PRM5 (YIL117C) is a 318-residue integral membrane protein of budding yeast with a single predicted transmembrane helix and a large, disordered, low-complexity C-terminal region. Its molecular function and biological role are not established. It was identified as one of a set of "pheromone-regulated membrane" (PRM) genes whose transcription is strongly induced by mating pheromone, and its expression is also induced by the cell wall integrity (Mpk1/Slt2–Rlm1) signalling pathway. It belongs to a fungal protein family (PANTHER PTHR36089; Pfam PF28230) that also contains its whole-genome-duplication paralog YNL058C and the chitin synthase III complex protein CSI2; family members are experimentally localized to fungal-type vacuole and bud-neck membranes, but the family carries no recognizable catalytic or binding motif and its shared molecular activity is unknown. PRM5 is phosphorylated on several serines in pheromone-arrested cells and is ubiquitinated, indicating it is expressed and post-translationally regulated, but no phenotype from large-scale deletion surveys (mild fitness, stress, and sporulation defects) has been mechanistically connected to a defined function.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0000324 fungal-type vacuole | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetically propagated cellular-component annotation. Per QuickGO, this IBA is propagated (with/from PANTHER:PTN002188658 | SGD:S000005367) from CSI2 (YOL007C), which has experimental (IDA/HDA) fungal-type-vacuole localization; the WGD paralog YNL058C also has experimental vacuole localization. Vacuolar-membrane localization is a reasonable inference for this membrane-protein family, but PRM5's own localization has not been directly determined, and this is a location, not a function. Keep as non-core, and note that the "is_active_in" qualifier overstates certainty for an uncharacterized protein (located_in would be more appropriate). Reason: Defensible family-level localization inference from experimentally localized paralogs (CSI2, YNL058C), but not directly verified for PRM5 and not a functional claim; retain as supporting localization context rather than a core function. |
| GO:0005935 cellular bud neck | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Phylogenetically propagated cellular-component annotation (with/from PANTHER:PTN002188659 | SGD:S000005367 = CSI2/YOL007C, which has experimental IDA bud-neck localization as a chitin synthase III complex protein). Because PRM5 is a WGD-era paralog whose molecular function has diverged and is unknown (ND), propagation of CSI2's bud-neck localization to PRM5 is a weaker inference than the vacuole call. Retain as non-core localization context; the "is_active_in" qualifier again overstates certainty for a dark protein. Reason: Weakly supported localization inference propagated from the bud-neck-localized paralog CSI2; not directly verified for PRM5 and not a functional claim. Keep as non-core context, flagged as lower confidence than the vacuole annotation. |
| GO:0016020 membrane | IEA GO_REF:0000044 | ACCEPT | Summary: Directly supported by sequence: UniProt annotates a single predicted transmembrane helix (FT TRANSMEM 75..98, ECO:0000255) and the subcellular location "Membrane; Single-pass membrane protein" (ECO:0000305), mapped to GO:0016020 via UniProtKB-SubCell SL-0162. This is the single most defensible annotation for this gene and is consistent with the entire PRM/PTHR36089 family being membrane proteins. Accept as-is. Reason: Membrane localization is directly grounded in the predicted transmembrane helix and UniProt subcellular-location curation; this is the best-supported annotation for PRM5. |
| GO:0003674 molecular_function | ND GO_REF:0000015 | ACCEPT | Summary: Root molecular_function with ND ("no biological data") is the correct, honest placeholder: PRM5 has no experimentally or computationally supportable molecular function. There is no catalytic or ligand-binding motif in the sequence, the PANTHER family (including the better-studied members CSI2 and YNL058C) also carries ND for molecular_function, and Heiman & Walter note PRM-family members have no recognizable motifs hinting at function. Retain the ND annotation to accurately record that molecular function is unknown. Reason: Molecular function is genuinely unknown; the ND root annotation correctly documents the absence of data and should be retained (do not invent an MF term or use protein binding). |
| GO:0008150 biological_process | ND GO_REF:0000015 | ACCEPT | Summary: Root biological_process with ND is the correct honest placeholder. PRM5 transcription is induced by mating pheromone and by cell wall integrity signalling, but induction is not evidence of participation, and no mating, cell-wall, or other biological-process phenotype has been demonstrated for a prm5 deletion beyond mild large-scale-survey effects. Retain the ND annotation; a specific BP term would be over-annotation. Reason: Biological process is unknown; being transcriptionally induced by pheromone/CWI signalling does not establish involvement in mating or cell-wall processes. The ND annotation correctly records the absence of data. |
Loading supporting content…
Download this section (compressed HTML)Q: Does PRM5 have any molecular activity beyond being a membrane component, and what is the ancestral activity shared across the PTHR36089 / PRM5-like family (PRM5, YNL058C, CSI2)?
Suggested experts: Heiman MG, Walter P
Q: Is PRM5 functionally involved in the mating/cell-fusion program or in cell-wall integrity responses, or is its dual induction by pheromone and Mpk1–Rlm1 signalling incidental regulon membership without a corresponding functional role?
Suggested experts: Levin DE
Experiment: Determine the subcellular localization of endogenously tagged PRM5 (C-terminal GFP under its native promoter) by fluorescence microscopy with organelle co-markers (FM4-64/vacuole, Cdc10/septin bud-neck, plasma-membrane markers), under basal, pheromone-induced, and CWI-induced conditions.
Hypothesis: PRM5 localizes to a specific membrane compartment (vacuolar membrane, bud neck, or plasma membrane) that constrains its function.
Type: fluorescence microscopy / subcellular localization
Experiment: Identify PRM5 physical partners by affinity purification–mass spectrometry and/or proximity labeling (e.g. TurboID) of tagged PRM5 expressed under inducing conditions, and test whether partners overlap with those of the paralog YNL058C or of CSI2 / the chitin synthase III complex.
Hypothesis: PRM5 acts within a physical module that reveals its molecular function.
Type: interaction proteomics (AP-MS / proximity labeling)
Experiment: Construct single (prm5 delta) and double (prm5 delta ynl058c delta) deletions and assay quantitative mating/cell-fusion efficiency and cell-wall-stress sensitivity (Calcofluor White, Congo Red, caspofungin, elevated temperature) to test for a redundant role masked by the paralog.
Hypothesis: PRM5 contributes to mating or cell-wall integrity, redundantly with its paralog YNL058C.
Type: genetic epistasis / phenotypic assay
What is not known — curated, literature-grounded statements of the open unknowns (the inverse of core functions).
Gap: The molecular function of PRM5 is entirely unknown. No catalytic activity, ligand/partner binding, transport, or scaffolding role has been demonstrated or can be inferred from sequence, and no informative GO molecular-function term is supportable (the annotation is the ND root, not "protein binding").
OPEN BIOLOGY MF_DARK
What is known: PRM5 is a 318-aa single-pass membrane protein with one predicted transmembrane helix and a large disordered/low-complexity C-terminal region. It belongs to fungal family PTHR36089 / Pfam PF28230, whose members (including the paralog YNL058C and CSI2) are membrane proteins but also carry ND for molecular function; the family founding paper noted such PRM proteins have no recognizable motifs hinting at function.
Significance: PRM5 is a conserved-in-fungi, whole-genome-duplication-retained membrane protein induced by two major signalling pathways (mating and cell wall integrity); a defined molecular activity would convert a recurrently-cited "pheromone-regulated membrane protein" from a name into a mechanism and would likely illuminate the shared activity of the whole PRM5/PTHR36089 family.
What would resolve it: Biochemical characterization of the purified protein and its membrane topology; affinity/ proximity proteomics to identify partners; and structure prediction/experimental structure to test for a cryptic domain. Comparison with the paralog YNL058C and with CSI2 may reveal the ancestral family activity.
Provenance (the field's own admissions):
Gap: The biological process PRM5 participates in is unknown. It is transcriptionally induced by mating pheromone and by the cell wall integrity (Mpk1–Rlm1) pathway, but it has not been shown to function in mating, cell fusion, cell-wall biogenesis, or any other process; a prm5-null mutant is viable with only mild, mechanistically unexplained phenotypes.
OPEN BIOLOGY BP_DARK
What is known: Induction by pheromone (PRM gene set) and by cell wall integrity signalling is experimentally established (UniProt INDUCTION, ECO:0000269|PubMed:10594829 and PubMed:11062271). Large-scale deletion surveys report decreased competitive fitness, oxidative-stress resistance, sporulation efficiency, and starvation resistance, but none is tied to a defined role.
Significance: Distinguishing whether PRM5 acts in the mating/cell-fusion program (like its namesake PRM1), in cell-wall remodelling (consistent with CWI induction), or elsewhere would resolve why the gene is co-regulated with these pathways and whether its co-regulation reflects a genuine functional role or incidental regulon membership.
Provenance (the field's own admissions):
Gap: PRM5's own subcellular localization has not been directly determined. Its current fungal-type-vacuole and bud-neck component annotations are phylogenetic (IBA) propagations from experimentally localized paralogs (CSI2, YNL058C), not direct observations of PRM5.
OPEN BIOLOGYCURATION CC_DARK
What is known: Membrane localization is well supported by the predicted transmembrane helix and UniProt subcellular-location curation. Whether PRM5 resides in the vacuolar membrane, at the bud neck, at the plasma membrane, or in another compartment is not experimentally established for PRM5 itself.
Significance: A definitive localization would sharpen functional hypotheses (vacuolar vs. bud-neck/cell- surface roles) and test whether PRM5 tracks the localization of its paralogs or has diverged after the whole-genome duplication.
What would resolve it: Direct localization of tagged PRM5 (e.g. GFP fusion under native regulation, or under pheromone/CWI induction) with organelle co-markers.
Loading supporting content…
Download this section (compressed HTML)Loading supporting content…
Download this section (compressed HTML)