{"gene":"PF3D7_1235200","run_date":"2026-09-08T14:19:06","timeline":{"discoveries":[{"year":2001,"finding":"VP2 (PfVP2) was identified and cloned from P. falciparum and inferred to encode a type II (K⁺-independent) V-type H⁺-translocating inorganic pyrophosphatase, phylogenetically and functionally distinct from the type I (K⁺-dependent) PfVP1.","method":"Gene cloning, sequence analysis, and phylogenetic comparison","journal":"Molecular and biochemical parasitology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — gene cloning and sequence/phylogenetic analysis establish identity and predicted biochemical class; functional inference (K⁺-independence) is extrapolated from sequence similarity to characterized plant AVP2, not directly assayed for PfVP2 itself","pmids":["11378198"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2011,"finding":"VP2 (PfVP2, the type II vacuolar proton-pumping pyrophosphatase gene) was successfully disrupted by double crossover recombination in P. falciparum blood stage parasites, demonstrating that VP2 is not essential for the survival of erythrocytic stage parasites.","method":"Gene disruption by double crossover recombination using the pUF-1 transfection vector with yDHODH positive selection and yCD-UPRT negative selection","journal":"Molecular and biochemical parasitology","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean double-crossover knockout with both positive and negative selection markers; definitive loss-of-function result with clear viability phenotype","pmids":["21251930"],"is_preprint":false,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2025,"finding":"VP2 (PfVP2) localizes to the parasite's subcellular membranes and functions as a proton pump in P. falciparum, where it hydrolyzes pyrophosphate as part of the parasite's pyrophosphate homeostasis machinery alongside PfVP1.","method":"Reverse genetics and biochemical approaches (specific subcellular localization details attributed to PfVP2 described in the context of the broader study)","journal":"bioRxiv","confidence":"Low","confidence_rationale":"Tier 3 / Weak — preprint abstract describes localization to subcellular membranes and proton pump function for PfVP2 but provides no granular experimental details specifically for PfVP2; primary mechanistic focus of the paper is on PfsPPases","pmids":["40027813"],"is_preprint":true,"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"finding":"In P. berghei, elevated mRNA transcript levels of vp2 (the VP2 ortholog) were associated with piperaquine and lumefantrine resistance, suggesting VP2 may contribute to drug resistance mechanisms, possibly by modulating proton gradients in the digestive vacuole.","method":"mRNA transcript quantification in drug-resistant P. berghei lines selected in vivo","journal":"Experimental parasitology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single method (transcript level measurement); association only, no direct functional experiment on VP2 protein activity or mechanism","pmids":["25448357"],"is_preprint":false,"attribution":[{"species":"Plasmodium berghei","strain":"ANKA"}]}],"current_model":"VP2 (PF3D7_1235200) is a K⁺-independent, type II V-type H⁺-translocating inorganic pyrophosphatase localized to parasite subcellular membranes in P. falciparum that hydrolyzes pyrophosphate coupled to proton pumping, but it is dispensable for erythrocytic stage survival as demonstrated by successful double-crossover gene disruption; its ortholog in P. berghei shows elevated expression in drug-resistant lines, suggesting a possible but unconfirmed role in antimalarial drug resistance."},"narrative":{"mechanistic_narrative":"VP2 (PF3D7_1235200) is a type II, K⁺-independent V-type H⁺-translocating inorganic pyrophosphatase of Plasmodium falciparum, cloned and assigned to this biochemical class by sequence and phylogenetic analysis that distinguished it from the K⁺-dependent type I enzyme PfVP1 [PMID:11378198]. It is dispensable for the intraerythrocytic stage: clean double-crossover disruption yields viable blood-stage parasites [PMID:21251930]. Beyond its predicted role in pyrophosphate hydrolysis coupled to proton pumping, direct mechanistic characterization of the VP2 protein itself is limited in the available corpus; a preprint places it at parasite subcellular membranes acting as a proton pump within pyrophosphate homeostasis alongside PfVP1 [PMID:40027813]. In P. berghei, elevated transcript levels of the VP2 ortholog accompany piperaquine and lumefantrine resistance, an association that has not been extended to a demonstrated functional role for the protein [PMID:25448357].","teleology":[{"year":2001,"claim":"Establishing that P. falciparum encodes a second, biochemically distinct pyrophosphatase answered whether the parasite's PPi-driven proton pumping was carried by a single enzyme, defining VP2 as a type II (K⁺-independent) counterpart to the K⁺-dependent PfVP1.","evidence":"Gene cloning, sequence analysis, and phylogenetic comparison in P. falciparum","pmids":["11378198"],"confidence":"Medium","gaps":["K⁺-independence and pyrophosphatase/proton-pump activity were inferred from sequence similarity to plant AVP2, not directly assayed for VP2","no biochemical reconstitution of VP2 enzymatic activity","subcellular localization not determined at this stage"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2011,"claim":"Determining whether VP2 is required for blood-stage growth showed the gene is not essential in erythrocytic parasites, constraining its physiological importance in that stage.","evidence":"Double-crossover gene disruption with yDHODH positive and yCD-UPRT negative selection in P. falciparum blood stages","pmids":["21251930"],"confidence":"High","gaps":["does not address a role in non-erythrocytic (mosquito or liver) stages","does not reveal what function VP2 serves when present","possible functional redundancy with PfVP1 not directly tested"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":2014,"claim":"Testing whether VP2 expression tracks with antimalarial resistance revealed elevated ortholog transcript levels in resistant lines, raising but not resolving a possible role in drug resistance.","evidence":"mRNA transcript quantification in piperaquine- and lumefantrine-resistant P. berghei ANKA lines selected in vivo","pmids":["25448357"],"confidence":"Low","gaps":["association only; no functional test of VP2 protein activity in resistance","shown in P. berghei ortholog, not in P. falciparum VP2","proposed link to digestive-vacuole proton gradients not experimentally demonstrated"],"attribution":[{"species":"Plasmodium berghei","strain":"ANKA"}]},{"year":2025,"claim":"Assigning subcellular localization and proton-pump function positioned VP2 at parasite membranes within pyrophosphate homeostasis alongside PfVP1.","evidence":"Reverse genetics and biochemical approaches in P. falciparum (preprint)","pmids":["40027813"],"confidence":"Low","gaps":["preprint provides no granular experimental detail specific to VP2","the study's primary focus is on soluble pyrophosphatases, not VP2","direct measurement of VP2 proton-pumping activity not reported"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]},{"year":null,"claim":"It remains unknown what physiological role VP2 serves given its dispensability, and whether its predicted K⁺-independent pyrophosphatase/proton-pump activity is directly demonstrable and mechanistically linked to antimalarial drug resistance.","evidence":"No direct enzymatic reconstitution or functional resistance experiment on VP2 protein is present in the corpus","pmids":[],"confidence":"Low","gaps":["no direct biochemical assay of VP2 pyrophosphatase or proton-pump activity","no functional demonstration of a resistance role for VP2 itself","stage-specific and redundancy relationships with PfVP1 uncharacterized"],"attribution":[{"species":"Plasmodium falciparum","strain":""}]}],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":["PFVP1 (TYPE I K+-DEPENDENT PYROPHOSPHATASE; CO-MEMBER OF PARASITE PYROPHOSPHATE HOMEOSTASIS MACHINERY PER #2, #0)"],"other_free_text":["Dispensable for P. falciparum erythrocytic-stage survival by double-crossover knockout [#1].","Classified as type II, K+-independent V-type H+-translocating pyrophosphatase by phylogeny/sequence, distinct from K+-dependent PfVP1 [#0].","Elevated transcript of the P. berghei ANKA vp2 ortholog associates with piperaquine/lumefantrine resistance; not functionally validated for the VP2 protein [#3]."]}},"prefetch_data":{},"corpus_meta":[{"pmid":"15774027","id":"PMC_15774027","title":"The 'permeome' of the malaria parasite: an overview of the membrane transport proteins of Plasmodium falciparum.","date":"2005","source":"Genome biology","url":"https://pubmed.ncbi.nlm.nih.gov/15774027","citation_count":146,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["curated_ref"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"21251930","id":"PMC_21251930","title":"Yeast dihydroorotate dehydrogenase as a new selectable marker for Plasmodium falciparum transfection.","date":"2011","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/21251930","citation_count":88,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfVP2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"10806252","id":"PMC_10806252","title":"AVP2, a sequence-divergent, K(+)-insensitive H(+)-translocating inorganic pyrophosphatase from Arabidopsis.","date":"2000","source":"Plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/10806252","citation_count":78,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["inorganic pyrophosphatase"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"11378198","id":"PMC_11378198","title":"Two classes of plant-like vacuolar-type H(+)-pyrophosphatases in malaria parasites.","date":"2001","source":"Molecular and biochemical parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/11378198","citation_count":69,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfVP2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"24657918","id":"PMC_24657918","title":"Single nucleotide polymorphisms in Plasmodium falciparum V type H(+) pyrophosphatase gene (pfvp2) and their associations with pfcrt and pfmdr1 polymorphisms.","date":"2014","source":"Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases","url":"https://pubmed.ncbi.nlm.nih.gov/24657918","citation_count":6,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfVP2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"25448357","id":"PMC_25448357","title":"Piperaquine and Lumefantrine resistance in Plasmodium berghei ANKA associated with increased expression of Ca2+/H+ antiporter and glutathione associated enzymes.","date":"2014","source":"Experimental parasitology","url":"https://pubmed.ncbi.nlm.nih.gov/25448357","citation_count":5,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["VP2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false},{"pmid":"40027813","id":"PMC_40027813","title":"Maintenance of pyrophosphate homeostasis in multiple subcellular compartments is essential in Plasmodium falciparum.","date":"2025","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/40027813","citation_count":0,"is_preprint":false,"source_species":["Pf"],"role":"primary","match_terms":["PfVP2"],"competing_organism_flag":false,"competing_organism_match":"","competing_organism_only":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":7005,"output_tokens":1174,"usd":0.019312,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":6040,"output_tokens":2325,"usd":0.044163,"stage2_stop_reason":"end_turn"},"total_usd":0.063475,"stage1_batch_id":"msgbatch_011BPjN2BL33F8cJXD1r7V7T","stage2_batch_id":"msgbatch_01Qwg6vP7qxkpL6Gsc7tajsb","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"VP2 (PfVP2) was identified and cloned from P. falciparum and inferred to encode a type II (K⁺-independent) V-type H⁺-translocating inorganic pyrophosphatase, phylogenetically and functionally distinct from the type I (K⁺-dependent) PfVP1.\",\n      \"method\": \"Gene cloning, sequence analysis, and phylogenetic comparison\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — gene cloning and sequence/phylogenetic analysis establish identity and predicted biochemical class; functional inference (K⁺-independence) is extrapolated from sequence similarity to characterized plant AVP2, not directly assayed for PfVP2 itself\",\n      \"pmids\": [\"11378198\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"VP2 (PfVP2, the type II vacuolar proton-pumping pyrophosphatase gene) was successfully disrupted by double crossover recombination in P. falciparum blood stage parasites, demonstrating that VP2 is not essential for the survival of erythrocytic stage parasites.\",\n      \"method\": \"Gene disruption by double crossover recombination using the pUF-1 transfection vector with yDHODH positive selection and yCD-UPRT negative selection\",\n      \"journal\": \"Molecular and biochemical parasitology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean double-crossover knockout with both positive and negative selection markers; definitive loss-of-function result with clear viability phenotype\",\n      \"pmids\": [\"21251930\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"VP2 (PfVP2) localizes to the parasite's subcellular membranes and functions as a proton pump in P. falciparum, where it hydrolyzes pyrophosphate as part of the parasite's pyrophosphate homeostasis machinery alongside PfVP1.\",\n      \"method\": \"Reverse genetics and biochemical approaches (specific subcellular localization details attributed to PfVP2 described in the context of the broader study)\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — preprint abstract describes localization to subcellular membranes and proton pump function for PfVP2 but provides no granular experimental details specifically for PfVP2; primary mechanistic focus of the paper is on PfsPPases\",\n      \"pmids\": [\"40027813\"],\n      \"is_preprint\": true,\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"In P. berghei, elevated mRNA transcript levels of vp2 (the VP2 ortholog) were associated with piperaquine and lumefantrine resistance, suggesting VP2 may contribute to drug resistance mechanisms, possibly by modulating proton gradients in the digestive vacuole.\",\n      \"method\": \"mRNA transcript quantification in drug-resistant P. berghei lines selected in vivo\",\n      \"journal\": \"Experimental parasitology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single method (transcript level measurement); association only, no direct functional experiment on VP2 protein activity or mechanism\",\n      \"pmids\": [\"25448357\"],\n      \"is_preprint\": false,\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"ANKA\"}]\n    }\n  ],\n  \"current_model\": \"VP2 (PF3D7_1235200) is a K⁺-independent, type II V-type H⁺-translocating inorganic pyrophosphatase localized to parasite subcellular membranes in P. falciparum that hydrolyzes pyrophosphate coupled to proton pumping, but it is dispensable for erythrocytic stage survival as demonstrated by successful double-crossover gene disruption; its ortholog in P. berghei shows elevated expression in drug-resistant lines, suggesting a possible but unconfirmed role in antimalarial drug resistance.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"VP2 (PF3D7_1235200) is a type II, K⁺-independent V-type H⁺-translocating inorganic pyrophosphatase of Plasmodium falciparum, cloned and assigned to this biochemical class by sequence and phylogenetic analysis that distinguished it from the K⁺-dependent type I enzyme PfVP1 [#0]. It is dispensable for the intraerythrocytic stage: clean double-crossover disruption yields viable blood-stage parasites [#1]. Beyond its predicted role in pyrophosphate hydrolysis coupled to proton pumping, direct mechanistic characterization of the VP2 protein itself is limited in the available corpus; a preprint places it at parasite subcellular membranes acting as a proton pump within pyrophosphate homeostasis alongside PfVP1 [#2]. In P. berghei, elevated transcript levels of the VP2 ortholog accompany piperaquine and lumefantrine resistance, an association that has not been extended to a demonstrated functional role for the protein [#3].\"\n  ,\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Establishing that P. falciparum encodes a second, biochemically distinct pyrophosphatase answered whether the parasite's PPi-driven proton pumping was carried by a single enzyme, defining VP2 as a type II (K⁺-independent) counterpart to the K⁺-dependent PfVP1.\",\n      \"evidence\": \"Gene cloning, sequence analysis, and phylogenetic comparison in P. falciparum\",\n      \"pmids\": [\"11378198\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"K⁺-independence and pyrophosphatase/proton-pump activity were inferred from sequence similarity to plant AVP2, not directly assayed for VP2\",\n        \"no biochemical reconstitution of VP2 enzymatic activity\",\n        \"subcellular localization not determined at this stage\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2011,\n      \"claim\": \"Determining whether VP2 is required for blood-stage growth showed the gene is not essential in erythrocytic parasites, constraining its physiological importance in that stage.\",\n      \"evidence\": \"Double-crossover gene disruption with yDHODH positive and yCD-UPRT negative selection in P. falciparum blood stages\",\n      \"pmids\": [\"21251930\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"does not address a role in non-erythrocytic (mosquito or liver) stages\",\n        \"does not reveal what function VP2 serves when present\",\n        \"possible functional redundancy with PfVP1 not directly tested\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Testing whether VP2 expression tracks with antimalarial resistance revealed elevated ortholog transcript levels in resistant lines, raising but not resolving a possible role in drug resistance.\",\n      \"evidence\": \"mRNA transcript quantification in piperaquine- and lumefantrine-resistant P. berghei ANKA lines selected in vivo\",\n      \"pmids\": [\"25448357\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"association only; no functional test of VP2 protein activity in resistance\",\n        \"shown in P. berghei ortholog, not in P. falciparum VP2\",\n        \"proposed link to digestive-vacuole proton gradients not experimentally demonstrated\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium berghei\", \"strain\": \"ANKA\"}]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Assigning subcellular localization and proton-pump function positioned VP2 at parasite membranes within pyrophosphate homeostasis alongside PfVP1.\",\n      \"evidence\": \"Reverse genetics and biochemical approaches in P. falciparum (preprint)\",\n      \"pmids\": [\"40027813\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"preprint provides no granular experimental detail specific to VP2\",\n        \"the study's primary focus is on soluble pyrophosphatases, not VP2\",\n        \"direct measurement of VP2 proton-pumping activity not reported\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown what physiological role VP2 serves given its dispensability, and whether its predicted K⁺-independent pyrophosphatase/proton-pump activity is directly demonstrable and mechanistically linked to antimalarial drug resistance.\",\n      \"evidence\": \"No direct enzymatic reconstitution or functional resistance experiment on VP2 protein is present in the corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"no direct biochemical assay of VP2 pyrophosphatase or proton-pump activity\",\n        \"no functional demonstration of a resistance role for VP2 itself\",\n        \"stage-specific and redundancy relationships with PfVP1 uncharacterized\"\n      ],\n      \"attribution\": [{\"species\": \"Plasmodium falciparum\", \"strain\": \"\"}]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0009678\", \"supporting_discovery_ids\": [0, 2]},\n      {\"term_id\": \"GO:0004427\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"GO:0015992\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0016020\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"GO:1902600\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\n      \"PfVP1 (type I K+-dependent pyrophosphatase; co-member of parasite pyrophosphate homeostasis machinery per #2, #0)\"\n    ],\n    \"other_free_text\": [\n      \"Dispensable for P. falciparum erythrocytic-stage survival by double-crossover knockout [#1].\",\n      \"Classified as type II, K+-independent V-type H+-translocating pyrophosphatase by phylogeny/sequence, distinct from K+-dependent PfVP1 [#0].\",\n      \"Elevated transcript of the P. berghei ANKA vp2 ortholog associates with piperaquine/lumefantrine resistance; not functionally validated for the VP2 protein [#3].\"\n    ]\n  }\n}","audit_flag":null,"strains":[{"strain":"Pf3D7","gene_id":"PF3D7_1235200","name":null,"product":"V-type K+-independent H+-translocating inorganic pyrophosphatase","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PbANKA","gene_id":"PBANKA_1449800","name":null,"product":"inorganic pyrophosphatase, putative","uniprot_acc":null,"chromosome":null,"start_pos":null},{"strain":"PkH","gene_id":"PKNH_1454900","name":null,"product":"vacuolar-type H+-translocating inorganic pyrophosphatase, putative","uniprot_acc":null,"chromosome":null,"start_pos":null}],"gene_symbol":"VP2","evaluation":null}