{"gene":"PF3D7_0815800","run_date":"2026-09-08T16:26:55","timeline":{"discoveries":[{"year":2025,"finding":"PF3D7_0815800 (VPS9) was identified as a co-immunoprecipitating interactor of PfVps16 in P. falciparum asexual stages by immunoprecipitation and mass spectrometry, placing VPS9 as an associated component of the PfVps-C/CORVET tethering complex alongside the canonical Vps-C subunits (Vps11, Vps16, Vps18, Vps33) and the CORVET subunit PfVps3.","method":"Immunoprecipitation and mass spectrometry (co-IP/MS of PfVps16)","journal":"mSphere","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/MS experiment, single lab, no orthogonal validation of the VPS9 interaction specifically","pmids":["40626728"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2020,"finding":"Peptides corresponding to VPS9 (PF3D7_0815800) were enriched in the clathrin heavy chain interactome of P. falciparum trophozoites by pulldown and mass spectrometry, suggesting VPS9 associates with clathrin-coated vesicle machinery in the parasite.","method":"Clathrin nanobody pulldown followed by mass spectrometry","journal":"mBio","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single pulldown/MS experiment, VPS9 enrichment reported without specific follow-up validation","pmids":["32098816"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"finding":"A P. berghei VPS9 homolog was found to be phosphorylated at S767 in a PKG-regulated manner in gliding ookinetes, as detected by phosphoproteomics, consistent with a role as a Rab5 GTPase activator in the endosomal pathway relevant to microneme biogenesis.","method":"Quantitative phosphoproteomics of P. berghei ookinetes with PKG perturbation","journal":"PLoS biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single phosphoproteomic dataset, no functional follow-up on VPS9 specifically; phosphosite likely not directly phosphorylated by PKG per the authors","pmids":["24594931"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"PF3D7_0815800 (VPS9) is a putative Rab5 GEF that co-purifies with the P. falciparum Vps-C/CORVET tethering complex (via PfVps16 immunoprecipitation) and with clathrin-coated vesicle components, and its P. berghei ortholog undergoes PKG-regulated phosphorylation in ookinetes, collectively suggesting a conserved role in endosomal/vesicular trafficking and potentially in apical organelle biogenesis, though no direct functional experiments on PF3D7_0815800 itself have been reported."},"narrative":{"mechanistic_narrative":"PF3D7_0815800 (VPS9) is a putative vacuolar protein sorting-associated protein implicated in endosomal/vesicular trafficking in Plasmodium, known in the available corpus only through its physical associations rather than direct functional assays. In P. falciparum asexual stages, VPS9 co-immunoprecipitates with PfVps16, placing it as an associated component of the PfVps-C/CORVET tethering complex that also contains Vps11, Vps16, Vps18, Vps33 and the CORVET subunit PfVps3 [PMID:40626728], and its peptides are enriched in the clathrin heavy chain interactome of trophozoites, consistent with an association with clathrin-coated vesicle machinery [PMID:32098816]. In P. berghei, a VPS9 homolog is phosphorylated at S767 in a PKG-regulated manner in gliding ookinetes [PMID:24594931]. Beyond these association and phosphosite observations, no direct functional experiments on PF3D7_0815800 itself have been reported in the available corpus, and its proposed Rab5 GEF activity has not been experimentally demonstrated.","teleology":[{"year":2014,"claim":"The first question was whether VPS9 participates in a regulated signaling pathway in the parasite; phosphoproteomics revealed a P. berghei VPS9 homolog is phosphorylated in a PKG-dependent context during ookinete gliding, linking it to a regulated trafficking process.","evidence":"Quantitative phosphoproteomics of P. berghei ookinetes with PKG perturbation, detecting phosphorylation at S767","pmids":["24594931"],"confidence":"Low","gaps":["Single phosphoproteomic dataset with no functional follow-up on VPS9 specifically; the authors note the phosphosite is likely not directly phosphorylated by PKG","The proposed Rab5 GEF activity is inferred, not demonstrated","Finding is in P. berghei, not directly in PF3D7_0815800"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2020,"claim":"To ask which trafficking machinery VPS9 associates with, a clathrin interactome was profiled, and VPS9 peptides were enriched, implicating it in clathrin-coated vesicle-associated transport.","evidence":"Clathrin nanobody pulldown followed by mass spectrometry in P. falciparum trophozoites","pmids":["32098816"],"confidence":"Low","gaps":["Single pulldown/MS experiment without orthogonal validation of the VPS9 enrichment","Does not establish direct binding versus co-enrichment as part of a larger assembly","No functional consequence of the clathrin association tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"claim":"To define VPS9's complex membership, PfVps16 was immunoprecipitated, and VPS9 co-purified with the canonical Vps-C/CORVET subunits, positioning it as an associated component of a tethering complex in asexual parasites.","evidence":"Co-immunoprecipitation and mass spectrometry of PfVps16 in P. falciparum asexual stages","pmids":["40626728"],"confidence":"Low","gaps":["Single Co-IP/MS from one lab with no orthogonal or reciprocal validation of the VPS9 interaction specifically","Does not establish whether VPS9 is a stoichiometric subunit or a transient associate","No functional role of VPS9 within the complex demonstrated"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether PF3D7_0815800 functions as a Rab5 GEF, and its direct role in endosomal trafficking or apical organelle biogenesis, remains untested by any direct functional or biochemical experiment.","evidence":"","pmids":[],"confidence":"Low","gaps":["No genetic knockout, knockdown, or conditional depletion of PF3D7_0815800 reported","No biochemical demonstration of guanine nucleotide exchange activity toward Rab5","No localization or trafficking-phenotype data specific to VPS9"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["PfVps-C/CORVET tethering complex (associated component, via PfVps16 co-IP) [#0]"],"partners":["PFVPS16 [#0]","CLATHRIN HEAVY CHAIN (INTERACTOME ENRICHMENT) [#1]"],"other_free_text":["P. berghei VPS9 homolog phosphorylated at S767 in a PKG-regulated manner in gliding ookinetes [#2]","Putative Rab5 GEF role is inferred from context and not experimentally demonstrated for PF3D7_0815800","No direct functional, genetic, or biochemical experiments on PF3D7_0815800 itself have been reported in the available corpus"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"32356940","id":"PMC_32356940","title":"Interaction of Plasmodium falciparum casein kinase 1 with components of host cell protein trafficking machinery.","date":"2020","source":"IUBMB life","url":"https://pubmed.ncbi.nlm.nih.gov/32356940","citation_count":7,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["VPS9"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40626728","id":"","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":["VPS9"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"32098816","id":"","title":"The Plasmodium falciparum Artemisinin Susceptibility-Associated AP-2 Adaptin μ Subunit is Clathrin Independent and Essential for Schizont Maturation.","date":"2020","source":"mBio","url":"https://pubmed.ncbi.nlm.nih.gov/32098816","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["VPS9"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24204248","id":"","title":"Protein trafficking through the endosomal system prepares intracellular parasites for a home invasion.","date":"2013","source":"PLoS pathogens","url":"https://pubmed.ncbi.nlm.nih.gov/24204248","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["VPS9"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"33869086","id":"","title":"Dangerous Duplicity: The Dual Functions of Casein Kinase 1 in Parasite Biology and Host Subversion.","date":"2021","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/33869086","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["VPS9"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24594931","id":"","title":"Phosphoinositide metabolism links cGMP-dependent protein kinase G to essential Ca²⁺ signals at key decision points in the life cycle of malaria parasites.","date":"2014","source":"PLoS biology","url":"https://pubmed.ncbi.nlm.nih.gov/24594931","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["VPS9"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26844642","id":"","title":"Vacuolar protein sorting mechanisms in apicomplexan parasites.","date":"2016","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/26844642","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["VPS9"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":9466,"output_tokens":939,"usd":0.021241,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5632,"output_tokens":1921,"usd":0.038093,"stage2_stop_reason":"end_turn"},"total_usd":0.059334,"stage1_batch_id":"msgbatch_01NE1MTa8x1hW7Lo4tAaNzY1","stage2_batch_id":"msgbatch_0141vaQdeFvbo2q39AinvXM9","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2025,\n      \"finding\": \"PF3D7_0815800 (VPS9) was identified as a co-immunoprecipitating interactor of PfVps16 in P. falciparum asexual stages by immunoprecipitation and mass spectrometry, placing VPS9 as an associated component of the PfVps-C/CORVET tethering complex alongside the canonical Vps-C subunits (Vps11, Vps16, Vps18, Vps33) and the CORVET subunit PfVps3.\",\n      \"method\": \"Immunoprecipitation and mass spectrometry (co-IP/MS of PfVps16)\",\n      \"journal\": \"mSphere\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/MS experiment, single lab, no orthogonal validation of the VPS9 interaction specifically\",\n      \"pmids\": [\"40626728\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Peptides corresponding to VPS9 (PF3D7_0815800) were enriched in the clathrin heavy chain interactome of P. falciparum trophozoites by pulldown and mass spectrometry, suggesting VPS9 associates with clathrin-coated vesicle machinery in the parasite.\",\n      \"method\": \"Clathrin nanobody pulldown followed by mass spectrometry\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single pulldown/MS experiment, VPS9 enrichment reported without specific follow-up validation\",\n      \"pmids\": [\"32098816\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"A P. berghei VPS9 homolog was found to be phosphorylated at S767 in a PKG-regulated manner in gliding ookinetes, as detected by phosphoproteomics, consistent with a role as a Rab5 GTPase activator in the endosomal pathway relevant to microneme biogenesis.\",\n      \"method\": \"Quantitative phosphoproteomics of P. berghei ookinetes with PKG perturbation\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single phosphoproteomic dataset, no functional follow-up on VPS9 specifically; phosphosite likely not directly phosphorylated by PKG per the authors\",\n      \"pmids\": [\"24594931\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_0815800 (VPS9) is a putative Rab5 GEF that co-purifies with the P. falciparum Vps-C/CORVET tethering complex (via PfVps16 immunoprecipitation) and with clathrin-coated vesicle components, and its P. berghei ortholog undergoes PKG-regulated phosphorylation in ookinetes, collectively suggesting a conserved role in endosomal/vesicular trafficking and potentially in apical organelle biogenesis, though no direct functional experiments on PF3D7_0815800 itself have been reported.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_0815800 (VPS9) is a putative vacuolar protein sorting-associated protein implicated in endosomal/vesicular trafficking in Plasmodium, known in the available corpus only through its physical associations rather than direct functional assays. In P. falciparum asexual stages, VPS9 co-immunoprecipitates with PfVps16, placing it as an associated component of the PfVps-C/CORVET tethering complex that also contains Vps11, Vps16, Vps18, Vps33 and the CORVET subunit PfVps3 [#0], and its peptides are enriched in the clathrin heavy chain interactome of trophozoites, consistent with an association with clathrin-coated vesicle machinery [#1]. In P. berghei, a VPS9 homolog is phosphorylated at S767 in a PKG-regulated manner in gliding ookinetes [#2]. Beyond these association and phosphosite observations, no direct functional experiments on PF3D7_0815800 itself have been reported in the available corpus, and its proposed Rab5 GEF activity has not been experimentally demonstrated.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"The first question was whether VPS9 participates in a regulated signaling pathway in the parasite; phosphoproteomics revealed a P. berghei VPS9 homolog is phosphorylated in a PKG-dependent context during ookinete gliding, linking it to a regulated trafficking process.\",\n      \"evidence\": \"Quantitative phosphoproteomics of P. berghei ookinetes with PKG perturbation, detecting phosphorylation at S767\",\n      \"pmids\": [\"24594931\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single phosphoproteomic dataset with no functional follow-up on VPS9 specifically; the authors note the phosphosite is likely not directly phosphorylated by PKG\",\n        \"The proposed Rab5 GEF activity is inferred, not demonstrated\",\n        \"Finding is in P. berghei, not directly in PF3D7_0815800\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"To ask which trafficking machinery VPS9 associates with, a clathrin interactome was profiled, and VPS9 peptides were enriched, implicating it in clathrin-coated vesicle-associated transport.\",\n      \"evidence\": \"Clathrin nanobody pulldown followed by mass spectrometry in P. falciparum trophozoites\",\n      \"pmids\": [\"32098816\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single pulldown/MS experiment without orthogonal validation of the VPS9 enrichment\",\n        \"Does not establish direct binding versus co-enrichment as part of a larger assembly\",\n        \"No functional consequence of the clathrin association tested\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"To define VPS9's complex membership, PfVps16 was immunoprecipitated, and VPS9 co-purified with the canonical Vps-C/CORVET subunits, positioning it as an associated component of a tethering complex in asexual parasites.\",\n      \"evidence\": \"Co-immunoprecipitation and mass spectrometry of PfVps16 in P. falciparum asexual stages\",\n      \"pmids\": [\"40626728\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Single Co-IP/MS from one lab with no orthogonal or reciprocal validation of the VPS9 interaction specifically\",\n        \"Does not establish whether VPS9 is a stoichiometric subunit or a transient associate\",\n        \"No functional role of VPS9 within the complex demonstrated\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether PF3D7_0815800 functions as a Rab5 GEF, and its direct role in endosomal trafficking or apical organelle biogenesis, remains untested by any direct functional or biochemical experiment.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No genetic knockout, knockdown, or conditional depletion of PF3D7_0815800 reported\",\n        \"No biochemical demonstration of guanine nucleotide exchange activity toward Rab5\",\n        \"No localization or trafficking-phenotype data specific to VPS9\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [\"PfVps-C/CORVET tethering complex (associated component, via PfVps16 co-IP) [#0]\"],\n    \"partners\": [\"PfVps16 [#0]\", \"clathrin heavy chain (interactome enrichment) [#1]\"],\n    \"other_free_text\": [\n      \"P. berghei VPS9 homolog phosphorylated at S767 in a PKG-regulated manner in gliding ookinetes [#2]\",\n      \"Putative Rab5 GEF role is inferred from context and not experimentally demonstrated for PF3D7_0815800\",\n      \"No direct functional, genetic, or biochemical experiments on PF3D7_0815800 itself have been reported in the available corpus\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_0815800","name":null,"product":"vacuolar protein sorting-associated protein 9, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0715000","name":null,"product":"vacuolar protein sorting-associated protein 9, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0504600","name":null,"product":"vacuolar protein sorting-associated protein 9, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"VPS9","evaluation":null}