{"gene":"PF3D7_1110500","run_date":"2026-09-08T19:44:17","timeline":{"discoveries":[{"year":2014,"finding":"PF3D7_1110500 (VPS35), as a component of the retromer complex, co-localizes with Rab7 to a small number of punctate endosomal structures in P. falciparum asexual blood-stage parasites. These endosomal structures lie in close proximity to but are distinct from the Golgi apparatus (retromer does not redistribute to the ER upon brefeldin A treatment). The retromer complex (including VPS35) is proposed to mediate retrograde transport of PfSortilin from the endosome back to the Golgi, and endosomes marked by retromer develop adjacent to nascent rhoptries, suggesting involvement in rhoptry biogenesis.","method":"Fluorescence co-localization microscopy of retromer components and Rab7; brefeldin A treatment to distinguish endosomal from Golgi compartment; immunofluorescence localization of PfSortilin","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — direct localization experiment with functional implication, single lab, but rhoptry biogenesis role is inferred from adjacency rather than direct functional perturbation of VPS35 itself","pmids":["24587025"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2018,"finding":"PF3D7_1110500 (VPS35) assembles into the retromer complex in P. falciparum asexual blood-stage parasites, as demonstrated by immunosensing Surface Plasmon Resonance: antibody against one retromer subunit captured the complex from whole-cell lysate, and antibodies against the other subunits (including VPS35) detected them in the trapped complex on the SPR chip.","method":"Immunosensing coupled to Surface Plasmon Resonance (SPR) using antibodies raised against retromer subunits including VPS35; complex captured from native P. falciparum lysate","journal":"Biochimica et biophysica acta. Proteins and proteomics","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — novel biosensing method detecting native complex assembly, single lab, single method; no reciprocal pulldown or orthogonal validation for VPS35 specifically","pmids":["29654975"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"finding":"The P. berghei ortholog of VPS35 undergoes regulated phosphorylation in gliding ookinetes in a PKG-dependent manner, linking VPS35 to the cGMP/PKG signaling pathway that controls vesicular trafficking during Plasmodium motility.","method":"Quantitative phosphoproteomics of P. berghei ookinetes with and without PKG inhibition; phosphosite T690 on VPS35 identified as PKG-pathway-regulated","journal":"PLoS biology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single phosphoproteomic dataset, single lab; authors explicitly note the regulated phosphosites are probably not direct PKG substrates, and no functional follow-up on VPS35 phosphorylation was performed","pmids":["24594931"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":""}]}],"current_model":"PF3D7_1110500 (VPS35) is a core subunit of the retromer complex in Plasmodium falciparum that localizes to discrete endosomal puncta adjacent to the Golgi apparatus in asexual blood-stage parasites, assembles into a native retromer complex with VPS26 and VPS29 as detected by SPR immunosensing, and is proposed to mediate retrograde transport of PfSortilin from endosomes to the Golgi and to contribute to rhoptry biogenesis; its P. berghei ortholog is additionally regulated by phosphorylation downstream of the PKG signaling pathway in ookinetes."},"narrative":{"mechanistic_narrative":"PF3D7_1110500 (VPS35) is a core subunit of the retromer complex in Plasmodium falciparum, functioning in endosome-to-Golgi retrograde membrane trafficking during asexual blood-stage growth [PMID:24587025, PMID:29654975]. It localizes to a small number of punctate Rab7-positive endosomal structures situated close to, but distinct from, the Golgi apparatus, and these retromer-marked endosomes develop adjacent to nascent rhoptries, implicating VPS35-containing retromer in retrograde transport of PfSortilin and in rhoptry biogenesis [PMID:24587025]. VPS35 physically assembles into a native retromer complex with the other retromer subunits, as detected by immunosensing surface plasmon resonance on parasite lysate [PMID:29654975]. In Plasmodium berghei, the VPS35 ortholog undergoes PKG-dependent regulated phosphorylation in gliding ookinetes, linking it to cGMP/PKG-controlled trafficking during parasite motility [PMID:24594931]. Beyond retromer membership, endosomal localization, and this ortholog phosphorylation, no further mechanistic detail on VPS35 has been characterized in the available corpus.","teleology":[{"year":2014,"claim":"Establishing where retromer acts in the parasite: the question of whether Plasmodium possesses a retromer-marked endosomal compartment was answered by placing VPS35-containing retromer at Rab7 puncta adjacent to the Golgi, defining a retrograde trafficking route toward rhoptry biogenesis.","evidence":"Fluorescence co-localization of retromer components with Rab7, brefeldin A treatment, and PfSortilin immunofluorescence in P. falciparum blood stages","pmids":["24587025"],"confidence":"Medium","gaps":["Rhoptry biogenesis role inferred from adjacency, not from direct functional perturbation of VPS35","PfSortilin retrograde transport is proposed, not demonstrated by VPS35 depletion","No genetic knockout or conditional knockdown of VPS35 itself"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"claim":"Connecting VPS35 to a signaling pathway: the question of whether retromer trafficking is regulated during motility was partially addressed by showing the P. berghei ortholog is phosphorylated in a PKG-dependent manner in gliding ookinetes.","evidence":"Quantitative phosphoproteomics of P. berghei ookinetes with PKG inhibition, identifying phosphosite T690","pmids":["24594931"],"confidence":"Low","gaps":["Authors note regulated phosphosites are probably not direct PKG substrates; no direct kinase-substrate demonstration","No functional follow-up on the consequence of VPS35 phosphorylation","Finding is in P. berghei ookinetes, not the P. falciparum blood stage where localization was defined"],"attribution":[{"species":"Plasmodium berghei","strain":""}]},{"year":2018,"claim":"Confirming physical complex assembly: the question of whether VPS35 is genuinely incorporated into an assembled native retromer, rather than merely co-localizing, was addressed by capturing the intact complex from parasite lysate and detecting VPS35 within it.","evidence":"Immunosensing surface plasmon resonance using antibodies against retromer subunits including VPS35, on native P. falciparum lysate","pmids":["29654975"],"confidence":"Medium","gaps":["Single method, single lab; no reciprocal pulldown or orthogonal validation specifically for VPS35","Does not define VPS35 stoichiometry, interaction interfaces, or subunit contacts","No structural model of the assembled complex"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"Whether VPS35 is functionally required for PfSortilin retrograde transport, rhoptry biogenesis, or blood-stage viability remains unresolved, as no direct loss-of-function perturbation of VPS35 has been reported in the corpus.","evidence":"","pmids":[],"confidence":"Low","gaps":["No conditional knockdown or knockout of VPS35 to test cargo transport or rhoptry phenotypes","Functional consequence of PKG-dependent phosphorylation unknown","No mapping of VPS35 cargo-recognition or membrane-recruitment mechanism in Plasmodium"],"attribution":[]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":["retromer complex"],"partners":["VPS26","VPS29","RAB7","PFSORTILIN"],"other_free_text":["Retromer-marked endosomes develop adjacent to nascent rhoptries, implicating VPS35 in rhoptry biogenesis [#0]","P. berghei VPS35 ortholog is phosphorylated at T690 in a PKG-dependent manner in gliding ookinetes [#2]"]}},"prefetch_data":{},"corpus_meta":[{"pmid":"24587025","id":"PMC_24587025","title":"Evidence for a Golgi-to-endosome protein sorting pathway in Plasmodium falciparum.","date":"2014","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/24587025","citation_count":40,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"29654975","id":"PMC_29654975","title":"Detection of retromer assembly in Plasmodium falciparum by immunosensing coupled to Surface Plasmon Resonance.","date":"2018","source":"Biochimica et biophysica acta. Proteins and proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/29654975","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"42515018","id":"","title":"Antibody Responses to the Conserved Plasmodium falciparum Vacuolar Sorting Protein 29 in the Brazilian Amazon.","date":"2026","source":"Pathogens (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/42515018","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["VPS35"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40075412","id":"","title":"Genome-wide scanning for genetic markers associated with anti-malarial drugs sensitivity of Plasmodium falciparum isolates from the China-Myanmar border region.","date":"2025","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/40075412","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["VPS35"],"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":["VPS35"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"25425018","id":"","title":"Genome wide in silico analysis of Plasmodium falciparum phosphatome.","date":"2014","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/25425018","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["VPS35"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"26289816","id":"","title":"Inhibition by stabilization: targeting the Plasmodium falciparum aldolase-TRAP complex.","date":"2015","source":"Malaria journal","url":"https://pubmed.ncbi.nlm.nih.gov/26289816","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["VPS35"],"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":["VPS35"],"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":["VPS35"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10722,"output_tokens":1115,"usd":0.024445,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":5923,"output_tokens":2068,"usd":0.040657,"stage2_stop_reason":"end_turn"},"total_usd":0.065102,"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\": 2014,\n      \"finding\": \"PF3D7_1110500 (VPS35), as a component of the retromer complex, co-localizes with Rab7 to a small number of punctate endosomal structures in P. falciparum asexual blood-stage parasites. These endosomal structures lie in close proximity to but are distinct from the Golgi apparatus (retromer does not redistribute to the ER upon brefeldin A treatment). The retromer complex (including VPS35) is proposed to mediate retrograde transport of PfSortilin from the endosome back to the Golgi, and endosomes marked by retromer develop adjacent to nascent rhoptries, suggesting involvement in rhoptry biogenesis.\",\n      \"method\": \"Fluorescence co-localization microscopy of retromer components and Rab7; brefeldin A treatment to distinguish endosomal from Golgi compartment; immunofluorescence localization of PfSortilin\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — direct localization experiment with functional implication, single lab, but rhoptry biogenesis role is inferred from adjacency rather than direct functional perturbation of VPS35 itself\",\n      \"pmids\": [\"24587025\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PF3D7_1110500 (VPS35) assembles into the retromer complex in P. falciparum asexual blood-stage parasites, as demonstrated by immunosensing Surface Plasmon Resonance: antibody against one retromer subunit captured the complex from whole-cell lysate, and antibodies against the other subunits (including VPS35) detected them in the trapped complex on the SPR chip.\",\n      \"method\": \"Immunosensing coupled to Surface Plasmon Resonance (SPR) using antibodies raised against retromer subunits including VPS35; complex captured from native P. falciparum lysate\",\n      \"journal\": \"Biochimica et biophysica acta. Proteins and proteomics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — novel biosensing method detecting native complex assembly, single lab, single method; no reciprocal pulldown or orthogonal validation for VPS35 specifically\",\n      \"pmids\": [\"29654975\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"The P. berghei ortholog of VPS35 undergoes regulated phosphorylation in gliding ookinetes in a PKG-dependent manner, linking VPS35 to the cGMP/PKG signaling pathway that controls vesicular trafficking during Plasmodium motility.\",\n      \"method\": \"Quantitative phosphoproteomics of P. berghei ookinetes with and without PKG inhibition; phosphosite T690 on VPS35 identified as PKG-pathway-regulated\",\n      \"journal\": \"PLoS biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single phosphoproteomic dataset, single lab; authors explicitly note the regulated phosphosites are probably not direct PKG substrates, and no functional follow-up on VPS35 phosphorylation was performed\",\n      \"pmids\": [\"24594931\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    }\n  ],\n  \"current_model\": \"PF3D7_1110500 (VPS35) is a core subunit of the retromer complex in Plasmodium falciparum that localizes to discrete endosomal puncta adjacent to the Golgi apparatus in asexual blood-stage parasites, assembles into a native retromer complex with VPS26 and VPS29 as detected by SPR immunosensing, and is proposed to mediate retrograde transport of PfSortilin from endosomes to the Golgi and to contribute to rhoptry biogenesis; its P. berghei ortholog is additionally regulated by phosphorylation downstream of the PKG signaling pathway in ookinetes.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PF3D7_1110500 (VPS35) is a core subunit of the retromer complex in Plasmodium falciparum, functioning in endosome-to-Golgi retrograde membrane trafficking during asexual blood-stage growth [#0, #1]. It localizes to a small number of punctate Rab7-positive endosomal structures situated close to, but distinct from, the Golgi apparatus, and these retromer-marked endosomes develop adjacent to nascent rhoptries, implicating VPS35-containing retromer in retrograde transport of PfSortilin and in rhoptry biogenesis [#0]. VPS35 physically assembles into a native retromer complex with the other retromer subunits, as detected by immunosensing surface plasmon resonance on parasite lysate [#1]. In Plasmodium berghei, the VPS35 ortholog undergoes PKG-dependent regulated phosphorylation in gliding ookinetes, linking it to cGMP/PKG-controlled trafficking during parasite motility [#2]. Beyond retromer membership, endosomal localization, and this ortholog phosphorylation, no further mechanistic detail on VPS35 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2014,\n      \"claim\": \"Establishing where retromer acts in the parasite: the question of whether Plasmodium possesses a retromer-marked endosomal compartment was answered by placing VPS35-containing retromer at Rab7 puncta adjacent to the Golgi, defining a retrograde trafficking route toward rhoptry biogenesis.\",\n      \"evidence\": \"Fluorescence co-localization of retromer components with Rab7, brefeldin A treatment, and PfSortilin immunofluorescence in P. falciparum blood stages\",\n      \"pmids\": [\"24587025\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Rhoptry biogenesis role inferred from adjacency, not from direct functional perturbation of VPS35\",\n        \"PfSortilin retrograde transport is proposed, not demonstrated by VPS35 depletion\",\n        \"No genetic knockout or conditional knockdown of VPS35 itself\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Connecting VPS35 to a signaling pathway: the question of whether retromer trafficking is regulated during motility was partially addressed by showing the P. berghei ortholog is phosphorylated in a PKG-dependent manner in gliding ookinetes.\",\n      \"evidence\": \"Quantitative phosphoproteomics of P. berghei ookinetes with PKG inhibition, identifying phosphosite T690\",\n      \"pmids\": [\"24594931\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Authors note regulated phosphosites are probably not direct PKG substrates; no direct kinase-substrate demonstration\",\n        \"No functional follow-up on the consequence of VPS35 phosphorylation\",\n        \"Finding is in P. berghei ookinetes, not the P. falciparum blood stage where localization was defined\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Confirming physical complex assembly: the question of whether VPS35 is genuinely incorporated into an assembled native retromer, rather than merely co-localizing, was addressed by capturing the intact complex from parasite lysate and detecting VPS35 within it.\",\n      \"evidence\": \"Immunosensing surface plasmon resonance using antibodies against retromer subunits including VPS35, on native P. falciparum lysate\",\n      \"pmids\": [\"29654975\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Single method, single lab; no reciprocal pulldown or orthogonal validation specifically for VPS35\",\n        \"Does not define VPS35 stoichiometry, interaction interfaces, or subunit contacts\",\n        \"No structural model of the assembled complex\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether VPS35 is functionally required for PfSortilin retrograde transport, rhoptry biogenesis, or blood-stage viability remains unresolved, as no direct loss-of-function perturbation of VPS35 has been reported in the corpus.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No conditional knockdown or knockout of VPS35 to test cargo transport or rhoptry phenotypes\",\n        \"Functional consequence of PKG-dependent phosphorylation unknown\",\n        \"No mapping of VPS35 cargo-recognition or membrane-recruitment mechanism in Plasmodium\"\n      ],\n      \"attribution\": []\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0030904\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0031901\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:0042147\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"retromer complex\"],\n    \"partners\": [\"VPS26\", \"VPS29\", \"Rab7\", \"PfSortilin\"],\n    \"other_free_text\": [\n      \"Retromer-marked endosomes develop adjacent to nascent rhoptries, implicating VPS35 in rhoptry biogenesis [#0]\",\n      \"P. berghei VPS35 ortholog is phosphorylated at T690 in a PKG-dependent manner in gliding ookinetes [#2]\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1110500","name":null,"product":"vacuolar protein sorting-associated protein 35, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_0937100","name":null,"product":"vacuolar protein sorting-associated protein 35, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_0908200","name":null,"product":"vacuolar protein sorting-associated protein 35, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"VPS35","evaluation":null}