Sandbox

• Description: Glyceraldehyde 3-phosphate dehydrogenase, NAD-dependent, glycolytic enzyme
  
  

Gene name	gapA
Synonyms
Essential	Yes (PubMed)
Product	glyceraldehyde 3-phosphate dehydrogenase
Function	catabolic enzyme in glycolysis
MW, pI	35.7 kDa, 5.03
Gene length, protein length	1005 bp, 335 amino acids
Immediate neighbours	cggR, pgk
Gene sequence (+200bp)	Protein sequence
Genetic context

The gene

Basic information

• Coordinates: 3480732 - 3481736

Phenotypes of a mutant

essential PubMed

essential PubMed

Database entries

• DBTBS entry: [1]

• SubtiList entry:[2]

The protein

Basic information/ Evolution

• Catalyzed reaction/ biological activity: glyceraldehyde-3-phosphate dehydrogenase, (NADH-dependent). Catalyzes the reaction from glyceraldehyde-3-phosphate to 1.3-bi-phosphoglycerate. This reaction is part of the glycolysis.

• Protein family:

• Paralogous protein(s): GapB

Extended information on the protein

• Kinetic information: K(M) for NAD: 5.7 mM, K(cat) for NAD: 70/sec (determined for GapA from Geobacillus stearothermophilus) PubMed

• Domains:

• Modification: Phosphorylation (STY) PubMed

• Cofactor(s):

• 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

• Localization: cytoplasm PubMed PubMed, loosely membrane associatedPubMed

Database entries

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

• Swiss prot entry: P09124

• KEGG entry: KEGG

• 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).

Expression and regulation

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

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. The processing event requires the Rny protein.

• Sigma factor: SigA

• Regulation: CggR represses the operon in the absence of glycolytic sugars PubMed

• Regulatory mechanism: repression

• 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).

Biological materials

• Mutant: essential

• Expression vector: pGP90 (N-terminal Strep-tag, purification from B. subtilis, in pGP380), 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

1. Blencke, H.-M., Homuth, G., Ludwig, H., Mäder, U., Hecker, M. & Stülke, J. (2003) Transcriptional profiling of gene expression in response to glucose in Bacillus subtilis: regulation of the central metabolic pathways. Metab. Engn. 5: 133-149. PubMed
2. Commichau, F. M., Rothe, F. M., Herzberg, C., Wagner, E., Hellwig, D., Lehnik-Habrink, M., Hammer, E., Völker, U. & Stülke, J. Novel activities of glycolytic enzymes in Bacillus subtilis: Interactions with essential proteins involved in mRNA processing. subm.
3. Doan, T., and S. Aymerich. 2003. Regulation of the central glycolytic pathways in Bacillus subtilis: binding of the repressor CggR to its single DNA target sequence is modulated by fructose-1,6-bisphosphate. Mol. Microbiol. 47: 1709-1721. PubMed
4. Evguenieva-Hackenberg, E., Schiltz, E., and Klug, G. (2002) Dehydrogenases from all three domains of life cleave RNA. J Biol Chem 277, 46145-46150. PubMed
5. Fillinger, S., Boschi-Muller, S., Azza, S., Dervyn, E., Branlant, G., and Aymerich, S. (2000) Two glyceraldehyde-3-phosphate dehydrogenases with opposite physiological roles in a nonphotosynthetic bacterium. J Biol Chem 275, 14031-14037. PubMed
6. Jannière, L., Canceill, D., Suski, C., Kanga, S., Dalmais, B., Lestini, R., Monnier, A. F., Chapuis, J., Bolotin, A., Titok, M., Le Chatelier, E., and Ehrlich, S. D. (2007) Genetic evidence for a link between glycolysis and DNA replication. PLoS ONE 2, e447. PubMed
7. Ludwig, H., Homuth, G., Schmalisch, M., Dyka, F. M., Hecker, M., and Stülke, J. (2001) Transcription of glycolytic genes and operons in Bacillus subtilis: evidence for the presence of multiple levels of control of the gapA operon. Mol Microbiol 41, 409-422.PubMed
8. Ludwig, H., Rebhan, N., Blencke, H.-M., Merzbacher, M. & Stülke, J. (2002). Control of the glycolytic gapA operon by the catabolite control protein A in Bacillus subtilis: a novel mechanism of CcpA-mediated regulation. Mol Microbiol 45, 543-553.PubMed
9. Macek et al. (2007) The serine/ threonine/ tyrosine phosphoproteome of the model bacterium Bacillus subtilis. Mol. Cell. Proteomics 6: 697-707 PubMed
10. Meinken, C., Blencke, H. M., Ludwig, H., and Stülke, J. (2003) Expression of the glycolytic gapA operon in Bacillus subtilis: differential synthesis of proteins encoded by the operon. Microbiology 149, 751-761. PubMed
11. Pompeo et al. (2007) Interaction of GapA with HPr and its homologue, Crh: Novel levels of regulation of a key step of glycolysis in Bacillus subtilis? J Bacteriol 189, 1154-1157.PubMed
12. Thomaides, H. B., Davison, E. J., Burston, L., Johnson, H., Brown, D. R., Hunt, A. C., Errington, J., and Czaplewski, L. (2007) Essential bacterial functions encoded by gene pairs. J Bacteriol 189, 591-602. PubMed
13. Tobisch, S., Zühlke, D., Bernhardt, J., Stülke, J., and Hecker, M. (1999) Role of CcpA in regulation of the central pathways of carbon catabolism in Bacillus subtilis. J Bacteriol 181, 6996-7004.PubMed