{"gene":"PF3D7_0935200","run_date":"2026-09-08T19:44:17","timeline":{"discoveries":[{"year":2013,"finding":"Bioinformatic analysis identified PF3D7_0935200 (VPS33) as a conserved subunit of the VpsC core of the HOPS and CORVET complexes in P. falciparum, establishing its presence as part of the ancient eukaryotic multi-subunit tethering complex complement retained in Apicomplexa.","method":"Comparative genomic/bioinformatic analysis across twelve apicomplexan genomes","journal":"PloS one","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational prediction only, no experimental validation of VPS33 function or interactions","pmids":["24086721"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"PF3D7_0935200 (VPS33) is one of the four canonical Vps-C core subunits (VPS11, VPS16, VPS18, VPS33) present in P. falciparum. Attempts to tag VPS33 at its C-terminus with GFP or the smaller HA-tag were unsuccessful, suggesting C-terminal tagging is detrimental to protein function.","method":"Attempted endogenous locus modification via selection-linked integration (SLI) for C-terminal tagging","journal":"PLoS pathogens","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single negative result (tagging failure); no functional data obtained for VPS33 itself","pmids":["40198740"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"Immunoprecipitation and mass spectrometry of PfVps16 demonstrated that PF3D7_0935200 (VPS33) is a binding partner of PfVps16, confirming its membership in the canonical Vps-C complex in P. falciparum together with VPS11, VPS18, and the CORVET component VPS3.","method":"Immunoprecipitation followed by mass spectrometry (PfVps16 as bait)","journal":"mSphere","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP/MS from a single lab; VPS33 detected as interactor of VPS16, consistent with canonical complex membership, but VPS33 itself was not independently validated as bait","pmids":["40626728"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"The HOPS/CORVET core subunits, of which VPS33 (PF3D7_0935200) is a member, are required for P. falciparum endocytosis and host cell cytosol uptake (early depletion caused developmental arrest and accumulation of endosomes failing to fuse with the digestive vacuole) and for protein trafficking to invasion-related apical organelles (rhoptries and micronemes) in schizonts (late depletion caused mistargeting of rhoptry/microneme proteins, reduced rhoptry volume, and vesicle accumulation).","method":"Conditional knockdown (FKBP-based degradation system) of core HOPS/CORVET subunits; ultrastructure-expansion microscopy; fluorescence co-localization with organelle markers","journal":"PLoS pathogens","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — rigorous loss-of-function with defined cellular phenotypes and multiple orthogonal readouts, but VPS33 itself could not be tagged/depleted independently; findings attributed to the complex as a whole, with VPS33's individual contribution inferred from complex membership","pmids":["40198740"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"current_model":"PF3D7_0935200 (VPS33) is a conserved core subunit of the P. falciparum Vps-C (HOPS/CORVET) tethering complex, confirmed as an interactor of PfVps16 by co-immunoprecipitation/mass spectrometry; the Vps-C complex as a whole is required for endocytosis/digestive vacuole fusion in trophozoites and for protein trafficking to rhoptries and micronemes in schizonts, but VPS33's individual molecular contribution could not be directly assessed because C-terminal tagging of VPS33 is detrimental to its function."},"narrative":{"mechanistic_narrative":"PF3D7_0935200 (VPS33) is a conserved core subunit of the Vps-C tethering module shared by the HOPS and CORVET complexes in Plasmodium falciparum [PMID:24086721, PMID:40626728]. Bioinformatic analysis across apicomplexan genomes first placed VPS33 among the four canonical Vps-C core subunits (VPS11, VPS16, VPS18, VPS33) retained from the ancestral eukaryotic tethering machinery [PMID:24086721, PMID:40198740], and immunoprecipitation-mass spectrometry using PfVps16 as bait experimentally confirmed VPS33 as a binding partner within this complex, alongside VPS11, VPS18, and the CORVET component VPS3 [PMID:40626728]. At the process level the Vps-C core is required for endocytosis and host-cell cytosol uptake in trophozoites — its depletion causes developmental arrest and accumulation of endosomes that fail to fuse with the digestive vacuole — and for trafficking of rhoptry and microneme proteins to apical invasion organelles in schizonts [PMID:40198740]. VPS33's individual molecular contribution has not been directly resolved in the available corpus: C-terminal tagging of VPS33 with GFP or HA was unsuccessful and appears detrimental to function, so the loss-of-function phenotypes are attributed to the complex as a whole rather than to VPS33 tested in isolation [PMID:40198740].","teleology":[{"year":2013,"claim":"Whether P. falciparum retains the ancestral multi-subunit tethering machinery was unknown; identifying VPS33 as a conserved Vps-C core subunit established that the HOPS/CORVET complement persists in Apicomplexa.","evidence":"Comparative genomic/bioinformatic analysis across twelve apicomplexan genomes","pmids":["24086721"],"confidence":"Low","gaps":["Computational prediction only, with no experimental validation of VPS33 expression, interactions, or function","Does not distinguish VPS33's role in HOPS versus CORVET","No subcellular localization established"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"To test whether the predicted VPS33 physically assembles into the Vps-C complex, PfVps16 was used as bait; recovery of VPS33 confirmed its membership in the canonical tethering complex in vivo.","evidence":"Immunoprecipitation followed by mass spectrometry with PfVps16 as bait","pmids":["40626728"],"confidence":"Medium","gaps":["VPS33 was detected as a VPS16 interactor but was not independently validated as bait, leaving direct binding partners of VPS33 undefined","Does not resolve whether VPS33 participates in HOPS, CORVET, or both","Stoichiometry and architecture of the complex not determined"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"The cellular requirement of the Vps-C core was addressed by conditional depletion, showing the complex is needed for endocytic fusion with the digestive vacuole and for apical organelle biogenesis, though VPS33's individual role could not be isolated because it could not be tagged.","evidence":"FKBP-based conditional knockdown of core HOPS/CORVET subunits with ultrastructure-expansion microscopy and organelle-marker co-localization; attempted C-terminal SLI tagging of VPS33 was unsuccessful","pmids":["40198740"],"confidence":"Medium","gaps":["Phenotypes are attributed to the complex as a whole; VPS33 itself could not be tagged or depleted, so its specific contribution is inferred not measured","C-terminal tagging is detrimental, leaving no working genetic handle on endogenous VPS33","No mechanistic detail on how VPS33 contributes to tethering or SNARE-mediated fusion"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"It remains unknown what VPS33 contributes to Vps-C function as an individual subunit, and how it can be genetically or biochemically interrogated without disrupting its function.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No tagging or depletion strategy exists that preserves VPS33 function","Direct binding partners and structural role of VPS33 within the complex are undefined","No discrimination of VPS33's function between the HOPS and CORVET complexes"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["Vps-C core (HOPS/CORVET) tethering complex"],"partners":["PFVPS16","VPS11","VPS18","VPS3"],"other_free_text":["Identified bioinformatically as a conserved Vps-C core subunit in Apicomplexa [#0].","Confirmed by Co-IP/MS as a binding partner of PfVps16 within the canonical Vps-C complex [#2].","C-terminal GFP/HA tagging of VPS33 is detrimental to function, precluding independent tagging or depletion; loss-of-function phenotypes are attributed to the complex as a whole [#1, #3].","Vps-C core depletion arrests development, blocks endosome fusion with the digestive vacuole, and mistargets rhoptry/microneme proteins in schizonts [#3]."]}},"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":["VPS33"],"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":["VPS33"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":5533,"output_tokens":1301,"usd":0.018057,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6132,"output_tokens":2148,"usd":0.04218,"stage2_stop_reason":"end_turn"},"total_usd":0.060237,"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\": 2013,\n      \"finding\": \"Bioinformatic analysis identified PF3D7_0935200 (VPS33) as a conserved subunit of the VpsC core of the HOPS and CORVET complexes in P. falciparum, establishing its presence as part of the ancient eukaryotic multi-subunit tethering complex complement retained in Apicomplexa.\",\n      \"method\": \"Comparative genomic/bioinformatic analysis across twelve apicomplexan genomes\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational prediction only, no experimental validation of VPS33 function or interactions\",\n      \"pmids\": [\"24086721\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PF3D7_0935200 (VPS33) is one of the four canonical Vps-C core subunits (VPS11, VPS16, VPS18, VPS33) present in P. falciparum. Attempts to tag VPS33 at its C-terminus with GFP or the smaller HA-tag were unsuccessful, suggesting C-terminal tagging is detrimental to protein function.\",\n      \"method\": \"Attempted endogenous locus modification via selection-linked integration (SLI) for C-terminal tagging\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single negative result (tagging failure); no functional data obtained for VPS33 itself\",\n      \"pmids\": [\"40198740\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Immunoprecipitation and mass spectrometry of PfVps16 demonstrated that PF3D7_0935200 (VPS33) is a binding partner of PfVps16, confirming its membership in the canonical Vps-C complex in P. falciparum together with VPS11, VPS18, and the CORVET component VPS3.\",\n      \"method\": \"Immunoprecipitation followed by mass spectrometry (PfVps16 as bait)\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP/MS from a single lab; VPS33 detected as interactor of VPS16, consistent with canonical complex membership, but VPS33 itself was not independently validated as bait\",\n      \"pmids\": [\"40626728\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The HOPS/CORVET core subunits, of which VPS33 (PF3D7_0935200) is a member, are required for P. falciparum endocytosis and host cell cytosol uptake (early depletion caused developmental arrest and accumulation of endosomes failing to fuse with the digestive vacuole) and for protein trafficking to invasion-related apical organelles (rhoptries and micronemes) in schizonts (late depletion caused mistargeting of rhoptry/microneme proteins, reduced rhoptry volume, and vesicle accumulation).\",\n      \"method\": \"Conditional knockdown (FKBP-based degradation system) of core HOPS/CORVET subunits; ultrastructure-expansion microscopy; fluorescence co-localization with organelle markers\",\n      \"journal\": \"PLoS pathogens\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — rigorous loss-of-function with defined cellular phenotypes and multiple orthogonal readouts, but VPS33 itself could not be tagged/depleted independently; findings attributed to the complex as a whole, with VPS33's individual contribution inferred from complex membership\",\n      \"pmids\": [\"40198740\"],\n      \"is_preprint\": false,\n      \"attribution\": [\n        {\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}\n      ]\n    }\n  ],\n  \"current_model\": \"PF3D7_0935200 (VPS33) is a conserved core subunit of the P. falciparum Vps-C (HOPS/CORVET) tethering complex, confirmed as an interactor of PfVps16 by co-immunoprecipitation/mass spectrometry; the Vps-C complex as a whole is required for endocytosis/digestive vacuole fusion in trophozoites and for protein trafficking to rhoptries and micronemes in schizonts, but VPS33's individual molecular contribution could not be directly assessed because C-terminal tagging of VPS33 is detrimental to its function.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0935200 (VPS33) is a conserved core subunit of the Vps-C tethering module shared by the HOPS and CORVET complexes in Plasmodium falciparum [#0, #2]. Bioinformatic analysis across apicomplexan genomes first placed VPS33 among the four canonical Vps-C core subunits (VPS11, VPS16, VPS18, VPS33) retained from the ancestral eukaryotic tethering machinery [#0, #1], and immunoprecipitation-mass spectrometry using PfVps16 as bait experimentally confirmed VPS33 as a binding partner within this complex, alongside VPS11, VPS18, and the CORVET component VPS3 [#2]. At the process level the Vps-C core is required for endocytosis and host-cell cytosol uptake in trophozoites — its depletion causes developmental arrest and accumulation of endosomes that fail to fuse with the digestive vacuole — and for trafficking of rhoptry and microneme proteins to apical invasion organelles in schizonts [#3]. VPS33's individual molecular contribution has not been directly resolved in the available corpus: C-terminal tagging of VPS33 with GFP or HA was unsuccessful and appears detrimental to function, so the loss-of-function phenotypes are attributed to the complex as a whole rather than to VPS33 tested in isolation [#1, #3].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"Whether P. falciparum retains the ancestral multi-subunit tethering machinery was unknown; identifying VPS33 as a conserved Vps-C core subunit established that the HOPS/CORVET complement persists in Apicomplexa.\",\n      \"evidence\": \"Comparative genomic/bioinformatic analysis across twelve apicomplexan genomes\",\n      \"pmids\": [\"24086721\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Computational prediction only, with no experimental validation of VPS33 expression, interactions, or function\",\n        \"Does not distinguish VPS33's role in HOPS versus CORVET\",\n        \"No subcellular localization established\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"To test whether the predicted VPS33 physically assembles into the Vps-C complex, PfVps16 was used as bait; recovery of VPS33 confirmed its membership in the canonical tethering complex in vivo.\",\n      \"evidence\": \"Immunoprecipitation followed by mass spectrometry with PfVps16 as bait\",\n      \"pmids\": [\"40626728\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"VPS33 was detected as a VPS16 interactor but was not independently validated as bait, leaving direct binding partners of VPS33 undefined\",\n        \"Does not resolve whether VPS33 participates in HOPS, CORVET, or both\",\n        \"Stoichiometry and architecture of the complex not determined\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"The cellular requirement of the Vps-C core was addressed by conditional depletion, showing the complex is needed for endocytic fusion with the digestive vacuole and for apical organelle biogenesis, though VPS33's individual role could not be isolated because it could not be tagged.\",\n      \"evidence\": \"FKBP-based conditional knockdown of core HOPS/CORVET subunits with ultrastructure-expansion microscopy and organelle-marker co-localization; attempted C-terminal SLI tagging of VPS33 was unsuccessful\",\n      \"pmids\": [\"40198740\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Phenotypes are attributed to the complex as a whole; VPS33 itself could not be tagged or depleted, so its specific contribution is inferred not measured\",\n        \"C-terminal tagging is detrimental, leaving no working genetic handle on endogenous VPS33\",\n        \"No mechanistic detail on how VPS33 contributes to tethering or SNARE-mediated fusion\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown what VPS33 contributes to Vps-C function as an individual subunit, and how it can be genetically or biochemically interrogated without disrupting its function.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No tagging or depletion strategy exists that preserves VPS33 function\",\n        \"Direct binding partners and structural role of VPS33 within the complex are undefined\",\n        \"No discrimination of VPS33's function between the HOPS and CORVET complexes\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"GO:0006897\", \"supporting_discovery_ids\": [3]},\n      {\"term_id\": \"GO:0006886\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\"Vps-C core (HOPS/CORVET) tethering complex\"],\n    \"partners\": [\"PfVps16\", \"VPS11\", \"VPS18\", \"VPS3\"],\n    \"other_free_text\": [\n      \"Identified bioinformatically as a conserved Vps-C core subunit in Apicomplexa [#0].\",\n      \"Confirmed by Co-IP/MS as a binding partner of PfVps16 within the canonical Vps-C complex [#2].\",\n      \"C-terminal GFP/HA tagging of VPS33 is detrimental to function, precluding independent tagging or depletion; loss-of-function phenotypes are attributed to the complex as a whole [#1, #3].\",\n      \"Vps-C core depletion arrests development, blocks endosome fusion with the digestive vacuole, and mistargets rhoptry/microneme proteins in schizonts [#3].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0935200","name":null,"product":"vacuolar protein sorting-associated protein 33, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0836000","name":null,"product":"vacuolar protein sorting-associated protein 33, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0733900","name":null,"product":"vacuolar protein sorting-associated protein 33, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"VPS33","evaluation":null}