{"gene":"TG_500179","gene_symbol":"PIKfyve","run_date":"2026-09-08T16:10:21","timeline":{"discoveries":[{"year":2014,"finding":"PIKfyve is a lipid kinase in Toxoplasma gondii that phosphorylates PI(3)P into PI(3,5)P2; conditional disruption of PIKfyve causes enlarged apicoplasts, establishing a role for PI(3,5)P2 in apicoplast homeostasis.","method":"Conditional gene disruption (knockdown) with morphological phenotypic readout (apicoplast size/inheritance)","journal":"Cellular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional KO with defined organelle phenotype and enzymatic activity inferred from substrate identity; single lab, two orthogonal approaches (PIKfyve KD and ArPIKfyve KD both phenocopy)","pmids":["25329540"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2014,"finding":"Conditional knockdown of ArPIKfyve (the PIKfyve regulatory protein) also induces enlarged apicoplasts, indicating that the PIKfyve–ArPIKfyve complex is required for apicoplast homeostasis in T. gondii.","method":"Conditional gene disruption (knockdown) of ArPIKfyve with apicoplast morphology readout","journal":"Cellular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean conditional KD with specific organelle phenotype; single lab, corroborated by parallel PIKfyve KD result","pmids":["25329540"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2014,"finding":"Six PX- and FYVE-domain-containing proteins (potential PI(3)P effectors) were identified in T. gondii; conditional depletion of these putative PI(3)P-binding proteins showed they are NOT essential for parasite growth or apicoplast biology, suggesting PI(3)P's primary apicoplast role is as a precursor for PI(3,5)P2 synthesis.","method":"Conditional gene disruption of PX/FYVE domain proteins with growth and apicoplast phenotype readout (negative result for essentiality)","journal":"Cellular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional KO panel with defined phenotypic readouts; single lab; negative result is mechanistically informative","pmids":["25329540"],"is_preprint":false,"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"current_model":"Toxoplasma gondii PIKfyve is a lipid kinase that phosphorylates PI(3)P to produce PI(3,5)P2; together with its regulatory protein ArPIKfyve, it is required for apicoplast homeostasis, as conditional disruption of either PIKfyve or ArPIKfyve causes apicoplast enlargement, and both PIKfyve and ArPIKfyve are absent in Cryptosporidium species that lack an apicoplast, supporting a direct role of PI(3,5)P2 in maintaining this organelle."},"narrative":{"mechanistic_narrative":"In Toxoplasma gondii, PIKfyve is a lipid kinase that phosphorylates PI(3)P to generate PI(3,5)P2, an activity required for apicoplast homeostasis, since conditional disruption of PIKfyve enlarges the apicoplast [PMID:25329540]. PIKfyve functions together with its regulatory protein ArPIKfyve, whose conditional knockdown phenocopies the enlarged-apicoplast defect, establishing that the PIKfyve–ArPIKfyve complex maintains this organelle [PMID:25329540]. The PI(3)P pool at the apicoplast appears to act principally as a precursor for PI(3,5)P2 synthesis rather than through PX/FYVE-domain effectors, as depletion of six candidate PI(3)P-binding proteins did not impair growth or apicoplast biology [PMID:25329540]. Beyond this apicoplast role and the inferred kinase reaction, no further mechanistic detail has been characterized in the available corpus.","teleology":[{"year":2014,"claim":"Established that PIKfyve provides the PI(3,5)P2-generating activity needed for apicoplast homeostasis, defining a specific lipid-signaling requirement for maintaining this organelle.","evidence":"Conditional gene disruption of PIKfyve with apicoplast morphology readout in T. gondii, with kinase activity inferred from substrate identity (PI(3)P → PI(3,5)P2)","pmids":["25329540"],"confidence":"Medium","gaps":["Kinase activity inferred from substrate identity rather than directly reconstituted in vitro","Mechanism by which PI(3,5)P2 controls apicoplast size not resolved","Subcellular localization of PIKfyve relative to the apicoplast not defined in the corpus"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2014,"claim":"Showed that PIKfyve acts within a complex with its regulatory partner ArPIKfyve, since knockdown of ArPIKfyve reproduces the apicoplast enlargement phenotype.","evidence":"Conditional knockdown of ArPIKfyve with apicoplast morphology readout in T. gondii","pmids":["25329540"],"confidence":"Medium","gaps":["Physical association of PIKfyve and ArPIKfyve not directly demonstrated by biochemical interaction data in the corpus","How ArPIKfyve regulates PIKfyve kinase output is unknown"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":2014,"claim":"Distinguished the biological function of PI(3)P at the apicoplast, indicating it serves mainly as a precursor for PI(3,5)P2 rather than acting through PX/FYVE-domain effectors.","evidence":"Conditional depletion panel of six PX/FYVE-domain candidate PI(3)P effectors with growth and apicoplast phenotype readout (negative result) in T. gondii","pmids":["25329540"],"confidence":"Medium","gaps":["Negative essentiality result does not exclude redundancy among the candidate effectors","Direct measurement of apicoplast PI(3)P versus PI(3,5)P2 pools not reported"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]},{"year":null,"claim":"How PI(3,5)P2 mechanistically maintains apicoplast size and inheritance, and the localization and direct enzymatic characterization of PIKfyve, remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No downstream effector of PI(3,5)P2 at the apicoplast identified","No in vitro reconstitution of the PIKfyve kinase reaction in the corpus","No structural or interaction data on the PIKfyve–ArPIKfyve complex"],"attribution":[{"species":"Toxoplasma gondii","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["PIKfyve–ArPIKfyve complex"],"partners":["ARPIKFYVE"],"other_free_text":["Phosphorylates PI(3)P to produce PI(3,5)P2 [#0].","Required for apicoplast homeostasis; disruption causes enlarged apicoplasts [#0, #1].","PI(3)P at the apicoplast acts primarily as a precursor for PI(3,5)P2 rather than through PX/FYVE-domain effectors [#2]."]},"strain_conflicts":[]},"prefetch_data":{},"corpus_meta":[{"pmid":"25329540","id":"PMC_25329540","title":"Lipid kinases are essential for apicoplast homeostasis in Toxoplasma gondii.","date":"2014","source":"Cellular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/25329540","citation_count":35,"is_preprint":false},{"pmid":"29870544","id":"PMC_29870544","title":"The PH domain from the Toxoplasma gondii PH-containing protein-1 (TgPH1) serves as an ectopic reporter of phosphatidylinositol 3-phosphate in mammalian cells.","date":"2018","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/29870544","citation_count":3,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3758,"output_tokens":924,"usd":0.012567,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5761,"output_tokens":1966,"usd":0.038977,"stage2_stop_reason":"end_turn"},"total_usd":0.051544,"stage1_batch_id":"msgbatch_01RQGfcbGqQD3GfCPaX8jpfW","stage2_batch_id":"msgbatch_019PABGEC4M9vU7v6jy6Fvwg","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2014,\n      \"finding\": \"PIKfyve is a lipid kinase in Toxoplasma gondii that phosphorylates PI(3)P into PI(3,5)P2; conditional disruption of PIKfyve causes enlarged apicoplasts, establishing a role for PI(3,5)P2 in apicoplast homeostasis.\",\n      \"method\": \"Conditional gene disruption (knockdown) with morphological phenotypic readout (apicoplast size/inheritance)\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO with defined organelle phenotype and enzymatic activity inferred from substrate identity; single lab, two orthogonal approaches (PIKfyve KD and ArPIKfyve KD both phenocopy)\",\n      \"pmids\": [\"25329540\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Conditional knockdown of ArPIKfyve (the PIKfyve regulatory protein) also induces enlarged apicoplasts, indicating that the PIKfyve–ArPIKfyve complex is required for apicoplast homeostasis in T. gondii.\",\n      \"method\": \"Conditional gene disruption (knockdown) of ArPIKfyve with apicoplast morphology readout\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean conditional KD with specific organelle phenotype; single lab, corroborated by parallel PIKfyve KD result\",\n      \"pmids\": [\"25329540\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Six PX- and FYVE-domain-containing proteins (potential PI(3)P effectors) were identified in T. gondii; conditional depletion of these putative PI(3)P-binding proteins showed they are NOT essential for parasite growth or apicoplast biology, suggesting PI(3)P's primary apicoplast role is as a precursor for PI(3,5)P2 synthesis.\",\n      \"method\": \"Conditional gene disruption of PX/FYVE domain proteins with growth and apicoplast phenotype readout (negative result for essentiality)\",\n      \"journal\": \"Cellular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional KO panel with defined phenotypic readouts; single lab; negative result is mechanistically informative\",\n      \"pmids\": [\"25329540\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"Toxoplasma gondii PIKfyve is a lipid kinase that phosphorylates PI(3)P to produce PI(3,5)P2; together with its regulatory protein ArPIKfyve, it is required for apicoplast homeostasis, as conditional disruption of either PIKfyve or ArPIKfyve causes apicoplast enlargement, and both PIKfyve and ArPIKfyve are absent in Cryptosporidium species that lack an apicoplast, supporting a direct role of PI(3,5)P2 in maintaining this organelle.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"In Toxoplasma gondii, PIKfyve is a lipid kinase that phosphorylates PI(3)P to generate PI(3,5)P2, an activity required for apicoplast homeostasis, since conditional disruption of PIKfyve enlarges the apicoplast [#0]. PIKfyve functions together with its regulatory protein ArPIKfyve, whose conditional knockdown phenocopies the enlarged-apicoplast defect, establishing that the PIKfyve\\u2013ArPIKfyve complex maintains this organelle [#1]. The PI(3)P pool at the apicoplast appears to act principally as a precursor for PI(3,5)P2 synthesis rather than through PX/FYVE-domain effectors, as depletion of six candidate PI(3)P-binding proteins did not impair growth or apicoplast biology [#2]. Beyond this apicoplast role and the inferred kinase reaction, no further mechanistic detail has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Established that PIKfyve provides the PI(3,5)P2-generating activity needed for apicoplast homeostasis, defining a specific lipid-signaling requirement for maintaining this organelle.\",\n      \"evidence\": \"Conditional gene disruption of PIKfyve with apicoplast morphology readout in T. gondii, with kinase activity inferred from substrate identity (PI(3)P \\u2192 PI(3,5)P2)\",\n      \"pmids\": [\"25329540\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Kinase activity inferred from substrate identity rather than directly reconstituted in vitro\",\n        \"Mechanism by which PI(3,5)P2 controls apicoplast size not resolved\",\n        \"Subcellular localization of PIKfyve relative to the apicoplast not defined in the corpus\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Showed that PIKfyve acts within a complex with its regulatory partner ArPIKfyve, since knockdown of ArPIKfyve reproduces the apicoplast enlargement phenotype.\",\n      \"evidence\": \"Conditional knockdown of ArPIKfyve with apicoplast morphology readout in T. gondii\",\n      \"pmids\": [\"25329540\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Physical association of PIKfyve and ArPIKfyve not directly demonstrated by biochemical interaction data in the corpus\",\n        \"How ArPIKfyve regulates PIKfyve kinase output is unknown\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Distinguished the biological function of PI(3)P at the apicoplast, indicating it serves mainly as a precursor for PI(3,5)P2 rather than acting through PX/FYVE-domain effectors.\",\n      \"evidence\": \"Conditional depletion panel of six PX/FYVE-domain candidate PI(3)P effectors with growth and apicoplast phenotype readout (negative result) in T. gondii\",\n      \"pmids\": [\"25329540\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Negative essentiality result does not exclude redundancy among the candidate effectors\",\n        \"Direct measurement of apicoplast PI(3)P versus PI(3,5)P2 pools not reported\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PI(3,5)P2 mechanistically maintains apicoplast size and inheritance, and the localization and direct enzymatic characterization of PIKfyve, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"No downstream effector of PI(3,5)P2 at the apicoplast identified\",\n        \"No in vitro reconstitution of the PIKfyve kinase reaction in the corpus\",\n        \"No structural or interaction data on the PIKfyve\\u2013ArPIKfyve complex\"\n      ],\n      \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0000285\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0046854\", \"supporting_discovery_ids\": [0], \"attribution\": [{\"species\": \"Toxoplasma gondii\", \"strain\": \"\"}]}\n    ],\n    \"complexes\": [\"PIKfyve\\u2013ArPIKfyve complex\"],\n    \"partners\": [\"ArPIKfyve\"],\n    \"other_free_text\": [\n      \"Phosphorylates PI(3)P to produce PI(3,5)P2 [#0].\",\n      \"Required for apicoplast homeostasis; disruption causes enlarged apicoplasts [#0, #1].\",\n      \"PI(3)P at the apicoplast acts primarily as a precursor for PI(3,5)P2 rather than through PX/FYVE-domain effectors [#2].\"\n    ]\n  },\n  \"strain_conflicts\": []\n}","audit_flag":null,"strains":[{"strain":"ME49","gene_id":"TGME49_500179","name":"PIKfyve","product":"FYVE zinc finger domain-containing protein","uniprot_acc":"A0A125YNH7","chromosome":"TGME49_chrVIIb","start_pos":4328780},{"strain":"GT1","gene_id":"TGGT1_256920","name":null,"product":"phosphatidylinositol-4-phosphate 5-Kinase","uniprot_acc":null,"chromosome":"TGGT1_chrVIIb","start_pos":4268265},{"strain":"RH88","gene_id":"TGRH88_072810","name":null,"product":"phosphatidylinositol-4-phosphate 5-Kinase","uniprot_acc":null,"chromosome":"CM023089","start_pos":4369782},{"strain":"VEG","gene_id":"TGVEG_256920","name":null,"product":"phosphatidylinositol-4-phosphate 5-Kinase","uniprot_acc":"V4YJS1","chromosome":"TGVEG_chrVIIb","start_pos":4353057}]}