{"gene":"PF3D7_1239900","run_date":"2026-09-08T19:44:17","timeline":{"discoveries":[{"year":2025,"finding":"PfVps16 (PF3D7_1239900) interacts with all four canonical members of the Vps-C complex (Vps11, Vps16, Vps18, Vps33) and the CORVET-specific component Vps3, as demonstrated by immunoprecipitation and mass spectrometry in P. falciparum.","method":"Immunoprecipitation and mass spectrometry","journal":"mSphere","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — reciprocal Co-IP/MS from a single lab, single study, no orthogonal validation of individual interactions","pmids":["40626728"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"PfVps16 (PF3D7_1239900) co-immunoprecipitates with three uncharacterized Plasmodium-specific proteins, two of which possess structural folds predicted to resemble those found in membrane tethering complex proteins, suggesting a parasite-specific extension of the canonical Vps-C complex.","method":"Immunoprecipitation, mass spectrometry, and structural prediction (AlphaFold or equivalent)","journal":"mSphere","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/MS study, structural prediction only for fold assignment, single lab","pmids":["40626728"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"PfVps16 (PF3D7_1239900) is expressed throughout the asexual erythrocytic cycle and is potentially associated with the Golgi apparatus and rhoptries in schizont-stage parasites.","method":"Immunofluorescence/co-localization imaging","journal":"mSphere","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single localization method, described as 'potentially associated' indicating incomplete certainty","pmids":["40626728"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"Conditional knockdown of VPS16 (PF3D7_1239900) as part of the HOPS/CORVET core leads to: (i) early depletion causing developmental arrest with accumulation of endosomes failing to fuse to the digestive vacuole, implicating VPS16 in endocytosis and host-cell cytosol uptake; (ii) late depletion causing severe defects in merozoite invasion due to mistargeting of proteins to rhoptries and micronemes, with reduced rhoptry volume and vesicle accumulation in schizonts.","method":"Conditional knockdown (knock-sideways or analogous), Giemsa smears, invasion assays, ultrastructure-expansion microscopy","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — conditional depletion with multiple readouts (endocytosis, invasion, ultrastructure), single lab but orthogonal phenotypic methods","pmids":["40198740"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2013,"finding":"Bioinformatic analysis identified PF3D7_1239900 (VPS16) as part of the conserved VpsC core of the HOPS/CORVET complexes retained in P. falciparum, placing it within a set of MTC subunits predicted to function in vesicle tethering/fusion in the apicomplexan endolysosomal system.","method":"Comparative genomic/bioinformatic analysis across twelve apicomplexan genomes","journal":"PloS one","confidence":"Low","confidence_rationale":"Tier 4 / Moderate — computational/bioinformatic prediction only, no direct functional experiment on this gene","pmids":["24086721"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PfVps16 (PF3D7_1239900) is a core subunit of the P. falciparum Vps-C/HOPS/CORVET tethering complex that physically interacts with Vps11, Vps18, Vps33, and Vps3, localizes to the Golgi and rhoptries in schizonts, and is required for endocytic fusion to the digestive vacuole in trophozoites and for trafficking of invasion-related cargo to rhoptries and micronemes in schizonts; additionally, it associates with three Plasmodium-specific proteins of unknown function that may represent parasite-specific extensions of the tethering machinery."},"narrative":{"mechanistic_narrative":"PF3D7_1239900 (VPS16) is a core subunit of the P. falciparum Vps-C/HOPS/CORVET membrane-tethering machinery that operates in the parasite's endolysosomal system across the asexual erythrocytic cycle [PMID:40626728, PMID:40198740]. It physically associates with the four canonical Vps-C members (Vps11, Vps16, Vps18, Vps33) and the CORVET-specific component Vps3 [PMID:40626728]. Functionally, VPS16 acts at two developmental stages: in trophozoites it is required for fusion of endosomes to the digestive vacuole, supporting endocytic uptake of host-cell cytosol, while in schizonts it is required for correct trafficking of cargo to rhoptries and micronemes, such that its depletion causes developmental arrest with unfused endosomes on one hand and defective merozoite invasion with reduced rhoptry volume on the other [PMID:40198740]. Beyond its role as a tethering-complex subunit, VPS16 also co-purifies with three Plasmodium-specific proteins of unknown function, two bearing folds predicted to resemble tethering-complex proteins, consistent with a parasite-specific extension of the canonical Vps-C complex [PMID:40626728].","teleology":[{"year":2013,"claim":"Before any functional work, it was unknown whether P. falciparum retained a canonical vesicle-tethering apparatus; comparative genomics placed PF3D7_1239900 within the conserved Vps-C core, establishing it as a candidate HOPS/CORVET subunit in the apicomplexan endolysosomal system.","evidence":"Comparative genomic/bioinformatic analysis across twelve apicomplexan genomes","pmids":["24086721"],"confidence":"Low","gaps":["Computational prediction only, no direct experiment on this gene","Does not establish physical assembly into a complex","No cellular localization or function tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"The predicted complex membership was tested directly, showing PF3D7_1239900 physically engages all four canonical Vps-C members and the CORVET-specific Vps3, confirming it as an assembled tethering-complex subunit rather than merely a sequence homolog.","evidence":"Reciprocal immunoprecipitation and mass spectrometry in P. falciparum","pmids":["40626728"],"confidence":"Medium","gaps":["Single lab, single study without orthogonal validation of individual interactions","Does not resolve HOPS versus CORVET stoichiometry","Does not map interaction interfaces"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"To test whether the parasite complex is more than the canonical core, co-IP identified three Plasmodium-specific interactors of PF3D7_1239900, two with tethering-like predicted folds, raising the possibility of a parasite-specific extension of Vps-C.","evidence":"Immunoprecipitation, mass spectrometry, and structural fold prediction","pmids":["40626728"],"confidence":"Low","gaps":["Structural assignment is prediction-only; folds not experimentally verified","Functions of the three proteins are unknown","Stable incorporation into the complex not demonstrated"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"Expression and localization were assessed to place the complex spatially, indicating PF3D7_1239900 is present throughout the asexual cycle and potentially associates with the Golgi and rhoptries in schizonts.","evidence":"Immunofluorescence/co-localization imaging","pmids":["40626728"],"confidence":"Low","gaps":["Localization described as 'potential' with a single method","Endosomal/digestive-vacuole localization not directly shown","No dynamic tracking across stages"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"The functional requirement was established by conditional depletion, revealing a stage-dependent dual role: endosome-to-digestive-vacuole fusion in trophozoites and rhoptry/microneme cargo delivery in schizonts, tying the tethering complex to both nutrient acquisition and merozoite invasion.","evidence":"Conditional knockdown of the HOPS/CORVET core with Giemsa smears, invasion assays, and ultrastructure-expansion microscopy","pmids":["40198740"],"confidence":"Medium","gaps":["Depletion was of the HOPS/CORVET core, not isolating VPS16-specific contribution","Molecular basis of cargo mistargeting not defined","Direct tethering activity not reconstituted"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"It remains unknown how PF3D7_1239900 switches between endocytic (digestive-vacuole fusion) and secretory (rhoptry/microneme) trafficking roles, and what the three Plasmodium-specific interactors contribute mechanistically.","evidence":"","pmids":[],"confidence":"Low","gaps":["No mechanism for stage-specific target-membrane selection","Roles of parasite-specific subunits uncharacterized","No structural model of the assembled parasite complex"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Vps-C core (HOPS/CORVET) tethering complex","CORVET complex (with Vps3)","putative Plasmodium-specific extended Vps-C complex"],"partners":["VPS11","VPS18","VPS33","VPS3","THREE UNCHARACTERIZED PLASMODIUM-SPECIFIC PROTEINS"],"other_free_text":["Required for endosome fusion to the digestive vacuole and host-cell cytosol uptake in trophozoites [#3]","Required for trafficking of invasion cargo to rhoptries and micronemes; depletion reduces rhoptry volume and impairs merozoite invasion [#3]","Expressed throughout the asexual erythrocytic cycle [#2]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"24086721","id":"PMC_24086721","title":"Comparative genomic analysis of multi-subunit tethering complexes demonstrates an ancient pan-eukaryotic complement and sculpting in Apicomplexa.","date":"2013","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24086721","citation_count":54,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40626728","id":"PMC_40626728","title":"The Plasmodium falciparum homolog of Vps16 interacts with the core members of the Vps-C tethering complex.","date":"2025","source":"mSphere","url":"https://pubmed.ncbi.nlm.nih.gov/40626728","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["VPS16","PfVPS16"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40198740","id":"","title":"HOPS/CORVET tethering complexes are critical for endocytosis and protein trafficking to invasion related organelles in malaria parasites.","date":"2025","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/40198740","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["VPS16"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26136076","id":"","title":"Disruption of cellular homeostasis induces organelle stress and triggers apoptosis like cell-death pathways in malaria parasite.","date":"2015","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/26136076","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["VPS16"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6474,"output_tokens":1394,"usd":0.020166,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6296,"output_tokens":2592,"usd":0.04814,"stage2_stop_reason":"end_turn"},"total_usd":0.068306,"stage1_batch_id":"msgbatch_01SRp5hyRc82zNjddxyCCXGk","stage2_batch_id":"msgbatch_01K3BTmBazRo3pRrMvyaPMTY","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2025,\n      \"finding\": \"PfVps16 (PF3D7_1239900) interacts with all four canonical members of the Vps-C complex (Vps11, Vps16, Vps18, Vps33) and the CORVET-specific component Vps3, as demonstrated by immunoprecipitation and mass spectrometry in P. falciparum.\",\n      \"method\": \"Immunoprecipitation and mass spectrometry\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — reciprocal Co-IP/MS from a single lab, single study, no orthogonal validation of individual interactions\",\n      \"pmids\": [\"40626728\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PfVps16 (PF3D7_1239900) co-immunoprecipitates with three uncharacterized Plasmodium-specific proteins, two of which possess structural folds predicted to resemble those found in membrane tethering complex proteins, suggesting a parasite-specific extension of the canonical Vps-C complex.\",\n      \"method\": \"Immunoprecipitation, mass spectrometry, and structural prediction (AlphaFold or equivalent)\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/MS study, structural prediction only for fold assignment, single lab\",\n      \"pmids\": [\"40626728\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PfVps16 (PF3D7_1239900) is expressed throughout the asexual erythrocytic cycle and is potentially associated with the Golgi apparatus and rhoptries in schizont-stage parasites.\",\n      \"method\": \"Immunofluorescence/co-localization imaging\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single localization method, described as 'potentially associated' indicating incomplete certainty\",\n      \"pmids\": [\"40626728\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Conditional knockdown of VPS16 (PF3D7_1239900) as part of the HOPS/CORVET core leads to: (i) early depletion causing developmental arrest with accumulation of endosomes failing to fuse to the digestive vacuole, implicating VPS16 in endocytosis and host-cell cytosol uptake; (ii) late depletion causing severe defects in merozoite invasion due to mistargeting of proteins to rhoptries and micronemes, with reduced rhoptry volume and vesicle accumulation in schizonts.\",\n      \"method\": \"Conditional knockdown (knock-sideways or analogous), Giemsa smears, invasion assays, ultrastructure-expansion microscopy\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — conditional depletion with multiple readouts (endocytosis, invasion, ultrastructure), single lab but orthogonal phenotypic methods\",\n      \"pmids\": [\"40198740\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Bioinformatic analysis identified PF3D7_1239900 (VPS16) as part of the conserved VpsC core of the HOPS/CORVET complexes retained in P. falciparum, placing it within a set of MTC subunits predicted to function in vesicle tethering/fusion in the apicomplexan endolysosomal system.\",\n      \"method\": \"Comparative genomic/bioinformatic analysis across twelve apicomplexan genomes\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Moderate — computational/bioinformatic prediction only, no direct functional experiment on this gene\",\n      \"pmids\": [\"24086721\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PfVps16 (PF3D7_1239900) is a core subunit of the P. falciparum Vps-C/HOPS/CORVET tethering complex that physically interacts with Vps11, Vps18, Vps33, and Vps3, localizes to the Golgi and rhoptries in schizonts, and is required for endocytic fusion to the digestive vacuole in trophozoites and for trafficking of invasion-related cargo to rhoptries and micronemes in schizonts; additionally, it associates with three Plasmodium-specific proteins of unknown function that may represent parasite-specific extensions of the tethering machinery.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1239900 (VPS16) is a core subunit of the P. falciparum Vps-C/HOPS/CORVET membrane-tethering machinery that operates in the parasite's endolysosomal system across the asexual erythrocytic cycle [#0, #3]. It physically associates with the four canonical Vps-C members (Vps11, Vps16, Vps18, Vps33) and the CORVET-specific component Vps3 [#0]. Functionally, VPS16 acts at two developmental stages: in trophozoites it is required for fusion of endosomes to the digestive vacuole, supporting endocytic uptake of host-cell cytosol, while in schizonts it is required for correct trafficking of cargo to rhoptries and micronemes, such that its depletion causes developmental arrest with unfused endosomes on one hand and defective merozoite invasion with reduced rhoptry volume on the other [#3]. Beyond its role as a tethering-complex subunit, VPS16 also co-purifies with three Plasmodium-specific proteins of unknown function, two bearing folds predicted to resemble tethering-complex proteins, consistent with a parasite-specific extension of the canonical Vps-C complex [#1].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Before any functional work, it was unknown whether P. falciparum retained a canonical vesicle-tethering apparatus; comparative genomics placed PF3D7_1239900 within the conserved Vps-C core, establishing it as a candidate HOPS/CORVET subunit in the apicomplexan endolysosomal system.\",\n      \"evidence\": \"Comparative genomic/bioinformatic analysis across twelve apicomplexan genomes\",\n      \"pmids\": [\"24086721\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Computational prediction only, no direct experiment on this gene\", \"Does not establish physical assembly into a complex\", \"No cellular localization or function tested\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The predicted complex membership was tested directly, showing PF3D7_1239900 physically engages all four canonical Vps-C members and the CORVET-specific Vps3, confirming it as an assembled tethering-complex subunit rather than merely a sequence homolog.\",\n      \"evidence\": \"Reciprocal immunoprecipitation and mass spectrometry in P. falciparum\",\n      \"pmids\": [\"40626728\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab, single study without orthogonal validation of individual interactions\", \"Does not resolve HOPS versus CORVET stoichiometry\", \"Does not map interaction interfaces\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"To test whether the parasite complex is more than the canonical core, co-IP identified three Plasmodium-specific interactors of PF3D7_1239900, two with tethering-like predicted folds, raising the possibility of a parasite-specific extension of Vps-C.\",\n      \"evidence\": \"Immunoprecipitation, mass spectrometry, and structural fold prediction\",\n      \"pmids\": [\"40626728\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Structural assignment is prediction-only; folds not experimentally verified\", \"Functions of the three proteins are unknown\", \"Stable incorporation into the complex not demonstrated\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Expression and localization were assessed to place the complex spatially, indicating PF3D7_1239900 is present throughout the asexual cycle and potentially associates with the Golgi and rhoptries in schizonts.\",\n      \"evidence\": \"Immunofluorescence/co-localization imaging\",\n      \"pmids\": [\"40626728\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Localization described as 'potential' with a single method\", \"Endosomal/digestive-vacuole localization not directly shown\", \"No dynamic tracking across stages\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The functional requirement was established by conditional depletion, revealing a stage-dependent dual role: endosome-to-digestive-vacuole fusion in trophozoites and rhoptry/microneme cargo delivery in schizonts, tying the tethering complex to both nutrient acquisition and merozoite invasion.\",\n      \"evidence\": \"Conditional knockdown of the HOPS/CORVET core with Giemsa smears, invasion assays, and ultrastructure-expansion microscopy\",\n      \"pmids\": [\"40198740\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Depletion was of the HOPS/CORVET core, not isolating VPS16-specific contribution\", \"Molecular basis of cargo mistargeting not defined\", \"Direct tethering activity not reconstituted\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how PF3D7_1239900 switches between endocytic (digestive-vacuole fusion) and secretory (rhoptry/microneme) trafficking roles, and what the three Plasmodium-specific interactors contribute mechanistically.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No mechanism for stage-specific target-membrane selection\", \"Roles of parasite-specific subunits uncharacterized\", \"No structural model of the assembled parasite complex\"],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005515\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005794\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0020008\", \"supporting_discovery_ids\": [2, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006897\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0006906\", \"supporting_discovery_ids\": [3, 4]},\n      {\"term_id\": \"GO:0006886\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\n      \"Vps-C core (HOPS/CORVET) tethering complex\",\n      \"CORVET complex (with Vps3)\",\n      \"putative Plasmodium-specific extended Vps-C complex\"\n    ],\n    \"partners\": [\n      \"Vps11\",\n      \"Vps18\",\n      \"Vps33\",\n      \"Vps3\",\n      \"three uncharacterized Plasmodium-specific proteins\"\n    ],\n    \"other_free_text\": [\n      \"Required for endosome fusion to the digestive vacuole and host-cell cytosol uptake in trophozoites [#3]\",\n      \"Required for trafficking of invasion cargo to rhoptries and micronemes; depletion reduces rhoptry volume and impairs merozoite invasion [#3]\",\n      \"Expressed throughout the asexual erythrocytic cycle [#2]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1239900","name":null,"product":"vacuolar protein sorting-associated protein 16, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1454300","name":null,"product":"vacuolar protein sorting-associated protein 16, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1460000","name":null,"product":"vacuolar protein sorting-associated protein 16, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"VPS16","evaluation":null}