{"gene":"PEF1","run_date":"2026-04-29T11:37:58","timeline":{"discoveries":[{"year":2019,"finding":"The penta-EF-hand protein PEF1 of Neurospora crassa accumulates at sites of plasma membrane injury in a Ca2+-dependent manner, as shown by live-cell fluorescence imaging of GFP-tagged PEF1. Site-directed mutagenesis of Ca2+-binding EF-hand domains abolished both the spatial recruitment dynamics and the membrane repair function, establishing that Ca2+ binding is essential for PEF1 activity at membrane damage sites.","method":"Live-cell fluorescence/GFP imaging, site-directed mutagenesis of Ca2+-binding domains, gene deletion in wild-type and lysis-prone mutant backgrounds","journal":"Genetics","confidence":"Medium","confidence_rationale":"Tier 2 — direct localization experiment tied to functional consequence, with mutagenesis validation; single lab, multiple orthogonal methods","pmids":["31270133"],"is_preprint":false},{"year":2019,"finding":"Deletion of pef1 in N. crassa sensitizes cells to membrane disruption during cell-cell fusion and in the presence of pore-forming drugs (e.g., the plant defense compound tomatine), demonstrating that PEF1 is required for plasma membrane integrity and repair in fungi.","method":"Gene knockout (pef1 deletion) in wild-type and lysis-prone mutant backgrounds; treatment with pore-forming drug tomatine; cell fusion assays","journal":"Genetics","confidence":"Medium","confidence_rationale":"Tier 2 — loss-of-function with specific phenotypic readout across multiple conditions; single lab","pmids":["31270133"],"is_preprint":false},{"year":2019,"finding":"PEF1-mediated membrane repair in N. crassa is associated with compartmentation of the syncytial fungal colony in response to antifungal treatment, as revealed by subcellular localization studies with GFP-PEF1.","method":"GFP tagging and fluorescence imaging during antifungal drug treatment","journal":"Genetics","confidence":"Low","confidence_rationale":"Tier 3 — localization observation with limited mechanistic follow-up; single lab, single method","pmids":["31270133"],"is_preprint":false},{"year":2026,"finding":"In Candida albicans, Pef1 (penta-EF-hand ortholog of human ALG-2/PEF1) localizes to sites of polarized growth in yeast and hyphal cells, and redistributes to punctate spots at the plasma membrane upon treatment with amphotericin B or tomatine, indicating Ca2+-dependent recruitment to sites of membrane perturbation.","method":"GFP-tagging and fluorescence microscopy; treatment with polyene drug amphotericin B and saponin tomatine; genetic deletion of calcineurin A (cna1) and its transcription factor crz1","journal":"G3 (Bethesda, Md.)","confidence":"Medium","confidence_rationale":"Tier 2 — direct localization tied to functional consequence with multiple perturbation conditions; single lab, multiple orthogonal approaches","pmids":["41920808"],"is_preprint":false},{"year":2026,"finding":"Deletion of PEF1 in C. albicans results in failure of hyphae to maintain plasma membrane integrity in serum, and the pef1Δ mutant shows attenuated virulence in an insect larvae infection model, establishing a role for Pef1 in membrane integrity during pathogenic growth.","method":"Gene deletion (pef1Δ), plasma membrane integrity assays in serum, insect larvae infection model (in vivo virulence assay)","journal":"G3 (Bethesda, Md.)","confidence":"Medium","confidence_rationale":"Tier 2 — loss-of-function with specific membrane integrity phenotype and in vivo virulence readout; single lab","pmids":["41920808"],"is_preprint":false},{"year":2026,"finding":"Loss of calcineurin A (Cna1), but not its downstream transcription factor Crz1, phenocopies the punctate membrane localization of GFP-Pef1 in C. albicans, placing Pef1 downstream of calcineurin in the membrane stress response pathway.","method":"Genetic deletion of cna1 and crz1; GFP-Pef1 localization imaging","journal":"G3 (Bethesda, Md.)","confidence":"Low","confidence_rationale":"Tier 3 — genetic epistasis via single localization readout; single lab, single method","pmids":["41920808"],"is_preprint":false}],"current_model":"PEF1 (penta-EF-hand protein, ortholog of human ALG-2) functions as a Ca2+-dependent membrane repair protein that is recruited to sites of plasma membrane injury and perturbation; its EF-hand Ca2+-binding domains are essential for both its spatial dynamics and protective function, and loss of PEF1 impairs membrane integrity during cell fusion, antifungal drug treatment, and pathogenic hyphal growth, with the calcineurin pathway acting upstream of Pef1 localization."},"narrative":{"teleology":[],"mechanism_profile":{"molecular_activity":[],"localization":[],"pathway":[],"complexes":[],"partners":[],"other_free_text":[]},"mechanistic_narrative":"Insufficient on-target evidence to synthesize a narrative — discovery timeline does not match the canonical PEF1 protein."},"prefetch_data":{"uniprot":{"accession":"Q9UBV8","full_name":"Peflin","aliases":["PEF protein with a long N-terminal hydrophobic domain","Penta-EF hand domain-containing protein 1"],"length_aa":284,"mass_kda":30.4,"function":"Calcium-binding protein that acts as an adapter that bridges unrelated proteins or stabilizes weak protein-protein complexes in response to calcium. Together with PDCD6, acts as a calcium-dependent adapter for the BCR(KLHL12) complex, a complex involved in endoplasmic reticulum (ER)-Golgi transport by regulating the size of COPII coats (PubMed:27716508). In response to cytosolic calcium increase, the heterodimer formed with PDCD6 interacts with, and bridges together the BCR(KLHL12) complex and SEC31 (SEC31A or SEC31B), promoting monoubiquitination of SEC31 and subsequent collagen export, which is required for neural crest specification (PubMed:27716508). Its role in the heterodimer formed with PDCD6 is however unclear: some evidence shows that PEF1 and PDCD6 work together and promote association between PDCD6 and SEC31 in presence of calcium (PubMed:27716508). Other reports show that PEF1 dissociates from PDCD6 in presence of calcium, and may act as a negative regulator of PDCD6 (PubMed:11278427). Also acts as a negative regulator of ER-Golgi transport; possibly by inhibiting interaction between PDCD6 and SEC31 (By similarity)","subcellular_location":"Cytoplasm; Endoplasmic reticulum; Membrane; Cytoplasmic vesicle, COPII-coated vesicle membrane","url":"https://www.uniprot.org/uniprotkb/Q9UBV8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/PEF1","classification":"Common Essential","n_dependent_lines":456,"n_total_lines":1208,"dependency_fraction":0.37748344370860926},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"PDCD6","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/PEF1","total_profiled":1310},"omim":[{"mim_id":"610033","title":"PENTA-EF-HAND DOMAIN-CONTAINING PROTEIN 1; PEF1","url":"https://www.omim.org/entry/610033"},{"mim_id":"601057","title":"PROGRAMMED CELL DEATH 6; PDCD6","url":"https://www.omim.org/entry/601057"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Vesicles","reliability":"Approved"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PEF1"},"hgnc":{"alias_symbol":["PEF1A"],"prev_symbol":[]},"alphafold":{"accession":"Q9UBV8","domains":[{"cath_id":"1.10.238.10","chopping":"116-280","consensus_level":"medium","plddt":94.1204,"start":116,"end":280}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UBV8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UBV8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UBV8-F1-predicted_aligned_error_v6.png","plddt_mean":73.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PEF1","jax_strain_url":"https://www.jax.org/strain/search?query=PEF1"},"sequence":{"accession":"Q9UBV8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UBV8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UBV8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UBV8"}},"corpus_meta":[{"pmid":"7769658","id":"PMC_7769658","title":"The enhancer in the long control region of human papillomavirus type 16 is up-regulated by PEF-1 and down-regulated by Oct-1.","date":"1995","source":"Journal of virology","url":"https://pubmed.ncbi.nlm.nih.gov/7769658","citation_count":38,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"32788233","id":"PMC_32788233","title":"The S. pombe CDK5 ortholog Pef1 regulates sexual differentiation through control of the TORC1 pathway and autophagy.","date":"2020","source":"Journal of cell science","url":"https://pubmed.ncbi.nlm.nih.gov/32788233","citation_count":11,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"16893567","id":"PMC_16893567","title":"Molecular analysis of the 21-kb bacteriocin-encoding plasmid pEF1 from Enterococcus faecium 6T1a.","date":"2006","source":"Plasmid","url":"https://pubmed.ncbi.nlm.nih.gov/16893567","citation_count":10,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31270133","id":"PMC_31270133","title":"Plasma Membrane Integrity During Cell-Cell Fusion and in Response to Pore-Forming Drugs Is Promoted by the Penta-EF-Hand Protein PEF1 in Neurospora crassa.","date":"2019","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31270133","citation_count":6,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"39335057","id":"PMC_39335057","title":"Characterization of Two Novel Endolysins from Bacteriophage PEF1 and Evaluation of Their Combined Effects on the Control of Enterococcus faecalis Planktonic and Biofilm Cells.","date":"2024","source":"Antibiotics (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/39335057","citation_count":4,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"33445784","id":"PMC_33445784","title":"The S. pombe CDK5 Orthologue Pef1 Cooperates with Three Cyclins, Clg1, Pas1 and Psl1, to Promote Pre-Meiotic DNA Replication.","date":"2021","source":"Biomolecules","url":"https://pubmed.ncbi.nlm.nih.gov/33445784","citation_count":3,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"31895039","id":"PMC_31895039","title":"The CDK Pef1 and protein phosphatase 4 oppose each other for regulating cohesin binding to fission yeast chromosomes.","date":"2020","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/31895039","citation_count":2,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"9820151","id":"PMC_9820151","title":"PEF-1, an epithelial cell transcription factor which activates the long control region of human papillomavirus type 16, is glycosylated with N-acetylglucosamine.","date":"1998","source":"The Journal of general virology","url":"https://pubmed.ncbi.nlm.nih.gov/9820151","citation_count":2,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"38915521","id":"PMC_38915521","title":"In Vivo Proximity Labeling Identifies a New Function for the Lifespan and Autophagy-regulating Kinase Pef1, an Ortholog of Human Cdk5.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38915521","citation_count":0,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":"41920808","id":"PMC_41920808","title":"The penta-EF-hand protein Pef1 of Candida albicans functions at sites of membrane perturbation to support polarized growth and membrane integrity.","date":"2026","source":"G3 (Bethesda, Md.)","url":"https://pubmed.ncbi.nlm.nih.gov/41920808","citation_count":0,"is_preprint":false,"source_track":"pubmed_title"},{"pmid":null,"id":"bio_10.1101_2024.09.06.611525","title":"The penta-EF-hand protein Pef1 of<i>Candida albicans</i>functions at sites of membrane perturbation to support polarized growth and membrane integrity","date":"2024-09-07","source":"bioRxiv","url":"https://doi.org/10.1101/2024.09.06.611525","citation_count":0,"is_preprint":true,"source_track":"pubmed_title"},{"pmid":null,"id":"bio_10.1101_2024.06.12.598664","title":"<i>In Vivo</i>Proximity Labeling Identifies a New Function for the Lifespan and Autophagy-regulating Kinase Pef1, an Ortholog of Human Cdk5","date":"2024-06-14","source":"bioRxiv","url":"https://doi.org/10.1101/2024.06.12.598664","citation_count":0,"is_preprint":true,"source_track":"pubmed_title"},{"pmid":"16189514","id":"PMC_16189514","title":"Towards a proteome-scale map of the human protein-protein interaction network.","date":"2005","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/16189514","citation_count":2090,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"12477932","id":"PMC_12477932","title":"Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.","date":"2002","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/12477932","citation_count":1479,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"26186194","id":"PMC_26186194","title":"The BioPlex Network: A Systematic Exploration of the Human Interactome.","date":"2015","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/26186194","citation_count":1118,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"28514442","id":"PMC_28514442","title":"Architecture of the human interactome defines protein communities and disease networks.","date":"2017","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/28514442","citation_count":1085,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"25416956","id":"PMC_25416956","title":"A proteome-scale map of the human interactome 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Interface.","date":"2015","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/26638075","citation_count":433,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"35271311","id":"PMC_35271311","title":"OpenCell: Endogenous tagging for the cartography of human cellular organization.","date":"2022","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/35271311","citation_count":432,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"16344560","id":"PMC_16344560","title":"Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes.","date":"2005","source":"Genome research","url":"https://pubmed.ncbi.nlm.nih.gov/16344560","citation_count":409,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"26344197","id":"PMC_26344197","title":"Panorama of ancient metazoan macromolecular complexes.","date":"2015","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/26344197","citation_count":407,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"14744259","id":"PMC_14744259","title":"14-3-3-affinity purification of over 200 human phosphoproteins reveals new links to regulation of cellular metabolism, proliferation and trafficking.","date":"2004","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/14744259","citation_count":372,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"22810586","id":"PMC_22810586","title":"Interpreting cancer genomes using systematic host network perturbations by tumour virus proteins.","date":"2012","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/22810586","citation_count":319,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21145461","id":"PMC_21145461","title":"Dynamics of cullin-RING ubiquitin ligase network revealed by systematic quantitative proteomics.","date":"2010","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/21145461","citation_count":318,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"16429158","id":"PMC_16429158","title":"Disrupted function and axonal distribution of mutant tyrosyl-tRNA synthetase in dominant intermediate Charcot-Marie-Tooth neuropathy.","date":"2006","source":"Nature genetics","url":"https://pubmed.ncbi.nlm.nih.gov/16429158","citation_count":317,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"31006538","id":"PMC_31006538","title":"Intrinsically Disordered Protein TEX264 Mediates ER-phagy.","date":"2019","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/31006538","citation_count":296,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"12975309","id":"PMC_12975309","title":"The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment.","date":"2003","source":"Genome research","url":"https://pubmed.ncbi.nlm.nih.gov/12975309","citation_count":285,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"17207965","id":"PMC_17207965","title":"hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes.","date":"2007","source":"Genomics","url":"https://pubmed.ncbi.nlm.nih.gov/17207965","citation_count":222,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"20458337","id":"PMC_20458337","title":"MHC class II-associated proteins in B-cell exosomes and potential functional implications for exosome biogenesis.","date":"2010","source":"Immunology and cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/20458337","citation_count":221,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21988832","id":"PMC_21988832","title":"Toward an understanding of the protein interaction network of the human liver.","date":"2011","source":"Molecular systems biology","url":"https://pubmed.ncbi.nlm.nih.gov/21988832","citation_count":207,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"21516116","id":"PMC_21516116","title":"Next-generation sequencing to generate interactome datasets.","date":"2011","source":"Nature methods","url":"https://pubmed.ncbi.nlm.nih.gov/21516116","citation_count":200,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"16196087","id":"PMC_16196087","title":"Large-scale analysis of the human ubiquitin-related proteome.","date":"2005","source":"Proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/16196087","citation_count":154,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"23533145","id":"PMC_23533145","title":"In-depth proteomic analyses of exosomes isolated from expressed prostatic secretions in urine.","date":"2013","source":"Proteomics","url":"https://pubmed.ncbi.nlm.nih.gov/23533145","citation_count":138,"is_preprint":false,"source_track":"gene2pubmed"},{"pmid":"30554943","id":"PMC_30554943","title":"Interactome Rewiring Following Pharmacological Targeting of BET Bromodomains.","date":"2018","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/30554943","citation_count":136,"is_preprint":false,"source_track":"gene2pubmed"}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":6895,"output_tokens":999,"usd":0.017835},"stage2":{"model":"claude-opus-4-6","input_tokens":3822,"output_tokens":1035,"usd":0.067477},"total_usd":0.17094,"stage1_batch_id":"msgbatch_012ZiiCUBfB62NCTQd4Bk1Jo","stage2_batch_id":"msgbatch_01Xuqq9aUHoQouS7UVGZNStZ","note":"batch pricing = 50% of standard","round2_stage1":{"model":"claude-sonnet-4-6","input_tokens":18500,"output_tokens":2269,"usd":0.044768},"round2_rules_fired":"R3","round2_stage2":{"model":"claude-opus-4-6","input_tokens":4913,"output_tokens":107,"usd":0.04086}},"stage1_raw":"Looking at the corpus, I need to identify which papers are about the human gene PEF1. \n\nThe human gene PEF1 encodes a penta-EF-hand calcium-binding protein (also known as ALG-2 interacting protein, or sorcin-like). The papers about S. pombe Pef1 (CDK5 ortholog) and HPV transcription factor PEF-1 appear to be symbol collisions with different proteins. Let me assess:\n\n- Papers 1, 8: HPV transcription factor \"PEF-1\" - this is a cellular transcription factor binding HPV LCR, not a penta-EF-hand protein. Symbol collision - SKIP.\n- Papers 2, 6, 7, 9, 12: S. pombe Pef1 as CDK5 ortholog - CDK5 is a kinase, not a penta-EF-hand protein. Symbol collision with human PEF1 (penta-EF-hand protein). SKIP.\n- Papers 3, 5: Bacteriophage/plasmid pEF1 - completely different. SKIP.\n- Papers 4, 10, 11: Neurospora crassa and Candida albicans PEF1 as penta-EF-hand protein, ortholog of human ALG-2/PEF1. These are consistent with the human PEF1 gene function. INCLUDE.\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2019,\n      \"finding\": \"The penta-EF-hand protein PEF1 of Neurospora crassa accumulates at sites of plasma membrane injury in a Ca2+-dependent manner, and site-directed mutagenesis of Ca2+-binding EF-hand domains abolished both the spatial dynamics and protective function of the protein. Loss of PEF1 impaired membrane integrity during cell-cell fusion and in response to pore-forming drugs such as tomatine.\",\n      \"method\": \"Fluorescence and live-cell imaging of GFP-tagged PEF1, site-directed mutagenesis of Ca2+-binding domains, gene deletion with defined membrane-integrity phenotypic readouts\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (live imaging, mutagenesis, KO phenotype) in a single rigorous study\",\n      \"pmids\": [\"31270133\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"In Candida albicans, the penta-EF-hand protein Pef1 (ortholog of human PEF1/ALG-2) localizes to sites of polarized growth and redistributes to punctate membrane spots upon treatment with amphotericin B or tomatine, or upon loss of calcineurin A (Cna1) but not its transcription factor Crz1. Deletion of PEF1 caused loss of plasma membrane integrity in hyphae grown in serum and attenuated virulence in an insect larvae infection model.\",\n      \"method\": \"GFP-tagging and live-cell fluorescence microscopy, pharmacological treatment (amphotericin B, tomatine), genetic deletion (pef1Δ, cna1Δ, crz1Δ) with membrane integrity and virulence readouts\",\n      \"journal\": \"G3 (Bethesda, Md.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (live imaging, drug treatment, epistasis with calcineurin pathway, KO phenotype) with functional consequence\",\n      \"pmids\": [\"41920808\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PEF1 encodes a penta-EF-hand Ca2+-binding protein that is recruited in a Ca2+-dependent manner to sites of plasma membrane damage, where it promotes membrane repair and integrity; its Ca2+-binding EF-hand domains are essential for both its dynamic localization and its protective function.\"\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\nI'll classify each paper first, then extract discoveries only from KEPT papers.\n\n**CLASSIFICATION:**\n\n**Retrieved Papers:**\n1. PMID:7769658 — \"PEF-1\" is a transcription factor binding HPV16 LCR. This is NOT the canonical human PEF1 (penta-EF-hand protein/ALG-2 family). This is an ALIAS COLLISION. → EXCLUDE\n2. PMID:32788233 — S. pombe Pef1, CDK5 ortholog. Domains/function incompatible with human PEF1 (penta-EF-hand protein). SYMBOL COLLISION. → EXCLUDE\n3. PMID:16893567 — Plasmid pEF1 from Enterococcus. Not a gene product. SYMBOL COLLISION. → EXCLUDE\n4. PMID:31270133 — Neurospora crassa penta-EF-hand protein PEF1. Compatible ortholog of human PEF1/ALG-2. → KEEP\n5. PMID:39335057 — Bacteriophage PEF1 endolysins. SYMBOL COLLISION. → EXCLUDE\n6. PMID:33445784 — S. pombe Pef1, CDK5 ortholog. SYMBOL COLLISION. → EXCLUDE\n7. PMID:31895039 — S. pombe Pef1 CDK. SYMBOL COLLISION. → EXCLUDE\n8. PMID:9820151 — \"PEF-1\" HPV transcription factor. ALIAS COLLISION. → EXCLUDE\n9. PMID:38915521 — S. pombe Pef1, CDK5 ortholog. SYMBOL COLLISION. → EXCLUDE\n10. PMID:41920808 — Candida albicans Pef1, penta-EF-hand protein, ortholog of human ALG-2/PEF1. → KEEP\n11. bio_10.1101_2024.09.06.611525 — Preprint version of PMID:41920808. → KEEP (but covered by peer-reviewed)\n12. bio_10.1101_2024.06.12.598664 — S. pombe Pef1, CDK5 ortholog. SYMBOL COLLISION. → EXCLUDE\n\n**Gene2pubmed Curated Papers:**\nThese are large-scale proteomics/interactome studies that detected PEF1 as part of broader screens. None describe direct mechanistic experiments specifically about PEF1's mechanism. They provide interaction data (e.g., BioPlex AP-MS) but no specific mechanistic characterization. I'll note any that contain actionable mechanistic data for PEF1 specifically — reviewing them: PMID:26186194, PMID:28514442, PMID:32296183, PMID:33961781 (BioPlex series) identified PEF1 interactions by AP-MS but no PEF1-specific mechanistic findings are described in the abstracts. PMID:26638075 (centrosome BioID) — no specific PEF1 finding. PMID:35271311 (OpenCell) — localization data possible. None of the gene2pubmed abstracts describe specific mechanistic findings about PEF1 beyond its detection in large-scale screens. → All EXCLUDE from discovery extraction (no PEF1-specific mechanistic data in abstracts).\n\n**DISCOVERIES from KEPT papers:**\n\n```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2019,\n      \"finding\": \"The penta-EF-hand protein PEF1 of Neurospora crassa accumulates at sites of plasma membrane injury in a Ca2+-dependent manner, as shown by live-cell fluorescence imaging of GFP-tagged PEF1. Site-directed mutagenesis of Ca2+-binding EF-hand domains abolished both the spatial recruitment dynamics and the membrane repair function, establishing that Ca2+ binding is essential for PEF1 activity at membrane damage sites.\",\n      \"method\": \"Live-cell fluorescence/GFP imaging, site-directed mutagenesis of Ca2+-binding domains, gene deletion in wild-type and lysis-prone mutant backgrounds\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct localization experiment tied to functional consequence, with mutagenesis validation; single lab, multiple orthogonal methods\",\n      \"pmids\": [\"31270133\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Deletion of pef1 in N. crassa sensitizes cells to membrane disruption during cell-cell fusion and in the presence of pore-forming drugs (e.g., the plant defense compound tomatine), demonstrating that PEF1 is required for plasma membrane integrity and repair in fungi.\",\n      \"method\": \"Gene knockout (pef1 deletion) in wild-type and lysis-prone mutant backgrounds; treatment with pore-forming drug tomatine; cell fusion assays\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function with specific phenotypic readout across multiple conditions; single lab\",\n      \"pmids\": [\"31270133\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"PEF1-mediated membrane repair in N. crassa is associated with compartmentation of the syncytial fungal colony in response to antifungal treatment, as revealed by subcellular localization studies with GFP-PEF1.\",\n      \"method\": \"GFP tagging and fluorescence imaging during antifungal drug treatment\",\n      \"journal\": \"Genetics\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — localization observation with limited mechanistic follow-up; single lab, single method\",\n      \"pmids\": [\"31270133\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"In Candida albicans, Pef1 (penta-EF-hand ortholog of human ALG-2/PEF1) localizes to sites of polarized growth in yeast and hyphal cells, and redistributes to punctate spots at the plasma membrane upon treatment with amphotericin B or tomatine, indicating Ca2+-dependent recruitment to sites of membrane perturbation.\",\n      \"method\": \"GFP-tagging and fluorescence microscopy; treatment with polyene drug amphotericin B and saponin tomatine; genetic deletion of calcineurin A (cna1) and its transcription factor crz1\",\n      \"journal\": \"G3 (Bethesda, Md.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — direct localization tied to functional consequence with multiple perturbation conditions; single lab, multiple orthogonal approaches\",\n      \"pmids\": [\"41920808\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Deletion of PEF1 in C. albicans results in failure of hyphae to maintain plasma membrane integrity in serum, and the pef1Δ mutant shows attenuated virulence in an insect larvae infection model, establishing a role for Pef1 in membrane integrity during pathogenic growth.\",\n      \"method\": \"Gene deletion (pef1Δ), plasma membrane integrity assays in serum, insect larvae infection model (in vivo virulence assay)\",\n      \"journal\": \"G3 (Bethesda, Md.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — loss-of-function with specific membrane integrity phenotype and in vivo virulence readout; single lab\",\n      \"pmids\": [\"41920808\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Loss of calcineurin A (Cna1), but not its downstream transcription factor Crz1, phenocopies the punctate membrane localization of GFP-Pef1 in C. albicans, placing Pef1 downstream of calcineurin in the membrane stress response pathway.\",\n      \"method\": \"Genetic deletion of cna1 and crz1; GFP-Pef1 localization imaging\",\n      \"journal\": \"G3 (Bethesda, Md.)\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 — genetic epistasis via single localization readout; single lab, single method\",\n      \"pmids\": [\"41920808\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PEF1 (penta-EF-hand protein, ortholog of human ALG-2) functions as a Ca2+-dependent membrane repair protein that is recruited to sites of plasma membrane injury and perturbation; its EF-hand Ca2+-binding domains are essential for both its spatial dynamics and protective function, and loss of PEF1 impairs membrane integrity during cell fusion, antifungal drug treatment, and pathogenic hyphal growth, with the calcineurin pathway acting upstream of Pef1 localization.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"PEF1 encodes a penta-EF-hand Ca²⁺-binding protein that functions in plasma membrane repair and integrity. PEF1 accumulates at sites of membrane damage in a Ca²⁺-dependent manner, and site-directed mutagenesis of its EF-hand Ca²⁺-binding domains abolishes both its dynamic relocalization and its protective function [PMID:31270133]. Loss of PEF1 impairs membrane integrity during cell-cell fusion, in response to pore-forming agents, and during hyphal growth, and attenuates virulence in a fungal pathogen infection model [PMID:31270133, PMID:41920808].\",\n  \"teleology\": [\n    {\n      \"year\": 2019,\n      \"claim\": \"Establishing that PEF1 is a Ca²⁺-dependent membrane repair factor: prior to this work, the cellular role of fungal penta-EF-hand proteins was unknown; this study demonstrated that PEF1 accumulates at plasma membrane damage sites in a Ca²⁺-dependent manner and that its EF-hand domains are essential for both relocalization and protection of membrane integrity during cell fusion and pore-forming drug challenge.\",\n      \"evidence\": \"Live-cell imaging of GFP-PEF1, site-directed mutagenesis of EF-hand domains, and gene deletion with membrane-integrity phenotypic assays in Neurospora crassa\",\n      \"pmids\": [\"31270133\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Downstream effectors or binding partners through which PEF1 promotes membrane repair are not identified\",\n        \"Whether the mechanism is conserved in mammalian cells has not been tested\",\n        \"The precise lipid or protein signals that recruit PEF1 to damage sites remain unknown\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Extending PEF1 function to a pathogenic fungus and linking it to virulence: this study showed that Candida albicans Pef1 localizes to polarized growth sites, redistributes to membrane puncta upon pore-forming drug treatment or loss of calcineurin (but not its downstream transcription factor Crz1), and is required for hyphal membrane integrity and full virulence in an insect infection model.\",\n      \"evidence\": \"GFP-tagging with live-cell microscopy, pharmacological perturbation (amphotericin B, tomatine), epistasis analysis with calcineurin pathway mutants, and in vivo Galleria mellonella infection model in Candida albicans\",\n      \"pmids\": [\"41920808\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"The mechanistic relationship between PEF1 and calcineurin signaling is not resolved beyond epistatic positioning\",\n        \"Whether PEF1 directly senses membrane damage or is recruited by an upstream Ca²⁺-sensing cascade is unclear\",\n        \"No structural model of PEF1 at the membrane has been generated\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"The direct molecular partners, substrates, and lipid interactions through which PEF1 mediates membrane repair remain unidentified, and whether this membrane repair function is conserved in mammalian PEF1/ALG-2 orthologs has not been tested.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No interactome or co-immunoprecipitation data for PEF1 in any organism\",\n        \"No reconstitution of PEF1 membrane repair activity in vitro\",\n        \"Functional conservation in mammalian systems is untested\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005886\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}\n```\n\n--- ROUND 2 (R2/R3, augmented corpus) ---\n\n```json\n{\n  \"mechanistic_narrative\": \"Insufficient on-target evidence to synthesize a narrative — discovery timeline does not match the canonical PEF1 protein.\",\n  \"teleology\": [],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [],\n    \"partners\": [],\n    \"other_free_text\": []\n  }\n}\n```"}