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: Central C-metabolism
MW, pI	35.7 kDa, 5.03
Gene length, protein length	1005 bp, 335 amino acids
Immediate neighbours	pgk, cggR
Get the DNA and protein sequences (Barbe et al., 2009)
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+ (do 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 Stülke lab
  • GP597 (gapA::erm), available in Stülke lab
  • GP703 (gapA::cat gapB::spec), available in Stülke lab
  • GM1501 (under p(spac) control), available in Stephane Aymerich lab
  • 1A1003 ( gapA::erm), PubMed, available at BGSC

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

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

• 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

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

Jörg Stülke, University of Göttingen, Germany homepage

References

Additional publications: PubMed

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)

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)

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