Ecm30 is a large HID1-family protein of Saccharomyces cerevisiae involved in membrane-trafficking homeostasis. It forms a complex with the ubiquitin protease Ubp15, and ecm30 deletion perturbs sorting and transport of the amino-acid permease Gap1 and alters cell-surface composition. A cytoplasmic pool is observed by GFP localization, while conserved HID1 ancestry supports peripheral membrane and Golgi association and a role in Golgi organization. Ecm30 is substantially diverged from some other HID1 proteins; its precise biochemical contribution, targeting determinants and relationship to the unstacked budding-yeast Golgi remain unresolved.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0005829 cytosol | IBA GO_REF:0000033 | ACCEPT | Summary: Cytosol is a supported major compartment of Ecm30. Reason: The actual PTHR21575 tree places Q06673/PTN001853777 below PTN000491103. The inherited cytosol assertion is consistent with the curated high-throughput cytoplasmic GFP localization. A location can represent the core biology even when the molecular mechanism is not established. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000491103 · PTN000491103 SUPPORTS TRANSFER Actual treeinfo lineage and the corresponding current PAINT IBD were checked. No target-specific loss of this assertion is established. Direct target experiments are distinguished from inherited function. |
| GO:0016020 membrane | IBA GO_REF:0000033 | ACCEPT | Summary: Peripheral membrane association is a supported HID1-family inference for Ecm30. Reason: GO:0016020 includes proteins attached to a lipid bilayer, not only integral membrane proteins. Lack of a transmembrane helix or signal peptide therefore does not refute it. Actual descent from PTN000491103 is verified; a cytoplasmic GFP pool does not exclude dynamic peripheral membrane association. Retain the inherited assertion rather than treat a broad valid parent as over-annotation. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000491103 · PTN000491103 SUPPORTS TRANSFER Actual treeinfo lineage and the corresponding current PAINT IBD were checked. No target-specific loss of this assertion is established. Direct target experiments are distinguished from inherited function. |
| GO:0007030 Golgi organization | IBA GO_REF:0000033 | ACCEPT | Summary: Ecm30 retains a phylogenetically inferred Golgi-organization role. Reason: Actual descent from PTN000491103 is verified. The ancestral assertion includes experimental fission-yeast SPAC17A5.16/Hid1 evidence; PMID:40899782 documents its Golgi phenotype and substantial ECM30 sequence divergence. That divergence and unstacked budding-yeast Golgi motivate mechanistic follow-up, but GO:0007030 encompasses organization beyond stacking, so they do not demonstrate loss of the broad function. Target Gap1 sorting and Ubp15 complex evidence is compatible with trafficking. Missing target experiments and metazoan dense-core-vesicle specialization do not negate this separately asserted conserved process. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000491103 · PTN000491103 SUPPORTS TRANSFER Actual treeinfo lineage and the corresponding current PAINT IBD were checked. No target-specific loss of this assertion is established. Direct target experiments are distinguished from inherited function. |
| GO:0000138 Golgi trans cisterna | IBA GO_REF:0000033 | ACCEPT | Summary: Trans-Golgi-cisterna association is retained as an inherited Ecm30 localization. Reason: PTN001853777 lies below the actual PTN000491103 Golgi-cisterna assertion. Budding-yeast cisternae need not form a stacked apparatus for a trans-Golgi compartment to exist, and the cytoplasmic GFP result is not an exclusion assay. PMID:40899782 provides a target-divergence lead for focused follow-up, not direct evidence that Ecm30 cannot associate with this compartment. The annotation remains phylogenetic, not a direct yeast localization measurement. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000491103 · PTN000491103 SUPPORTS TRANSFER Actual treeinfo lineage and the corresponding current PAINT IBD were checked. No target-specific loss of this assertion is established. Direct target experiments are distinguished from inherited function. |
| GO:0005797 Golgi medial cisterna | IBA GO_REF:0000033 | ACCEPT | Summary: Medial-Golgi-cisterna association is retained as an inherited Ecm30 localization. Reason: The current tree confirms descent from the ancestral medial-Golgi assertion at PTN000491103. Unstacked Golgi morphology does not abolish cisternal maturation compartments, and primary cytoplasmic localization does not establish exclusivity. Specific target sequence divergence is recorded for adjudication, but no demonstrated functional or localization loss justifies rejecting the inherited annotation. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000491103 · PTN000491103 SUPPORTS TRANSFER Actual treeinfo lineage and the corresponding current PAINT IBD were checked. No target-specific loss of this assertion is established. Direct target experiments are distinguished from inherited function. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: Electronic mapping from the UniProt SUBCELLULAR LOCATION "Cytoplasm" vocabulary, which itself is backed by the experimental GFP result. Correct and redundant with the HDA cytoplasm annotation. Reason: Accurate localization consistent with the experimental (HDA) cytoplasm annotation to the same term; retained for consistency. |
| GO:0005737 cytoplasm | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: Best-supported localization for ECM30: high-throughput GFP-fusion analysis (Huh et al.) places the protein in the cytoplasm. This is the primary experimental cellular-component evidence. Reason: Directly supported experimental (HDA) localization; the correct and best-evidenced compartment annotation for ECM30. |
| GO:0003674 molecular_function | ND GO_REF:0000015 | ACCEPT | Summary: Root "molecular_function" with ND correctly records that no molecular function has been experimentally established for ECM30 (a protein of unknown function). Reason: The ND root annotation accurately captures the MF-dark status of this gene; an appropriate placeholder given the absence of any assigned biochemical activity. |
| GO:0008150 biological_process | ND GO_REF:0000015 | ACCEPT | Summary: Root "biological_process" with ND correctly records that no biological process has been experimentally assigned to ECM30. Phenotypes (cell-wall composition, Gap1 sorting) and genetic interactions suggest a role in membrane trafficking, but no process has been directly established. Reason: The ND root annotation appropriately represents the BP-dark status; existing clues are phenotypic/genetic, not a curated experimental process assignment. |
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Download this section (compressed HTML)Q: Does ECM30 physically associate with the Golgi/TGN or endosomal membranes in S. cerevisiae, as its metazoan HID1 ortholog does at the trans-Golgi network?
Q: Is the cell-wall (mannose/glucose) phenotype of ecm30 mutants a direct effect on wall biogenesis or an indirect consequence of defective intracellular sorting of trafficking cargo such as Gap1?
Experiment: Perform affinity-purification mass spectrometry on endogenously tagged ECM30 to identify a specific, reproducible interaction partner set (filtering high-throughput background), combined with fluorescent co-localization to Golgi/TGN, endosome and vacuole markers, and cargo-trafficking assays (Gap1-GFP itinerary; cell-wall biosynthetic enzyme localization) in the ecm30 null.
Hypothesis: ECM30 functions as a peripheral membrane-trafficking scaffold at the Golgi/ endosome, and its cell-wall and Gap1 phenotypes are downstream of impaired cargo sorting.
Type: affinity purification-mass spectrometry, fluorescence microscopy, cargo-trafficking assay
Experiment: Systematically test genetic epistasis and cargo phenotypes of ecm30 in combination with GET1/GET2/GET3, ARL1, SEC14 and VPS mutants to place ECM30 in a defined trafficking step.
Hypothesis: ECM30 acts in the same functional module as the GET pathway and Golgi trafficking machinery revealed by its genetic interactions.
Type: genetic epistasis analysis
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: Ecm30 forms a validated complex with Ubp15, but its biochemical contribution to that complex is unresolved; neither intrinsic enzyme activity nor a particular adaptor mechanism has been established.
OPEN BIOLOGY MF_DARK
What is known: What is firmly established is only the domain architecture and localization: ECM30 is a 1274-aa HID1-family protein (Pfam Hid1; InterPro IPR026705 HID1/Ecm30; PANTHER PTHR21575), with several internal disordered/low-complexity segments, no transmembrane domain, no signal peptide, and no catalytic-domain signature; it is experimentally cytoplasmic.
Significance: HID1 is a conserved, disease-linked family whose molecular activity is undefined in every organism; establishing an activity for the tractable single-copy yeast member would anchor function for the whole family.
What would resolve it: Determine the composition, targeting and biochemical effect of the Ecm30-Ubp15 complex, then reconstitute candidate cargo or membrane interactions.
Provenance (the field's own admissions):
Gap: The biological process ECM30 acts in, and the mechanism linking it to the cell-wall phenotype, are unknown. It is unresolved whether ECM30 contributes directly to cell-wall (mannan/glucan) biogenesis or does so indirectly by supporting the intracellular sorting of cell-wall-biosynthetic and permease cargo (e.g. the Gap1 sorting/transport defect of ecm30 mutants).
OPEN BIOLOGY BP_DARK
What is known: What is established phenotypically is that ecm30 loss alters calcofluor-white sensitivity and the relative mannose/glucose content of the cell wall, and that ecm30 mutants mis-sort the general amino acid permease Gap1; genetic interactions connect ECM30 to the GET pathway (GET1/GET2/GET3), Golgi/secretory factors (ARL1, SEC14, COPI subunits SEC26/SEC28) and vacuolar sorting (VPS1/VPS9/VPS17).
Significance: Distinguishing a direct cell-wall-biosynthetic role from an upstream membrane-trafficking role would explain a decades-old "extracellular mutant" phenotype and clarify how a cytosolic HID1-family protein controls cell-surface composition.
What would resolve it: Epistasis and cargo-trafficking assays (Gap1 and cell-wall enzyme itineraries) in ecm30 versus GET/Golgi/VPS mutants, and direct measurement of cell-wall polysaccharide biosynthesis in the ecm30 null.
Provenance (the field's own admissions):
Gap: Determine the native Ecm30 distribution across cytosol, Golgi cisternae and other membranes and how sequence divergence affects dynamic targeting.
OPEN BIOLOGYCURATION CC_DARK
What is known: The cytoplasmic GFP observation coexists with verified positive ancestral Golgi/membrane assertions. Neither absent target colocalization data nor unstacked Golgi morphology establishes functional loss.
Significance: Direct localization and separation-of-function assays would refine a supported evolutionary inference and explain how the divergent budding-yeast protein contributes to membrane traffic.
What would resolve it: Endogenous fluorescent-protein co-localization with Golgi/TGN and endosome markers under native and stressed conditions, and fractionation to test peripheral membrane association.
Provenance (the field's own admissions):
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