{"gene":"ATP6V1F","run_date":"2026-06-09T22:02:44","timeline":{"discoveries":[{"year":1994,"finding":"VMA7 (yeast ortholog of ATP6V1F) encodes a novel 14-kDa subunit of the vacuolar H(+)-ATPase V1 catalytic sector. In vma7Δ null mutants, vacuolar membranes contained no V-ATPase activity; V0 subunit levels were greatly reduced while V1 subunits remained normal but failed to associate with the vacuolar membrane. Vma7p was easily stripped from vacuolar membranes and co-fractionated only with the fully assembled V-ATPase, not with a separate V0 subcomplex, indicating a critical role in stabilizing V0 and bridging V1 and V0 complexes.","method":"Null mutant generation, vacuolar membrane isolation, V-ATPase activity assay, Western blot fractionation, density gradient fractionation","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro enzymatic assay, subcellular fractionation, null mutant with defined biochemical phenotype, replicated across two independent 1994 papers","pmids":["7929308"],"is_preprint":false},{"year":1994,"finding":"VMA7 (yeast ortholog of ATP6V1F) encodes subunit F of the V-ATPase catalytic sector. The δvma7::URA3 null mutant cannot grow at pH 7.5, fails to accumulate quinacrine in vacuoles, and V1 catalytic subunits are not assembled onto the vacuolar membrane in its absence. A monoclonal antibody against an epitope-tagged Vma7p markedly inhibited proton uptake activity of isolated vacuoles. Cold inactivation experiments confirmed Vma7p is a genuine subunit of the catalytic sector.","method":"Null mutant characterization, quinacrine accumulation assay, antibody inhibition of proton uptake, cold inactivation, epitope tagging","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple orthogonal in vitro and genetic methods, two independent labs reporting consistent findings in the same year","pmids":["7929071"],"is_preprint":false},{"year":2005,"finding":"In Candida albicans, Vma7p (ortholog of ATP6V1F) is required for vacuole acidification; vma7 null mutants show reduced vacuolar acidification, defective growth at alkaline pH, defects in degradation of intravacuolar endosomal structures, sensitivity to metal ions, and are avirulent in a mouse model of systemic candidiasis. Vma7p interacts genetically with the phosphatidylinositol 3-kinase Vps34p, as vma7 and vps34 null mutants showed similar phenotypes.","method":"Null mutant generation, vacuole acidification assay, pH growth assay, mouse virulence model, genetic epistasis with Vps34p","journal":"Microbiology (Reading, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with defined cellular and in vivo phenotypes, genetic epistasis, single lab","pmids":["15870472"],"is_preprint":false},{"year":2008,"finding":"In zebrafish, atp6v1f (ortholog of mammalian ATP6V1F) is required for v-ATPase complex function in the eye. Loss-of-function mutants are oculocutaneous albinos with defects in melanosome formation/survival, malformed RPE with compromised melanosome distribution, microphthalmia, impaired retinoblast cell cycle exit, sustained ciliary marginal zone proliferation defects, elevated retinal/brain apoptosis, abnormal photoreceptor outer segment morphology, and accumulation of undigested outer segment material in RPE vacuoles. In situ hybridization localized atp6v1f transcripts in the RPE.","method":"Zebrafish mutant characterization, histology, BrdU incorporation assay, ultrastructural analysis, in situ hybridization","journal":"Investigative ophthalmology & visual science","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function zebrafish mutant with multiple defined cellular phenotypes and localization, single study","pmids":["18836173"],"is_preprint":false},{"year":2024,"finding":"CANX regulates expression of ATP6V1F (V1 domain) and ATP6V0B (V0 domain) in hepatocellular carcinoma cells, affecting mitochondrial function and energy metabolism. Dihydroartemisinin (DHA) decreased expression of CANX, ATP6V0B, and ATP6V1F, and inhibited ATP production, mitochondrial membrane potential, and NAD+/NADH ratio, promoting apoptosis and inhibiting metastasis.","method":"CANX overexpression and siRNA knockdown in HCC cells, Western blotting, ATP production assay, mitochondrial membrane potential (JC-1), NAD+/NADH ratio measurement, ROS assay","journal":"Oncology letters","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, indirect regulatory relationship, no direct mechanistic assay of ATP6V1F itself","pmids":["39161338"],"is_preprint":false}],"current_model":"ATP6V1F (subunit F) is an essential component of the V1 catalytic sector of the vacuolar H(+)-ATPase complex; it is required for assembly of V1 subunits onto the vacuolar membrane, stabilization of the V0 complex, and bridging of V1 and V0 subcomplexes to form a functional proton-pumping V-ATPase, as established by null mutant biochemistry and in vitro enzymatic assays in yeast orthologs and confirmed by loss-of-function studies in zebrafish and Candida albicans."},"narrative":{"mechanistic_narrative":"ATP6V1F is an essential subunit of the V1 catalytic sector of the vacuolar H(+)-ATPase, the multisubunit proton pump that acidifies intracellular compartments [PMID:7929308, PMID:7929071]. In yeast, the ortholog Vma7p is required to assemble the V1 catalytic subunits onto the vacuolar membrane and to stabilize the membrane-embedded V0 sector; in its absence vacuolar membranes have no V-ATPase activity, V0 levels collapse, and the V1 subunits remain present but fail to attach to the membrane, identifying ATP6V1F as a bridge that couples V1 to V0 to form a functional pump [PMID:7929308]. Cold-inactivation and antibody-inhibition experiments confirm it is a genuine subunit of the catalytic sector whose loss abolishes proton uptake and prevents vacuolar acidification and growth at alkaline pH [PMID:7929071]. This acidification function is conserved: loss in Candida albicans impairs vacuole acidification, intravacuolar degradation, and virulence, and interacts genetically with the PI3-kinase Vps34p [PMID:15870472], while loss in zebrafish disrupts melanosome formation, RPE function, retinal cell-cycle exit, and clearance of photoreceptor outer-segment material in lysosome-like RPE vacuoles [PMID:18836173]. Beyond its role as a V-ATPase assembly and bridging subunit, no additional biochemical activity for ATP6V1F has been characterized in the available corpus.","teleology":[{"year":1994,"claim":"Established that ATP6V1F's ortholog is a bona fide V1 catalytic-sector subunit whose primary role is to assemble V1 onto the membrane and bridge/stabilize the V0 sector, defining why the protein is essential for proton pumping.","evidence":"vma7Δ yeast null mutant with vacuolar membrane isolation, V-ATPase activity assay, and density-gradient/Western fractionation","pmids":["7929308"],"confidence":"High","gaps":["Atomic-resolution structure of how subunit F bridges V1 and V0 not resolved","Mechanism by which V0 is destabilized in its absence not defined at the molecular level"]},{"year":1994,"claim":"Confirmed by orthogonal genetic and biochemical methods that the protein is a genuine catalytic-sector subunit required for vacuolar acidification, ruling out a peripheral or regulatory-only role.","evidence":"δvma7::URA3 null mutant characterized by quinacrine accumulation, antibody inhibition of proton uptake, cold inactivation, and epitope tagging in yeast","pmids":["7929071"],"confidence":"High","gaps":["Does not establish whether the human ortholog behaves identically","Stoichiometry within the V1 sector not quantified"]},{"year":2005,"claim":"Extended the acidification function to a pathogen and linked it to physiology, showing the subunit is required for fungal vacuole acidification, stress resistance, and virulence and acts in a pathway shared with Vps34p.","evidence":"Candida albicans vma7 null mutant with acidification, pH-growth, metal-sensitivity assays, mouse systemic candidiasis model, and genetic epistasis with Vps34p","pmids":["15870472"],"confidence":"Medium","gaps":["Genetic interaction with Vps34p is epistatic, not biochemical/physical","Single lab; not confirmed in mammalian system"]},{"year":2008,"claim":"Demonstrated that the conserved acidification function is required for vertebrate organelle biology, tying V-ATPase loss to melanosome formation, RPE maintenance, and retinal development.","evidence":"Zebrafish atp6v1f loss-of-function mutant analyzed by histology, BrdU labeling, ultrastructure, and in situ hybridization","pmids":["18836173"],"confidence":"Medium","gaps":["Phenotypes are downstream consequences of failed acidification rather than direct molecular readouts","No human disease link established","Single study"]},{"year":2024,"claim":"Placed ATP6V1F within a cancer regulatory context, indicating its expression can be controlled by CANX and modulated pharmacologically to affect mitochondrial energetics.","evidence":"CANX overexpression/siRNA in hepatocellular carcinoma cells with Western blotting, ATP/mitochondrial membrane potential/NAD+:NADH assays under dihydroartemisinin treatment","pmids":["39161338"],"confidence":"Low","gaps":["Indirect regulatory correlation, not a direct mechanistic assay of ATP6V1F","No demonstration that ATP6V1F mediates the mitochondrial phenotype","Single lab, not independently confirmed"]},{"year":null,"claim":"How ATP6V1F is assembled and regulated in mammalian cells, its structural mode of bridging V1 to V0, and any human disease association remain uncharacterized in this corpus.","evidence":"","pmids":[],"confidence":"Low","gaps":["No mammalian biochemical reconstitution","No structural model of the F subunit in human V-ATPase","No causative human Mendelian disease evidence"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[0,1]}],"localization":[{"term_id":"GO:0005773","term_label":"vacuole","supporting_discovery_ids":[0,1,2]}],"pathway":[{"term_id":"R-HSA-382551","term_label":"Transport of small molecules","supporting_discovery_ids":[0,1]}],"complexes":["vacuolar H(+)-ATPase (V-ATPase) V1 sector"],"partners":[],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q16864","full_name":"V-type proton ATPase subunit F","aliases":["V-ATPase 14 kDa subunit","Vacuolar proton pump subunit F"],"length_aa":119,"mass_kda":13.4,"function":"Subunit of the V1 complex of vacuolar(H+)-ATPase (V-ATPase), a multisubunit enzyme composed of a peripheral complex (V1) that hydrolyzes ATP and a membrane integral complex (V0) that translocates protons (PubMed:33065002). V-ATPase is responsible for acidifying and maintaining the pH of intracellular compartments and in some cell types, is targeted to the plasma membrane, where it is responsible for acidifying the extracellular environment (By similarity)","subcellular_location":"Cytoplasmic vesicle, secretory vesicle, synaptic vesicle membrane; Cytoplasmic vesicle, clathrin-coated vesicle membrane","url":"https://www.uniprot.org/uniprotkb/Q16864/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/ATP6V1F","classification":"Common Essential","n_dependent_lines":1193,"n_total_lines":1208,"dependency_fraction":0.9875827814569537},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000128524","cell_line_id":"CID001650","localizations":[{"compartment":"cytoplasmic","grade":3},{"compartment":"nucleoplasm","grade":3},{"compartment":"vesicles","grade":2}],"interactors":[{"gene":"ATP6V0A2","stoichiometry":10.0},{"gene":"ATP6V1H","stoichiometry":10.0},{"gene":"C9ORF16","stoichiometry":10.0},{"gene":"ATP6V1G1","stoichiometry":10.0},{"gene":"ATP6V1A","stoichiometry":4.0},{"gene":"ATP6V1E1","stoichiometry":4.0},{"gene":"ATP6V1B2","stoichiometry":0.2},{"gene":"ATP6AP1","stoichiometry":0.2},{"gene":"VMA21","stoichiometry":0.2},{"gene":"DMXL1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001650","total_profiled":1310},"omim":[{"mim_id":"607160","title":"ATPase, H+ TRANSPORTING, LYSOSOMAL, 14-KD, V1 SUBUNIT F; ATP6V1F","url":"https://www.omim.org/entry/607160"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"","locations":[],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ATP6V1F"},"hgnc":{"alias_symbol":["ATP6S14","VATF","Vma7"],"prev_symbol":[]},"alphafold":{"accession":"Q16864","domains":[{"cath_id":"3.40.50.10580","chopping":"1-81","consensus_level":"medium","plddt":91.8225,"start":1,"end":81}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q16864","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q16864-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q16864-F1-predicted_aligned_error_v6.png","plddt_mean":86.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ATP6V1F","jax_strain_url":"https://www.jax.org/strain/search?query=ATP6V1F"},"sequence":{"accession":"Q16864","fasta_url":"https://rest.uniprot.org/uniprotkb/Q16864.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q16864/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q16864"}},"corpus_meta":[{"pmid":"14654946","id":"PMC_14654946","title":"Up-regulated expression of the MAT-8 gene in prostate cancer and its siRNA-mediated inhibition of expression induces a decrease in proliferation of human prostate carcinoma cells.","date":"2004","source":"International journal of oncology","url":"https://pubmed.ncbi.nlm.nih.gov/14654946","citation_count":82,"is_preprint":false},{"pmid":"18836173","id":"PMC_18836173","title":"The vacuolar-ATPase complex regulates retinoblast proliferation and survival, photoreceptor morphogenesis, and pigmentation in the zebrafish eye.","date":"2008","source":"Investigative ophthalmology & visual science","url":"https://pubmed.ncbi.nlm.nih.gov/18836173","citation_count":78,"is_preprint":false},{"pmid":"26740819","id":"PMC_26740819","title":"Polygenic analysis and targeted improvement of the complex trait of high acetic acid tolerance in the yeast Saccharomyces cerevisiae.","date":"2016","source":"Biotechnology for biofuels","url":"https://pubmed.ncbi.nlm.nih.gov/26740819","citation_count":71,"is_preprint":false},{"pmid":"7929308","id":"PMC_7929308","title":"VMA7 encodes a novel 14-kDa subunit of the Saccharomyces cerevisiae vacuolar H(+)-ATPase complex.","date":"1994","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/7929308","citation_count":62,"is_preprint":false},{"pmid":"7929071","id":"PMC_7929071","title":"The Saccharomyces cerevisiae VMA7 gene encodes a 14-kDa subunit of the vacuolar H(+)-ATPase catalytic sector.","date":"1994","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/7929071","citation_count":52,"is_preprint":false},{"pmid":"15870472","id":"PMC_15870472","title":"The putative vacuolar ATPase subunit Vma7p of Candida albicans is involved in vacuole acidification, hyphal development and virulence.","date":"2005","source":"Microbiology (Reading, England)","url":"https://pubmed.ncbi.nlm.nih.gov/15870472","citation_count":51,"is_preprint":false},{"pmid":"32766165","id":"PMC_32766165","title":"Identification of Antimicrobial Resistance Determinants in Aeromonas veronii Strain MS-17-88 Recovered From Channel Catfish (Ictalurus punctatus).","date":"2020","source":"Frontiers in cellular and infection microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/32766165","citation_count":33,"is_preprint":false},{"pmid":"35905627","id":"PMC_35905627","title":"Triphenyltin exposure induced abnormal morphological colouration in adult male guppies (Poecilia reticulata).","date":"2022","source":"Ecotoxicology and environmental safety","url":"https://pubmed.ncbi.nlm.nih.gov/35905627","citation_count":13,"is_preprint":false},{"pmid":"38429903","id":"PMC_38429903","title":"Identification of key regulatory molecules in the early development stage of Alzheimer's disease.","date":"2024","source":"Journal of cellular and molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/38429903","citation_count":11,"is_preprint":false},{"pmid":"32090358","id":"PMC_32090358","title":"RNA-Seq Analysis of Genetic and Transcriptome Network Effects of Dual-Trait Selection for Ethanol Preference and Withdrawal Using SOT and NOT Genetic Models.","date":"2020","source":"Alcoholism, clinical and experimental research","url":"https://pubmed.ncbi.nlm.nih.gov/32090358","citation_count":11,"is_preprint":false},{"pmid":"40205686","id":"PMC_40205686","title":"Neutrophil-derived serine proteases induce FOXA2-mediated autophagy dysfunction and exacerbate colitis-associated carcinogenesis via protease activated receptor 2.","date":"2025","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/40205686","citation_count":7,"is_preprint":false},{"pmid":"38266420","id":"PMC_38266420","title":"Study on the mechanism of arsenic-induced renal injury based on SWATH proteomics technology.","date":"2024","source":"Journal of trace elements in medicine and biology : organ of the Society for Minerals and Trace Elements (GMS)","url":"https://pubmed.ncbi.nlm.nih.gov/38266420","citation_count":7,"is_preprint":false},{"pmid":"38201093","id":"PMC_38201093","title":"Hunted Wild Boars in Sardinia: Prevalence, Antimicrobial Resistance and Genomic Analysis of Salmonella and Yersinia enterocolitica.","date":"2023","source":"Foods (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/38201093","citation_count":5,"is_preprint":false},{"pmid":"39161338","id":"PMC_39161338","title":"Dihydroartemisinin inhibits ATP6 activity, reduces energy metabolism of hepatocellular carcinoma cells, promotes apoptosis and inhibits metastasis via CANX.","date":"2024","source":"Oncology letters","url":"https://pubmed.ncbi.nlm.nih.gov/39161338","citation_count":4,"is_preprint":false},{"pmid":"40382034","id":"PMC_40382034","title":"Phylogenetic relationship, genomic heterogeneity, and population structure of Yersinia enterocolitica biotype 1A isolated from pork and poultry meat.","date":"2025","source":"Food research international (Ottawa, Ont.)","url":"https://pubmed.ncbi.nlm.nih.gov/40382034","citation_count":4,"is_preprint":false},{"pmid":"22212708","id":"PMC_22212708","title":"Cloning and overexpression of an important functional gene ATP6V1F encoding a component of vacuolar ATPase from the Giant Panda (Ailuropoda melanoleuca).","date":"2012","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/22212708","citation_count":2,"is_preprint":false},{"pmid":"39798383","id":"PMC_39798383","title":"Genomic characteristics and virulence of common but overlooked Yersinia intermedia, Y. frederiksenii, and Y. kristensenii in food.","date":"2025","source":"International journal of food microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/39798383","citation_count":1,"is_preprint":false},{"pmid":"42129839","id":"PMC_42129839","title":"Plasma extracellular vesicle proteins biomarker for cerebral small vessel disease related cognitive impairment.","date":"2026","source":"Alzheimer's research & therapy","url":"https://pubmed.ncbi.nlm.nih.gov/42129839","citation_count":0,"is_preprint":false},{"pmid":"41580526","id":"PMC_41580526","title":"A single-cell derived spheroid approach to dissect intratumoural heterogeneity in colorectal cancer: cell lines show changes in proteomes and therapeutic response to 5-FU.","date":"2026","source":"Journal of cancer research and clinical oncology","url":"https://pubmed.ncbi.nlm.nih.gov/41580526","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":13848,"output_tokens":1629,"usd":0.032989,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8391,"output_tokens":2173,"usd":0.04814,"stage2_stop_reason":"end_turn"},"total_usd":0.081129,"stage1_batch_id":"msgbatch_0179Z2pxRYBsXi2xADneafRw","stage2_batch_id":"msgbatch_01LaY9ZaVdgjWArcZo9eqQE5","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 1994,\n      \"finding\": \"VMA7 (yeast ortholog of ATP6V1F) encodes a novel 14-kDa subunit of the vacuolar H(+)-ATPase V1 catalytic sector. In vma7Δ null mutants, vacuolar membranes contained no V-ATPase activity; V0 subunit levels were greatly reduced while V1 subunits remained normal but failed to associate with the vacuolar membrane. Vma7p was easily stripped from vacuolar membranes and co-fractionated only with the fully assembled V-ATPase, not with a separate V0 subcomplex, indicating a critical role in stabilizing V0 and bridging V1 and V0 complexes.\",\n      \"method\": \"Null mutant generation, vacuolar membrane isolation, V-ATPase activity assay, Western blot fractionation, density gradient fractionation\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro enzymatic assay, subcellular fractionation, null mutant with defined biochemical phenotype, replicated across two independent 1994 papers\",\n      \"pmids\": [\"7929308\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"VMA7 (yeast ortholog of ATP6V1F) encodes subunit F of the V-ATPase catalytic sector. The δvma7::URA3 null mutant cannot grow at pH 7.5, fails to accumulate quinacrine in vacuoles, and V1 catalytic subunits are not assembled onto the vacuolar membrane in its absence. A monoclonal antibody against an epitope-tagged Vma7p markedly inhibited proton uptake activity of isolated vacuoles. Cold inactivation experiments confirmed Vma7p is a genuine subunit of the catalytic sector.\",\n      \"method\": \"Null mutant characterization, quinacrine accumulation assay, antibody inhibition of proton uptake, cold inactivation, epitope tagging\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple orthogonal in vitro and genetic methods, two independent labs reporting consistent findings in the same year\",\n      \"pmids\": [\"7929071\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"In Candida albicans, Vma7p (ortholog of ATP6V1F) is required for vacuole acidification; vma7 null mutants show reduced vacuolar acidification, defective growth at alkaline pH, defects in degradation of intravacuolar endosomal structures, sensitivity to metal ions, and are avirulent in a mouse model of systemic candidiasis. Vma7p interacts genetically with the phosphatidylinositol 3-kinase Vps34p, as vma7 and vps34 null mutants showed similar phenotypes.\",\n      \"method\": \"Null mutant generation, vacuole acidification assay, pH growth assay, mouse virulence model, genetic epistasis with Vps34p\",\n      \"journal\": \"Microbiology (Reading, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined cellular and in vivo phenotypes, genetic epistasis, single lab\",\n      \"pmids\": [\"15870472\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"In zebrafish, atp6v1f (ortholog of mammalian ATP6V1F) is required for v-ATPase complex function in the eye. Loss-of-function mutants are oculocutaneous albinos with defects in melanosome formation/survival, malformed RPE with compromised melanosome distribution, microphthalmia, impaired retinoblast cell cycle exit, sustained ciliary marginal zone proliferation defects, elevated retinal/brain apoptosis, abnormal photoreceptor outer segment morphology, and accumulation of undigested outer segment material in RPE vacuoles. In situ hybridization localized atp6v1f transcripts in the RPE.\",\n      \"method\": \"Zebrafish mutant characterization, histology, BrdU incorporation assay, ultrastructural analysis, in situ hybridization\",\n      \"journal\": \"Investigative ophthalmology & visual science\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function zebrafish mutant with multiple defined cellular phenotypes and localization, single study\",\n      \"pmids\": [\"18836173\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CANX regulates expression of ATP6V1F (V1 domain) and ATP6V0B (V0 domain) in hepatocellular carcinoma cells, affecting mitochondrial function and energy metabolism. Dihydroartemisinin (DHA) decreased expression of CANX, ATP6V0B, and ATP6V1F, and inhibited ATP production, mitochondrial membrane potential, and NAD+/NADH ratio, promoting apoptosis and inhibiting metastasis.\",\n      \"method\": \"CANX overexpression and siRNA knockdown in HCC cells, Western blotting, ATP production assay, mitochondrial membrane potential (JC-1), NAD+/NADH ratio measurement, ROS assay\",\n      \"journal\": \"Oncology letters\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, indirect regulatory relationship, no direct mechanistic assay of ATP6V1F itself\",\n      \"pmids\": [\"39161338\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ATP6V1F (subunit F) is an essential component of the V1 catalytic sector of the vacuolar H(+)-ATPase complex; it is required for assembly of V1 subunits onto the vacuolar membrane, stabilization of the V0 complex, and bridging of V1 and V0 subcomplexes to form a functional proton-pumping V-ATPase, as established by null mutant biochemistry and in vitro enzymatic assays in yeast orthologs and confirmed by loss-of-function studies in zebrafish and Candida albicans.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ATP6V1F is an essential subunit of the V1 catalytic sector of the vacuolar H(+)-ATPase, the multisubunit proton pump that acidifies intracellular compartments [#0, #1]. In yeast, the ortholog Vma7p is required to assemble the V1 catalytic subunits onto the vacuolar membrane and to stabilize the membrane-embedded V0 sector; in its absence vacuolar membranes have no V-ATPase activity, V0 levels collapse, and the V1 subunits remain present but fail to attach to the membrane, identifying ATP6V1F as a bridge that couples V1 to V0 to form a functional pump [#0]. Cold-inactivation and antibody-inhibition experiments confirm it is a genuine subunit of the catalytic sector whose loss abolishes proton uptake and prevents vacuolar acidification and growth at alkaline pH [#1]. This acidification function is conserved: loss in Candida albicans impairs vacuole acidification, intravacuolar degradation, and virulence, and interacts genetically with the PI3-kinase Vps34p [#2], while loss in zebrafish disrupts melanosome formation, RPE function, retinal cell-cycle exit, and clearance of photoreceptor outer-segment material in lysosome-like RPE vacuoles [#3]. Beyond its role as a V-ATPase assembly and bridging subunit, no additional biochemical activity for ATP6V1F has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 1994,\n      \"claim\": \"Established that ATP6V1F's ortholog is a bona fide V1 catalytic-sector subunit whose primary role is to assemble V1 onto the membrane and bridge/stabilize the V0 sector, defining why the protein is essential for proton pumping.\",\n      \"evidence\": \"vma7\\u0394 yeast null mutant with vacuolar membrane isolation, V-ATPase activity assay, and density-gradient/Western fractionation\",\n      \"pmids\": [\"7929308\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic-resolution structure of how subunit F bridges V1 and V0 not resolved\", \"Mechanism by which V0 is destabilized in its absence not defined at the molecular level\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Confirmed by orthogonal genetic and biochemical methods that the protein is a genuine catalytic-sector subunit required for vacuolar acidification, ruling out a peripheral or regulatory-only role.\",\n      \"evidence\": \"\\u03b4vma7::URA3 null mutant characterized by quinacrine accumulation, antibody inhibition of proton uptake, cold inactivation, and epitope tagging in yeast\",\n      \"pmids\": [\"7929071\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not establish whether the human ortholog behaves identically\", \"Stoichiometry within the V1 sector not quantified\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Extended the acidification function to a pathogen and linked it to physiology, showing the subunit is required for fungal vacuole acidification, stress resistance, and virulence and acts in a pathway shared with Vps34p.\",\n      \"evidence\": \"Candida albicans vma7 null mutant with acidification, pH-growth, metal-sensitivity assays, mouse systemic candidiasis model, and genetic epistasis with Vps34p\",\n      \"pmids\": [\"15870472\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Genetic interaction with Vps34p is epistatic, not biochemical/physical\", \"Single lab; not confirmed in mammalian system\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Demonstrated that the conserved acidification function is required for vertebrate organelle biology, tying V-ATPase loss to melanosome formation, RPE maintenance, and retinal development.\",\n      \"evidence\": \"Zebrafish atp6v1f loss-of-function mutant analyzed by histology, BrdU labeling, ultrastructure, and in situ hybridization\",\n      \"pmids\": [\"18836173\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Phenotypes are downstream consequences of failed acidification rather than direct molecular readouts\", \"No human disease link established\", \"Single study\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placed ATP6V1F within a cancer regulatory context, indicating its expression can be controlled by CANX and modulated pharmacologically to affect mitochondrial energetics.\",\n      \"evidence\": \"CANX overexpression/siRNA in hepatocellular carcinoma cells with Western blotting, ATP/mitochondrial membrane potential/NAD+:NADH assays under dihydroartemisinin treatment\",\n      \"pmids\": [\"39161338\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Indirect regulatory correlation, not a direct mechanistic assay of ATP6V1F\", \"No demonstration that ATP6V1F mediates the mitochondrial phenotype\", \"Single lab, not independently confirmed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How ATP6V1F is assembled and regulated in mammalian cells, its structural mode of bridging V1 to V0, and any human disease association remain uncharacterized in this corpus.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No mammalian biochemical reconstitution\", \"No structural model of the F subunit in human V-ATPase\", \"No causative human Mendelian disease evidence\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005773\", \"supporting_discovery_ids\": [0, 1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-382551\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [\"vacuolar H(+)-ATPase (V-ATPase) V1 sector\"],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":4,"faith_pct":100.0}}