Ymr1 (YJR110W) is the single myotubularin-family lipid phosphatase of Saccharomyces cerevisiae. Its CX5R protein-tyrosine-phosphatase-like domain hydrolyses the 3-phosphate of phosphatidylinositol 3-phosphate to yield phosphatidylinositol (EC 3.1.3.64). Ymr1 is a cytoplasmic protein; ymr1 deletion raises cellular PtdIns3P, and together with the synaptojanin-like phosphatases Sjl2/Inp52 and Sjl3/Inp53 it limits the level and restricts the distribution of Vps34-generated PtdIns3P. ymr1 sjl3 double mutants accumulate PtdIns3P on the vacuole membrane, with vacuolar protein sorting defects and vacuole fragmentation, and ymr1 sjl2 sjl3 triple mutants are inviable, showing that phosphatase-mediated PtdIns3P turnover is essential for endosomal system integrity.
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0003729 mRNA binding | IDA PMID:21124907 A screen for RNA-binding proteins in yeast indicates dual fu... | KEEP AS NON CORE | Summary: Scherrer et al. recovered Ymr1 in a proteome-wide screen for RNA-binding proteins and found its associated mRNAs enriched for translation-related messages. No follow-up links mRNA binding to Ymr1 function; retained as non-core rather than overruling the experimental annotation. Reason: Proteome-wide RIP-chip in S. cerevisiae identified Ymr1-associated mRNAs enriched for translation-related transcripts (PMID:21124907); retained as non-core in deference to the experimental assay, as Ymr1's primary role is lipid 3-phosphatase catalysis. Supporting Evidence: PMID:21124907 messages associated with Map1p, Pot1p, and Ymr1p are commonly related to translation |
| GO:0004438 phosphatidylinositol-3-phosphate phosphatase activity | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the myotubularin clade (MTM1/MTMR family); Ymr1 has its own experimental support for PtdIns3P phosphatase activity, so the inference is sound. Reason: Core catalytic activity of Ymr1, directly demonstrated in vitro with recombinant yeast enzyme and in vivo by PtdIns3P accumulation in ymr1 mutants (PMID:10900271, PMID:15169871); SGD:S000003871 (YMR1) is itself an experimental seed of PTN000086845. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000086845 SUPPORTS TRANSFER Active myotubularin clade node; PtdIns3P 3-phosphatase activity is conserved and directly demonstrated for S. cerevisiae Ymr1. SGD:S000003871 SUPPORTS TRANSFER Target's own experimental PtdIns3P phosphatase activity (PMID:10900271) grounds the clade annotation. UniProtKB:Q13496 SUPPORTS TRANSFER Human MTM1 PtdIns3P 3-phosphatase activity supports clade conservation. Supporting Evidence: PMID:10900271 Both the recombinant yeast enzyme and a human myotubularin-related protein (KIAA0371) are able to dephosphorylate PI(3)P in vitro file:yeast/YMR1/YMR1-uniprot.txt receptor class myotubularin subfamily |
| GO:0004438 phosphatidylinositol-3-phosphate phosphatase activity | IEA GO_REF:0000120 | ACCEPT | Summary: EC 3.1.3.64/RHEA:12316 mapping; matches the established Ymr1 activity. Reason: Electronic mapping from EC 3.1.3.64 / RHEA:12316 matches the directly assayed phosphatidylinositol-3-phosphate phosphatase activity of Ymr1 (PMID:10900271). Supporting Evidence: file:yeast/YMR1/YMR1-uniprot.txt Lipid phosphatase which dephosphorylates phosphatidylinositol |
| GO:0004438 phosphatidylinositol-3-phosphate phosphatase activity | IMP PMID:10900271 Myotubularin, a protein tyrosine phosphatase mutated in myot... | ACCEPT | Summary: Taylor et al. showed recombinant Ymr1 dephosphorylates PtdIns3P in vitro and that its disruption raises PtdIns3P. Reason: Recombinant Ymr1 dephosphorylates PtdIns3P in vitro and ymr1 disruption increases cellular PtdIns3P levels in S. cerevisiae (PMID:10900271). Supporting Evidence: PMID:10900271 Both the recombinant yeast enzyme and a human myotubularin-related protein (KIAA0371) are able to dephosphorylate PI(3)P in vitro PMID:10900271 a Saccharomyces cerevisiae strain in which the myotubularin-like gene (YJR110w) is disrupted also exhibits increased PI(3)P levels |
| GO:0004438 phosphatidylinositol-3-phosphate phosphatase activity | IMP PMID:15169871 Essential role for the myotubularin-related phosphatase Ymr1... | ACCEPT | Summary: Parrish et al.: ymr1 sjl3 double mutants accumulate PtdIns3P, establishing Ymr1 as a physiological PtdIns3P phosphatase. Reason: ymr1 sjl3 double mutants aberrantly accumulate PtdIns3P in vivo, confirming Ymr1's physiological phosphatidylinositol-3-phosphate phosphatase activity (PMID:15169871). Supporting Evidence: PMID:15169871 the ymr1Delta sjl3Delta double mutant aberrantly accumulated PI(3)P |
| GO:0004438 phosphatidylinositol-3-phosphate phosphatase activity | RCA GO_REF:0000123 | ACCEPT | Summary: YeastPathways PWY3O-242 assigns Ymr1 to PI3P + H2O -> PI (EC 3.1.3.64); correct step. Reason: YeastPathways reaction assignment matches the experimentally established PtdIns3P 3-phosphatase activity (PMID:10900271). Supporting Evidence: PMID:10900271 Both the recombinant yeast enzyme and a human myotubularin-related protein (KIAA0371) are able to dephosphorylate PI(3)P in vitro file:yeast/YMR1/YMR1-uniprot.txt Lipid phosphatase which dephosphorylates phosphatidylinositol |
| GO:0005737 cytoplasm | HDA PMID:14562095 Global analysis of protein localization in budding yeast. | ACCEPT | Summary: Huh et al. GFP library localised Ymr1 to the cytoplasm. Reason: Direct high-throughput GFP imaging in S. cerevisiae localizes Ymr1 to the cytoplasm (PMID:14562095). Supporting Evidence: file:yeast/YMR1/YMR1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. |
| GO:0005737 cytoplasm | IBA GO_REF:0000033 | ACCEPT | Summary: IBA 'is_active_in cytoplasm' from the myotubularin clade; consistent with the cytoplasmic localization of Ymr1. Reason: Corroborated by the direct S. cerevisiae GFP localization of Ymr1 in the cytoplasm (PMID:14562095). Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000743854 SUPPORTS TRANSFER Myotubularin family node; cytoplasmic localization is conserved and directly corroborated in S. cerevisiae (PMID:14562095). UniProtKB:Q13496 SUPPORTS TRANSFER Human MTM1 cytoplasmic localization supports family-wide conservation. Supporting Evidence: file:yeast/YMR1/YMR1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. |
| GO:0005737 cytoplasm | IEA GO_REF:0000044 | ACCEPT | Summary: UniProt SubCell mapping to cytoplasm; consistent with HTP localization. Reason: UniProt SubCell mapping from the experimentally determined cytoplasmic localization in S. cerevisiae (PMID:14562095). Supporting Evidence: file:yeast/YMR1/YMR1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. |
| GO:0005829 cytosol | RCA GO_REF:0000123 | KEEP AS NON CORE | Summary: YeastPathways RCA assignment to cytosol. Ymr1 is a soluble cytoplasmic protein that acts transiently on membrane-bound PtdIns3P. Reason: GFP-tagged Ymr1 localizes to the cytoplasm in S. cerevisiae (PMID:14562095) and the protein has no annotated transmembrane segments in UniProt (P47147), so cytosolic residence of the soluble pool is biologically plausible, while its lipid substrate PtdIns3P resides on endosomal and vacuolar membranes; retained as non-core alongside GO:0005737 (cytoplasm). Supporting Evidence: file:yeast/YMR1/YMR1-uniprot.txt SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:14562095}. |
| GO:0016020 membrane | IBA GO_REF:0000033 | KEEP AS NON CORE | Summary: Membrane IBA from the myotubularin clade (PTN000086845); Ymr1 acts on membrane-bound PtdIns3P in the endosomal/vacuolar system, while no specific membrane compartment has been directly localized for Ymr1 in yeast. Reason: Myotubularin phosphatases act on membrane-embedded PtdIns3P via their PH-GRAM/catalytic domains, and Ymr1 regulates PtdIns3P on endosomal and vacuolar membranes in vivo (PMID:15169871). Because direct localization of Ymr1 to a specific organelle membrane has not been demonstrated in S. cerevisiae (where GFP-tagged Ymr1 is cytoplasmic, PMID:14562095), the general GO:0016020 (membrane) term is as precise as the localization evidence allows and is kept as non-core, matching the human MTMR12 and rat Mtmr12 reviews on PTN000086845. Propagation Review Root cause: NO FAILURE NON CORE Sources checked: PANTHER:PTN000086845 SUPPORTS TRANSFER Myotubularin clade node; transient peripheral membrane action on PtdIns3P transfers as a non-core location. UniProtKB:Q13496 SUPPORTS TRANSFER Human MTM1 membrane association supports the clade-level inference as non-core. Supporting Evidence: PMID:15169871 Ymr1p, a myotubularin phosphatase family member, functions in the control of PI(3)P-dependent signaling and the maintenance of endosomal system integrity |
| GO:0046854 phosphatidylinositol phosphate biosynthetic process | RCA GO_REF:0000123 | MODIFY | Summary: YeastPathways RCA places all PWY3O-242 enzymes in 'phosphatidylinositol phosphate biosynthetic process'. Ymr1 converts PtdIns3P to PI, i.e. it degrades a PIP; its process is phosphatidylinositol dephosphorylation (already annotated). Reason: YeastPathways PWY3O-242 groups phosphoinositide kinases and phosphatases under a single pathway label; Ymr1 hydrolyses the D-3 phosphate of PtdIns3P to produce unphosphorylated phosphatidylinositol (PMID:10900271), which is a catabolic dephosphorylation rather than phosphatidylinositol phosphate biosynthesis. This is a lateral replacement to GO:0046856 (phosphatidylinositol dephosphorylation), which the gene already carries. Proposed replacements: phosphatidylinositol dephosphorylation Supporting Evidence: PMID:10900271 Both the recombinant yeast enzyme and a human myotubularin-related protein (KIAA0371) are able to dephosphorylate PI(3)P in vitro |
| GO:0046856 phosphatidylinositol dephosphorylation | IBA GO_REF:0000033 | ACCEPT | Summary: IBA from the myotubularin clade; correct for a PtdIns3P phosphatase. Reason: Core biological process of Ymr1, directly supported in S. cerevisiae by in vitro and in vivo PtdIns3P dephosphorylation assays (PMID:10900271, PMID:15169871); SGD:S000003871 is itself an experimental seed of PTN000086845. Propagation Review Root cause: NO FAILURE CORE Sources checked: PANTHER:PTN000086845 SUPPORTS TRANSFER Active myotubularin clade node; phosphatidylinositol dephosphorylation is conserved and directly demonstrated for S. cerevisiae Ymr1. SGD:S000003871 SUPPORTS TRANSFER Target's own experimental dephosphorylation evidence (PMID:10900271, PMID:15169871) grounds the clade annotation. UniProtKB:Q13496 SUPPORTS TRANSFER Human MTM1 phosphatidylinositol dephosphorylation evidence supports clade conservation. Supporting Evidence: PMID:10900271 Both the recombinant yeast enzyme and a human myotubularin-related protein (KIAA0371) are able to dephosphorylate PI(3)P in vitro |
| GO:0046856 phosphatidylinositol dephosphorylation | IGI PMID:15169871 Essential role for the myotubularin-related phosphatase Ymr1... | ACCEPT | Summary: IGI with the synaptojanin-like phosphatase Sjl2/Inp52 (with/from SGD:S000005050): ymr1 sjl2 sjl3 triple deletion is lethal and is rescued by a PtdIns3P-targeted Sac1 domain, showing overlapping PtdIns3P dephosphorylation. Reason: Synthetic lethality of ymr1 sjl2 sjl3 and rescue by a PtdIns3P-targeted phosphatase domain demonstrate overlapping physiological PtdIns3P dephosphorylation in vivo (PMID:15169871). Supporting Evidence: PMID:15169871 Triple deletion of YMR1, SJL2, and SJL3 was lethal, suggesting an essential requirement for phosphatase-mediated PI(3)P regulation. |
| GO:0046856 phosphatidylinositol dephosphorylation | IMP PMID:10900271 Myotubularin, a protein tyrosine phosphatase mutated in myot... | ACCEPT | Summary: Taylor et al.: ymr1 disruption raises PtdIns3P levels. Reason: Disruption of YMR1 in S. cerevisiae increases cellular PtdIns3P levels, demonstrating in vivo phosphatidylinositol dephosphorylation (PMID:10900271). Supporting Evidence: PMID:10900271 a Saccharomyces cerevisiae strain in which the myotubularin-like gene (YJR110w) is disrupted also exhibits increased PI(3)P levels |
| GO:0046856 phosphatidylinositol dephosphorylation | IMP PMID:15169871 Essential role for the myotubularin-related phosphatase Ymr1... | ACCEPT | Summary: Parrish et al.: Ymr1 loss contributes to PtdIns3P accumulation and redistribution. Reason: Loss of Ymr1 (especially in combination with Sjl3) causes aberrant PtdIns3P accumulation on vacuolar and endosomal membranes in vivo (PMID:15169871). Supporting Evidence: PMID:15169871 the ymr1Delta sjl3Delta double mutant aberrantly accumulated PI(3)P PMID:15169871 Triple deletion of YMR1, SJL2, and SJL3 was lethal, suggesting an essential requirement for phosphatase-mediated PI(3)P regulation. |
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Download this section (compressed HTML)Phosphatidylinositol 3-phosphate (PI3P) phosphatase; involved in various protein sorting pathways, including CVT targeting and endosome to vacuole transport; has similarity to the conserved myotubularin dual specificity phosphatase family
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