Gpd2p is the second NAD+-dependent glycerol-3-phosphate dehydrogenase (EC 1.1.1.8) of S. cerevisiae. Like Gpd1p it reduces dihydroxyacetone phosphate to sn-glycerol 3-phosphate with NADH, but GPD2 is not osmotically regulated; it is induced under anoxia and other conditions of cytosolic NADH excess, independently of the HOG pathway. Glycerol formation by Gpd2p is the main redox sink that reoxidizes surplus NADH during anaerobic fermentation: gpd2 mutants grow poorly anaerobically and gpd1 gpd2 double mutants make no glycerol and cannot grow without oxygen. Gpd2p is mostly cytosolic but has an N-terminal mitochondrial presequence that directs a fraction into mitochondria, making respiratory-deficient cells dependent on Gpd2p. It can also act as the cytosolic half of the glycerol-3-phosphate shuttle with mitochondrial Gut2p. Gpd2p activity is curtailed when nutrients are limiting by inhibitory phosphorylation (at Ser72) by the AMP-activated protein kinase Snf1, whereas its paralog Gpd1p is regulated by the TORC2-dependent kinases Ypk1 and Ypk2.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005634 nucleus | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: IBA is_active_in nucleus from PTN000919785; the only experimental donor is Gpd1p (SGD:S000002180), whose stress-induced nuclear relocation depends on its own PTS2/phospho-regulated N-terminus. Gpd2p has a different N-terminus (a mitochondrial presequence) and there is no evidence it enters the nucleus. Likely paralog over-propagation. Reason: No Gpd2p-specific nuclear evidence; the inherited trait is tied to Gpd1p-specific targeting. Propagation Review Root cause: PROPAGATION BAD Failure modes: COMPARTMENT OR COMPLEX MISMATCH FUNCTIONAL DIVERGENCE Sources checked: SGD:S000002180 SUPPORTS SOURCE BUT NOT TARGET Gpd1p nuclear relocation under osmotic stress is real but depends on its PTS2 N-terminus, which Gpd2p lacks. Supporting Evidence: PMID:15210723 Gpd2p is known to be a cytosolic protein but possesses a classical mitochondrial presequence, which we show is sufficient for mitochondrial targeting. PMID:20026609 Exposure of cells to osmotic stress induces changes in the subcellular distribution of Gpd1p to the cytosol and nucleus. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell mapping of the curated 'Cytoplasm' location; Gpd2p is largely cytosolic. Supporting Evidence: file:yeast/GPD2/GPD2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm. Mitochondrion. |
| GO:0005739 mitochondrion | HDA PMID:14576278 The proteome of Saccharomyces cerevisiae mitochondria. | ACCEPT | Summary: HDA, mitochondrial proteome (Sickmann 2003). Consistent with the classical presequence of Gpd2p that is sufficient for mitochondrial targeting (partial mitochondrial pool). Supporting Evidence: PMID:14576278 The proteins of highly pure yeast mitochondria were separated by several independent methods and analyzed by tandem MS. PMID:15210723 Gpd2p is known to be a cytosolic protein but possesses a classical mitochondrial presequence, which we show is sufficient for mitochondrial targeting. |
| GO:0005739 mitochondrion | HDA PMID:16823961 Toward the complete yeast mitochondrial proteome: multidimen... | ACCEPT | Summary: HDA, PROMITO mitochondrial proteome (Reinders 2006). Consistent with partial mitochondrial targeting. Supporting Evidence: PMID:16823961 A total of 851 different proteins (PROMITO dataset) were identified PMID:15210723 Gpd2p is known to be a cytosolic protein but possesses a classical mitochondrial presequence, which we show is sufficient for mitochondrial targeting. |
| GO:0005739 mitochondrion | HDA PMID:24769239 Quantitative variations of the mitochondrial proteome and ph... | ACCEPT | Summary: HDA, quantitative mitochondrial proteome (Renvoise 2014). Consistent with partial mitochondrial targeting. 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 Gpd2p is known to be a cytosolic protein but possesses a classical mitochondrial presequence, which we show is sufficient for mitochondrial targeting. |
| GO:0005739 mitochondrion | IDA PMID:17054397 Assessing systems properties of yeast mitochondria through a... | ACCEPT | Summary: IDA (Perocchi 2006): in vitro mitochondrial import of Gpd2p confirmed, implying dual cytosolic and mitochondrial localization. Supporting Evidence: PMID:17054397 we performed mitochondrial import experiments and confirmed import of both Gut1p and Gpd2p, implying a novel dual cytosolic and mitochondrial localization PMID:15210723 A partial mitochondrial localization of Gpd2p will provide for establishment of intramitochondrial redox balance under non-respiratory conditions. |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell mapping of 'Mitochondrion'; correct. Supporting Evidence: file:yeast/GPD2/GPD2-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm. Mitochondrion. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: IBA is_active_in cytosol from PTN000198006 (cytosolic NAD-GPDH clade). Gpd2p is mainly cytosolic, where it reoxidizes glycolytic NADH by producing glycerol-3-phosphate. Supporting Evidence: PMID:15210723 Gpd2p is known to be a cytosolic protein but possesses a classical mitochondrial presequence, which we show is sufficient for mitochondrial targeting. PMID:9171333 Thus, glycerol formation is strictly required as a redox sink for excess cytosolic NADH during anaerobic metabolism. |
| GO:0005829 cytosol | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA cytosol prediction; agrees with experimental localization. Supporting Evidence: PMID:15210723 Gpd2p is known to be a cytosolic protein but possesses a classical mitochondrial presequence, which we show is sufficient for mitochondrial targeting. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways glycerol biosynthesis (PWY3O-48), cytosolic compartment. Correct. Supporting Evidence: PMID:9171333 Thus, glycerol formation is strictly required as a redox sink for excess cytosolic NADH during anaerobic metabolism. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways superpathway of phosphatidate biosynthesis (PWY3O-6499); redundant but correct. Supporting Evidence: PMID:15210723 Gpd2p is known to be a cytosolic protein but possesses a classical mitochondrial presequence, which we show is sufficient for mitochondrial targeting. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | ACCEPT | Summary: RCA from YeastPathways phosphatidate biosynthesis II (PWY3O-6635); cytosolic step. Correct. Supporting Evidence: PMID:15210723 Gpd2p is known to be a cytosolic protein but possesses a classical mitochondrial presequence, which we show is sufficient for mitochondrial targeting. |
| GO:0005829 cytosol | TAS PMID:10781551 In vivo analysis of the mechanisms for oxidation of cytosoli... | ACCEPT | Summary: TAS (Overkamp 2000) describing the soluble Gpd1p/Gpd2p component of the glycerol-3-phosphate shuttle. Correct. Supporting Evidence: PMID:10781551 a glycerol-3-phosphate shuttle consisting of soluble (Gpd1p or Gpd2p) and membrane-bound (Gut2p) glycerol-3-phosphate dehydrogenases |
| GO:0005975 carbohydrate metabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO (IPR006109) broad 'carbohydrate metabolic process'; the specific process is glycerol biosynthesis. Proposed replacements: glycerol biosynthetic process Supporting Evidence: 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:0006071 glycerol metabolic process | IMP PMID:9171333 The two isoenzymes for yeast NAD+-dependent glycerol 3-phosp... | MODIFY | Summary: IMP (Ansell 1997): gpd1 gpd2 mutants make no detectable glycerol and gpd2 mutants grow poorly anaerobically. The evidence supports the more specific glycerol biosynthetic process. Proposed replacements: glycerol biosynthetic process Supporting Evidence: PMID:9171333 Mutants deleted for both GPD1 and GPD2 do not produce detectable glycerol, are highly osmosensitive and fail to grow under anoxic conditions. PMID:9171333 Mutants lacking GPD2 show poor growth under anaerobic conditions. |
| GO:0006072 glycerol-3-phosphate metabolic process | IBA GO_REF:0000033 | TOO GENERAL | Summary: IBA from PTN000198006; correct but general (Gpd2p makes sn-glycerol 3-phosphate). Supporting Evidence: file:yeast/GPD2/GPD2-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0006072 glycerol-3-phosphate metabolic process | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO NAD-GPDH family signatures; correct, general. Supporting Evidence: file:yeast/GPD2/GPD2-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0006654 phosphatidic acid biosynthetic process | RCA GO_REF:0000123 | KEEP AS NON CORE | Summary: RCA from YeastPathways phosphatidate biosynthesis II; Gpd2p supplies the G3P backbone acylated by Gat1/Gat2. Defensible pathway-step participation, no Gpd2-specific lipid phenotype. Non-core. Supporting Evidence: file:yeast/GPD2/GPD2-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0008654 phospholipid biosynthetic process | RCA GO_REF:0000123 | MARK AS OVER ANNOTATED | Summary: RCA inherited from the YeastPathways superpathway of phosphatidate biosynthesis; broad ancestor adding nothing beyond the PA row. Superpathway inflation. Supporting Evidence: file:yeast/GPD2/GPD2-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO generic CH-OH/NAD(P) oxidoreductase; replace with the specific NAD+-GPDH activity. Proposed replacements: glycerol-3-phosphate dehydrogenase (NAD+) activity Supporting Evidence: file:yeast/GPD2/GPD2-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) homodimerization; plausible family property of eukaryotic NAD-GPDHs, no Gpd2p-specific data. Supporting Evidence: file:yeast/GPD2/GPD2-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0046168 glycerol-3-phosphate catabolic process | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO glycerol-3-phosphate catabolic process reflects the oxidative reaction direction. Physiologically Gpd2p reduces DHAP to G3P as an NADH sink, i.e. G3P biosynthesis. Proposed replacements: glycerol-3-phosphate biosynthetic process Supporting Evidence: PMID:9171333 Thus, glycerol formation is strictly required as a redox sink for excess cytosolic NADH during anaerobic metabolism. |
| GO:0047952 glycerol-3-phosphate dehydrogenase [NAD(P)+] activity | IBA GO_REF:0000033 | MODIFY | Summary: IBA from PTN000919759 (fungal NAD-GPDH node). Use NAD+-specific child term (EC 1.1.1.8). 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/GPD2/GPD2-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
| GO:0047952 glycerol-3-phosphate dehydrogenase [NAD(P)+] activity | IMP PMID:9171333 The two isoenzymes for yeast NAD+-dependent glycerol 3-phosp... | MODIFY | Summary: IMP (Ansell 1997): Gpd2p is an NAD-dependent GPDH isoenzyme. NAD+-specific child term is more precise (already present as EXP from the same paper). Proposed replacements: glycerol-3-phosphate dehydrogenase (NAD+) activity Supporting Evidence: PMID:9171333 The two homologous genes GPD1 and GPD2 encode the isoenzymes of NAD-dependent glycerol 3-phosphate dehydrogenase in the yeast Saccharomyces cerevisiae. |
| 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); use NAD+-specific term. Proposed replacements: glycerol-3-phosphate dehydrogenase (NAD+) activity Supporting Evidence: file:yeast/GPD2/GPD2-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; use NAD+-specific term. Proposed replacements: glycerol-3-phosphate dehydrogenase (NAD+) activity Supporting Evidence: file:yeast/GPD2/GPD2-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; use NAD+-specific term. Proposed replacements: glycerol-3-phosphate dehydrogenase (NAD+) activity Supporting Evidence: file:yeast/GPD2/GPD2-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; true but implied by the catalytic activity. Supporting Evidence: file:yeast/GPD2/GPD2-uniprot.txt KM=0.018 mM for NADH |
| GO:0141152 glycerol-3-phosphate dehydrogenase (NAD+) activity | EXP PMID:9171333 The two isoenzymes for yeast NAD+-dependent glycerol 3-phosp... | ACCEPT | Summary: EXP (Ansell 1997): GPD2 encodes an NAD-dependent GPDH isoenzyme (UniProt kinetics: Km 18 uM NADH, 0.86 mM DHAP). Core molecular function. Supporting Evidence: PMID:9171333 The two homologous genes GPD1 and GPD2 encode the isoenzymes of NAD-dependent glycerol 3-phosphate dehydrogenase in the yeast Saccharomyces cerevisiae. file:yeast/GPD2/GPD2-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate file:yeast/GPD2/GPD2-uniprot.txt KM=0.018 mM for NADH |
| 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. Supporting Evidence: file:yeast/GPD2/GPD2-uniprot.txt Reaction=sn-glycerol 3-phosphate + NAD(+) = dihydroxyacetone phosphate |
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Download this section (compressed HTML)Q: Which reactions does the mitochondrial pool of Gpd2p balance (intramitochondrial NADH from lysine/glutamate synthesis), and is the alternative initiator Met-49 used to make a cytosol-only form?
Q: Should GPD1/GPD2 carry 'glycerol-3-phosphate shuttle' (GO:0006127), given that Gut2p does and Overkamp 2000 names Gpd1p/Gpd2p as the soluble component?
Experiment: Compare anaerobic growth and glycerol yield of gpd1 gpd2 strains complemented with cytosol-only (presequence-deleted) versus mitochondria-only Gpd2p.
NAD-dependent glycerol 3-phosphate dehydrogenase; expression is controlled by an oxygen-independent signaling pathway required to regulate metabolism under anoxic conditions; located in cytosol and mitochondria; constitutively active but is inactivated via phosphorylation by energy-stress responsive kinase SNF1; GPD2 has a paralog, GPD1, that arose from the whole genome duplication
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