Use of the ND evidence code for Gene Ontology (GO) terms

Basis for the molecular_function ND placeholder, which this review proposes to replace with an orthology-inferred tRNA nuclease activity

Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity

Source of the ISS and ISO transfers from S. cerevisiae Vms1 for mitochondrial, ER-membrane and Cdc48-Npl4-Vms1 complex annotations

GO_REF:0000033

Annotation inferences using phylogenetic trees

Source of the single PTHR16036 IBA (ERAD pathway) that this review proposes to re-term to rescue of stalled cytosolic ribosome

GO_REF:0000044

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt

Produces IEA localisation annotations that duplicate the ISS and EXP localisation annotations

GO_REF:0000111

Gene Ontology annotations Inferred by Curator (IC) using at least one Inferred by Sequence Similarity (ISS) annotation to support the inference

Basis for the cytoplasmic side of mitochondrial outer membrane annotation, inferred from the Cdc48p-Npl4p-Vms1p complex annotation

PMID:16823372

ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.

Genome-wide YFP tagging that provides the only fission-yeast experimental localisation data for vms1 (cytoplasm and cytosol)

"we determined the localization of 4,431 proteins"

PMID:18257517

Phosphoproteome analysis of fission yeast.

Identifies Ser-38 of fission-yeast vms1 as a phosphorylation site; the regulatory significance is unknown

"2887 distinct phosphorylation sites were identified from 1194 proteins"

PMID:21148305

A Cdc48p-associated factor modulates endoplasmic reticulum-associated degradation, cell stress, and ubiquitinated protein homeostasis.

Reports the S. cerevisiae Vms1p (Ydr049p) ERAD contribution that seeds the PTHR16036 ERAD IBD, and characterises it as a modest, post-ubiquitination effect acting in parallel with the canonical Cdc48 ERAD cofactors

"Loss of YDR049 modestly slows the degradation of the cystic fibrosis"
Places Vms1p at the ER membrane and in the cytosol via Cdc48p binding, the basis of the transferred ER-membrane localisation

"Ydr049p, also known as Vms1p, which binds Cdc48p at both the ER membrane and in the cytosol under non-stressed conditions."

PMID:21070972

A stress-responsive system for mitochondrial protein degradation.

Establishes the Cdc48-Npl4-Vms1 complex and stress-responsive mitochondria-associated degradation in S. cerevisiae, the basis of the transferred GO:0036266 and mitochondrial-outer-membrane annotations

"Vms1 stably associates with both Cdc48 and its cofactor Npl4"
Frames the mitochondrial degradation role as conserved

"Vms1 plays a conserved role in recruiting the ubiquitin/ proteasome"

PMID:29632312

Vms1 and ANKZF1 peptidyl-tRNA hydrolases release nascent chains from stalled ribosomes.

Defines the VLRF1 clade and shows that activity depends on a conserved catalytic glutamine, the residue whose fission-yeast counterpart (Q249) is verified in this review's alignment analysis

"Vms1 activity is dependent on a conserved catalytic glutamine."
Identifies Vms1 as the founding member of a clade of eRF1 homologs

"Vms1 is the founding member of a clade of eRF1 homologs"

PMID:31011209

Mechanism for recycling tRNAs on stalled ribosomes.

Shows that ANKZF1 and Vms1p sever polypeptidyl-tRNAs on RQC complexes by cleaving the terminal 3'-CCA nucleotides, establishing the family's molecular function as a tRNA nuclease rather than a peptidyl-tRNA hydrolase

"polypeptidyl-tRNAs on RQC complexes by precisely cleaving off"
Places the activity squarely in ribosome-associated quality control

"During RQC, ANKZF1 (yeast Vms1p) releases"

PMID:31189955

Structure and function of Vms1 and Arb1 in RQC and mitochondrial proteome homeostasis.

Structural work on S. cerevisiae Vms1 bound to 60S subunits before and after peptidyl-tRNA cleavage, confirming the ribosome-rescue mechanism in the budding-yeast ortholog that seeds the PAINT node

"with 60S subunits in pre- and post-peptidyl-tRNA cleavage states."
Links cleavage and release to counteracting CAT-tailing of nuclear-encoded mitochondrial proteins

"addition of CAT tails10-12. In doing so, Vms1 counteracts CAT-tailing of"

PMID:29107329

Cytosolic Protein Vms1 Links Ribosome Quality Control to Mitochondrial and Cellular Homeostasis.

Connects the cytosolic ribosome-rescue activity to protection of mitochondrial function, explaining why the family has both RQC and mitochondrial associations without those being separate pathways

"together with the E3 ligase Ltn1, protects against the mitochondrial toxicity of"

file:SCHPO/vms1/vms1-bioinformatics/RESULTS.md

S. pombe vms1 (O74977): VLRF1 catalytic-site conservation

Pairwise alignment projects human ANKZF1 Q246 onto S. pombe Q249 and S. cerevisiae Q295, independently reproducing both UniProt ACT_SITE calls and showing the catalytic glutamine is retained in fission yeast

"S. pombe vms1 retains the catalytic residue required for"