed
  • Cys152-Cys156 form intramolecular disulfide in response to disulfide stress (diamide, NaOCl-stress) PubMed

• Cofactor(s): NAD⁺ (does not accept NADP⁺) PubMed

• Effectors of protein activity:

• Interactions:
  • GapA-PtsH: HPr(Ser-46-P) binds GapA resulting in a slight inhibition of enzymatic activity PubMed
  • GapA-Crh: Crh(Ser-46-P) binds GapA resulting in a slight inhibition of enzymatic activity.PubMed
  • GapA-YkzW PubMed

• Localization:
  • cytoplasm (Homogeneous) PubMed PubMed
  • loosely membrane associated PubMed

Database entries

• Structure:
  • 1GD1 (from Geobacillus stearothermophilus)
  • 1NQO (from Geobacillus stearothermophilus, mutant with cys 149 replaced by ser, complex with NAD+ und D-Glyceraldehyde-3-Phosphate)

• UniProt: P09124

• KEGG entry: [3]

• E.C. number: 1.2.1.12

Additional information

• GAP dehydrogenases from different sources (incl. Geobacillus stearothermophilus) were shown to cleave RNA (PubMed)
• Moreover, mutations in gapA from B. subtilis can suppress mutations in genes involved in DNA replication (PubMed).
• extensive information on the structure and enzymatic properties of GapA can be found at Proteopedia

Expression and regulation

• Operon:
  • cggR-gapA-pgk-tpi-pgm-eno PubMed
  • cggR-gapA PubMed

• Expression browser: gapA PubMed

• Sigma factor: SigA PubMed

• Regulation:
  • expression activated by glucose (10 fold) (CggR) PubMed

• Regulatory mechanism:
  • CggR: transcription repression PubMed

• Database entries: DBTBS

• Additional information:
  • GapA is one of the most abundant proteins in the cell. In the presence of glucose, there are about 25,000 GapA molecules per cell (PubMed).
  • 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 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:
  • GP592 (gapA::cat), available in Jörg Stülke's lab, PubMed
  • GP597 (gapA::erm), available in Jörg Stülke's lab, PubMed
  • GP703 (gapA::cat gapB::spec), available in Jörg Stülke's lab, PubMed
  • GM1501 (under p(spac) control), available in Stephane Aymerich's lab
  • 1A1003 ( gapA::erm), available at BGSC

• Expression vector:
  • pGP1424 (expression in B. subtilis, in pBQ200) (available in Jörg Stülke's lab)
  • pGP90 (N-terminal Strep-tag, for SPINE, purification from B. subtilis, in pGP380) (available in Jörg Stülke's lab)
  • pGP704 (N-terminal His-tag, in pWH844) (available in Jörg Stülke's lab)

• lacZ fusion: pGP506 (in pAC7), pGP512 (in pAC6) (available in Jörg Stülke's lab)

• GFP fusion:

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

• Antibody: available in Jörg Stülke's lab

Labs working on this gene/protein

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

Jörg Stülke, University of Göttingen, Germany homepage

References

Fabian M Commichau, Nico Pietack, Jörg Stülke
Essential genes in Bacillus subtilis: a re-evaluation after ten years.
Mol Biosyst: 2013, 9(6);1068-75
[PubMed:23420519] [WorldCat.org] [DOI] (I p)

Matthias Gimpel, Heike Preis, Emanuel Barth, Lydia Gramzow, Sabine Brantl
SR1--a small RNA with two remarkably conserved functions.
Nucleic Acids Res: 2012, 40(22);11659-72
[PubMed:23034808] [WorldCat.org] [DOI] (I p)

Martin Rühl, Dominique Le Coq, Stéphane Aymerich, Uwe Sauer
13C-flux analysis reveals NADPH-balancing transhydrogenation cycles in stationary phase of nitrogen-starving Bacillus subtilis.
J Biol Chem: 2012, 287(33);27959-70
[PubMed:22740702] [WorldCat.org] [DOI] (I p)

Alexander K W Elsholz, Kürsad Turgay, Stephan Michalik, Bernd Hessling, Katrin Gronau, Dan Oertel, Ulrike Mäder, Jörg Bernhardt, Dörte Becher, Michael Hecker, Ulf Gerth
Global impact of protein arginine phosphorylation on the physiology of Bacillus subtilis.
Proc Natl Acad Sci U S A: 2012, 109(19);7451-6
[PubMed:22517742] [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)

Bui Khanh Chi, Katrin Gronau, Ulrike Mäder, Bernd Hessling, Dörte Becher, Haike Antelmann
S-bacillithiolation protects against hypochlorite stress in Bacillus subtilis as revealed by transcriptomics and redox proteomics.
Mol Cell Proteomics: 2011, 10(11);M111.009506
[PubMed:21749987] [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)

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)

Manuel Liebeke, Dierk-Christoph Pöther, Nguyen van Duy, Dirk Albrecht, Dörte Becher, Falko Hochgräfe, Michael Lalk, Michael Hecker, Haike Antelmann
Depletion of thiol-containing proteins in response to quinones in Bacillus subtilis.
Mol Microbiol: 2008, 69(6);1513-29
[PubMed:18673455] [WorldCat.org] [DOI] (I p)

Christine Eymann, Dörte Becher, Jörg Bernhardt, Katrin Gronau, Anja Klutzny, Michael Hecker
Dynamics of protein phosphorylation on Ser/Thr/Tyr in Bacillus subtilis.
Proteomics: 2007, 7(19);3509-26
[PubMed:17726680] [WorldCat.org] [DOI] (P p)

Laurent Jannière, Danielle Canceill, Catherine Suski, Sophie Kanga, Bérengère Dalmais, Roxane Lestini, Anne-Françoise Monnier, Jérôme Chapuis, Alexander Bolotin, Marina Titok, Emmanuelle Le Chatelier, S Dusko Ehrlich
Genetic evidence for a link between glycolysis and DNA replication.
PLoS One: 2007, 2(5);e447
[PubMed:17505547] [WorldCat.org] [DOI] (I e)

Boris Macek, Ivan Mijakovic, Jesper V Olsen, Florian Gnad, Chanchal Kumar, Peter R Jensen, Matthias Mann
The serine/threonine/tyrosine phosphoproteome of the model bacterium Bacillus subtilis.
Mol Cell Proteomics: 2007, 6(4);697-707
[PubMed:17218307] [WorldCat.org] [DOI] (P p)

Frédérique Pompeo, Jennifer Luciano, Anne Galinier
Interaction of GapA with HPr and its homologue, Crh: Novel levels of regulation of a key step of glycolysis in Bacillus subtilis?
J Bacteriol: 2007, 189(3);1154-7
[PubMed:17142398] [WorldCat.org] [DOI] (P p)

Helena B Thomaides, Ella J Davison, Lisa Burston, Hazel Johnson, David R Brown, Alison C Hunt, Jeffery Errington, Lloyd Czaplewski
Essential bacterial functions encoded by gene pairs.
J Bacteriol: 2007, 189(2);591-602
[PubMed:17114254] [WorldCat.org] [DOI] (P p)

Jean-Christophe Meile, Ling Juan Wu, S Dusko Ehrlich, Jeff Errington, Philippe Noirot
Systematic localisation of proteins fused to the green fluorescent protein in Bacillus subtilis: identification of new proteins at the DNA replication factory.
Proteomics: 2006, 6(7);2135-46
[PubMed:16479537] [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)

Elena Evguenieva-Hackenberg, Emile Schiltz, Gabriele Klug
Dehydrogenases from all three domains of life cleave RNA.
J Biol Chem: 2002, 277(48);46145-50
[PubMed:12359717] [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)

S Tobisch, D Zühlke, J Bernhardt, J Stülke, M Hecker
Role of CcpA in regulation of the central pathways of carbon catabolism in Bacillus subtilis.
J Bacteriol: 1999, 181(22);6996-7004
[PubMed:10559165] [WorldCat.org] [DOI] (P p)