{"gene":"PRELID1","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2013,"finding":"PRELID1 (PRELI) forms a complex with TRIAP1 in the mitochondrial intermembrane space (IMS) that transfers phosphatidic acid (PA) to the inner membrane for cardiolipin (CL) synthesis. Loss of PRELI impairs CL accumulation, facilitates cytochrome c release, and renders cells vulnerable to apoptosis; survival is rescued by exogenous phosphatidylglycerol.","method":"Co-immunoprecipitation of TRIAP1/PRELI complex; in vitro lipid transfer assay; loss-of-function (siRNA knockdown) with measurement of CL levels, cytochrome c release, and apoptosis; rescue by exogenous phosphatidylglycerol","journal":"Cell metabolism","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro lipid transfer reconstitution combined with genetic loss-of-function and metabolic rescue, multiple orthogonal methods in one rigorous study","pmids":["23931759"],"is_preprint":false},{"year":2010,"finding":"The yeast ortholog Ups1 (PRELID1 homologue) is an intrinsically unstable IMS protein that regulates cardiolipin accumulation. Its stability and import are protected by binding to Mdm35 (a twin Cx9C protein), and its turnover is mediated by the metallopeptidase Atp23 and the i-AAA protease Yme1.","method":"Yeast genetic interaction and epistasis; co-immunoprecipitation of Ups1/Mdm35 complex; protease mutant analysis (Δyme1, Δatp23) measuring protein turnover by pulse-chase/steady-state levels","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, genetic epistasis, protease mutants, replicated across multiple experimental approaches in one rigorous study; conserved pathway noted in higher eukaryotes","pmids":["20657548"],"is_preprint":false},{"year":2010,"finding":"PRELI associates with the dynamin-like GTPase OPA1 and contributes to maintenance of mitochondrial morphology, mitochondrial membrane potential (ΔΨm), and respiratory chain function (complex I/NADH dehydrogenase and ATP synthase expression, oxygen consumption, ROS reduction). The LEA motif is required for these functions; dominant-negative PRELI/LEA(-) or PRELI knockdown renders cells vulnerable to apoptosis.","method":"Co-immunoprecipitation (PRELI–OPA1); dominant-negative overexpression of PRELI/LEA(-) mutant; siRNA knockdown; measurement of ΔΨm, oxygen consumption, ROS, complex I/ATP synthase expression; in vivo mouse embryo lethality with dominant-negative construct","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — co-IP for OPA1 interaction, multiple functional readouts in single lab; dominant-negative approach has caveats; no structural or reconstitution-level validation of the interaction","pmids":["21364629"],"is_preprint":false},{"year":2008,"finding":"PRELI induces oxidative stress and a mitochondrial apoptosis pathway in human primary T helper cells, inhibits Th2-cell development, and down-regulates STAT6; the STAT6 down-regulation involves calpain, an oxidative stress-induced cysteine protease.","method":"PRELI overexpression in primary human Th cells; measurement of apoptosis markers, ROS, STAT6 protein levels; calpain inhibitor experiments linking oxidative stress to STAT6 degradation","journal":"Blood","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — overexpression plus pharmacological inhibition in primary cells, single lab, multiple readouts but no reconstitution or structural validation","pmids":["18945965"],"is_preprint":false},{"year":2004,"finding":"PRELI is localized to mitochondria via an N-terminal mitochondrial targeting signal, as demonstrated by GFP-fusion protein imaging and subcellular fractionation.","method":"GFP-fusion protein live imaging; subcellular fractionation; bioinformatic identification of mitochondrial targeting signal","journal":"The Biochemical journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization by live fluorescence imaging and fractionation, single lab, two orthogonal methods","pmids":["14640972"],"is_preprint":false},{"year":2005,"finding":"Drosophila Preli-like (Prel) protein, a member of the PRELI/MSF1 family, localizes to mitochondria, indicating the PRELI/MSF1 domain function is mitochondria-specific.","method":"Subcellular localization of GFP-tagged Prel in Drosophila cells","journal":"Development genes and evolution","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single localization experiment in Drosophila, no functional mechanistic follow-up for PRELID1 specifically","pmids":["15700158"],"is_preprint":false},{"year":2009,"finding":"Drosophila Preli-like (Prel) loss-of-function in neurons decreases cellular ATP levels, causes mitochondrial fragmentation and sparse distribution in dendrites/axons, and leads to simplified/retracted dendritic arbors. Overexpression of Drob-1 (Bax-like) phenocopies this, while expression of Drob-1 antagonist Buffy in prel mutants restores dendritic morphology, placing Prel upstream of Bcl-2 family regulation of mitochondrial activity.","method":"Genetic loss-of-function (prel mutant Drosophila); ATP measurement; mitochondrial morphology imaging; genetic epistasis with Drob-1 and Buffy; measurement of respiratory chain complex IV activity","journal":"Development (Cambridge, England)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis in Drosophila model with multiple orthogonal readouts (ATP, morphology, complex IV activity), single lab","pmids":["19855018"],"is_preprint":false},{"year":2017,"finding":"An alternative polyadenylation (APA) event in PRELID1 mRNA enhances its steady-state level and translational efficiency; PRELID1 regulates mitochondrial reactive oxygen species (ROS) production in a cell-type-specific manner.","method":"PAS-seq (polyadenylation site sequencing) in primary breast tumor specimens; PRELID1 modulation (knockdown/overexpression) with measurement of mitochondrial ROS","journal":"Molecular cancer research : MCR","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, ROS phenotype established but molecular mechanism of how PRELID1 regulates ROS not mechanistically defined beyond PA/CL pathway inference","pmids":["28912168"],"is_preprint":false},{"year":2015,"finding":"PRELID1 knockdown in HepG2 cells under oxidative stress leads to up-regulation of caspase-3 and down-regulation of SOD-1, increased mitochondrial apoptosis, and enhanced cellular senescence, demonstrating PRELID1 suppresses apoptosis and senescence in hepatocellular carcinoma cells.","method":"siRNA knockdown of PRELID1 in HepG2 cells; RT-PCR for caspase-3 and SOD-1; fluorescence-based mitochondrial apoptosis assay; senescence assay","journal":"Annals of clinical and laboratory science","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single knockdown approach, limited mechanistic resolution beyond phenotypic gene expression changes","pmids":["26275693"],"is_preprint":false},{"year":2025,"finding":"PRELID1 (the mammalian Ups1 ortholog) is required for pathological accumulation of cardiolipin within mitochondria when the phospholipid efflux transporter BLTP1 is absent; depleting PRELID1 prevents apoptosis caused by BLTP1 deficiency, genetically placing PRELID1 downstream of BLTP1-mediated lipid efflux and upstream of CL-driven apoptosis.","method":"Genetic epistasis (double depletion of BLTP1 and PRELID1); measurement of PA, PG, and CL levels; apoptosis assays; ROS measurement","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean epistasis with defined molecular phenotype (lipid accumulation + apoptosis), preprint not yet peer-reviewed","pmids":["bio_10.1101_2025.09.30.679455"],"is_preprint":true},{"year":2025,"finding":"Ups1 (yeast PRELID1 ortholog) preferentially binds positively curved membrane regions for phosphatidic acid extraction; PA extraction is energetically favored at high-positive-curvature domains; events at the donor membrane are rate-limiting for the lipid transfer cycle; membrane binding is modulated by pH, lipid composition, and membrane morphology.","method":"In vitro lipid transfer assays with membranes of defined curvature; biophysical binding measurements; computational/MD modeling","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — in vitro reconstitution with curvature-defined membranes is rigorous but preprint, single lab, not yet peer-reviewed","pmids":["bio_10.1101_2025.04.03.647039"],"is_preprint":true}],"current_model":"PRELID1 (PRELI) is a mitochondrial intermembrane space lipid transfer protein that forms a complex with TRIAP1, transfers phosphatidic acid from the outer to the inner mitochondrial membrane for cardiolipin synthesis, and thereby prevents cytochrome c release and apoptosis; its stability is regulated by binding to the chaperone Mdm35 (TRIAP1 in mammals) and by mitochondrial proteases, while its PA-extraction activity is tuned by membrane curvature, pH, and lipid composition at the donor membrane."},"narrative":{"mechanistic_narrative":"PRELID1 (PRELI) is a mitochondrial intermembrane-space lipid transfer protein that controls cardiolipin homeostasis and thereby sets the threshold for mitochondrial apoptosis [PMID:23931759]. It forms a complex with TRIAP1 that extracts phosphatidic acid and transfers it across the IMS to the inner membrane for cardiolipin synthesis; loss of PRELID1 impairs cardiolipin accumulation, facilitates cytochrome c release, and sensitizes cells to apoptosis, with survival rescued by exogenous phosphatidylglycerol [PMID:23931759]. PRELID1 is targeted to mitochondria by an N-terminal mitochondrial targeting signal [PMID:14640972]. Work on the yeast ortholog Ups1 established the conserved logic of this pathway: Ups1 is an intrinsically unstable IMS protein whose stability and import are protected by binding the twin Cx9C protein Mdm35 (TRIAP1 in mammals), with turnover executed by the proteases Atp23 and Yme1 [PMID:20657548], and its phosphatidic-acid extraction is rate-limited by donor-membrane events, favored at positively curved membrane domains and tuned by pH and lipid composition [PMID:bio_10.1101_2025.04.03.647039]. Consistent with its role in cardiolipin-driven death, PRELID1 acts downstream of BLTP1-mediated phospholipid efflux: depleting PRELID1 blocks the pathological cardiolipin accumulation and apoptosis caused by BLTP1 loss [PMID:bio_10.1101_2025.09.30.679455]. Beyond cardiolipin transfer, PRELID1 associates with the dynamin-like GTPase OPA1 and supports mitochondrial morphology, membrane potential, and respiratory chain function in a manner requiring its LEA motif [PMID:21364629], and it modulates mitochondrial ROS and apoptotic/senescence responses across cell types [PMID:18945965, PMID:26275693].","teleology":[{"year":2004,"claim":"Establishing where PRELI acts was the first step; demonstrating mitochondrial residence framed all subsequent mechanistic work.","evidence":"GFP-fusion live imaging and subcellular fractionation identifying an N-terminal mitochondrial targeting signal","pmids":["14640972"],"confidence":"Medium","gaps":["Did not resolve sub-mitochondrial localization (IMS vs matrix)","No functional role assigned"]},{"year":2010,"claim":"Yeast genetics resolved how the unstable PRELI/Ups1 protein is stabilized and degraded, defining the chaperone-protease control of cardiolipin regulation.","evidence":"Yeast genetic epistasis, reciprocal Ups1/Mdm35 co-IP, and protease mutant (Δyme1, Δatp23) turnover analysis","pmids":["20657548"],"confidence":"High","gaps":["Did not directly demonstrate lipid transfer biochemistry","Mammalian protease equivalents not tested here"]},{"year":2010,"claim":"A parallel line tied PRELI to OPA1 and bioenergetics, linking it to mitochondrial morphology and respiratory function beyond a purely structural role.","evidence":"PRELI–OPA1 co-IP, dominant-negative LEA(-) mutant, siRNA knockdown with ΔΨm/O2/ROS/complex readouts, and mouse embryo lethality","pmids":["21364629"],"confidence":"Medium","gaps":["OPA1 interaction not validated structurally or by reconstitution","Dominant-negative approach carries interpretive caveats"]},{"year":2013,"claim":"The central mechanism was defined: PRELI/TRIAP1 directly transfers phosphatidic acid for cardiolipin synthesis, mechanistically coupling lipid handling to apoptosis sensitivity.","evidence":"TRIAP1/PRELI co-IP, in vitro lipid transfer assay, siRNA loss-of-function with CL/cytochrome c/apoptosis measurement, and phosphatidylglycerol rescue","pmids":["23931759"],"confidence":"High","gaps":["Structural basis of PA binding not resolved","Regulation of transfer in cells not defined"]},{"year":2017,"claim":"Post-transcriptional control was identified, showing alternative polyadenylation raises PRELID1 levels and links it to cell-type-specific ROS regulation.","evidence":"PAS-seq in breast tumor specimens with PRELID1 modulation and mitochondrial ROS measurement","pmids":["28912168"],"confidence":"Low","gaps":["Molecular mechanism of ROS regulation not defined beyond inference to the PA/CL pathway","Single-lab correlative tumor data"]},{"year":2025,"claim":"Genetic epistasis placed PRELID1 in a defined lipid-flux circuit, showing it is required downstream of BLTP1 for pathological cardiolipin accumulation and apoptosis.","evidence":"Double depletion of BLTP1 and PRELID1 with PA/PG/CL, apoptosis, and ROS measurement (preprint)","pmids":["bio_10.1101_2025.09.30.679455"],"confidence":"Medium","gaps":["Preprint, not peer-reviewed","Direct physical relationship between BLTP1 and PRELID1 not established"]},{"year":2025,"claim":"Biophysical reconstitution refined the transfer mechanism, showing donor-membrane curvature is the rate-limiting determinant of PA extraction.","evidence":"In vitro lipid transfer with curvature-defined membranes, biophysical binding, and MD modeling (preprint)","pmids":["bio_10.1101_2025.04.03.647039"],"confidence":"Medium","gaps":["Preprint, not peer-reviewed","Performed on yeast Ups1; mammalian PRELID1 curvature preference not confirmed"]},{"year":null,"claim":"How PRELID1's lipid transfer activity, OPA1 association, and ROS/apoptosis outputs are integrated and regulated in mammalian cells remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of mammalian PRELID1/TRIAP1 bound to PA","Mechanism connecting cardiolipin transfer to OPA1-dependent morphology unclear","In vivo physiological role beyond embryonic lethality uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[0,10]},{"term_id":"GO:0140104","term_label":"molecular carrier activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[0,4,5]}],"pathway":[{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[0]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[0]}],"complexes":["PRELID1–TRIAP1 (Ups1–Mdm35) lipid transfer complex"],"partners":["TRIAP1","OPA1"],"other_free_text":[]}},"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":143,"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":"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":"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":"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":9465,"output_tokens":2886,"usd":0.035842,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10295,"output_tokens":2743,"usd":0.060025,"stage2_stop_reason":"end_turn"},"total_usd":0.095867,"stage1_batch_id":"msgbatch_01CNoDbkChHEkgrJnL7BwtGJ","stage2_batch_id":"msgbatch_016Y4x9E9Wg5VQDANj9quSQD","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"PRELID1 (PRELI) forms a complex with TRIAP1 in the mitochondrial intermembrane space (IMS) that transfers phosphatidic acid (PA) to the inner membrane for cardiolipin (CL) synthesis. Loss of PRELI impairs CL accumulation, facilitates cytochrome c release, and renders cells vulnerable to apoptosis; survival is rescued by exogenous phosphatidylglycerol.\",\n      \"method\": \"Co-immunoprecipitation of TRIAP1/PRELI complex; in vitro lipid transfer assay; loss-of-function (siRNA knockdown) with measurement of CL levels, cytochrome c release, and apoptosis; rescue by exogenous phosphatidylglycerol\",\n      \"journal\": \"Cell metabolism\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro lipid transfer reconstitution combined with genetic loss-of-function and metabolic rescue, multiple orthogonal methods in one rigorous study\",\n      \"pmids\": [\"23931759\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"The yeast ortholog Ups1 (PRELID1 homologue) is an intrinsically unstable IMS protein that regulates cardiolipin accumulation. Its stability and import are protected by binding to Mdm35 (a twin Cx9C protein), and its turnover is mediated by the metallopeptidase Atp23 and the i-AAA protease Yme1.\",\n      \"method\": \"Yeast genetic interaction and epistasis; co-immunoprecipitation of Ups1/Mdm35 complex; protease mutant analysis (Δyme1, Δatp23) measuring protein turnover by pulse-chase/steady-state levels\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, genetic epistasis, protease mutants, replicated across multiple experimental approaches in one rigorous study; conserved pathway noted in higher eukaryotes\",\n      \"pmids\": [\"20657548\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"PRELI associates with the dynamin-like GTPase OPA1 and contributes to maintenance of mitochondrial morphology, mitochondrial membrane potential (ΔΨm), and respiratory chain function (complex I/NADH dehydrogenase and ATP synthase expression, oxygen consumption, ROS reduction). The LEA motif is required for these functions; dominant-negative PRELI/LEA(-) or PRELI knockdown renders cells vulnerable to apoptosis.\",\n      \"method\": \"Co-immunoprecipitation (PRELI–OPA1); dominant-negative overexpression of PRELI/LEA(-) mutant; siRNA knockdown; measurement of ΔΨm, oxygen consumption, ROS, complex I/ATP synthase expression; in vivo mouse embryo lethality with dominant-negative construct\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — co-IP for OPA1 interaction, multiple functional readouts in single lab; dominant-negative approach has caveats; no structural or reconstitution-level validation of the interaction\",\n      \"pmids\": [\"21364629\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"PRELI induces oxidative stress and a mitochondrial apoptosis pathway in human primary T helper cells, inhibits Th2-cell development, and down-regulates STAT6; the STAT6 down-regulation involves calpain, an oxidative stress-induced cysteine protease.\",\n      \"method\": \"PRELI overexpression in primary human Th cells; measurement of apoptosis markers, ROS, STAT6 protein levels; calpain inhibitor experiments linking oxidative stress to STAT6 degradation\",\n      \"journal\": \"Blood\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — overexpression plus pharmacological inhibition in primary cells, single lab, multiple readouts but no reconstitution or structural validation\",\n      \"pmids\": [\"18945965\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"PRELI is localized to mitochondria via an N-terminal mitochondrial targeting signal, as demonstrated by GFP-fusion protein imaging and subcellular fractionation.\",\n      \"method\": \"GFP-fusion protein live imaging; subcellular fractionation; bioinformatic identification of mitochondrial targeting signal\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization by live fluorescence imaging and fractionation, single lab, two orthogonal methods\",\n      \"pmids\": [\"14640972\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"Drosophila Preli-like (Prel) protein, a member of the PRELI/MSF1 family, localizes to mitochondria, indicating the PRELI/MSF1 domain function is mitochondria-specific.\",\n      \"method\": \"Subcellular localization of GFP-tagged Prel in Drosophila cells\",\n      \"journal\": \"Development genes and evolution\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single localization experiment in Drosophila, no functional mechanistic follow-up for PRELID1 specifically\",\n      \"pmids\": [\"15700158\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"Drosophila Preli-like (Prel) loss-of-function in neurons decreases cellular ATP levels, causes mitochondrial fragmentation and sparse distribution in dendrites/axons, and leads to simplified/retracted dendritic arbors. Overexpression of Drob-1 (Bax-like) phenocopies this, while expression of Drob-1 antagonist Buffy in prel mutants restores dendritic morphology, placing Prel upstream of Bcl-2 family regulation of mitochondrial activity.\",\n      \"method\": \"Genetic loss-of-function (prel mutant Drosophila); ATP measurement; mitochondrial morphology imaging; genetic epistasis with Drob-1 and Buffy; measurement of respiratory chain complex IV activity\",\n      \"journal\": \"Development (Cambridge, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis in Drosophila model with multiple orthogonal readouts (ATP, morphology, complex IV activity), single lab\",\n      \"pmids\": [\"19855018\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"An alternative polyadenylation (APA) event in PRELID1 mRNA enhances its steady-state level and translational efficiency; PRELID1 regulates mitochondrial reactive oxygen species (ROS) production in a cell-type-specific manner.\",\n      \"method\": \"PAS-seq (polyadenylation site sequencing) in primary breast tumor specimens; PRELID1 modulation (knockdown/overexpression) with measurement of mitochondrial ROS\",\n      \"journal\": \"Molecular cancer research : MCR\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, ROS phenotype established but molecular mechanism of how PRELID1 regulates ROS not mechanistically defined beyond PA/CL pathway inference\",\n      \"pmids\": [\"28912168\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"PRELID1 knockdown in HepG2 cells under oxidative stress leads to up-regulation of caspase-3 and down-regulation of SOD-1, increased mitochondrial apoptosis, and enhanced cellular senescence, demonstrating PRELID1 suppresses apoptosis and senescence in hepatocellular carcinoma cells.\",\n      \"method\": \"siRNA knockdown of PRELID1 in HepG2 cells; RT-PCR for caspase-3 and SOD-1; fluorescence-based mitochondrial apoptosis assay; senescence assay\",\n      \"journal\": \"Annals of clinical and laboratory science\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single knockdown approach, limited mechanistic resolution beyond phenotypic gene expression changes\",\n      \"pmids\": [\"26275693\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PRELID1 (the mammalian Ups1 ortholog) is required for pathological accumulation of cardiolipin within mitochondria when the phospholipid efflux transporter BLTP1 is absent; depleting PRELID1 prevents apoptosis caused by BLTP1 deficiency, genetically placing PRELID1 downstream of BLTP1-mediated lipid efflux and upstream of CL-driven apoptosis.\",\n      \"method\": \"Genetic epistasis (double depletion of BLTP1 and PRELID1); measurement of PA, PG, and CL levels; apoptosis assays; ROS measurement\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean epistasis with defined molecular phenotype (lipid accumulation + apoptosis), preprint not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.09.30.679455\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Ups1 (yeast PRELID1 ortholog) preferentially binds positively curved membrane regions for phosphatidic acid extraction; PA extraction is energetically favored at high-positive-curvature domains; events at the donor membrane are rate-limiting for the lipid transfer cycle; membrane binding is modulated by pH, lipid composition, and membrane morphology.\",\n      \"method\": \"In vitro lipid transfer assays with membranes of defined curvature; biophysical binding measurements; computational/MD modeling\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — in vitro reconstitution with curvature-defined membranes is rigorous but preprint, single lab, not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.04.03.647039\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"PRELID1 (PRELI) is a mitochondrial intermembrane space lipid transfer protein that forms a complex with TRIAP1, transfers phosphatidic acid from the outer to the inner mitochondrial membrane for cardiolipin synthesis, and thereby prevents cytochrome c release and apoptosis; its stability is regulated by binding to the chaperone Mdm35 (TRIAP1 in mammals) and by mitochondrial proteases, while its PA-extraction activity is tuned by membrane curvature, pH, and lipid composition at the donor membrane.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PRELID1 (PRELI) is a mitochondrial intermembrane-space lipid transfer protein that controls cardiolipin homeostasis and thereby sets the threshold for mitochondrial apoptosis [#0]. It forms a complex with TRIAP1 that extracts phosphatidic acid and transfers it across the IMS to the inner membrane for cardiolipin synthesis; loss of PRELID1 impairs cardiolipin accumulation, facilitates cytochrome c release, and sensitizes cells to apoptosis, with survival rescued by exogenous phosphatidylglycerol [#0]. PRELID1 is targeted to mitochondria by an N-terminal mitochondrial targeting signal [#4]. Work on the yeast ortholog Ups1 established the conserved logic of this pathway: Ups1 is an intrinsically unstable IMS protein whose stability and import are protected by binding the twin Cx9C protein Mdm35 (TRIAP1 in mammals), with turnover executed by the proteases Atp23 and Yme1 [#1], and its phosphatidic-acid extraction is rate-limited by donor-membrane events, favored at positively curved membrane domains and tuned by pH and lipid composition [#10]. Consistent with its role in cardiolipin-driven death, PRELID1 acts downstream of BLTP1-mediated phospholipid efflux: depleting PRELID1 blocks the pathological cardiolipin accumulation and apoptosis caused by BLTP1 loss [#9]. Beyond cardiolipin transfer, PRELID1 associates with the dynamin-like GTPase OPA1 and supports mitochondrial morphology, membrane potential, and respiratory chain function in a manner requiring its LEA motif [#2], and it modulates mitochondrial ROS and apoptotic/senescence responses across cell types [#3, #8].\",\n  \"teleology\": [\n    {\n      \"year\": 2004,\n      \"claim\": \"Establishing where PRELI acts was the first step; demonstrating mitochondrial residence framed all subsequent mechanistic work.\",\n      \"evidence\": \"GFP-fusion live imaging and subcellular fractionation identifying an N-terminal mitochondrial targeting signal\",\n      \"pmids\": [\"14640972\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not resolve sub-mitochondrial localization (IMS vs matrix)\", \"No functional role assigned\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Yeast genetics resolved how the unstable PRELI/Ups1 protein is stabilized and degraded, defining the chaperone-protease control of cardiolipin regulation.\",\n      \"evidence\": \"Yeast genetic epistasis, reciprocal Ups1/Mdm35 co-IP, and protease mutant (\\u0394yme1, \\u0394atp23) turnover analysis\",\n      \"pmids\": [\"20657548\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not directly demonstrate lipid transfer biochemistry\", \"Mammalian protease equivalents not tested here\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"A parallel line tied PRELI to OPA1 and bioenergetics, linking it to mitochondrial morphology and respiratory function beyond a purely structural role.\",\n      \"evidence\": \"PRELI\\u2013OPA1 co-IP, dominant-negative LEA(-) mutant, siRNA knockdown with \\u0394\\u03a8m/O2/ROS/complex readouts, and mouse embryo lethality\",\n      \"pmids\": [\"21364629\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"OPA1 interaction not validated structurally or by reconstitution\", \"Dominant-negative approach carries interpretive caveats\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"The central mechanism was defined: PRELI/TRIAP1 directly transfers phosphatidic acid for cardiolipin synthesis, mechanistically coupling lipid handling to apoptosis sensitivity.\",\n      \"evidence\": \"TRIAP1/PRELI co-IP, in vitro lipid transfer assay, siRNA loss-of-function with CL/cytochrome c/apoptosis measurement, and phosphatidylglycerol rescue\",\n      \"pmids\": [\"23931759\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of PA binding not resolved\", \"Regulation of transfer in cells not defined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Post-transcriptional control was identified, showing alternative polyadenylation raises PRELID1 levels and links it to cell-type-specific ROS regulation.\",\n      \"evidence\": \"PAS-seq in breast tumor specimens with PRELID1 modulation and mitochondrial ROS measurement\",\n      \"pmids\": [\"28912168\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Molecular mechanism of ROS regulation not defined beyond inference to the PA/CL pathway\", \"Single-lab correlative tumor data\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Genetic epistasis placed PRELID1 in a defined lipid-flux circuit, showing it is required downstream of BLTP1 for pathological cardiolipin accumulation and apoptosis.\",\n      \"evidence\": \"Double depletion of BLTP1 and PRELID1 with PA/PG/CL, apoptosis, and ROS measurement (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.09.30.679455\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not peer-reviewed\", \"Direct physical relationship between BLTP1 and PRELID1 not established\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Biophysical reconstitution refined the transfer mechanism, showing donor-membrane curvature is the rate-limiting determinant of PA extraction.\",\n      \"evidence\": \"In vitro lipid transfer with curvature-defined membranes, biophysical binding, and MD modeling (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.04.03.647039\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not peer-reviewed\", \"Performed on yeast Ups1; mammalian PRELID1 curvature preference not confirmed\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PRELID1's lipid transfer activity, OPA1 association, and ROS/apoptosis outputs are integrated and regulated in mammalian cells remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of mammalian PRELID1/TRIAP1 bound to PA\", \"Mechanism connecting cardiolipin transfer to OPA1-dependent morphology unclear\", \"In vivo physiological role beyond embryonic lethality uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [0, 10]},\n      {\"term_id\": \"GO:0140104\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [0, 4, 5]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [0]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"complexes\": [\"PRELID1\\u2013TRIAP1 (Ups1\\u2013Mdm35) lipid transfer complex\"],\n    \"partners\": [\"TRIAP1\", \"OPA1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":5,"faith_total":5,"faith_pct":100.0}}