dpm-1 (Y66H1A.2) encodes the full-length 239-residue Caenorhabditis elegans orthologue of DPM1, the catalytic subunit of dolichol-phosphate-mannose (Dol-P-Man) synthase. It is a GT2-family glycosyltransferase in PANTHER subfamily PTHR43398:SF1, together with human DPM1 and yeast Dpm1, and it retains the conserved acidic DXD-type motifs of the family. By homology it transfers mannose from GDP-mannose to dolichyl phosphate on the cytosolic face of the endoplasmic reticulum, producing Dol-P-Man, the lipid-linked mannosyl donor for lumenal steps of N-glycan precursor assembly, GPI-anchor synthesis and protein O- and C-mannosylation. Like human DPM1, and unlike S. cerevisiae Dpm1, it lacks a C-terminal transmembrane anchor, so its ER-membrane association is expected to depend on a partner such as the worm DPM3 orthologue DPM-3. None of these properties has been measured directly on the C. elegans protein; the assignments rest on subfamily membership, PAINT phylogenetic inference and experiments on yeast and mammalian orthologues.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0004582 dolichyl-phosphate beta-D-mannosyltransferase activity | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT places Dol-P-Man synthase activity at PTN002459128, seeded by experimentally characterised yeast Dpm1, human and mouse DPM1 and microbial relatives. Q9TYJ7 is a full-length member of the same subfamily (PTHR43398:SF1) as human DPM1 and yeast Dpm1, with the catalytic acidic motifs intact. Reason: The target sits inside the clade that inherited the activity, and nothing in its sequence suggests loss: both conserved aspartate-containing motifs (VDDAS at 41, MDAD at 95) are present and the protein has the human-class architecture, which is functional in vivo (human-class and yeast-class synthases complement each other in S. pombe). This is the core activity of the gene. It is inferred, not measured, in C. elegans. Supporting Evidence: PMID:3053713 DPM1 is the structural gene for yeast Dol-P-Man synthase since Escherichia coli transformants harboring this gene express Dol-P-Man synthase activity in vitro PMID:10835346 mammalian DPM synthase contains catalytic DPM1 and regulatory DPM2 subunits PMID:9223280 The two classes of synthase are functionally equivalent, because S. cerevisiae DPM1 and its human counterpart both complement the lethal null mutation in S. pombe dpm1 + file:worm/dpm-1__Q9TYJ7/dpm-1__Q9TYJ7-bioinformatics/RESULTS.md Q9TYJ7 retains both acidic motifs (VDDAS at 41, MDAD at 95) |
| GO:0004582 dolichyl-phosphate beta-D-mannosyltransferase activity | IEA GO_REF:0000120 | ACCEPT | Summary: Combined electronic annotation (InterPro DPM1-like IPR039528, UniRule RU365083, EC 2.4.1.83 / RHEA 21184) to the same activity as the IBA row. Reason: Consistent with the PAINT inference and with the protein's subfamily membership and retained catalytic motifs; the DPM1-like InterPro signature and UniRule assignment are valid family-level support. Same claim as the IBA row, so the same action. Supporting Evidence: file:worm/dpm-1__Q9TYJ7/dpm-1__Q9TYJ7-uniprot.txt Transfers mannose from GDP-mannose to dolichol monophosphate to form dolichol phosphate mannose (Dol-P-Man) file:worm/dpm-1__Q9TYJ7/dpm-1__Q9TYJ7-uniprot.txt DR InterPro; IPR039528; DPM1-like. |
| GO:0005783 endoplasmic reticulum | IEA GO_REF:0000044 | MODIFY | Summary: UniProt subcellular-location mapping (from the UniRule ER location) to endoplasmic reticulum. Reason: Correct but less specific than supported. DPM1-class enzymes act at the cytosolic face of the ER membrane, and the gene already carries endoplasmic reticulum membrane (GO:0005789) by IBA; that more specific term is proposed as the replacement. Proposed replacements: endoplasmic reticulum membrane Supporting Evidence: PMID:16280320 A coiled-coil domain near the C terminus of DPM3 was important for tethering DPM1, the catalytic subunit of the enzyme, to the endoplasmic reticulum membrane |
| GO:0005789 endoplasmic reticulum membrane | IBA GO_REF:0000033 | ACCEPT | Summary: PAINT assigns ER membrane at the eukaryotic node PTN000092441, seeded by Arabidopsis DPMS1, yeast Dpm1 and human DPM1. Reason: The node spans both membrane-anchored (yeast-class) and anchor-less (human-class) synthases, so the assertion is about where the enzyme acts, not about how it is attached. Worm DPM-1 is human-class (no transmembrane-strength hydrophobic segment), so it is expected to be a peripheral protein on the cytosolic face of the ER membrane, held there by a partner as human DPM1 is held by DPM3; C. elegans has a DPM3 orthologue (dpm-3). Worm localisation has not been examined experimentally. Supporting Evidence: PMID:9223280 suggest that S. cerevisiae Dol- P -Man synthase faces the cytoplasm and is anchored in the ER membrane by its COOH-terminal hydrophobic domain PMID:16280320 A coiled-coil domain near the C terminus of DPM3 was important for tethering DPM1, the catalytic subunit of the enzyme, to the endoplasmic reticulum membrane file:worm/dpm-1__Q9TYJ7/dpm-1__Q9TYJ7-bioinformatics/RESULTS.md The worm protein therefore has the human-class architecture (no C-terminal |
| GO:0006488 dolichol-linked oligosaccharide biosynthetic process | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT places dolichol-linked oligosaccharide biosynthesis at PTN000092440, seeded by yeast DPM1 and Candida DPM1 experimental annotations. Dol-P-Man donates the four lumenal mannoses of the N-glycan precursor. Reason: DPM-1 makes the mannosyl donor consumed by the lumenal ALG mannosyltransferases; it does not itself extend the oligosaccharide. Its own reaction is captured more precisely by dolichol phosphate mannose biosynthetic process (GO:0180047, proposed below), which is not a descendant of GO:0006488, so this is not a MODIFY. The pathway assignment is a considered PAINT placement (it is also given to worm DPM-3) and is kept, as one of several Dol-P-Man-consuming pathways the enzyme feeds, but not as the core function. Supporting Evidence: PMID:9535917 It donates four mannosyl residues in the N-linked oligosaccharide precursor and all three mannosyl residues in the core of the glycosylphosphatidylinositol anchor. PMID:2146492 Dol-P-Man synthase is also required in vivo for N |
| GO:0180047 dolichol phosphate mannose biosynthetic process | ISS PMID:10835346 Human dolichol-phosphate-mannose synthase consists of three ... | NEW | Summary: Proposed process annotation for the reaction the enzyme itself catalyses: formation of Dol-P-Man from GDP-mannose and dolichyl phosphate. Reason: Participation, not necessity: the catalytic DPM1 subunit performs the single step that defines this process. Comparator check: human DPM1 (IDA) and DPM2 (IDA, PMID:10835346) and yeast Dpm1 (ISS) carry this term; the term is recent and PAINT has not yet placed an IBD for it in PTHR43398, so its absence from worm reflects ontology lag rather than a curator decision against it. It is the process counterpart of the accepted GO:0004582 activity, inferred by subfamily membership (PTHR43398:SF1) and not demonstrated in C. elegans. Supporting Evidence: PMID:3053713 Dolichol phosphate mannose (Dol-P-Man) synthase (EC 2.4.1.83) catalyzes the formation of Dol-P-Man from Dol-P and GDP-Man. PMID:10835346 mammalian DPM synthase contains catalytic DPM1 and regulatory DPM2 subunits file:worm/dpm-1__Q9TYJ7/dpm-1__Q9TYJ7-bioinformatics/RESULTS.md Q9TYJ7, human DPM1 and yeast Dpm1 all fall in the same PANTHER subfamily, PTHR43398:SF1. |
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Download this section (compressed HTML)Q: Does C. elegans DPM-1 form a complex with DPM-3 (Q9XVV5), and does the worm, which has no detectable DPM2 (PF07297) protein, use a DPM2-independent complex or a divergent DPM2?
Q: PAINT propagates GO:0033185 (DPM synthase complex) to DPM3-family members but not to the DPM1 family node, which also contains single-subunit yeast-class enzymes. Would an animal-level DPM1 node be the right place to propagate complex membership and the human GPI-anchor and O-mannosylation process annotations?
Q: Which Dol-P-Man-consuming pathways (N-glycan precursor, GPI anchor, O- and C-mannosylation) are most sensitive to loss of dpm-1 in C. elegans?
Experiment: Express full-length Y66H1A.2a (Q9TYJ7) alone and with DPM-3 in a Dol-P-Man-deficient host (e.g. S. pombe dpm1 null or mammalian class E cells) and measure Dol-P-Man formation from GDP-mannose and dolichyl phosphate, with a DXD-motif (D96A/D98A in the MDAD motif) mutant as negative control.
Experiment: Tag endogenous DPM-1 and DPM-3 by CRISPR, test ER-membrane co-localisation and co-immunoprecipitation, and test whether DPM-1 membrane association is lost after dpm-3 depletion.
Experiment: Profile lipid-linked oligosaccharides, GPI-anchored proteins and O-mannosylated proteins in a conditional dpm-1 loss-of-function background to define which pathways depend on it in worms.
dpm-1 encodes a putative catalytic subunit of dolichol phosphate mannosyltransferase, orthologous to budding yeast and human DPM1 (OMIM:603503, mutated in congenital disorder of glycosylation type Ie); in mass RNAi assays, DPM-1 is required for embryonic viability and proper cortical motion in the early embryo.
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