{"gene":"PRELID1","run_date":"2026-04-28T19:45:45","timeline":{"discoveries":[{"year":2013,"finding":"TRIAP1/PRELI (PRELID1) complexes localized in the mitochondrial intermembrane space (IMS) exert lipid transfer activity in vitro, supplying phosphatidic acid (PA) to the inner membrane for cardiolipin (CL) synthesis. Loss of TRIAP1 or PRELI impairs CL accumulation, facilitates cytochrome c release, and renders cells vulnerable to apoptosis; survival is restored by exogenous phosphatidylglycerol.","method":"In vitro lipid transfer assay, genetic loss-of-function (siRNA knockdown), phospholipid rescue experiment, cytochrome c release assay, fractionation/localization","journal":"Cell metabolism","confidence":"High","confidence_rationale":"Tier 1 — in vitro lipid transfer reconstitution plus multiple orthogonal genetic and biochemical validations; replicated context of yeast orthologs","pmids":["23931759"],"is_preprint":false},{"year":2010,"finding":"Mdm35 (TRIAP1 ortholog), a twin Cx9C protein, is identified as a novel interaction partner of the PRELID1 ortholog Ups1 in yeast IMS; binding to Mdm35 ensures import of Ups1 and protects it against proteolytic degradation by Yme1 (i-AAA protease) and Atp23 metallopeptidase, thereby regulating cardiolipin and phosphatidylethanolamine levels in mitochondrial membranes.","method":"Co-immunoprecipitation, protease activity assays, genetic deletion of Yme1/Atp23, protein stability/turnover assays in yeast","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP, protease mutant epistasis, and protein turnover assays; conserved in higher eukaryotes per the authors","pmids":["20657548"],"is_preprint":false},{"year":2004,"finding":"PRELI (PRELID1) is localized to mitochondria; a mitochondrial targeting signal is identified at its N-terminus using GFP-fusion proteins and subcellular fractionation.","method":"GFP-fusion live imaging, subcellular fractionation, mitochondrial targeting sequence analysis","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 2 — direct localization by GFP fusion and fractionation in mammalian/mouse system; single lab","pmids":["14640972"],"is_preprint":false},{"year":2010,"finding":"PRELI (PRELID1) associates with dynamin-like GTPase OPA1, contributes to maintenance of mitochondrial morphology, upholds mitochondrial membrane potential (ΔΨm), and enhances respiratory chain function (complex I/NADH dehydrogenase and ATP synthase expression, oxygen consumption, reduced ROS). The LEA motif of PRELI is essential for these cytoprotective functions, as dominant-negative LEA-deficient PRELI mutant and PRELI knockdown render cells vulnerable to apoptosis.","method":"Co-immunoprecipitation (PRELI–OPA1 association), dominant-negative overexpression of PRELI/LEA(-) mutant, siRNA knockdown, mitochondrial membrane potential assay, oxygen consumption measurement, ROS measurement, apoptosis assays","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2/3 — Co-IP plus multiple functional readouts in one lab; single-lab study with multiple orthogonal methods","pmids":["21364629"],"is_preprint":false},{"year":2008,"finding":"PRELI (PRELID1) induces oxidative stress and a mitochondrial apoptosis pathway in human primary T helper cells, inhibits Th2-cell development, and down-regulates STAT6 through a mechanism involving calpain (an oxidative stress-induced cysteine protease).","method":"Overexpression and knockdown in primary human Th cells, STAT6 protein measurement, calpain inhibitor experiments, flow cytometry for apoptosis and Th subset markers","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 2/3 — loss-of-function and gain-of-function with defined molecular pathway (calpain-STAT6); single lab, multiple readouts","pmids":["18945965"],"is_preprint":false},{"year":2009,"finding":"Drosophila Preli-like (ortholog of PRELID1) is required for mitochondrial structural integrity, activity of respiratory chain complex IV, and cellular ATP levels in neurons; loss of Prel leads to mitochondrial fragmentation, sparse mitochondrial distribution in dendrites/axons, and dendritic arbor simplification. Epistasis with the Bax-like protein Drob-1 and its antagonist Buffy places Prel upstream of Bcl-2 family-mediated apoptosis in this context.","method":"Genetic loss-of-function in Drosophila neurons (in vivo), respiratory chain complex IV activity assay, ATP measurement, live imaging of mitochondria, genetic epistasis (Drob-1 overexpression, Buffy rescue of prel mutant)","journal":"Development (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 2 — in vivo genetic loss-of-function with enzymatic assay, ATP measurement, live imaging, and epistasis; ortholog of PRELID1 in Drosophila","pmids":["19855018"],"is_preprint":false},{"year":2017,"finding":"PRELID1 regulates mitochondrial reactive oxygen species (ROS) production in a cell-type-specific manner; an alternative polyadenylation (APA) event in PRELID1 mRNA enhances its steady-state level and translational efficiency, providing a posttranscriptional mechanism controlling PRELID1-dependent stress response.","method":"PAS-seq (polyadenylation site sequencing), PRELID1 modulation by overexpression/knockdown, mitochondrial ROS measurement","journal":"Molecular cancer research : MCR","confidence":"Medium","confidence_rationale":"Tier 2/3 — direct measurement of ROS upon PRELID1 modulation with identification of APA regulatory mechanism; single lab","pmids":["28912168"],"is_preprint":false},{"year":2025,"finding":"PRELID1 (Ups1) exhibits a strong preference for binding positively curved membrane regions; phosphatidic acid extraction is energetically favored at these domains, and lipid extraction is the rate-limiting step in the PA transfer cycle. Membrane binding by Ups1/PRELID1 is modulated by pH, lipid composition, and membrane morphology.","method":"In vitro lipid transfer assay with defined curvature membranes, coarse-grained MD simulations, giant unilamellar vesicle binding assay","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 — in vitro reconstitution with curvature-defined membranes plus computational modeling; preprint, not yet peer-reviewed","pmids":["bio_10.1101_2025.04.03.647039"],"is_preprint":true},{"year":2025,"finding":"Depleting PRELID1 (intramitochondrial lipid transfer protein) prevents apoptosis caused by BLTP1 deficiency, establishing PRELID1 as a required effector in the pathway by which excess PA/PG/CL accumulation leads to mitochondrial ROS elevation and cell death. This places PRELID1 downstream of BLTP1-mediated phospholipid efflux.","method":"PRELID1 siRNA knockdown epistasis in BLTP1-deficient cells; mitochondrial ROS, bioenergetics, and apoptosis assays","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 — epistasis experiment with defined phenotypic readout; preprint, single lab","pmids":["bio_10.1101_2025.09.30.679455"],"is_preprint":true}],"current_model":"PRELID1 (PRELI) is a mitochondrial intermembrane space lipid transfer protein that, in complex with TRIAP1 (Mdm35 in yeast), transfers phosphatidic acid (PA) from the outer to the inner mitochondrial membrane to support cardiolipin synthesis; this activity is regulated by membrane curvature and proteolytic turnover, and is essential for maintaining cardiolipin levels, mitochondrial integrity, and cell survival against apoptosis."},"narrative":{"teleology":[{"year":2004,"claim":"Establishing that PRELID1 is a mitochondrial protein resolved the subcellular context for its function, ruling out cytosolic or ER roles.","evidence":"GFP-fusion imaging and subcellular fractionation in mammalian cells identified an N-terminal mitochondrial targeting signal","pmids":["14640972"],"confidence":"Medium","gaps":["Sub-mitochondrial localization (outer membrane vs. IMS vs. matrix) not resolved","No functional phenotype reported"]},{"year":2008,"claim":"Linking PRELID1 overexpression to oxidative stress, calpain activation, and STAT6 degradation in T helper cells provided the first mechanistic connection between PRELID1 and ROS-dependent signaling.","evidence":"Gain- and loss-of-function in primary human Th cells with calpain inhibitor rescue","pmids":["18945965"],"confidence":"Medium","gaps":["Mechanism by which PRELID1 generates ROS not identified","Relevance beyond Th cells not tested","No lipid-level measurements"]},{"year":2009,"claim":"In vivo loss-of-function of the Drosophila ortholog demonstrated that PRELID1 family members are essential for mitochondrial structural integrity, respiratory complex IV activity, and neuronal morphogenesis, placing the gene upstream of Bcl-2 family apoptotic regulators.","evidence":"Genetic knockout in Drosophila neurons with complex IV activity, ATP, live mitochondrial imaging, and epistasis with Drob-1/Buffy","pmids":["19855018"],"confidence":"Medium","gaps":["PA/CL lipid levels not measured in fly neurons","Whether dendritic simplification is secondary to energy deficit or a direct lipid signaling defect is unclear"]},{"year":2010,"claim":"Identifying Mdm35 (TRIAP1) as a binding partner that protects Ups1 (PRELID1) from IMS proteases established the regulatory logic controlling PRELID1 stability and, consequently, cardiolipin homeostasis.","evidence":"Co-immunoprecipitation, protease mutant epistasis (Yme1, Atp23), and protein turnover assays in yeast","pmids":["20657548"],"confidence":"High","gaps":["Mammalian protease counterparts for PRELID1 degradation not identified","Stoichiometry of the TRIAP1–PRELID1 complex not determined"]},{"year":2010,"claim":"Demonstrating that PRELID1 physically associates with OPA1 and that its LEA motif is required for maintaining membrane potential and respiratory function connected PRELID1 to mitochondrial dynamics and cristae organization.","evidence":"Co-IP of PRELI–OPA1, dominant-negative LEA-deficient mutant, membrane potential and oxygen consumption assays in mammalian cells","pmids":["21364629"],"confidence":"Medium","gaps":["Whether PRELI–OPA1 interaction is direct or mediated by lipid intermediates is unresolved","Structural basis of the LEA motif function unknown"]},{"year":2013,"claim":"Reconstituting PA transfer by the TRIAP1–PRELID1 complex in vitro established the core molecular activity: intermembrane lipid transport supplying PA for cardiolipin synthesis, linking prior genetic phenotypes to a defined biochemical function.","evidence":"In vitro lipid transfer assay between donor and acceptor liposomes, siRNA knockdown, cytochrome c release, and phosphatidylglycerol rescue in mammalian cells","pmids":["23931759"],"confidence":"High","gaps":["Structural mechanism of PA extraction and insertion not resolved","Whether PRELID1 also transfers other phospholipids in vivo remains debated"]},{"year":2017,"claim":"Identifying alternative polyadenylation as a posttranscriptional mechanism that tunes PRELID1 mRNA levels and translational output revealed how cells modulate PA transfer capacity under stress.","evidence":"PAS-seq, PRELID1 overexpression/knockdown, and mitochondrial ROS measurement","pmids":["28912168"],"confidence":"Medium","gaps":["Signaling pathways that trigger the APA switch are unknown","Impact on cardiolipin levels not directly measured"]},{"year":2025,"claim":"Showing that PRELID1/Ups1 preferentially extracts PA from positively curved membranes, with extraction as the rate-limiting step, provided a biophysical framework explaining how mitochondrial membrane topology regulates lipid transfer efficiency.","evidence":"In vitro lipid transfer with defined-curvature liposomes and coarse-grained MD simulations (preprint)","pmids":["bio_10.1101_2025.04.03.647039"],"confidence":"Medium","gaps":["Awaits peer review","In vivo validation of curvature-dependent transfer not performed","Whether cristae curvature modulates PRELID1 activity in cells is untested"]},{"year":2025,"claim":"Epistasis experiments placing PRELID1 downstream of the ER–mitochondria lipid transporter BLTP1 established that PRELID1-mediated PA import is required for the toxic accumulation of mitochondrial phospholipids when ER-to-OMM lipid efflux is blocked.","evidence":"PRELID1 siRNA knockdown in BLTP1-deficient cells with ROS, bioenergetics, and apoptosis readouts (preprint)","pmids":["bio_10.1101_2025.09.30.679455"],"confidence":"Medium","gaps":["Awaits peer review","Direct measurement of PA flux in this epistasis context not shown","Whether other PRELID family members compensate is unknown"]},{"year":null,"claim":"A high-resolution structural mechanism for PA extraction and delivery by the TRIAP1–PRELID1 complex in the context of native mitochondrial membranes, and the physiological signals that dynamically regulate this transfer in vivo, remain to be determined.","evidence":"","pmids":[],"confidence":"High","gaps":["No high-resolution structure of the human TRIAP1–PRELID1–PA ternary complex","In vivo real-time measurement of PA transfer rates is lacking","Whether PRELID1 participates in inter-organelle lipid transport beyond the IMS is unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[0,7]},{"term_id":"GO:0140104","term_label":"molecular carrier activity","supporting_discovery_ids":[0,7]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,2,3,5]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[0,3,5]}],"complexes":["TRIAP1-PRELID1"],"partners":["TRIAP1","OPA1"],"other_free_text":[]},"mechanistic_narrative":"PRELID1 is a mitochondrial intermembrane space lipid transfer protein that, in complex with TRIAP1, shuttles phosphatidic acid (PA) from the outer to the inner mitochondrial membrane, thereby fueling cardiolipin biosynthesis and sustaining mitochondrial membrane integrity [PMID:23931759]. TRIAP1 binding stabilizes PRELID1 by protecting it from proteolytic degradation by IMS proteases, a regulatory mechanism conserved from yeast to mammals [PMID:20657548]. PRELID1 associates with the dynamin-like GTPase OPA1 and is required for maintaining mitochondrial membrane potential, respiratory chain activity, and normal mitochondrial morphology; its loss causes cytochrome c release, elevated reactive oxygen species, and sensitization to apoptosis [PMID:21364629, PMID:23931759]. In Drosophila neurons, the PRELID1 ortholog is essential for mitochondrial distribution in neurites and dendritic arbor complexity, acting upstream of Bcl-2 family–mediated cell death [PMID:19855018]."},"prefetch_data":{"uniprot":{"accession":"Q9Y255","full_name":"PRELI domain-containing protein 1, mitochondrial","aliases":["25 kDa protein of relevant evolutionary and lymphoid interest","Px19-like protein"],"length_aa":219,"mass_kda":25.2,"function":"Involved in the modulation of the mitochondrial apoptotic pathway by ensuring the accumulation of cardiolipin (CL) in mitochondrial membranes. In vitro, the TRIAP1:PRELID1 complex mediates the transfer of phosphatidic acid (PA) between liposomes and probably functions as a PA transporter across the mitochondrion intermembrane space to provide PA for CL synthesis in the inner membrane. Regulates the mitochondrial apoptotic pathway in primary Th cells. Regulates Th cell differentiation by down-regulating STAT6 thereby reducing IL-4-induced Th2 cell number. May be important for the development of vital and immunocompetent organs","subcellular_location":"Mitochondrion; Mitochondrion intermembrane space","url":"https://www.uniprot.org/uniprotkb/Q9Y255/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/PRELID1","classification":"Common Essential","n_dependent_lines":1208,"n_total_lines":1208,"dependency_fraction":1.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/PRELID1","total_profiled":1310},"omim":[{"mim_id":"620754","title":"PRELI DOMAIN-CONTAINING PROTEIN 3B; PRELID3B","url":"https://www.omim.org/entry/620754"},{"mim_id":"617302","title":"OPTIC ATROPHY 11; OPA11","url":"https://www.omim.org/entry/617302"},{"mim_id":"607472","title":"MITOCHONDRIAL ESCAPE 1-LIKE 1; YME1L1","url":"https://www.omim.org/entry/607472"},{"mim_id":"605733","title":"PRELI DOMAIN-CONTAINING PROTEIN 1; PRELID1","url":"https://www.omim.org/entry/605733"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Mitochondria","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PRELID1"},"hgnc":{"alias_symbol":["CGI-106","PX19","PRELI"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y255","domains":[{"cath_id":"3.30.530.20","chopping":"2-169","consensus_level":"high","plddt":93.6934,"start":2,"end":169},{"cath_id":"1.20.5","chopping":"176-219","consensus_level":"medium","plddt":78.0686,"start":176,"end":219}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y255","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y255-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y255-F1-predicted_aligned_error_v6.png","plddt_mean":90.56},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PRELID1","jax_strain_url":"https://www.jax.org/strain/search?query=PRELID1"},"sequence":{"accession":"Q9Y255","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y255.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y255/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y255"}},"corpus_meta":[{"pmid":"23931759","id":"PMC_23931759","title":"TRIAP1/PRELI complexes prevent apoptosis by mediating intramitochondrial transport of phosphatidic acid.","date":"2013","source":"Cell metabolism","url":"https://pubmed.ncbi.nlm.nih.gov/23931759","citation_count":167,"is_preprint":false},{"pmid":"20657548","id":"PMC_20657548","title":"Regulation of mitochondrial phospholipids by Ups1/PRELI-like proteins depends on proteolysis and Mdm35.","date":"2010","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/20657548","citation_count":141,"is_preprint":false},{"pmid":"15700158","id":"PMC_15700158","title":"A novel family of mitochondrial proteins is represented by the Drosophila genes slmo, preli-like and real-time.","date":"2005","source":"Development genes and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/15700158","citation_count":33,"is_preprint":false},{"pmid":"19855018","id":"PMC_19855018","title":"Mitochondrial protein Preli-like is required for development of dendritic arbors and prevents their regression in the Drosophila sensory nervous system.","date":"2009","source":"Development (Cambridge, England)","url":"https://pubmed.ncbi.nlm.nih.gov/19855018","citation_count":26,"is_preprint":false},{"pmid":"18945965","id":"PMC_18945965","title":"PRELI is a mitochondrial regulator of human primary T-helper cell apoptosis, STAT6, and Th2-cell differentiation.","date":"2008","source":"Blood","url":"https://pubmed.ncbi.nlm.nih.gov/18945965","citation_count":25,"is_preprint":false},{"pmid":"10784606","id":"PMC_10784606","title":"PRELI, the human homologue of the avian px19, is expressed by germinal center B lymphocytes.","date":"2000","source":"International immunology","url":"https://pubmed.ncbi.nlm.nih.gov/10784606","citation_count":24,"is_preprint":false},{"pmid":"14640972","id":"PMC_14640972","title":"PRELI (protein of relevant evolutionary and lymphoid interest) is located within an evolutionarily conserved gene cluster on chromosome 5q34-q35 and encodes a novel mitochondrial protein.","date":"2004","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/14640972","citation_count":24,"is_preprint":false},{"pmid":"28912168","id":"PMC_28912168","title":"Alternative Polyadenylation of PRELID1 Regulates Mitochondrial ROS Signaling and Cancer Outcomes.","date":"2017","source":"Molecular cancer research : MCR","url":"https://pubmed.ncbi.nlm.nih.gov/28912168","citation_count":22,"is_preprint":false},{"pmid":"21364629","id":"PMC_21364629","title":"Vital function of PRELI and essential requirement of its LEA motif.","date":"2010","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/21364629","citation_count":19,"is_preprint":false},{"pmid":"26275693","id":"PMC_26275693","title":"Effects of PRELI in Oxidative-Stressed HepG2 Cells.","date":"2015","source":"Annals of clinical and laboratory science","url":"https://pubmed.ncbi.nlm.nih.gov/26275693","citation_count":8,"is_preprint":false},{"pmid":"19847657","id":"PMC_19847657","title":"Conserved expression of the PRELI domain containing 2 gene (Prelid2) during mid-later-gestation mouse embryogenesis.","date":"2009","source":"Journal of molecular histology","url":"https://pubmed.ncbi.nlm.nih.gov/19847657","citation_count":7,"is_preprint":false},{"pmid":"22666421","id":"PMC_22666421","title":"Spare PRELI gene loci: failsafe chromosome insurance?","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/22666421","citation_count":1,"is_preprint":false},{"pmid":"39769068","id":"PMC_39769068","title":"MicroRNA Profiling of PRELI-Modulated Exosomes and Effects on Hepatic Cancer Stem Cells.","date":"2024","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/39769068","citation_count":1,"is_preprint":false},{"pmid":"41706757","id":"PMC_41706757","title":"PRELID1 and VDAC3 Coordinate a Senescence-Like State in Germinal Center B Cells to Promote IL-7-Driven Antitumor Immunity in Colorectal Cancer.","date":"2026","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/41706757","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.09.30.679455","title":"BLTP1-dependent phospholipid efflux prevents mitochondrial lipid overload and apoptosis at FKBP8-tethered ER-mitochondrial contact","date":"2025-09-30","source":"bioRxiv","url":"https://doi.org/10.1101/2025.09.30.679455","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.04.03.647039","title":"Membrane curvature regulates Ups1 dependent phosphatidic acid transfer across lipid bilayers","date":"2025-04-04","source":"bioRxiv","url":"https://doi.org/10.1101/2025.04.03.647039","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8702,"output_tokens":2389,"usd":0.030971},"stage2":{"model":"claude-opus-4-6","input_tokens":5685,"output_tokens":2373,"usd":0.131625},"total_usd":0.162596,"stage1_batch_id":"msgbatch_01SUR8NDzVrNmyszWyJeCct7","stage2_batch_id":"msgbatch_01G7Yfutko3cDWzejrwH5AMx","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"TRIAP1/PRELI (PRELID1) complexes localized in the mitochondrial intermembrane space (IMS) exert lipid transfer activity in vitro, supplying phosphatidic acid (PA) to the inner membrane for cardiolipin (CL) synthesis. Loss of TRIAP1 or PRELI impairs CL accumulation, facilitates cytochrome c release, and renders cells vulnerable to apoptosis; survival is restored by exogenous phosphatidylglycerol.\",\n      \"method\": \"In vitro lipid transfer assay, genetic loss-of-function (siRNA knockdown), phospholipid rescue experiment, cytochrome c release assay, fractionation/localization\",\n      \"journal\": \"Cell metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — in vitro lipid transfer reconstitution plus multiple orthogonal genetic and biochemical validations; replicated context of yeast orthologs\",\n      \"pmids\": [\"23931759\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Mdm35 (TRIAP1 ortholog), a twin Cx9C protein, is identified as a novel interaction partner of the PRELID1 ortholog Ups1 in yeast IMS; binding to Mdm35 ensures import of Ups1 and protects it against proteolytic degradation by Yme1 (i-AAA protease) and Atp23 metallopeptidase, thereby regulating cardiolipin and phosphatidylethanolamine levels in mitochondrial membranes.\",\n      \"method\": \"Co-immunoprecipitation, protease activity assays, genetic deletion of Yme1/Atp23, protein stability/turnover assays in yeast\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP, protease mutant epistasis, and protein turnover assays; conserved in higher eukaryotes per the authors\",\n      \"pmids\": [\"20657548\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"PRELI (PRELID1) is localized to mitochondria; a mitochondrial targeting signal is identified at its N-terminus using GFP-fusion proteins and subcellular fractionation.\",\n      \"method\": \"GFP-fusion live imaging, subcellular fractionation, mitochondrial targeting sequence analysis\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct localization by GFP fusion and fractionation in mammalian/mouse system; single lab\",\n      \"pmids\": [\"14640972\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"PRELI (PRELID1) associates with dynamin-like GTPase OPA1, contributes to maintenance of mitochondrial morphology, upholds mitochondrial membrane potential (ΔΨm), and enhances respiratory chain function (complex I/NADH dehydrogenase and ATP synthase expression, oxygen consumption, reduced ROS). The LEA motif of PRELI is essential for these cytoprotective functions, as dominant-negative LEA-deficient PRELI mutant and PRELI knockdown render cells vulnerable to apoptosis.\",\n      \"method\": \"Co-immunoprecipitation (PRELI–OPA1 association), dominant-negative overexpression of PRELI/LEA(-) mutant, siRNA knockdown, mitochondrial membrane potential assay, oxygen consumption measurement, ROS measurement, apoptosis assays\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — Co-IP plus multiple functional readouts in one lab; single-lab study with multiple orthogonal methods\",\n      \"pmids\": [\"21364629\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"PRELI (PRELID1) induces oxidative stress and a mitochondrial apoptosis pathway in human primary T helper cells, inhibits Th2-cell development, and down-regulates STAT6 through a mechanism involving calpain (an oxidative stress-induced cysteine protease).\",\n      \"method\": \"Overexpression and knockdown in primary human Th cells, STAT6 protein measurement, calpain inhibitor experiments, flow cytometry for apoptosis and Th subset markers\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — loss-of-function and gain-of-function with defined molecular pathway (calpain-STAT6); single lab, multiple readouts\",\n      \"pmids\": [\"18945965\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Drosophila Preli-like (ortholog of PRELID1) is required for mitochondrial structural integrity, activity of respiratory chain complex IV, and cellular ATP levels in neurons; loss of Prel leads to mitochondrial fragmentation, sparse mitochondrial distribution in dendrites/axons, and dendritic arbor simplification. Epistasis with the Bax-like protein Drob-1 and its antagonist Buffy places Prel upstream of Bcl-2 family-mediated apoptosis in this context.\",\n      \"method\": \"Genetic loss-of-function in Drosophila neurons (in vivo), respiratory chain complex IV activity assay, ATP measurement, live imaging of mitochondria, genetic epistasis (Drob-1 overexpression, Buffy rescue of prel mutant)\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — in vivo genetic loss-of-function with enzymatic assay, ATP measurement, live imaging, and epistasis; ortholog of PRELID1 in Drosophila\",\n      \"pmids\": [\"19855018\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"PRELID1 regulates mitochondrial reactive oxygen species (ROS) production in a cell-type-specific manner; an alternative polyadenylation (APA) event in PRELID1 mRNA enhances its steady-state level and translational efficiency, providing a posttranscriptional mechanism controlling PRELID1-dependent stress response.\",\n      \"method\": \"PAS-seq (polyadenylation site sequencing), PRELID1 modulation by overexpression/knockdown, mitochondrial ROS measurement\",\n      \"journal\": \"Molecular cancer research : MCR\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2/3 — direct measurement of ROS upon PRELID1 modulation with identification of APA regulatory mechanism; single lab\",\n      \"pmids\": [\"28912168\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PRELID1 (Ups1) exhibits a strong preference for binding positively curved membrane regions; phosphatidic acid extraction is energetically favored at these domains, and lipid extraction is the rate-limiting step in the PA transfer cycle. Membrane binding by Ups1/PRELID1 is modulated by pH, lipid composition, and membrane morphology.\",\n      \"method\": \"In vitro lipid transfer assay with defined curvature membranes, coarse-grained MD simulations, giant unilamellar vesicle binding assay\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 — in vitro reconstitution with curvature-defined membranes plus computational modeling; preprint, not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.04.03.647039\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Depleting PRELID1 (intramitochondrial lipid transfer protein) prevents apoptosis caused by BLTP1 deficiency, establishing PRELID1 as a required effector in the pathway by which excess PA/PG/CL accumulation leads to mitochondrial ROS elevation and cell death. This places PRELID1 downstream of BLTP1-mediated phospholipid efflux.\",\n      \"method\": \"PRELID1 siRNA knockdown epistasis in BLTP1-deficient cells; mitochondrial ROS, bioenergetics, and apoptosis assays\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — epistasis experiment with defined phenotypic readout; preprint, single lab\",\n      \"pmids\": [\"bio_10.1101_2025.09.30.679455\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"PRELID1 (PRELI) is a mitochondrial intermembrane space lipid transfer protein that, in complex with TRIAP1 (Mdm35 in yeast), transfers phosphatidic acid (PA) from the outer to the inner mitochondrial membrane to support cardiolipin synthesis; this activity is regulated by membrane curvature and proteolytic turnover, and is essential for maintaining cardiolipin levels, mitochondrial integrity, and cell survival against apoptosis.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"PRELID1 is a mitochondrial intermembrane space lipid transfer protein that, in complex with TRIAP1, shuttles phosphatidic acid (PA) from the outer to the inner mitochondrial membrane, thereby fueling cardiolipin biosynthesis and sustaining mitochondrial membrane integrity [PMID:23931759]. TRIAP1 binding stabilizes PRELID1 by protecting it from proteolytic degradation by IMS proteases, a regulatory mechanism conserved from yeast to mammals [PMID:20657548]. PRELID1 associates with the dynamin-like GTPase OPA1 and is required for maintaining mitochondrial membrane potential, respiratory chain activity, and normal mitochondrial morphology; its loss causes cytochrome c release, elevated reactive oxygen species, and sensitization to apoptosis [PMID:21364629, PMID:23931759]. In Drosophila neurons, the PRELID1 ortholog is essential for mitochondrial distribution in neurites and dendritic arbor complexity, acting upstream of Bcl-2 family–mediated cell death [PMID:19855018].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Establishing that PRELID1 is a mitochondrial protein resolved the subcellular context for its function, ruling out cytosolic or ER roles.\",\n      \"evidence\": \"GFP-fusion imaging and subcellular fractionation in mammalian cells identified an N-terminal mitochondrial targeting signal\",\n      \"pmids\": [\"14640972\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Sub-mitochondrial localization (outer membrane vs. IMS vs. matrix) not resolved\",\n        \"No functional phenotype reported\"\n      ]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Linking PRELID1 overexpression to oxidative stress, calpain activation, and STAT6 degradation in T helper cells provided the first mechanistic connection between PRELID1 and ROS-dependent signaling.\",\n      \"evidence\": \"Gain- and loss-of-function in primary human Th cells with calpain inhibitor rescue\",\n      \"pmids\": [\"18945965\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanism by which PRELID1 generates ROS not identified\",\n        \"Relevance beyond Th cells not tested\",\n        \"No lipid-level measurements\"\n      ]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"In vivo loss-of-function of the Drosophila ortholog demonstrated that PRELID1 family members are essential for mitochondrial structural integrity, respiratory complex IV activity, and neuronal morphogenesis, placing the gene upstream of Bcl-2 family apoptotic regulators.\",\n      \"evidence\": \"Genetic knockout in Drosophila neurons with complex IV activity, ATP, live mitochondrial imaging, and epistasis with Drob-1/Buffy\",\n      \"pmids\": [\"19855018\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"PA/CL lipid levels not measured in fly neurons\",\n        \"Whether dendritic simplification is secondary to energy deficit or a direct lipid signaling defect is unclear\"\n      ]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Identifying Mdm35 (TRIAP1) as a binding partner that protects Ups1 (PRELID1) from IMS proteases established the regulatory logic controlling PRELID1 stability and, consequently, cardiolipin homeostasis.\",\n      \"evidence\": \"Co-immunoprecipitation, protease mutant epistasis (Yme1, Atp23), and protein turnover assays in yeast\",\n      \"pmids\": [\"20657548\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Mammalian protease counterparts for PRELID1 degradation not identified\",\n        \"Stoichiometry of the TRIAP1–PRELID1 complex not determined\"\n      ]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Demonstrating that PRELID1 physically associates with OPA1 and that its LEA motif is required for maintaining membrane potential and respiratory function connected PRELID1 to mitochondrial dynamics and cristae organization.\",\n      \"evidence\": \"Co-IP of PRELI–OPA1, dominant-negative LEA-deficient mutant, membrane potential and oxygen consumption assays in mammalian cells\",\n      \"pmids\": [\"21364629\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether PRELI–OPA1 interaction is direct or mediated by lipid intermediates is unresolved\",\n        \"Structural basis of the LEA motif function unknown\"\n      ]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Reconstituting PA transfer by the TRIAP1–PRELID1 complex in vitro established the core molecular activity: intermembrane lipid transport supplying PA for cardiolipin synthesis, linking prior genetic phenotypes to a defined biochemical function.\",\n      \"evidence\": \"In vitro lipid transfer assay between donor and acceptor liposomes, siRNA knockdown, cytochrome c release, and phosphatidylglycerol rescue in mammalian cells\",\n      \"pmids\": [\"23931759\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Structural mechanism of PA extraction and insertion not resolved\",\n        \"Whether PRELID1 also transfers other phospholipids in vivo remains debated\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Identifying alternative polyadenylation as a posttranscriptional mechanism that tunes PRELID1 mRNA levels and translational output revealed how cells modulate PA transfer capacity under stress.\",\n      \"evidence\": \"PAS-seq, PRELID1 overexpression/knockdown, and mitochondrial ROS measurement\",\n      \"pmids\": [\"28912168\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Signaling pathways that trigger the APA switch are unknown\",\n        \"Impact on cardiolipin levels not directly measured\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Showing that PRELID1/Ups1 preferentially extracts PA from positively curved membranes, with extraction as the rate-limiting step, provided a biophysical framework explaining how mitochondrial membrane topology regulates lipid transfer efficiency.\",\n      \"evidence\": \"In vitro lipid transfer with defined-curvature liposomes and coarse-grained MD simulations (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.04.03.647039\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Awaits peer review\",\n        \"In vivo validation of curvature-dependent transfer not performed\",\n        \"Whether cristae curvature modulates PRELID1 activity in cells is untested\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Epistasis experiments placing PRELID1 downstream of the ER–mitochondria lipid transporter BLTP1 established that PRELID1-mediated PA import is required for the toxic accumulation of mitochondrial phospholipids when ER-to-OMM lipid efflux is blocked.\",\n      \"evidence\": \"PRELID1 siRNA knockdown in BLTP1-deficient cells with ROS, bioenergetics, and apoptosis readouts (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.09.30.679455\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Awaits peer review\",\n        \"Direct measurement of PA flux in this epistasis context not shown\",\n        \"Whether other PRELID family members compensate is unknown\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"A high-resolution structural mechanism for PA extraction and delivery by the TRIAP1–PRELID1 complex in the context of native mitochondrial membranes, and the physiological signals that dynamically regulate this transfer in vivo, remain to be determined.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No high-resolution structure of the human TRIAP1–PRELID1–PA ternary complex\",\n        \"In vivo real-time measurement of PA transfer rates is lacking\",\n        \"Whether PRELID1 participates in inter-organelle lipid transport beyond the IMS is unknown\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"GO:0140104\", \"supporting_discovery_ids\": [0, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 2, 3, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [0, 3, 5]}\n    ],\n    \"complexes\": [\n      \"TRIAP1-PRELID1\"\n    ],\n    \"partners\": [\n      \"TRIAP1\",\n      \"OPA1\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}