Glycerol dehydrogenase 1 of Schizosaccharomyces pombe, a zinc-dependent member of the iron-containing alcohol dehydrogenase (bacterial GldA-type) family. It oxidizes glycerol to dihydroxyacetone with NAD+ as acceptor, the first step of the dihydroxyacetone route by which fission yeast assimilates glycerol; the dihydroxyacetone is then phosphorylated by the dihydroxyacetone kinases dak1 and dak2. Deletion of gld1 lowers glycerol dehydrogenase activity and abolishes glycerol assimilation without affecting growth on dihydroxyacetone. Expression is repressed by glucose. Fission yeast has no GCY1-type aldo-keto reductase for this step. Large-scale YFP tagging placed the protein in mitochondria, and its N-terminal extension relative to bacterial GldA has presequence-like composition, but its compartment has not been established by targeted experiments.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell mapping from the ORFeome-wide YFP localization (PMID:16823372), which called gld1 mitochondrial. The gld1 N-terminus (residues 1-45) is Arg/Lys-rich with no acidic residue before position 47 and is absent from bacterial GldA, consistent with a mitochondrial presequence. Retained, though a targeted localization experiment is lacking. Reason: The only experimental localization data (high-throughput) say mitochondrion, and the sequence has a presequence-like N-terminal extension. This conflicts with the PomBase cytosol IC and the GO-CAM; flagged as a question rather than overruled. Supporting Evidence: file:SCHPO/gld1/gld1-uniprot.txt CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:16823372}. |
| GO:0005829 cytosol | IC GO_REF:0000111 | UNDECIDED | Summary: PomBase curator inference that gld1 acts in the cytosol, made from its ISS-supported glycerol dehydrogenase activity (the bacterial GldA homologs are cytosolic). The only experimental localization for gld1 (ORFeome YFP) is mitochondrial, and gld1 carries an N-terminal extension absent from GldA with presequence-like composition. Reason: Curator inference conflicts with HTP experimental data and a sequence feature; neither side has a targeted experiment. Kept undecided pending fractionation or tagged-allele localization. Supporting Evidence: file:SCHPO/gld1/gld1-uniprot.txt CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:16823372}. |
| GO:0008888 glycerol dehydrogenase (NAD+) activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT node PTN000161157 seeded by E. coli GldA and by gld1 itself (whose own IMP annotations ground the inference). Correct core activity. Supporting Evidence: PMID:20396879 Deletion of gld1 caused a reduction in glycerol dehydrogenase activity and prevented glycerol assimilation. |
| GO:0008888 glycerol dehydrogenase (NAD+) activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined automated mapping from EC 1.1.1.6 / RHEA:13769 assigned in the UniProt entry, where the catalytic activity is backed by the gld1 deletion study. Correct. Supporting Evidence: file:SCHPO/gld1/gld1-uniprot.txt CC Reaction=glycerol + NAD(+) = dihydroxyacetone + NADH + H(+); |
| GO:0008888 glycerol dehydrogenase (NAD+) activity | IMP PMID:20396879 The gld1+ gene encoding glycerol dehydrogenase is required f... | ACCEPT | Summary: Matsuzawa et al. 2010: gld1 deletion reduced cellular glycerol dehydrogenase activity and abolished glycerol assimilation, while DHA still supported growth, placing gld1 at the glycerol-to-DHA step. Supporting Evidence: PMID:20396879 Deletion of gld1 caused a reduction in glycerol dehydrogenase activity and prevented glycerol assimilation. PMID:20396879 The gld1 Delta cells grew on 50 mM DHA as the sole carbon source |
| GO:0008888 glycerol dehydrogenase (NAD+) activity | IMP PMID:3017714 Isolation and characterization of mutants from Schyzosacchar... | ACCEPT | Summary: Gancedo et al. 1986 isolated glycerol-negative, DHA-positive mutants lacking glycerol dehydrogenase activity; revertants regained the activity. The abstract does not name the mutated locus; the PomBase curator linked these mutants to gld1 (full text not available here), and the phenotype matches the later gld1 deletion. Reason: Experimental annotation consistent with the gld1 deletion phenotype; deferring to the curator on locus assignment. Supporting Evidence: PMID:3017714 The first type of mutants was defective in glycerol dehydrogenase while the second one was affected both in the glycerol dehydrogenase and in dihydroxyacetone kinase. |
| GO:0016491 oxidoreductase activity | IEA GO_REF:0000002 | MARK AS OVER ANNOTATED | Summary: InterPro2GO from the Fe-ADH domain (IPR001670/IPR018211). True but uninformative root of the oxidoreductase branch; GO:0008888 captures the activity. Reason: Redundant high-level parent of the experimentally supported GO:0008888. |
| GO:0016614 oxidoreductase activity, acting on CH-OH group of donors | IEA GO_REF:0000002 | TOO GENERAL | Summary: InterPro2GO from the glycerol dehydrogenase family signature IPR016205. Correct parent of GO:0008888 (glycerol is a CH-OH donor) but less specific. Reason: Correct but general; the specific activity is GO:0008888. |
| GO:0019563 glycerol catabolic process | IMP PMID:20396879 The gld1+ gene encoding glycerol dehydrogenase is required f... | ACCEPT | Summary: gld1 deletion abolished glycerol assimilation; gld1 catalyses the first step of the glycerol-to-DHAP route. Supporting Evidence: PMID:20396879 indicating that the glycerol dehydrogenase encoded by gld1 (+) is essential for glycerol assimilation in S. pombe |
| GO:0019588 anaerobic glycerol catabolic process | IEA GO_REF:0000041 | MODIFY | Summary: UniPathway UPA00617 ("glycerol fermentation; glycerone phosphate from glycerol (oxidative route)") maps to the anaerobic glycerol catabolism term, which describes bacterial glycerol fermentation. In S. pombe glycerol assimilation is studied on respirable co-substrates (galactose, ethanol) and is not shown to be anaerobic. Reason: The pathway mapping imposes an anaerobic context with no fission-yeast support; the generic glycerol catabolic process is correct. Proposed replacements: glycerol catabolic process Supporting Evidence: PMID:20396879 in the presence of other carbon sources such as galactose and ethanol, S. pombe could assimilate glycerol |
| GO:0046872 metal ion binding | IEA GO_REF:0000002 | MODIFY | Summary: InterPro2GO metal binding for the Fe-ADH/GldA family. The gld1 crystal structure shows one zinc per subunit, as the catalytic metal; zinc ion binding is the more precise term. Reason: The metal is identified structurally as Zn2+. Proposed replacements: zinc ion binding Supporting Evidence: file:SCHPO/gld1/gld1-uniprot.txt CC Note=Binds 1 zinc ion per subunit. {ECO:0000269|Ref.4}; |
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Download this section (compressed HTML)Q: Is gld1 mitochondrial (ORFeome YFP call; presequence-like N-terminus absent from bacterial GldA) or cytosolic (PomBase IC and GO-CAM)? If mitochondrial, how does the DHA it produces reach the cytosolic dak1/dak2?
Experiment: Localize endogenously tagged gld1 (C-terminal tag, native promoter, glucose-derepressed conditions) by microscopy with a mitochondrial marker and by subcellular fractionation; test whether deleting residues 1-45 changes localization and complementation of gld1-delta glycerol assimilation.
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