{"gene":"TG_310190","gene_symbol":"VPS15","run_date":"2026-09-08T15:15:13","timeline":{"discoveries":[{"year":2022,"finding":"TgVPS15 promotes PI3P (phosphatidylinositol-3-phosphate) generation in Toxoplasma gondii, acting as a regulator of the single PI3-kinase activity in the parasite.","method":"Genetic/functional characterization of TgVPS15 with PI3P level measurements","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — single lab, multiple functional readouts (PI3P formation, organelle biogenesis, autophagy) with active-site mutagenesis supporting mechanistic conclusions","pmids":["36318587"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"finding":"TgVPS15 possesses a protein kinase domain, but two critical active-site residues (lacking conservation with conventional kinases) are required for PI3P formation and parasitic functions, as shown by active-site mutagenesis.","method":"Active-site mutagenesis of the kinase domain combined with PI3P formation and functional assays","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — active-site mutagenesis with functional readout, single lab","pmids":["36318587"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"finding":"TgVPS15 regulates apicoplast biogenesis and inheritance by promoting PI3P generation, which controls trafficking and conjugation of TgATG8 to the apicoplast via the PI3P-binding protein TgATG18.","method":"Loss-of-function studies, localization of TgATG8 and TgATG18 to apicoplast, organelle inheritance assays","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — single lab, multiple orthogonal readouts (organelle inheritance, protein trafficking, epistatic placement with TgATG18 and TgATG8)","pmids":["36318587"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"finding":"TgVPS15 regulates autophagy under nutrient-limiting conditions by promoting autophagosome formation, using TgATG18 and controlling TgATG8 conjugation to autophagosomes.","method":"Loss-of-function studies under nutrient-limiting conditions, autophagosome formation assays, TgATG8 localization","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — single lab, defined cellular phenotype (autophagosome formation) with pathway placement via TgATG18 and TgATG8","pmids":["36318587"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"TgVPS15 is a protein kinase-domain-containing regulator of PI3-kinase activity in Toxoplasma gondii that promotes PI3P generation; two critical active-site residues drive this activity, and the resulting PI3P pool recruits TgATG18 to control TgATG8 trafficking/conjugation, thereby governing both apicoplast biogenesis/inheritance and autophagosome formation under nutrient stress."},"narrative":{"mechanistic_narrative":"TgVPS15 is a protein kinase-domain-containing regulator of the single PI3-kinase activity in Toxoplasma gondii, driving generation of the phosphatidylinositol-3-phosphate (PI3P) pool that governs membrane-trafficking events in the parasite [PMID:36318587]. Its kinase domain carries two active-site residues that diverge from conventional kinases yet are required for PI3P formation and parasite function, as demonstrated by active-site mutagenesis [PMID:36318587]. The PI3P generated by TgVPS15 recruits the PI3P-binding protein TgATG18, which in turn controls trafficking and conjugation of TgATG8, thereby directing both apicoplast biogenesis/inheritance [PMID:36318587] and, under nutrient-limiting conditions, autophagosome formation [PMID:36318587]. All available evidence derives from a single study in T. gondii; no structural, biochemical-reconstitution, or cross-species data are present in the corpus.","teleology":[{"year":2022,"claim":"Establishing whether TgVPS15 contributes to lipid signaling, this work showed it regulates the parasite's single PI3-kinase activity and promotes PI3P generation, defining it as a control point for PI3P-dependent membrane biology.","evidence":"Genetic/functional characterization with direct PI3P level measurements in T. gondii","pmids":["36318587"],"confidence":"Medium","gaps":["No direct biochemical demonstration that TgVPS15 physically associates with or activates the PI3-kinase","Strain unspecified","No structural model of the enzyme complex"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"claim":"To test whether the kinase domain is functionally required, active-site mutagenesis identified two non-canonical residues essential for PI3P formation and parasite functions, establishing a catalytic determinant distinct from conventional kinases.","evidence":"Active-site mutagenesis coupled to PI3P and functional assays in T. gondii","pmids":["36318587"],"confidence":"Medium","gaps":["Whether these residues confer intrinsic kinase activity versus a scaffolding/regulatory role is not resolved","No in vitro reconstitution of the mutant enzyme"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"claim":"To place TgVPS15 in organelle biology, loss-of-function studies showed it controls apicoplast biogenesis and inheritance by generating PI3P that recruits TgATG18 to direct TgATG8 trafficking/conjugation to the apicoplast, linking lipid signaling to organelle maintenance.","evidence":"Loss-of-function, TgATG8/TgATG18 localization, and organelle inheritance assays in T. gondii","pmids":["36318587"],"confidence":"Medium","gaps":["Direct interaction between TgVPS15 and TgATG18/TgATG8 not biochemically demonstrated","Mechanism of PI3P-mediated TgATG18 recruitment to the apicoplast not resolved at molecular detail"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2022,"claim":"To extend the pathway to stress adaptation, the same system showed TgVPS15 promotes autophagosome formation under nutrient limitation via TgATG18 and TgATG8 conjugation, indicating a dual role of the PI3P pool in constitutive organelle biology and induced autophagy.","evidence":"Loss-of-function under nutrient-limiting conditions with autophagosome formation and TgATG8 localization assays in T. gondii","pmids":["36318587"],"confidence":"Medium","gaps":["How the same PI3P pool is partitioned between apicoplast and autophagosome pathways is unknown","Upstream signals coupling nutrient status to TgVPS15 activity not identified"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"Whether TgVPS15 possesses intrinsic catalytic activity, how it physically engages the PI3-kinase and the ATG machinery, and its structural organization remain uncharacterized in the available corpus.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural or reconstituted-biochemistry evidence","No direct binding partner map","All evidence from a single study/lab"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["TGATG18","TGATG8"],"other_free_text":["Promotes PI3P generation as regulator of the single Toxoplasma PI3-kinase activity [#0].","Two non-canonical kinase-domain active-site residues required for PI3P formation and parasite function [#1].","PI3P-dependent recruitment of TgATG18 controls TgATG8 trafficking/conjugation to the apicoplast, governing apicoplast biogenesis and inheritance [#2].","Under nutrient limitation, drives autophagosome formation via TgATG18 and TgATG8 conjugation [#3]."]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"36318587","id":"PMC_36318587","title":"A VPS15-like kinase regulates apicoplast biogenesis and autophagy by promoting PI3P generation in Toxoplasma gondii.","date":"2022","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/36318587","citation_count":5,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":2981,"output_tokens":1009,"usd":0.012039,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5892,"output_tokens":2481,"usd":0.045742,"stage2_stop_reason":"end_turn"},"total_usd":0.057781,"stage1_batch_id":"msgbatch_01S6GjoYQm8LTPUsdhASdqag","stage2_batch_id":"msgbatch_01VX63RTMdBJqsG6gQMqoCjz","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2022,\n      \"finding\": \"TgVPS15 promotes PI3P (phosphatidylinositol-3-phosphate) generation in Toxoplasma gondii, acting as a regulator of the single PI3-kinase activity in the parasite.\",\n      \"method\": \"Genetic/functional characterization of TgVPS15 with PI3P level measurements\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — single lab, multiple functional readouts (PI3P formation, organelle biogenesis, autophagy) with active-site mutagenesis supporting mechanistic conclusions\",\n      \"pmids\": [\"36318587\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TgVPS15 possesses a protein kinase domain, but two critical active-site residues (lacking conservation with conventional kinases) are required for PI3P formation and parasitic functions, as shown by active-site mutagenesis.\",\n      \"method\": \"Active-site mutagenesis of the kinase domain combined with PI3P formation and functional assays\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — active-site mutagenesis with functional readout, single lab\",\n      \"pmids\": [\"36318587\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TgVPS15 regulates apicoplast biogenesis and inheritance by promoting PI3P generation, which controls trafficking and conjugation of TgATG8 to the apicoplast via the PI3P-binding protein TgATG18.\",\n      \"method\": \"Loss-of-function studies, localization of TgATG8 and TgATG18 to apicoplast, organelle inheritance assays\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — single lab, multiple orthogonal readouts (organelle inheritance, protein trafficking, epistatic placement with TgATG18 and TgATG8)\",\n      \"pmids\": [\"36318587\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TgVPS15 regulates autophagy under nutrient-limiting conditions by promoting autophagosome formation, using TgATG18 and controlling TgATG8 conjugation to autophagosomes.\",\n      \"method\": \"Loss-of-function studies under nutrient-limiting conditions, autophagosome formation assays, TgATG8 localization\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — single lab, defined cellular phenotype (autophagosome formation) with pathway placement via TgATG18 and TgATG8\",\n      \"pmids\": [\"36318587\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"TgVPS15 is a protein kinase-domain-containing regulator of PI3-kinase activity in Toxoplasma gondii that promotes PI3P generation; two critical active-site residues drive this activity, and the resulting PI3P pool recruits TgATG18 to control TgATG8 trafficking/conjugation, thereby governing both apicoplast biogenesis/inheritance and autophagosome formation under nutrient stress.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TgVPS15 is a protein kinase-domain-containing regulator of the single PI3-kinase activity in Toxoplasma gondii, driving generation of the phosphatidylinositol-3-phosphate (PI3P) pool that governs membrane-trafficking events in the parasite [#0]. Its kinase domain carries two active-site residues that diverge from conventional kinases yet are required for PI3P formation and parasite function, as demonstrated by active-site mutagenesis [#1]. The PI3P generated by TgVPS15 recruits the PI3P-binding protein TgATG18, which in turn controls trafficking and conjugation of TgATG8, thereby directing both apicoplast biogenesis/inheritance [#2] and, under nutrient-limiting conditions, autophagosome formation [#3]. All available evidence derives from a single study in T. gondii; no structural, biochemical-reconstitution, or cross-species data are present in the corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2022,\n      \"claim\": \"Establishing whether TgVPS15 contributes to lipid signaling, this work showed it regulates the parasite's single PI3-kinase activity and promotes PI3P generation, defining it as a control point for PI3P-dependent membrane biology.\",\n      \"evidence\": \"Genetic/functional characterization with direct PI3P level measurements in T. gondii\",\n      \"pmids\": [\"36318587\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate\",\n      \"gaps\": [\"No direct biochemical demonstration that TgVPS15 physically associates with or activates the PI3-kinase\", \"Strain unspecified\", \"No structural model of the enzyme complex\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"To test whether the kinase domain is functionally required, active-site mutagenesis identified two non-canonical residues essential for PI3P formation and parasite functions, establishing a catalytic determinant distinct from conventional kinases.\",\n      \"evidence\": \"Active-site mutagenesis coupled to PI3P and functional assays in T. gondii\",\n      \"pmids\": [\"36318587\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate\",\n      \"gaps\": [\"Whether these residues confer intrinsic kinase activity versus a scaffolding/regulatory role is not resolved\", \"No in vitro reconstitution of the mutant enzyme\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"To place TgVPS15 in organelle biology, loss-of-function studies showed it controls apicoplast biogenesis and inheritance by generating PI3P that recruits TgATG18 to direct TgATG8 trafficking/conjugation to the apicoplast, linking lipid signaling to organelle maintenance.\",\n      \"evidence\": \"Loss-of-function, TgATG8/TgATG18 localization, and organelle inheritance assays in T. gondii\",\n      \"pmids\": [\"36318587\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate\",\n      \"gaps\": [\"Direct interaction between TgVPS15 and TgATG18/TgATG8 not biochemically demonstrated\", \"Mechanism of PI3P-mediated TgATG18 recruitment to the apicoplast not resolved at molecular detail\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"To extend the pathway to stress adaptation, the same system showed TgVPS15 promotes autophagosome formation under nutrient limitation via TgATG18 and TgATG8 conjugation, indicating a dual role of the PI3P pool in constitutive organelle biology and induced autophagy.\",\n      \"evidence\": \"Loss-of-function under nutrient-limiting conditions with autophagosome formation and TgATG8 localization assays in T. gondii\",\n      \"pmids\": [\"36318587\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate\",\n      \"gaps\": [\"How the same PI3P pool is partitioned between apicoplast and autophagosome pathways is unknown\", \"Upstream signals coupling nutrient status to TgVPS15 activity not identified\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether TgVPS15 possesses intrinsic catalytic activity, how it physically engages the PI3-kinase and the ATG machinery, and its structural organization remain uncharacterized in the available corpus.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural or reconstituted-biochemistry evidence\", \"No direct binding partner map\", \"All evidence from a single study/lab\"],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0004672\", \"supporting_discovery_ids\": [1], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0035004\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0020011\", \"supporting_discovery_ids\": [2], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006914\", \"supporting_discovery_ids\": [3], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0000045\", \"supporting_discovery_ids\": [3], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]},\n      {\"term_id\": \"GO:0036258\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"TgATG18\", \"TgATG8\"],\n    \"other_free_text\": [\n      \"Promotes PI3P generation as regulator of the single Toxoplasma PI3-kinase activity [#0].\",\n      \"Two non-canonical kinase-domain active-site residues required for PI3P formation and parasite function [#1].\",\n      \"PI3P-dependent recruitment of TgATG18 controls TgATG8 trafficking/conjugation to the apicoplast, governing apicoplast biogenesis and inheritance [#2].\",\n      \"Under nutrient limitation, drives autophagosome formation via TgATG18 and TgATG8 conjugation [#3].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_310190","name":"VPS15","product":"VPS15-like kinase","uniprot_acc":"S8GCT6","chromosome":"TGME49_chrXI","start_pos":1126974},{"strain":"GT1","gene_id":"TGGT1_310190","name":null,"product":"PIK3R4 kinase-related protein (incomplete catalytic triad)","uniprot_acc":null,"chromosome":"TGGT1_chrXI","start_pos":1090626},{"strain":"RH88","gene_id":"TGRH88_049700","name":null,"product":"PIK3R4 kinase-related protein (incomplete catalytic triad)","uniprot_acc":null,"chromosome":"CM023092","start_pos":1176191},{"strain":"VEG","gene_id":"TGVEG_310190","name":null,"product":"PIK3R4 kinase-related protein (incomplete catalytic triad)","uniprot_acc":"A0A125YYI8","chromosome":"TGVEG_chrXI","start_pos":1136775}]}