Gpd1p is the osmotically induced, NAD+-dependent glycerol-3-phosphate dehydrogenase (EC 1.1.1.8) of S. cerevisiae. It reduces dihydroxyacetone phosphate to sn-glycerol 3-phosphate using NADH, the first and rate-limiting step of glycerol synthesis; glycerol-3-phosphatases (Gpp1p/Gpp2p) then release glycerol. GPD1 transcription is induced through the HOG MAP kinase pathway, and gpd1 mutants make little glycerol and are osmosensitive, so Gpd1p is the main supplier of glycerol as a compatible solute during hyperosmotic stress. Gpd1p activity is also controlled post-translationally, because the TORC2-dependent kinases Ypk1 and Ypk2 phosphorylate and inhibit it; hyperosmotic shock inactivates Ypk1, and the resulting dephosphorylation activates Gpd1p and speeds glycerol accumulation. The reaction also reoxidizes cytosolic NADH and provides the glycerol-3-phosphate backbone for glycerolipid synthesis. Gpd1p is cytosolic and also imported into peroxisomes by an N-terminal PTS2 (Pex7/Pex21-dependent), where it piggybacks the nicotinamidase Pnc1p; under osmotic stress a fraction moves to the nucleus. Its paralog Gpd2p has similar kinetics but is anaerobically induced and partly mitochondrial.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: IBA is_active_in nucleus from PANTHER node PTN000919785, whose only experimental donor is Gpd1p itself (SGD:S000002180). Gpd1p does relocate partly to the nucleus under osmotic stress, but no nuclear function has been demonstrated; the catalytic role is cytosolic/peroxisomal. Supporting Evidence: PMID:20026609 Exposure of cells to osmotic stress induces changes in the subcellular distribution of Gpd1p to the cytosol and nucleus. PMID:26276932 The glycerol-producing PTS2 protein glycerol-3-phosphate dehydrogenase Gpd1p shows a tripartite localization in peroxisomes, in the cytosol, and in the nucleus under osmotic stress conditions. |
| GO:0005634 nucleus | IDA PMID:20026609 Dynamic changes in the subcellular distribution of Gpd1p in ... | KEEP AS NON CORE | Summary: IDA (GFP microscopy, Jung et al. 2010): Gpd1p redistributes to cytosol and nucleus on osmotic stress. Localization is real but stress-conditional and no nuclear activity is known. Supporting Evidence: PMID:20026609 Exposure of cells to osmotic stress induces changes in the subcellular distribution of Gpd1p to the cytosol and nucleus. |
| GO:0005737 cytoplasm | EXP PMID:15210723 Distinct intracellular localization of Gpd1p and Gpd2p, the ... | ACCEPT | Summary: EXP from Valadi et al. 2004: Gpd1p is partly cytosolic and partly peroxisomal. Cytoplasm is correct (cytosol is the more specific compartment, annotated separately). Supporting Evidence: PMID:15210723 Gpd1p, the other Gpd isoform, is partly cytosolic and partly peroxisomal and becomes more strictly peroxisomal in respiratory-deficient mutants. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell mapping (SL-0086) from the curated 'Cytoplasm' location; correct for Gpd1p. Supporting Evidence: file:yeast/GPD1/GPD1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:15210723}. |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | MARK AS OVER ANNOTATED | Summary: HDA from a quantitative proteome of isolated mitochondria (Renvoise 2014). Gpd1p carries a PTS2 and is cytosolic/peroxisomal/nuclear; unlike its paralog Gpd2p it has no mitochondrial presequence and no targeted study places it in mitochondria. Most likely co-purification of an abundant cytosolic/peroxisomal enzyme. Reason: Single high-throughput organelle-proteomics hit contradicted by targeted localization studies (PTS2-dependent peroxisomal + cytosolic). Not removed because the curator saw the dataset. Supporting Evidence: PMID:24769239 we performed an overall quantitative proteomic and phosphoproteomic study of isolated mitochondria extracted from yeast grown on fermentative (glucose or galactose) and respiratory (lactate) media PMID:15210723 Gpd1p, the other Gpd isoform, is partly cytosolic and partly peroxisomal and becomes more strictly peroxisomal in respiratory-deficient mutants. |
| GO:0005777 peroxisome | EXP PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: EXP from the genome-wide GFP localization screen (Huh 2003); consistent with targeted studies showing PTS2/Pex7-dependent peroxisomal import of Gpd1p. Supporting Evidence: PMID:14562095 Here we describe the construction and analysis of a collection of yeast strains expressing full-length, chromosomally tagged green fluorescent protein fusion proteins. PMID:20026609 Here, we show that Gpd1p is directed to peroxisomes by virtue of an N-terminal type 2 peroxisomal targeting signal (PTS2) in a Pex7p-dependent manner. |
| GO:0005777 peroxisome | IDA PMID:15210723 Distinct intracellular localization of Gpd1p and Gpd2p, the ... | ACCEPT | Summary: IDA (Valadi 2004): Gpd1p is partly peroxisomal, more strictly so in respiratory-deficient cells. Supporting Evidence: PMID:15210723 Gpd1p, the other Gpd isoform, is partly cytosolic and partly peroxisomal and becomes more strictly peroxisomal in respiratory-deficient mutants. |
| GO:0005777 peroxisome | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell mapping of the curated 'Peroxisome' location; supported by PTS2-dependent import data. Supporting Evidence: file:yeast/GPD1/GPD1-uniprot.txt Peroxisome {ECO:0000269|PubMed:14562095, ECO:0000269|PubMed:15210723}. PMID:20026609 Here, we show that Gpd1p is directed to peroxisomes by virtue of an N-terminal type 2 peroxisomal targeting signal (PTS2) in a Pex7p-dependent manner. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: IBA is_active_in cytosol from PTN000198006 (cytosolic NAD-GPDH clade incl. plant and animal GPD1). Gpd1p is the classical cytosolic NADH-dependent GPDH that makes glycerol-3-phosphate for glycerol synthesis. Supporting Evidence: PMID:8196651 We have cloned a gene encoding the key enzyme of glycerol synthesis, the NADH-dependent cytosolic glycerol-3-phosphate dehydrogenase, and we named it GPD1. |
| GO:0005829 cytosol | IDA PMID:15210723 Distinct intracellular localization of Gpd1p and Gpd2p, the ... | ACCEPT | Summary: IDA (Valadi 2004): cytosolic pool of Gpd1p demonstrated by fractionation/microscopy. Supporting Evidence: PMID:15210723 Gpd1p, the other Gpd isoform, is partly cytosolic and partly peroxisomal and becomes more strictly peroxisomal in respiratory-deficient mutants. |
| GO:0005829 cytosol | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA machine-learning cytosol prediction; agrees with experimental data for Gpd1p. Supporting Evidence: PMID:15210723 Gpd1p, the other Gpd isoform, is partly cytosolic and partly peroxisomal and becomes more strictly peroxisomal in respiratory-deficient mutants. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways 'glycerol biosynthesis' (PWY3O-48): reaction compartment cytosol. Correct for Gpd1p. Supporting Evidence: PMID:8196651 We have cloned a gene encoding the key enzyme of glycerol synthesis, the NADH-dependent cytosolic glycerol-3-phosphate dehydrogenase, and we named it GPD1. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways superpathway of phosphatidate biosynthesis (PWY3O-6499); same cytosolic DHAP reduction step. Redundant with other cytosol rows but correct. Supporting Evidence: PMID:8196651 We have cloned a gene encoding the key enzyme of glycerol synthesis, the NADH-dependent cytosolic glycerol-3-phosphate dehydrogenase, and we named it GPD1. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways phosphatidate biosynthesis II (PWY3O-6635); cytosolic compartment for the DHAP to glycerol-3-phosphate step. Correct. Supporting Evidence: PMID:8196651 We have cloned a gene encoding the key enzyme of glycerol synthesis, the NADH-dependent cytosolic glycerol-3-phosphate dehydrogenase, and we named it GPD1. |
| GO:0005975 carbohydrate metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO (IPR006109 NAD-GPDH C-terminal) maps to the very broad 'carbohydrate metabolic process'. Gpd1p's process is glycerol biosynthesis (a descendant), which should replace it. Proposed replacements: glycerol biosynthetic process Supporting Evidence: PMID:8196651 We have cloned a gene encoding the key enzyme of glycerol synthesis, the NADH-dependent cytosolic glycerol-3-phosphate dehydrogenase, and we named it GPD1. PMID:9171333 Mutants deleted for both GPD1 and GPD2 do not produce detectable glycerol, are highly osmosensitive and fail to grow under anoxic conditions. |
| GO:0006072 glycerol-3-phosphate metabolic process | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from PTN000198006: glycerol-3-phosphate metabolism is correct (Gpd1p produces sn-glycerol 3-phosphate from DHAP), though general; glycerol biosynthesis is the core process. Supporting Evidence: file:yeast/GPD1/GPD1-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0006072 glycerol-3-phosphate metabolic process | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO (NAD-dependent GPDH family signatures). Correct, general. Supporting Evidence: file:yeast/GPD1/GPD1-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0006114 glycerol biosynthetic process | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways glycerol biosynthesis (PWY3O-48), reaction EC 1.1.1.8 in the DHAP -> glycerol-3-phosphate direction. Matches the genetics: gpd1 mutants make very little glycerol and gpd1 gpd2 mutants none. Core process. Supporting Evidence: PMID:8196651 gpd1 delta mutants produced very little glycerol, and they were sensitive to osmotic stress. PMID:9171333 Mutants deleted for both GPD1 and GPD2 do not produce detectable glycerol, are highly osmosensitive and fail to grow under anoxic conditions. |
| GO:0006654 phosphatidic acid biosynthetic process | RCA GO_REF:0000123 | KEEP AS NON CORE | Summary: RCA from YeastPathways 'phosphatidate biosynthesis II (glycerol-3-phosphate pathway)', in which Gpd1/Gpd2 supply the sn-glycerol 3-phosphate backbone that Gat1/Gat2 acylate. The step is catalysed by Gpd1p, so participation is defensible, but no Gpd1-specific lipid phenotype is documented; glycerol-3-phosphate can also come from Gut1p. Non-core. Supporting Evidence: file:yeast/GPD1/GPD1-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0006973 intracellular accumulation of glycerol | IMP PMID:8196651 GPD1, which encodes glycerol-3-phosphate dehydrogenase, is e... | ACCEPT | Summary: IMP (Albertyn 1994): gpd1 deletion abolishes most glycerol production and causes osmosensitivity; GPD1 is HOG-induced. Gpd1p catalyses the rate-limiting step of osmotically induced glycerol accumulation. Core for the GPD1 (osmo) isoform. Supporting Evidence: PMID:8196651 gpd1 delta mutants produced very little glycerol, and they were sensitive to osmotic stress. PMID:8196651 hog1 delta mutants lacking a protein kinase involved in osmostress-induced signal transduction (the high-osmolarity glycerol response [HOG] pathway) failed to increase glycerol-3-phosphate dehydrogenase activity and mRNA levels when osmotic stress was imposed. PMID:11676566 These results demonstrate that GPDH, but not the glycerol 3-phosphatase, is rate-limiting for glycerol production. |
| GO:0008654 phospholipid biosynthetic process | RCA GO_REF:0000123 | MARK AS OVER ANNOTATED | Summary: RCA inherited from the YeastPathways superpathway of phosphatidate biosynthesis (PWY3O-6499). Adds only a broad ancestor of the phosphatidic acid biosynthesis row; Gpd1p makes the glycerol backbone precursor, not phospholipids per se. Superpathway inflation. Supporting Evidence: file:yeast/GPD1/GPD1-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0016558 protein import into peroxisome matrix | IMP PMID:26276932 Role of Pex21p for Piggyback Import of Gpd1p and Pnc1p into ... | KEEP AS NON CORE | Summary: IMP (Effelsberg 2015): Gpd1p, a PTS2 cargo, carries the PTS2-less nicotinamidase Pnc1p into peroxisomes by piggyback import; Gpd1p therefore does part of the work of importing another matrix protein. Genuine but peripheral to its metabolic role. Supporting Evidence: PMID:26276932 Pnc1p, a nicotinamidase without functional PTS2, is co-imported into peroxisomes by piggyback transport via Gpd1p. PMID:26276932 Pex21p is required for peroxisomal import of Gpd1p as well as a key enzyme of the NAD(+) salvage pathway, Pnc1p |
| GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO (IPR011128) gives the generic CH-OH/NAD(P) oxidoreductase parent. The specific activity is NAD+-linked glycerol-3-phosphate dehydrogenase (EC 1.1.1.8). Proposed replacements: glycerol-3-phosphate dehydrogenase (NAD+) activity Supporting Evidence: file:yeast/GPD1/GPD1-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0042803 protein homodimerization activity | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO (IPR017751 eukaryotic NAD-GPDH) homodimerization. Eukaryotic NAD-GPDHs are homodimers and nothing argues against this for Gpd1p, but there is no yeast-specific experimental evidence and it is not a functional activity in its own right. Supporting Evidence: file:yeast/GPD1/GPD1-uniprot.txt Belongs to the NAD-dependent glycerol-3-phosphate |
| GO:0046168 glycerol-3-phosphate catabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO (IPR011128) assigns glycerol-3-phosphate catabolic process, reflecting the reaction written in the oxidative direction. In vivo Gpd1p runs DHAP + NADH -> sn-glycerol 3-phosphate (glycerol synthesis, NADH reoxidation), i.e. it makes rather than breaks down G3P. Replace with glycerol-3-phosphate biosynthetic process. Proposed replacements: glycerol-3-phosphate biosynthetic process Supporting Evidence: PMID:8196651 We have cloned a gene encoding the key enzyme of glycerol synthesis, the NADH-dependent cytosolic glycerol-3-phosphate dehydrogenase, and we named it GPD1. PMID:12032156 dihydroxyacetone phosphate is reduced to glycerol 3-phosphate by the cytosolic Gpd1p |
| GO:0047952 glycerol-3-phosphate dehydrogenase [NAD(P)+] activity | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN000919759 (fungal NAD-GPDH node; donors Gpd1p, Gpd2p, S. pombe gpd1). Correct in essence but the [NAD(P)+] term is the EC 1.1.1.94 parent; yeast Gpd1p is the NAD+-specific EC 1.1.1.8 enzyme. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000919759 SUPPORTS SOURCE BUT NOT TARGET Node correctly carries NAD(P)-GPDH activity; the NAD+-specific child GO:0141152 is the precise term for the yeast enzymes. Proposed replacements: glycerol-3-phosphate dehydrogenase (NAD+) activity Supporting Evidence: file:yeast/GPD1/GPD1-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0047952 glycerol-3-phosphate dehydrogenase [NAD(P)+] activity | IMP PMID:8196651 GPD1, which encodes glycerol-3-phosphate dehydrogenase, is e... | MODIFY | Summary: IMP (Albertyn 1994): gpd1 mutants lose NADH-dependent GPDH activity. The activity is NAD+-specific, so the child term GO:0141152 is the better fit (already present as EXP from the same paper). Proposed replacements: glycerol-3-phosphate dehydrogenase (NAD+) activity Supporting Evidence: PMID:8196651 We have cloned a gene encoding the key enzyme of glycerol synthesis, the NADH-dependent cytosolic glycerol-3-phosphate dehydrogenase, and we named it GPD1. |
| GO:0047952 glycerol-3-phosphate dehydrogenase [NAD(P)+] activity | RCA GO_REF:0000123 | MODIFY | Summary: RCA from YeastPathways glycerol biosynthesis (EC 1.1.1.8 reaction). The pathway reaction uses NADH, so the NAD+-specific term is more accurate. Proposed replacements: glycerol-3-phosphate dehydrogenase (NAD+) activity Supporting Evidence: file:yeast/GPD1/GPD1-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0047952 glycerol-3-phosphate dehydrogenase [NAD(P)+] activity | RCA GO_REF:0000123 | MODIFY | Summary: RCA from YeastPathways superpathway of phosphatidate biosynthesis; same EC 1.1.1.8 step. Use the NAD+-specific term. Proposed replacements: glycerol-3-phosphate dehydrogenase (NAD+) activity Supporting Evidence: file:yeast/GPD1/GPD1-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0047952 glycerol-3-phosphate dehydrogenase [NAD(P)+] activity | RCA GO_REF:0000123 | MODIFY | Summary: RCA from YeastPathways phosphatidate biosynthesis II; same EC 1.1.1.8 step. Use the NAD+-specific term. Proposed replacements: glycerol-3-phosphate dehydrogenase (NAD+) activity Supporting Evidence: file:yeast/GPD1/GPD1-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0051287 NAD binding | IEA GO_REF:0000002 | KEEP AS NON CORE | Summary: InterPro2GO NAD binding (Rossmann NAD-GPDH N-terminal domain). True (NADH is the cosubstrate) but implied by the catalytic activity term. Supporting Evidence: file:yeast/GPD1/GPD1-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0141152 glycerol-3-phosphate dehydrogenase (NAD+) activity | EXP PMID:8196651 GPD1, which encodes glycerol-3-phosphate dehydrogenase, is e... | ACCEPT | Summary: EXP (Albertyn 1994): GPD1 encodes the NADH-dependent cytosolic GPDH; activity lost in mutants and regulated via HOG. Core molecular function (EC 1.1.1.8, RHEA:11092). Supporting Evidence: PMID:8196651 We have cloned a gene encoding the key enzyme of glycerol synthesis, the NADH-dependent cytosolic glycerol-3-phosphate dehydrogenase, and we named it GPD1. file:yeast/GPD1/GPD1-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0141152 glycerol-3-phosphate dehydrogenase (NAD+) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined IEA (ARBA / RHEA:11092 / EC:1.1.1.8). Correct and specific. Supporting Evidence: file:yeast/GPD1/GPD1-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
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Download this section (compressed HTML)Q: What does the peroxisomal pool of Gpd1p do metabolically (NADH reoxidation inside peroxisomes, a peroxisomal G3P shuttle), given that peroxisomal targeting is dispensable for beta-oxidation?
Q: Does nuclear Gpd1p under osmotic stress have a function beyond sequestration, e.g. linked to co-transported Pnc1p and chromatin silencing?
Experiment: Express Gpd1p variants restricted to cytosol, peroxisome or nucleus (PTS2 deletion, PTS1/NLS fusions) in a gpd1 gpd2 background and measure glycerol production, osmotolerance and compartmental NADH/NAD+ ratios.
NAD-dependent glycerol-3-phosphate dehydrogenase; key enzyme of glycerol synthesis, essential for growth under osmotic stress; expression regulated by high-osmolarity glycerol response pathway; protein abundance increases in response to DNA replication stress; constitutively inactivated via phosphorylation by the protein kinases Ypk1p and Ypk2p, dephosphorylation increases catalytic activity; forms a heterodimer with Pnc1p to facilitate its peroxisomal import
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