Vps74p (also called Mnn3p) is the budding-yeast member of the GOLPH3/GPP34 family and the orthologue of human GOLPH3 and GOLPH3L. It is a soluble, tetrameric protein recruited to the cytosolic face of Golgi membranes by direct recognition of phosphatidylinositol 4-phosphate through a basic pocket in its GPP34 fold, so its Golgi residence depends on ongoing PtdIns4P synthesis by the Pik1 PI 4-kinase. On the membrane it works as a cargo adaptor, or sorting receptor: one surface binds a short pentameric motif in the N-terminal cytosolic tails of cis- and medial-Golgi mannosyltransferases such as Kre2p, Mnn2p, Mnn5p, Och1p, Ktr3p and Mnn4p, while an N-terminal arginine cluster binds COPI coatomer, coupling those enzymes to retrograde COPI vesicles and thereby holding them in their resident cisternae instead of letting them escape to the vacuole, where they are degraded. Vps74p also binds the catalytic domain of the Sac1 phosphoinositide phosphatase and, with it, keeps PtdIns4P low on medial-Golgi cisternae, linking Golgi enzyme sorting to local phosphoinositide and sphingolipid homeostasis. Because the glycosyltransferases it retains build N- and O-linked mannose chains, cells lacking Vps74p secrete hypoglycosylated proteins and have altered cell-wall mannan, even though Vps74p itself is cytosolic and performs no glycosylation chemistry. In mammalian cells the same fold additionally links Golgi membranes to the actomyosin motor MYO18A, a partner that budding yeast lacks.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000139 Golgi membrane | IEA GO_REF:0000108 | ACCEPT | Summary: Inter-ontology inference from Golgi vesicle budding. Vps74p is a peripheral protein of the cytosolic face of Golgi membranes, so the location is correct. Reason: Although derived by logical inference rather than observation, the conclusion is independently established, since Vps74p is recruited to Golgi membranes by PtdIns4P and behaves as a peripheral membrane protein on the cytoplasmic side, and mutations that abolish lipid binding abolish Golgi membrane association. Golgi membrane is the location at which the cargo-adaptor activity acts. Supporting Evidence: file:yeast/VPS74/VPS74-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus, Golgi stack membrane PMID:20026658 Golgi mannosyltransferases that depend on Vps74 for Golgi localization are not retained in the Golgi in mutant cells that express a form of Vps74 that does not bind PtdIns4P. |
| GO:0005515 protein binding | IPI PMID:16429126 Proteome survey reveals modularity of the yeast cell machine... | REMOVE | Summary: High-throughput TAP-MS co-purification of Vps74p with the Hsp70 chaperone Ssa2p (P10592). Reason: Bare GO:0005515 protein binding carries no functional information and is removed under the project's protein-binding policy. This is not a claim that the reported Ssa2p association is false; Ssa2p is an abundant cytosolic chaperone that co-purifies very widely, and no study assigns Vps74p a chaperone-related activity, so no informative replacement molecular function can be justified from this interaction. The informative molecular functions of Vps74p (cargo adaptor activity, PtdIns4P binding) are annotated separately in this review. |
| GO:0005515 protein binding | IPI PMID:37968396 The social and structural architecture of the yeast protein ... | REMOVE | Summary: The same Vps74p-Ssa2p association recovered by the Michaelis et al. saturating GFP-pulldown interactome. Reason: Removed for the same reason as the other GO:0005515 row, namely that the term is uninformative rather than wrong. A second high-throughput recovery of an Hsp70 association does not identify a molecular function, and nothing in the Vps74p literature suggests the interaction is functionally central. |
| GO:0005634 nucleus | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | MARK AS OVER ANNOTATED | Summary: Assignment from the genome-wide GFP-fusion localization survey of Huh et al. Reason: Vps74p is a peripheral Golgi membrane protein with a large soluble pool; every dedicated imaging study localizes it to Golgi puncta plus diffuse cytosol, and none reports nuclear enrichment or any nuclear function. A diffuse cytosolic GFP signal is readily binned as nuclear-plus-cytoplasmic in a high-throughput survey. The cached record for this screen is abstract-only, so the row is marked as an over-annotation rather than removed. Supporting Evidence: PMID:18410729 A substantial amount of GFP-Vps74p is also seen in the cytosol |
| GO:0005737 cytoplasm | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | TOO GENERAL | Summary: Cytoplasmic signal for Vps74p-GFP in the genome-wide localization survey. Reason: True but uninformative here, because the more specific GO:0005829 cytosol is asserted by direct imaging elsewhere in this review and entails cytoplasm, as do the Golgi and Golgi-membrane rows. The claim itself is not in doubt. Supporting Evidence: PMID:18410729 A substantial amount of GFP-Vps74p is also seen in the cytosol |
| GO:0005794 Golgi apparatus | IDA PMID:18410729 Golgi localization of glycosyltransferases requires a Vps74p... | ACCEPT | Summary: GFP-Vps74p co-localizes with the Golgi markers Arf1p, Cop1p and Sec7p (Fig. S1 of Schmitz et al.). Reason: Direct imaging in the paper that defined the Vps74p mechanism. Under the root-organelle policy the Golgi apparatus term is informative in its own right, and it is kept alongside the finer cis/medial cisternal rows rather than being replaced by them. This is the compartment in which the core cargo-adaptor activity operates. Supporting Evidence: PMID:18410729 N-terminally GFP-tagged Vps74p (GFP-Vps74p) localizes to the Golgi apparatus as judged by its co-localization with Arf1p-mCherry, Cop1p-mCherry, and Sec7p-mCherry |
| GO:0005794 Golgi apparatus | IDA PMID:19837035 GOLPH3 bridges phosphatidylinositol-4- phosphate and actomyo... | ACCEPT | Summary: EGFP-Vps74p imaged on yeast Golgi and shown to leave the Golgi when PtdIns4P synthesis is switched off in a pik1 temperature-sensitive strain. Reason: A second independent IDA for the same compartment, with the additional value that it establishes the recruitment mechanism, since acute loss of Pik1 activity strips Vps74p off the Golgi within minutes, which is exactly what a PtdIns4P-dependent peripheral Golgi protein should do. Supporting Evidence: PMID:19837035 EGFP-Vps74p dissociates from the Golgi within five minutes after shift to the non-permissive temperature |
| GO:0005794 Golgi apparatus | IDA PMID:24019977 The N-terminus of Vps74p is essential for the retention of g... | ACCEPT | Summary: CACAO row. Figure 2 of Hsu et al. images GFP-tagged wild-type Vps74p against Arf1p-mRFP and Arl1p-mRFP in vps74-delta cells: Vps74p gives Golgi puncta that partially overlap both markers. Reason: CACAO assessment: the cited paper is about this gene in this organism, the assay is a direct co-localization experiment with two independent Golgi markers (Fig. 2 and Fig. S1), and GO:0005794 is exactly what that figure shows. The term is neither too downstream nor the wrong granularity; the figure resolves cis and trans markers but Vps74p overlaps both, so stopping at the organelle is the honest reading. The same figure panel is the control for the paper's real point, that the N-terminal 66 residues are dispensable for Golgi association. The row agrees with the independent UniProt and SGD IDA rows for this term. The GONUTS wiki page for this PMID was checked on 2026-10-29 and gowiki.tamu.edu is offline for maintenance, but the cached full text is sufficient. Supporting Evidence: PMID:24019977 Wild-type Vps74p partially co-localized with Arf1p and Arl1p (Figures 2 and S1), indicating that Vps74p localizes to both the cis- and trans-Golgi networks. PMID:24019977 These findings clearly indicated that the N-terminal 66 amino acids are not required for the association of Vps74p with the Golgi. |
| GO:0005794 Golgi apparatus | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA rule-based assignment of the family-wide Golgi location. Reason: An electronic restatement of a location that three independent IDA rows in this review establish directly. GOLPH3-family membership does predict Golgi localization, and here the prediction is correct, so the row is kept even though it adds nothing beyond the experimental rows. Supporting Evidence: PMID:18410729 N-terminally GFP-tagged Vps74p (GFP-Vps74p) localizes to the Golgi apparatus as judged by its co-localization with Arf1p-mCherry, Cop1p-mCherry, and Sec7p-mCherry |
| GO:0005797 Golgi medial cisterna | IDA PMID:22553352 Local control of phosphatidylinositol 4-phosphate signaling ... | ACCEPT | Summary: Quantitative intra-Golgi profiling (Pearson correlation of GFP-Vps74 against mKate-tagged cisternal markers) places Vps74 on cis and medial cisternae, correlating best with Cop1 and with the medial-Golgi enzyme Aur1. Reason: This is the most informative cellular-component assertion for the gene and the one that matches its function, since the mannosyltransferase clients it retains are cis/medial residents and its Sac1-dependent control of PtdIns4P is exerted on medial cisternae. It is a sub-compartment row added alongside, not instead of, the Golgi apparatus rows. Supporting Evidence: PMID:22553352 Vps74 is enriched on cis and medial compartments of the Golgi. PMID:18410729 These results implicate Vps74p in specific retention of mannosyltransferases that reside in cis and medial Golgi compartments. |
| GO:0005802 trans-Golgi network | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: PAINT assertion at the GOLPH3-family ancestral node PTN000294961, with rat Golph3, human GOLPH3L and VPS74 itself among the descendant evidences. Reason: The node placement is sound, since TGN localization is a documented property across the family, and the appearance of SGD:S000002780 in the WITH/FROM column reflects that VPS74's own IDA row was one of the descendant evidences the PAINT curator used, which is expected rather than circular. It is kept as non-core because the quantitative cisternal profiling in Wood et al. shows the yeast protein's steady-state pool peaks on cis/medial rather than trans cisternae, so the TGN is a real but peripheral station for Vps74p. Supporting Evidence: PMID:19837035 In yeast, EGFP-Vps74p colocalizes with the late Golgi marker Sec7p-dsRed (Figure S2B). PMID:22553352 Vps74 is enriched on cis and medial compartments of the Golgi. |
| GO:0005802 trans-Golgi network | IDA PMID:19837035 GOLPH3 bridges phosphatidylinositol-4- phosphate and actomyo... | KEEP AS NON CORE | Summary: CACAO row. Figure S2B of Dippold et al. shows EGFP-Vps74p co-localizing with the late-Golgi/TGN marker Sec7p-dsRed in S. cerevisiae. Reason: CACAO assessment: the paper is a GOLPH3 paper but it contains a dedicated yeast panel for this protein, and that panel is a direct co-localization with a bona fide late-Golgi marker, so the evidence code and the term both fit what was done. This is not phenotype-read-as-process and not a case of a paper that does not assay the gene. The only reservation is granularity in the other direction. A later quantitative study of the same protein finds its steady-state distribution is skewed to cis and medial cisternae, with the lowest correlation to late-Golgi markers, so the TGN is kept as a genuine but non-core location rather than accepted as a site of the core activity. GONUTS could not be consulted (gowiki.tamu.edu offline, checked 2026-10-29); the cached full text was sufficient. Supporting Evidence: PMID:19837035 In yeast, EGFP-Vps74p colocalizes with the late Golgi marker Sec7p-dsRed (Figure S2B). PMID:22553352 Vps74 is enriched on cis and medial compartments of the Golgi. |
| GO:0005829 cytosol | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Family-level assertion of a cytosolic pool, propagated from the GOLPH3 ancestral node. Reason: Correct, in that GOLPH3-family proteins are soluble and partition between a membrane-bound and a cytosolic pool, and the yeast protein is directly observed to do so. Kept as non-core because the cytosolic pool is the unengaged reservoir; the cargo-adaptor and Sac1-regulatory activities require recruitment onto the Golgi membrane by PtdIns4P, and a Vps74p variant that cannot be recruited is non-functional. Supporting Evidence: PMID:18410729 A substantial amount of GFP-Vps74p is also seen in the cytosol PMID:20026658 Golgi mannosyltransferases that depend on Vps74 for Golgi localization are not retained in the Golgi in mutant cells that express a form of Vps74 that does not bind PtdIns4P. |
| GO:0005829 cytosol | IDA PMID:18410729 Golgi localization of glycosyltransferases requires a Vps74p... | KEEP AS NON CORE | Summary: GFP-Vps74p shows substantial diffuse cytosolic signal in addition to Golgi puncta, and does not overlap the endosomal retromer marker Vps17p. Reason: Direct observation of the soluble pool, and a useful negative control against an endosomal assignment. Non-core for the same reason as the IBA row, namely that the protein must be on the membrane to work. Supporting Evidence: PMID:18410729 A substantial amount of GFP-Vps74p is also seen in the cytosol |
| GO:0005829 cytosol | IEA GO_REF:0000117 | KEEP AS NON CORE | Summary: ARBA rule-based cytosol assignment for the family. Reason: An electronic restatement of a correct and directly observed location. Kept, at the same non-core status as the IDA and IBA rows for this term, so the three rows agree. Supporting Evidence: PMID:18410729 A substantial amount of GFP-Vps74p is also seen in the cytosol |
| GO:0006487 protein N-linked glycosylation | IMP PMID:18410729 Golgi localization of glycosyltransferases requires a Vps74p... | MARK AS OVER ANNOTATED | Summary: CACAO row. Figures 1A-1C of Schmitz et al.: 35S pulse-chase of secreted proteins from vps74-delta cells shows faster-migrating species; immunoprecipitated invertase migrates faster from the mutant and is collapsed to a common size by N-glycosidase F; mature CPY is also shortened while its ER-derived p1 form is not. Reason: CACAO assessment: the paper is the right paper, the gene is the right gene and the IMP code fits the deletion-mutant assay, so this is not a mis-attribution. The failure is the choice of term, which reads a phenotype as a process. Vps74p sits on the cytosolic face of the Golgi and performs no step of N-glycan assembly, which happens in the lumen; the authors say so explicitly in the same paper. The hypoglycosylation of invertase and CPY is the downstream consequence of mannosyltransferases escaping the Golgi, and the process Vps74p actually executes is GO:0045053 protein retention in Golgi apparatus, which SGD annotated from this very paper. Marked as over-annotated rather than removed, in deference to the student curator and because the underlying requirement is real; the mechanistic term already carries the claim. Comparator check: GO:0006487 in yeast is annotated to the glycosyltransferases and OST subunits that do the chemistry, not to the cytosolic factors that position them. GONUTS was unavailable (offline, checked 2026-10-29), but the full text is cached. Supporting Evidence: PMID:18410729 Therefore, the higher mobility of untreated invertase from vps74 Ξ cells is a consequence of reduced N-linked glycosylation. PMID:18410729 Since Vps74p exists on the cytosolic side, and protein glycosylation occurs on the luminal side of secretory organelles, the role that Vps74p plays in glycosylation must be indirect. PMID:18410729 These results implicate Vps74p in specific retention of mannosyltransferases that reside in cis and medial Golgi compartments. |
| GO:0006890 retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | IMP PMID:18635803 Signal-mediated dynamic retention of glycosyltransferases in... | MODIFY | Summary: Tu et al. showed that Vps74p binds a pentameric motif in glycosyltransferase cytosolic tails and also binds COPI, and proposed that it maintains their steady-state Golgi localization by promoting their incorporation into COPI-coated vesicles. Reason: The essence is right, in that Vps74p acts in COPI-dependent retrograde traffic, but the compartment pair is wrong. What the paper describes, and what every subsequent study supports, is recycling of resident enzymes between Golgi cisternae, not transport from the Golgi back to the endoplasmic reticulum. Consistent with this, deleting VPS74 does not disturb the ER glycosyltransferase Alg5p or other ER residents. GO:0000301 retrograde transport, vesicle recycling within Golgi is the term that matches the mechanism. The cached record is abstract-only, so this is a lateral correction of the term rather than a challenge to the curator's reading of the experiment. Proposed replacements: retrograde transport, vesicle recycling within Golgi Supporting Evidence: PMID:18635803 cytoplasmic tails of the majority of yeast Golgi-localized glycosyltransferases, PMID:22889169 Vps74p, a member of the GOLPH3 protein family, binds directly to coatomer and PMID:18410729 Similarly, localization of several peripheral Golgi membrane proteins (Arf1p, Cop1p and Sec7p) and of Alg5p-GFP, an ER-localized glycosyltransferase, are unaffected by VPS74 deletion. |
| GO:0007030 Golgi organization | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Family-level assertion that GOLPH3 proteins shape the Golgi, placed at PTN000294961 from Drosophila and human descendant evidence. Reason: The node placement is defensible, since human GOLPH3 knockdown condenses the whole Golgi ribbon and the Drosophila protein behaves similarly, and yeast Vps74p is inside the clade, so the inheritance claim stands. It is non-core for the yeast protein, however, because the mammalian effect on Golgi shape is mediated by MYO18A, which budding yeast does not encode, and no comparable gross Golgi morphology defect is reported for vps74-delta. The organizational contribution in yeast is at the level of cisternal enzyme composition rather than overall architecture. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000294961 SUPPORTS TRANSFER Ancestral GOLPH3-family node, soundly placed. The membrane-shaping aspect of the ancestral assertion depends in mammals on a MYO18A partner absent from budding yeast, so the term is kept but as non-core. Supporting Evidence: PMID:19837035 In mammals, we observe that GOLPH3 functions through its interaction with MYO18A, but the S. cerevisiae genome does not encode an ortholog of MYO18A, having only type I, II, and V myosins (Berg et al., 2001). |
| GO:0019899 enzyme binding | IPI PMID:18410729 Golgi localization of glycosyltransferases requires a Vps74p... | MODIFY | Summary: GST pull-down (Fig. 3) with the first 15 residues of Mnn2p (SGD:S000000219, alpha-1,2-mannosyltransferase) fused to GST; purified Vps74p binds in a bait-dose-dependent manner, while GST alone and a Cps1p tail control do not. Reason: The interaction is real and important, but enzyme binding describes only the identity of the partner, not what Vps74p does. The informative molecular function is GO:0140312 cargo adaptor activity, since Vps74p is the sorting receptor that reads these enzymes' cytosolic tails on one surface and coatomer on another, coupling them to COPI vesicles. GO:0140312 is already asserted for this gene by IBA, so the replacement is a term the gene carries. The fact that the four partners happen to be enzymes is incidental; they are cargo. Proposed replacements: cargo adaptor activity Supporting Evidence: PMID:18410729 Vps74p binds strongly to the Kre2p fusion protein and significantly to a number of the other fusion proteins. PMID:22889169 Vps74p, a member of the GOLPH3 protein family, binds directly to coatomer and |
| GO:0019899 enzyme binding | IPI PMID:18410729 Golgi localization of glycosyltransferases requires a Vps74p... | MODIFY | Summary: Same Fig. 3 GST pull-down with the Kre2p tail (SGD:S000002891, medial-Golgi alpha-1,2-mannosyltransferase), the strongest binder of the set and the client whose mislocalization is best characterized. Reason: Modified to GO:0140312 cargo adaptor activity for the same reason as the other three rows from this experiment, in that the binding is the mechanism of a cargo-sorting activity and that activity is the informative claim. Kre2p is the archetypal client, whose Golgi retention is lost in vps74-delta, whose tail binds Vps74p most strongly, and whose binding is abolished by the beta-hairpin deletions that inactivate the protein. Proposed replacements: cargo adaptor activity Supporting Evidence: PMID:18410729 Vps74p binds strongly to the Kre2p fusion protein and significantly to a number of the other fusion proteins. PMID:18410729 These results implicate Vps74p in specific retention of mannosyltransferases that reside in cis and medial Golgi compartments. |
| GO:0019899 enzyme binding | IPI PMID:18410729 Golgi localization of glycosyltransferases requires a Vps74p... | MODIFY | Summary: Same Fig. 3 GST pull-down with the Och1p tail (SGD:S000003006, cis-Golgi mannosyltransferase that initiates outer-chain elongation). Reason: Modified to GO:0140312 cargo adaptor activity, as for the other tail-binding rows. Worth noting that a later study found Och1p's Golgi retention to be largely Vps74p-independent in vivo, which does not contradict the in vitro tail binding recorded here but does show that binding and functional dependence are separable across clients. Proposed replacements: cargo adaptor activity Supporting Evidence: PMID:18410729 Vps74p binds strongly to the Kre2p fusion protein and significantly to a number of the other fusion proteins. PMID:32673164 Nevertheless, the Golgi retention of Och1p appears to be largely independent of Vps74p, but rather to require Bre5p/Ubp3p, as unlike Ktr3-9myc there is no synthetic loss of Och1-9myc in vps74Ξ bre5Ξ cells |
| GO:0019899 enzyme binding | IPI PMID:18410729 Golgi localization of glycosyltransferases requires a Vps74p... | MODIFY | Summary: Same Fig. 3 GST pull-down with the Mnn5p tail (SGD:S000003722, alpha-1,2-mannosyltransferase); Mnn5p-GFP is among the enzymes delivered to the vacuole in vps74-delta cells. Reason: Modified to GO:0140312 cargo adaptor activity, consistent with the other three rows from the same figure. The pairing of tail binding in vitro with mislocalization in vivo is what converts a binding observation into an adaptor activity. Proposed replacements: cargo adaptor activity Supporting Evidence: PMID:18410729 Vps74p binds strongly to the Kre2p fusion protein and significantly to a number of the other fusion proteins. PMID:18410729 The GFP reporters localize to the lumen of the lysosome-like vacuole in addition to faint puncta resembling Golgi or endosomal compartments |
| GO:0030968 endoplasmic reticulum unfolded protein response | IMP PMID:16582425 Genomic analysis of the Opi- phenotype. | MARK AS OVER ANNOTATED | Summary: vps74 was recovered among 89 Opi- (inositol-excreting) deletion mutants and, in a UPRE-reporter assay, behaved like hac1 and ire1 in failing to respond to tunicamycin and inositol depletion. Reason: A genome-wide screen phenotype whose mechanism the authors themselves frame as indirect, proposing only that VPS74 is somehow required for HAC1 or IRE1 function or expression. Vps74p is a cytosolic Golgi sorting receptor with no assayed role in Ire1 activation, HAC1 splicing or UPRE transcription, and a secretory-pathway mutant with widespread glycosylation defects can perturb a UPR reporter for many reasons. The requirement is real, so the row is marked as an over-annotation rather than removed, but it does not represent participation in the response. Supporting Evidence: PMID:16582425 This suggests that VPS74 is required for the function/expression of either HAC1 or IRE1 ( Figure 9 ) PMID:18410729 Since Vps74p exists on the cytosolic side, and protein glycosylation occurs on the luminal side of secretory organelles, the role that Vps74p plays in glycosylation must be indirect. |
| GO:0032580 Golgi cisterna membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Mapped from the UniProt subcellular-location annotation for the Golgi stack membrane, which is itself curated from three experimental papers. Reason: Accurate and at the right granularity. Vps74p is a peripheral protein on the cytosolic face of Golgi stack cisternae, enriched on cis and medial cisternae, and the SubCell-to-GO mapping reproduces that faithfully rather than over-reaching. Supporting Evidence: file:yeast/VPS74/VPS74-uniprot.txt SUBCELLULAR LOCATION: Golgi apparatus, Golgi stack membrane PMID:22553352 Vps74 is enriched on cis and medial compartments of the Golgi. |
| GO:0034067 protein localization to Golgi apparatus | IEA GO_REF:0000117 | ACCEPT | Summary: ARBA rule assigning the family role in localizing proteins to the Golgi. Reason: Unusually, the ARBA rule lands on exactly the right process. Vps74p's defining activity is keeping a defined set of membrane proteins localized to the Golgi. The more specific GO:0045053 protein retention in Golgi apparatus is also annotated with experimental evidence, and this broader term remains a true statement about what the gene does rather than a restatement of a phenotype. Supporting Evidence: PMID:18410729 These results implicate Vps74p in specific retention of mannosyltransferases that reside in cis and medial Golgi compartments. PMID:18410729 The GFP reporters localize to the lumen of the lysosome-like vacuole in addition to faint puncta resembling Golgi or endosomal compartments |
| GO:0035269 protein O-linked glycosylation via mannose | IMP PMID:18410729 Golgi localization of glycosyltransferases requires a Vps74p... | MARK AS OVER ANNOTATED | Summary: CACAO row. Figure 1D of Schmitz et al.: HA-tagged Hsp150p, an extensively O-mannosylated secreted protein, runs as a single band of about 150 kDa in wild type but as multiple shorter species in vps74-delta cells. Reason: CACAO assessment: the same shape of error as the companion N-glycosylation row from this paper, and judged the same way. The experiment is real, the gene and organism are right, and the IMP code fits; but Vps74p is a cytosolic protein that catalyses no mannosyl transfer, and the paper states that its role in glycosylation must be indirect. The O-mannosylation defect follows from Kre2p, an alpha-1,2-mannosyltransferase acting in both N- and O-linked mannosylation, escaping the Golgi, which is the Vps74p-dependent step and is captured by GO:0045053. Comparator check: the yeast PMT and KTR/MNN family enzymes that perform O-mannosylation carry this term, whereas the cytosolic factors that position them do not. Marked as over-annotated rather than removed, deferring to the student curator. GONUTS offline on 2026-10-29; full text cached. Supporting Evidence: PMID:18410729 These data indicate that Vps74p is required for proper mannosylation of O-linked as well as N-linked mannoproteins. PMID:18410729 Since Vps74p exists on the cytosolic side, and protein glycosylation occurs on the luminal side of secretory organelles, the role that Vps74p plays in glycosylation must be indirect. PMID:18410729 KRE2 encodes an Ξ±-1,2-mannosyltransferase of the medial Golgi that functions in both N- and O-linked mannosylation |
| GO:0043001 Golgi to plasma membrane protein transport | IBA GO_REF:0000033 | MARK AS OVER ANNOTATED | Summary: Family-level anterograde-transport assertion propagated from the GOLPH3 ancestral node, resting on mammalian GOLPH3/GOLPH3L vesicle-budding data. Reason: This is the aspect of the ancestral assertion that transfers worst to budding yeast. In mammals the anterograde contribution runs through the GOLPH3-MYO18A actomyosin link, and the authors of that work note that S. cerevisiae encodes no MYO18A orthologue. Directly, bulk secretion is not grossly impaired when VPS74 is deleted, since the secreted-protein profile of vps74-delta cells is shifted in mobility but not in composition or abundance. Vps74p's documented traffic role is retrograde and intra-Golgi. Marked as over-annotated rather than removed because the GOLPH3 family does act in Golgi export and a modest, undetected yeast contribution cannot be excluded. Propagation Review Root cause: PROPAGATION BAD Failure modes: PSEUDO OR SUBACTIVITY LOSS Sources checked: PANTHER:PTN000294961 SUPPORTS SOURCE BUT NOT TARGET Ancestral node is well placed for the family, but the anterograde Golgi-to-PM aspect depends on the MYO18A partnership, and budding yeast has no MYO18A orthologue. Supporting Evidence: PMID:19837035 In mammals, we observe that GOLPH3 functions through its interaction with MYO18A, but the S. cerevisiae genome does not encode an ortholog of MYO18A, having only type I, II, and V myosins (Berg et al., 2001). PMID:18410729 although the number of proteins and their relative abundances are similar |
| GO:0045053 protein retention in Golgi apparatus | IGI PMID:32673164 A novel mechanism for the retention of Golgi membrane protei... | ACCEPT | Summary: Genetic interaction with UBP3 (SGD:S000000953). vps74-delta ubp3-delta double mutants show synthetic glycosylation and Golgi-retention defects, and Ktr3p and Mnn4p require both Vps74p and the Bre5p/Ubp3p deubiquitinase for robust Golgi retention. Reason: This is the core process for the gene, and the IGI row adds the important refinement that Vps74p-dependent retention operates in parallel with a deubiquitinase-dependent pathway, with additive effects on shared clients. Wang et al. also describe Vps74p in exactly the role GO intends, as a COPI-coatomer-affiliated sorting receptor. Supporting Evidence: PMID:32673164 Moreover, Ktr3p and Mnn4p employ a dual retention mechanism that requires both Bre5p/Ubp3p as well as Vps74p for their robust Golgi retention. |
| GO:0045053 protein retention in Golgi apparatus | IGI PMID:32673164 A novel mechanism for the retention of Golgi membrane protei... | ACCEPT | Summary: The matching genetic interaction with BRE5 (SGD:S000005334), the partner subunit of the Ubp3p deubiquitinase. Reason: Accepted for the same reason as the UBP3 row; the two partners are subunits of one complex and the two rows record one genetic result. Core process for the gene. Supporting Evidence: PMID:32673164 Moreover, Ktr3p and Mnn4p employ a dual retention mechanism that requires both Bre5p/Ubp3p as well as Vps74p for their robust Golgi retention. |
| GO:0045053 protein retention in Golgi apparatus | IMP PMID:18410729 Golgi localization of glycosyltransferases requires a Vps74p... | ACCEPT | Summary: Deleting VPS74 sends Kre2p-GFP, Mnn2p-GFP, Mnn5p-GFP and Och1p-GFP to the vacuolar lumen while leaving multi-TM Golgi proteins, TGN proteins, peripheral Golgi proteins and an ER glycosyltransferase in place (Fig. 2); a Kre2p(1-118)-GFP minimal reporter behaves the same way. Reason: The defining experiment for the gene, and the term that correctly names what Vps74p does rather than what fails downstream. The specificity controls are what make it strong, since only a defined set of cis/medial enzymes is affected and the effect is not a secondary consequence of defective glycosylation, because deleting the Golgi calcium and manganese transporter PMR1 does not reproduce it. Supporting Evidence: PMID:18410729 These results implicate Vps74p in specific retention of mannosyltransferases that reside in cis and medial Golgi compartments. PMID:18410729 The GFP reporters localize to the lumen of the lysosome-like vacuole in addition to faint puncta resembling Golgi or endosomal compartments PMID:18410729 Loss of Golgi localization of these mannosyltransferases is not due to defective glycosylation. |
| GO:0045053 protein retention in Golgi apparatus | IMP PMID:32673164 A novel mechanism for the retention of Golgi membrane protei... | ACCEPT | Summary: Wang et al. show nutrient-dependent Vps74p requirements for the Golgi retention of Ktr3p and Mnn11p and an additive Vps74p/Bre5p-Ubp3p requirement for Mnn4p. Reason: An independent laboratory, a decade later, confirming and extending the same process assignment with new clients. The nutrient dependence is a genuinely new finding about the activity and a good reason to keep this row alongside the 2008 IMP. Supporting Evidence: PMID:32673164 Moreover, Ktr3p and Mnn4p employ a dual retention mechanism that requires both Bre5p/Ubp3p as well as Vps74p for their robust Golgi retention. PMID:32673164 it nonetheless displays a nutrient-dependent requirement for Vps74p (as was also the case for Ktr3p; Figure 2) |
| GO:0048194 Golgi vesicle budding | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Family-level assertion that GOLPH3 proteins act in budding of Golgi-derived vesicles. Reason: Defensible for the yeast protein on different grounds than for the mammalian ones. Vps74p binds coatomer through an N-terminal arginine cluster and loads its clients into COPI vesicles, so it does act at the stage of COPI vesicle formation, even though yeast lacks the MYO18A-dependent tensile mechanism the mammalian evidence rests on. Kept as non-core because Vps74p's role there is cargo selection rather than driving budding itself, and vps74-delta cells have no reported general vesicle-formation defect. Supporting Evidence: PMID:22889169 Vps74p, a member of the GOLPH3 protein family, binds directly to coatomer and PMID:18635803 cytoplasmic tails of the majority of yeast Golgi-localized glycosyltransferases, |
| GO:0060304 regulation of phosphatidylinositol dephosphorylation | IMP PMID:22553352 Local control of phosphatidylinositol 4-phosphate signaling ... | ACCEPT | Summary: Vps74 binds the cytoplasmic N-terminal region of the Sac1 phosphoinositide phosphatase directly (SPR dissociation constant 3.8 micromolar, plus GST pull-down and two-hybrid), and PtdIns4P is elevated on medial-Golgi cisternae in cells lacking either VPS74 or SAC1. Reason: A second, genuinely distinct function, supported by direct binding measurements and by metabolic labelling of PtdIns4P in the deletion mutant, with the SAC1 genetic partner recorded in WITH/FROM. Vps74p does work here rather than merely being required, in that it is the PtdIns4P sensor that recruits or engages the phosphatase on medial cisternae, so the regulation term is apt. It also closes a satisfying loop, in that the lipid which recruits Vps74p is the lipid whose turnover Vps74p directs. Supporting Evidence: PMID:22553352 Surface plasmon resonance (SPR) experiments employing untagged recombinant proteins indicated that Vps74 binds Sac1 (amino acids 2β521) with a KD value of 3.8 Β± 0.4 ΞΌM (Figure 2B). PMID:22553352 These results indicate that both Vps74 and Sac1 function to maintain a low level of PtdIns4P on medial Golgi compartments. |
| GO:0070273 phosphatidylinositol-4-phosphate binding | IBA GO_REF:0000033 | ACCEPT | Summary: Family-wide PtdIns4P-binding assertion at the GOLPH3 ancestral node, with Drosophila, human GOLPH3 and GOLPH3L, and VPS74 itself among the descendant evidences. Reason: The best-supported node assertion for this family, since the lipid-binding pocket is structurally conserved and has been assayed directly in yeast, fly and human members, and it names a core molecular function of the yeast protein. The presence of SGD:S000002780 in WITH/FROM reflects that VPS74's own IDA rows were descendant evidence for the node, which is the expected marker of experimental grounding on the target itself. Supporting Evidence: PMID:20026658 in vitroβtranslated radiolabeled Vps74 and GOLPH3 bind to immobilized PtdIns4P PMID:19837035 Our data demonstrate that Vps74p binds PtdIns(4)P in vitro and is downstream of PIK1 in vivo. |
| GO:0070273 phosphatidylinositol-4-phosphate binding | IDA PMID:19837035 GOLPH3 bridges phosphatidylinositol-4- phosphate and actomyo... | ACCEPT | Summary: Dippold et al. identified GOLPH3/Vps74p in a proteomic lipid-binding screen and showed direct PtdIns(4)P binding in vitro for the yeast protein. Reason: Direct in vitro lipid binding for this protein, corroborated in the same paper by the in vivo requirement for Pik1-made PtdIns4P to keep Vps74p on the Golgi. Core molecular function. Supporting Evidence: PMID:19837035 Our data demonstrate that Vps74p binds PtdIns(4)P in vitro and is downstream of PIK1 in vivo. PMID:19837035 EGFP-Vps74p dissociates from the Golgi within five minutes after shift to the non-permissive temperature |
| GO:0070273 phosphatidylinositol-4-phosphate binding | IDA PMID:20026658 PtdIns4P recognition by Vps74/GOLPH3 links PtdIns 4-kinase s... | ACCEPT | Summary: Dot-blot assay with in vitro translated radiolabelled Vps74 shows specific binding to immobilized PtdIns4P, with only weak signals for PtdIns3P, PtdIns5P and PtdIns(4,5)P2, alongside a Snx3/Grd19 PtdIns3P-binding specificity control. Reason: The most rigorous specificity data for this activity, and it is paired in the same paper with the identification of the binding pocket (W88, R97, K178, R181) whose mutation abolishes binding. Core molecular function. Supporting Evidence: PMID:20026658 in vitroβtranslated radiolabeled Vps74 and GOLPH3 bind to immobilized PtdIns4P PMID:20026658 Golgi mannosyltransferases that depend on Vps74 for Golgi localization are not retained in the Golgi in mutant cells that express a form of Vps74 that does not bind PtdIns4P. |
| GO:0070273 phosphatidylinositol-4-phosphate binding | IEA GO_REF:0000002 | ACCEPT | Summary: InterPro2GO mapping from IPR008628 (GPP34-like domain) to PtdIns4P binding. Reason: A domain-to-function mapping that is correct here, because the GPP34 fold is the PtdIns4P-binding module itself and the lipid-binding residues identified in the yeast structure are conserved across the family. Agrees with the IDA, IMP and IBA rows for this term. Supporting Evidence: PMID:20026658 in vitroβtranslated radiolabeled Vps74 and GOLPH3 bind to immobilized PtdIns4P |
| GO:0070273 phosphatidylinositol-4-phosphate binding | IMP PMID:20026658 PtdIns4P recognition by Vps74/GOLPH3 links PtdIns 4-kinase s... | ACCEPT | Summary: Charge-neutralizing substitutions in the predicted pocket (W88A/R97A and K178A/R181A) abolish phosphoinositide binding in vitro and Vps74 function in vivo, and the mutant protein no longer retains its mannosyltransferase clients. Reason: The structure-function complement to the IDA rows, tying the binding activity to a defined site and showing that the activity is required for the cargo-adaptor process. Consistent with the other four rows for this term; core molecular function. Supporting Evidence: PMID:20026658 Golgi mannosyltransferases that depend on Vps74 for Golgi localization are not retained in the Golgi in mutant cells that express a form of Vps74 that does not bind PtdIns4P. |
| GO:0140312 cargo adaptor activity | IBA GO_REF:0000033 | ACCEPT | Summary: Family-level cargo-adaptor assertion at the GOLPH3 ancestral node. Reason: The single most informative molecular-function term for this gene, and the one the yeast experimental data support most directly even though the row itself is a phylogenetic inference. Vps74p binds a pentameric motif in client cytosolic tails on one surface and COPI coatomer through an N-terminal arginine cluster, and loss of either contact inactivates retention, which is an adaptor rather than merely a binder. This is the term to which the four GO:0019899 enzyme-binding rows are modified. Supporting Evidence: PMID:18410729 Vps74p binds strongly to the Kre2p fusion protein and significantly to a number of the other fusion proteins. PMID:22889169 Vps74p, a member of the GOLPH3 protein family, binds directly to coatomer and PMID:22889169 for glycosyltransferase retention, the Golgi membrane-binding capabilities of |
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Download this section (compressed HTML)Q: Should the two CACAO glycosylation rows for VPS74 (GO:0006487 and GO:0035269, both IMP from PMID:18410729) be retained at all, given that the cited paper states the role in glycosylation must be indirect and that the mechanistic term GO:0045053 was annotated by SGD from the same figures?
Q: Is the SGD row GO:0006890, retrograde vesicle-mediated transport from Golgi to endoplasmic reticulum (IMP from PMID:18635803), supported by an assay of Golgi-to-ER traffic in the full text, or should it be GO:0000301, retrograde transport and vesicle recycling within Golgi, which is what the abstract describes?
Q: What determines whether a Golgi glycosyltransferase is a Vps74p client, a Bre5p/Ubp3p client, both, or neither? Och1p binds Vps74p in vitro yet its retention in vivo is largely Vps74p-independent, and Ktr3p and Mnn11p depend on Vps74p only under some nutrient conditions.
Q: Does Vps74p engage Sac1 in cis on Golgi membranes or in trans at ER-Golgi contact sites, and is the Vps74p-Sac1 complex the physiological route by which medial-Golgi PtdIns4P is turned over?
Q: Which yeast myosin, if any, substitutes for the MYO18A link that GOLPH3 uses in mammals, and does Vps74p contribute to Golgi membrane tension or shape in budding yeast at all?
Experiment: Tether Kre2p, Mnn2p and Mnn5p in the Golgi independently of Vps74p, for example by appending a Vps74p-independent retention determinant or by fusing them to a resident multi-TM Golgi protein, in a vps74-delta background, then assay invertase and Hsp150p mobility. Full rescue of glycosylation without restoring Vps74p would settle the phenotype-versus-process question behind the two CACAO rows.
Hypothesis: The glycosylation defect of vps74-delta cells is wholly attributable to loss of mannosyltransferase retention, not to any direct role of Vps74p in glycan synthesis.
Type: genetic rescue and glycoprotein mobility assay
Experiment: Compare vps74-delta with ret1 and sec21 COPI mutants in a direct Golgi-to-ER retrieval assay, for example HDEL-reporter retrieval or cisternal maturation followed by live four-dimensional imaging of Och1p and Mnn9p, scoring intra-Golgi recycling and Golgi-to-ER return separately.
Hypothesis: Vps74p acts in intra-Golgi retrograde recycling and not in Golgi-to-ER transport.
Type: trafficking assay and live-cell imaging
Experiment: Quantify ubiquitination of Ktr3p, Mnn4p and Mnn11p in wild-type, vps74-delta, bre5-delta and double mutants grown in rich versus synthetic medium, in parallel with mNeon imaging of their Golgi versus vacuolar distribution.
Hypothesis: Nutrient status switches clients between the Vps74p and Bre5p/Ubp3p retention pathways by changing client ubiquitination.
Type: ubiquitination profiling and quantitative imaging
Experiment: Use split-fluorophore or proximity-labelling reporters to localize the Vps74-Sac1 complex relative to ER-Golgi contact sites, combined with a Sac1 variant anchored exclusively in the ER or exclusively in the Golgi, and measure medial-Golgi PtdIns4P with a quantitative reporter in each case.
Hypothesis: Vps74p recruits the Sac1 catalytic domain to medial-Golgi membranes in trans from the ER.
Type: proximity labelling and phosphoinositide reporter imaging
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