vms1 is the fission-yeast member of the Vms1/ANKZF1 family, a clade of eRF1 homologs (VLRF1) that act in ribosome-associated quality control. In the characterised orthologs, the protein binds the 60S ribosomal subunit of stalled ribosome-nascent-chain complexes through its VLRF1 domain and cleaves the polypeptidyl-tRNA, severing the terminal 3'-CCA nucleotides of the tRNA so that the incomplete nascent chain is released for proteasomal degradation and the tRNA fragment can be repaired and recycled. Release also limits C-terminal Ala/Thr extension (CAT-tailing) of stalled mitochondrial precursor proteins, linking the activity to mitochondrial proteome integrity. The protein is a Cdc48/p97 cofactor and, in budding yeast, is a subunit of the Cdc48-Npl4-Vms1 complex that acts in stress-responsive mitochondria-associated degradation. Fission-yeast vms1 is cytoplasmic and cytosolic and retains the conserved catalytic glutamine of the family, but no fission-yeast-specific biochemical or genetic characterisation of its function has been published; its assignments therefore rest on orthology.
Definition: Catalysis of the endonucleolytic removal of the terminal 3'-CCA nucleotides from the tRNA moiety of a polypeptidyl-tRNA bound in the P site of a 60S ribosomal subunit, releasing the nascent polypeptide still esterified to a truncated tRNA and leaving a tRNA fragment that requires CCA re-addition before it can be re-aminoacylated.
Justification: The Vms1/ANKZF1 reaction is more specific than GO:0004549 tRNA-specific ribonuclease activity, and it is not a peptidyl-tRNA hydrolase reaction (GO:0004045) because the peptidyl-tRNA ester bond is not broken. GO currently has no term for this chemistry, so the family can only be annotated with a parent term that loses the mechanistic detail.
Parent term: tRNA-specific ribonuclease activity
Supporting Evidence:
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0036503 ERAD pathway | IBA GO_REF:0000033 | MODIFY | Summary: The inherited function is real but the term is wrong. The PTHR16036 IBD behind this IBA (node PTN000411325) is placed at the eukaryotic root and seeded only by S. cerevisiae VMS1, whose ERAD evidence is a modest, modulatory, post-ubiquitination effect reported before the family's catalytic activity was known. The conserved, mechanistically defined family function - cleavage of polypeptidyl-tRNA to rescue stalled cytosolic ribosomes - is not propagated by PAINT at all. Replace ERAD with rescue of stalled cytosolic ribosome. Reason: ERAD and ribosome-associated quality control are distinct pathways. The S. cerevisiae seed annotation shows Vms1p acting in parallel with the canonical Cdc48 ERAD cofactors and only modestly slowing substrate degradation, which is an accessory budding-yeast role rather than the ancestral eukaryotic function asserted at this node. The activity that is conserved from budding yeast to human, and for which fission-yeast vms1 retains the catalytic glutamine, is release of nascent chains from stalled 60S complexes. MODIFY rather than REMOVE because inheritance from the family node is genuine and vms1 would otherwise be left with no biological-process annotation at all. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: ROLE CONFLATION SOURCE EVIDENCE WEAK Sources checked: PANTHER:PTN000411325 · PTHR16036 ancestral node (Eukaryota) SUPPORTS SOURCE BUT NOT TARGET Cached PAINT export shows this IBD is the family's only PAINT annotation and is placed at taxon:2759, so an accessory budding-yeast role is projected to all eukaryotes while the conserved RQC function is propagated nowhere. SGD:S000002456 · S. cerevisiae VMS1 SOURCE WEAK OR INFERRED The seed ERAD annotation rests on PMID:21148305, which reports only a modest slowing of substrate degradation acting in parallel with the canonical Cdc48 ERAD cofactors; the same protein's principal characterised activity is ribosome rescue. Proposed replacements: rescue of stalled cytosolic ribosome Supporting Evidence: PMID:21148305 Loss of YDR049 modestly slows the degradation of the cystic fibrosis PMID:21148305 acts in parallel with Cdc48p partners to modulate ERAD PMID:31011209 During RQC, ANKZF1 (yeast Vms1p) releases PMID:31189955 Vms1 catalyses cleavage and release of the peptidyl-tRNA before or after file:SCHPO/vms1/vms1-bioinformatics/RESULTS.md S. pombe vms1 retains the catalytic residue required for |
| GO:0003674 molecular_function | ND GO_REF:0000015 | MODIFY | Summary: The ND (no data) placeholder understates what is known. vms1 carries an intact VLRF1 domain and the catalytic glutamine (Q249) whose equivalent in human ANKZF1 (Q246) is required for polypeptidyl-tRNA cleavage, so an orthology-based tRNA nuclease molecular function is better than asserting no data. Reason: ND should be replaced once a defensible molecular function can be inferred. Own alignment work reproduces the UniProt ACT_SITE assignments for both yeasts and shows the fission-yeast catalytic context (RKQGGSQ) is identical to the budding-yeast one, so vms1 is not a degenerate pseudoenzyme. The replacement should be made at ISS strength (from UniProtKB:Q04311 or UniProtKB:Q9H8Y5), not as an experimental claim, since no fission-yeast biochemistry exists. This is the same molecular-function term this project proposes for the human ortholog ANKZF1, keeping the two reviews consistent. Proposed replacements: tRNA-specific ribonuclease activity Supporting Evidence: PMID:31011209 polypeptidyl-tRNAs on RQC complexes by precisely cleaving off PMID:29632312 Vms1 activity is dependent on a conserved catalytic glutamine. file:SCHPO/vms1/vms1-bioinformatics/RESULTS.md The glutamine is present in S. pombe vms1, in an `RKQGGSQ` motif |
| GO:0005737 cytoplasm | EXP PMID:16823372 ORFeome cloning and global analysis of protein localization ... | KEEP AS NON CORE | Summary: Directly observed in fission yeast by genome-wide YFP tagging. This is the only experimental annotation vms1 has, and it is consistent with the family's cytosolic RQC role. Reason: Correct and fission-yeast-specific, but cytoplasm is a broad compartment term; the more informative cytosol annotation from the same study captures the location for core-function purposes. Supporting Evidence: PMID:16823372 we determined the localization of 4,431 proteins |
| GO:0005829 cytosol | HDA PMID:16823372 ORFeome cloning and global analysis of protein localization ... | ACCEPT | Summary: Cytosolic localisation observed in the fission-yeast ORFeome localisation screen. This is where ribosome-associated quality control takes place and is the location in which vms1 is expected to act. Reason: Fission-yeast-specific experimental support for the compartment in which the inferred core function operates. Supporting Evidence: PMID:16823372 we determined the localization of 4,431 proteins |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt subcellular-location keyword mapping restating the cytoplasmic localisation that is already supported experimentally in fission yeast. Reason: Not wrong, but redundant with the EXP and HDA localisation annotations from PMID:16823372 and less informative than cytosol. |
| GO:0005739 mitochondrion | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Transferred from S. cerevisiae Vms1 (UniProtKB:Q04311), which relocalises to mitochondria under oxidative stress as part of the mitochondria-associated degradation system. No fission-yeast evidence exists, and in budding yeast the localisation is stress-conditional rather than constitutive. Reason: The budding-yeast evidence for a mitochondrial pool is solid, so the transfer is defensible, but it describes a stress-responsive accessory location rather than where fission-yeast vms1 has been shown to act. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: UniProtKB:Q04311 · S. cerevisiae Vms1 SUPPORTS TRANSFER Mitochondrial pool is well documented in budding yeast but is induced by stress rather than constitutive, so the transferred location is contextual. Supporting Evidence: PMID:21070972 Vms1 plays a conserved role in recruiting the ubiquitin/ proteasome |
| GO:0005739 mitochondrion | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt keyword mapping restating the same ortholog-derived mitochondrial localisation as the ISS annotation. Reason: Redundant with the ISS annotation from UniProtKB:Q04311 and carries no independent evidence. |
| GO:0032473 cytoplasmic side of mitochondrial outer membrane | IC GO_REF:0000111 | KEEP AS NON CORE | Summary: Curator inference from the Cdc48p-Npl4p-Vms1p complex annotation. In budding yeast the complex extracts ubiquitinated proteins from the outer mitochondrial membrane, so the topology is right, but the whole chain rests on ortholog transfer with no fission-yeast data. Reason: Internally consistent with the GO:0036266 annotation it is inferred from, and it correctly places the protein on the cytosolic face rather than inside the organelle. It describes the stress-responsive mitochondria-associated degradation role, not the core ribosome-rescue role. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: CONTEXT OR TISSUE MISMATCH Sources checked: GO:0036266 · Cdc48p-Npl4p-Vms1p AAA ATPase complex (the ISO annotation this IC is inferred from) SUPPORTS TRANSFER The inference is sound given the complex annotation, but it inherits that annotation's ortholog-transfer basis, so it is no stronger than the ISO it depends on. Supporting Evidence: PMID:21070972 Vms1 stably associates with both Cdc48 and its cofactor Npl4 |
| GO:0036266 Cdc48p-Npl4p-Vms1p AAA ATPase complex | ISO GO_REF:0000024 | KEEP AS NON CORE | Summary: Transferred from S. cerevisiae, where Vms1 stably associates with Cdc48 and Npl4 in the complex that mediates stress-responsive mitochondria-associated degradation. The Cdc48-binding VIM interaction is a conserved feature of the family. Reason: The budding-yeast complex is experimentally well established and the Cdc48-cofactor relationship is conserved, so the transfer is reasonable. It is not core for fission yeast because the complex has not been demonstrated there and it represents the mitochondrial-degradation branch rather than the ribosome-rescue activity that defines the family. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: SGD:S000002456 · S. cerevisiae VMS1 SUPPORTS TRANSFER Complex membership is solidly established in budding yeast; the fission-yeast counterpart complex has not been isolated, so membership is plausible but undemonstrated. Supporting Evidence: PMID:21070972 Vms1 stably associates with both Cdc48 and its cofactor Npl4 |
| GO:0005789 endoplasmic reticulum membrane | ISS GO_REF:0000024 | KEEP AS NON CORE | Summary: Transferred from S. cerevisiae Vms1, which was reported to bind Cdc48p at the ER membrane in the same study that produced the ERAD annotation. That study predates the discovery of the family's ribosome-rescue activity, and no fission-yeast evidence supports an ER pool. Reason: The budding-yeast observation is real, so this is not an outright error, but it belongs to the same modest, modulatory ERAD-adjacent body of evidence whose biological-process term is being corrected in this review. It should not be treated as a core location for fission-yeast vms1. Propagation Review Root cause: NO FAILURE NON CORE Failure modes: COMPARTMENT OR COMPLEX MISMATCH Sources checked: UniProtKB:Q04311 · S. cerevisiae Vms1 SUPPORTS TRANSFER Source shows an ER-membrane Cdc48p interaction in budding yeast; the protein is predominantly cytosolic and the ER pool is secondary. Supporting Evidence: PMID:21148305 Ydr049p, also known as Vms1p, which binds Cdc48p at both the ER membrane and in the cytosol under non-stressed conditions. |
| GO:0005789 endoplasmic reticulum membrane | ISO GO_REF:0000024 | KEEP AS NON CORE | Summary: An is_active_in ISO transfer from SGD:S000002456 asserting that fission-yeast vms1 acts at the ER membrane. The underlying budding-yeast data support presence at the ER membrane through Cdc48p binding, not that this is where the fission-yeast protein executes its function. Reason: Retained on the same basis as the ISS transfer of the same term, but the is_active_in qualifier over-states what ortholog transfer can support here. Given that the accompanying ERAD process term is being corrected to ribosome rescue, located_in would be the defensible qualifier for this annotation and curators should consider weakening it. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: COMPARTMENT OR COMPLEX MISMATCH ROLE CONFLATION Sources checked: SGD:S000002456 · S. cerevisiae VMS1 SUPPORTS SOURCE BUT NOT TARGET Source supports an ER-membrane location for budding-yeast Vms1p, but not an is_active_in claim for the fission-yeast protein, whose characterised family activity is cytosolic ribosome rescue. Supporting Evidence: PMID:21148305 Ydr049p acts at a postubiquitination step in the ERAD pathway |
| GO:0005789 endoplasmic reticulum membrane | IEA GO_REF:0000044 | KEEP AS NON CORE | Summary: UniProt keyword mapping restating the ortholog-derived ER-membrane localisation. Reason: Redundant with the ISS annotation from UniProtKB:Q04311 and carries no independent evidence for fission yeast. |
| GO:0006515 protein quality control for misfolded or incompletely synthesized proteins | ISS | NEW | Summary: Proposed new annotation. Releasing incompletely synthesized nascent chains from stalled 60S subunits so they can be degraded is the quality-control outcome of the family's activity, and human ANKZF1 carries this term with four independent IDA annotations. Reason: Proposed at ISS strength from UniProtKB:Q9H8Y5 and UniProtKB:Q04311, not as a fission-yeast experimental claim. It complements the proposed GO:0072344 replacement, which captures freeing of the ribosome, whereas this term captures the fate of the incomplete polypeptide. Curators may reasonably decide that GO:0072344 alone is sufficient for a gene with no fission-yeast functional data. Supporting Evidence: PMID:31011209 During RQC, ANKZF1 (yeast Vms1p) releases PMID:31189955 Vms1 catalyses cleavage and release of the peptidyl-tRNA before or after file:SCHPO/vms1/vms1-bioinformatics/RESULTS.md S. pombe vms1 retains the catalytic residue required for |
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Download this section (compressed HTML)Q: Does fission-yeast vms1 actually cleave polypeptidyl-tRNA on 60S ribosome-nascent-chain complexes, or has the fission-yeast lineage repurposed the conserved catalytic glutamine for something else?
Q: Should the PTHR16036 IBD at PTN000411325 be re-placed rather than re-termed, that is, should an RQC IBD be added at the eukaryotic root where both human and budding-yeast experimental evidence sits, and the ERAD IBD restricted or dropped given that its only seed is a modulatory budding-yeast result?
Q: Is the budding-yeast ERAD contribution of Vms1p a genuinely separate pathway role, or a downstream consequence of Cdc48 cofactor competition that would be better captured without an ERAD process term?
Q: Does fission yeast perform CAT-tailing, and if so does vms1 antagonise it as the budding-yeast ortholog does?
Experiment: Reconstitute fission-yeast 60S ribosome-nascent-chain complexes and test purified vms1 and a vms1-Q249L point mutant for cleavage of the P-site polypeptidyl-tRNA, resolving products to determine whether the 3'-CCA is removed.
Hypothesis: Fission-yeast vms1 is an active tRNA endonuclease that removes the 3'-CCA from polypeptidyl-tRNA on stalled 60S subunits, and this depends on Q249.
Experiment: Compare accumulation of stalled nascent chains and of aggregated mitochondrial precursor proteins in wild-type, vms1-delta and vms1-Q249L fission yeast under respiratory growth.
Hypothesis: Loss of vms1 catalytic activity, not just of the protein, causes accumulation of unreleased nascent chains and mitochondrial proteotoxicity.
Experiment: Assay degradation of a defined fission-yeast ERAD substrate in vms1-delta cells, with and without simultaneous loss of the fission-yeast Ufd1 and Npl4 cofactors, to test whether an ERAD contribution exists in this lineage at all.
Hypothesis: Fission-yeast vms1 makes no measurable contribution to ERAD, supporting removal rather than retention of an ERAD process term across the family.
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