Glycerol synthesis and utilisation via glycerol 3-phosphate and dihydroxyacetone

Glycerol metabolism in eukaryotic microbes connects the triose-phosphate pool of glycolysis with free glycerol through two opposing arms. In the synthetic arm, a cytosolic NAD-dependent glycerol-3-phosphate dehydrogenase reduces dihydroxyacetone phosphate (DHAP) to sn-glycerol 3-phosphate, and a specific glycerol-3-phosphate phosphatase releases glycerol. The arm reoxidizes cytosolic NADH, which makes it a redox sink under anaerobic or respiration-deficient conditions, and it produces glycerol as the main compatible solute during hyperosmotic stress. In the utilisation arm, glycerol is returned to DHAP by one of two routes. In the phosphorylating route, glycerol kinase forms sn-glycerol 3-phosphate in the cytosol, and a FAD-dependent glycerol-3-phosphate:quinone oxidoreductase on the outer face of the mitochondrial inner membrane oxidizes it to DHAP, passing electrons to ubiquinone. In the oxidative (dihydroxyacetone) route, a glycerol dehydrogenase oxidizes glycerol to dihydroxyacetone, which a dihydroxyacetone kinase phosphorylates to DHAP. Organisms use one or both routes. Both arms share DHAP with glycolysis and gluconeogenesis, and the dehydrogenase pair at the centre of the module is the same pair that forms the glycerol-3-phosphate shuttle.

NEW (YeastPathways project, 2026-10). The module joins the two YeastCyc frames because synthesis and utilisation share the sn-glycerol 3-phosphate/DHAP couple and are reciprocally regulated (GPD1/GPP2 are HOG-induced; GUT1/GUT2 are glucose-repressed). Boundary: glycerol transport (Fps1 channel, Stl1 symporter), the HOG signalling pathway, triose-phosphate isomerase and lipid-backbone use of glycerol 3-phosphate are outside the module. The existing glycerol_phosphate_shuttle module (human GPD1 + GPD2) reuses the same two dehydrogenase activities for redox shuttling rather than net glycerol flux and is not edited here; bacterial GlpF/GlpK/GlpD catabolism is modelled in bacterial_glycerol_uptake_catabolism. The utilisation arm is an ONE_OR_MORE variant set: S. cerevisiae has both the glycerol 3-phosphate route (GUT1-GUT2, the main aerobic route) and the dihydroxyacetone route (GCY1-DAK1/DAK2, osmotically induced and also needed to detoxify DHA), while S. pombe lacks a glycerol kinase (PANTHER PTHR10196 contains only xks1 in S. pombe) and assimilates glycerol through gld1 and dak1/dak2 (PMID:20396879). The glycerol dehydrogenase step has two unrelated enzyme families: the NAD-dependent iron-containing GldA-type enzyme (S. pombe gld1, E. coli gldA; PTHR43616) and the NADP-dependent aldo-keto reductase GCY1 of S. cerevisiae (EC 1.1.1.156); the GCY1 assignment rests on metabolite profiling (PMID:22979944) and YPR1, a GCY1 paralog proposed in PMID:9038161, is not used as an exemplar. Locations: GPD1 is dual cytosolic/peroxisomal and GPD2 partly mitochondrial (PMID:15210723), so the NAD-dependent dehydrogenase annoton carries cytosol as the principal site; GUT2 is placed at the mitochondrial inner membrane facing the intermembrane space (PMID:11502169). UniProt places S. pombe gld1 in mitochondria, whereas the PomBase GO-CAM places its activity in the cytosol; the annoton carries no location. YeastCyc corrections: added the dihydroxyacetone route (GCY1, DAK1, DAK2), which YeastCyc omits; the GPP reaction substrate is corrected to sn-glycerol 3-phosphate. GO-CAM disagreements: YeastPathways_AERO-GLYCEROL-CAT-PWY places GUT2 only in "mitochondrion", consistent with but less specific than the module. The PomBase model 6796b94c00004743 has the glycerol-3-phosphatase activity enabled by an unspecified protein (CHEBI:36080), places gut2 in the mitochondrial outer membrane and as part of the glycerol-3-phosphate shuttle, puts gpd1/gpd2 in GO:0006072 (glycerol-3-phosphate metabolic process) rather than glycerol biosynthesis, and includes tpi1 (glycolysis), which is outside this module.