{"gene":"PLAA","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":2009,"finding":"The C-terminal PUL domain of PLAA (human ortholog of yeast Doa1/Ufd3) forms a 6-mer Armadillo-containing domain whose positively charged inner ridge binds the C-terminus of p97/Cdc48; Tyr805 of p97 is buried in this ridge and implicated in phosphorylation-dependent regulation. Point mutants disrupting this interaction display only partial loss-of-function phenotypes, indicating the p97-PLAA interaction is required for a subset of PLAA-dependent processes.","method":"Crystal structure of PUL domain–p97 C-terminal peptide complex; structure-guided mutagenesis of yeast Doa1; functional complementation assays in doa1Δ cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution crystal structure combined with mutagenesis and in vivo functional validation in a single rigorous study","pmids":["19887378"],"is_preprint":false},{"year":2010,"finding":"Crystal structure of the PFU-PUL domain pair of yeast Doa1 at 1.9 Å reveals that the PUL domain adopts an Armadillo-like repeat fold with a positively charged concave surface that binds the negatively charged C-terminus of Cdc48; the PFU domain conserved surface is implicated in binding ubiquitin and Hse1. Structural comparison with Ufd2 suggests Doa1 and Ufd2 compete for Cdc48 binding to dictate fate of ubiquitinated proteins.","method":"X-ray crystallography at 1.9 Å resolution; structural comparison","journal":"The Kobe journal of medical sciences","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — high-quality structural data but single lab, limited functional validation reported in abstract","pmids":["21063153"],"is_preprint":false},{"year":2008,"finding":"The PFU domain of yeast Doa1 binds directly to the SH3 domain of Hse1 (component of the ESCRT machinery), mediating Doa1's role in endosomal sorting. Loss of Doa1 causes missorting of MVB cargo GFP-Cps1 and reduces flux of ubiquitinated membrane proteins through the MVB pathway. This function is genetically separable from Doa1's role in maintaining ubiquitin levels.","method":"Direct binding assay (Hse1-SH3 pulldown of Doa1-PFU); site-directed mutations blocking PFU–SH3 interaction; GFP-Cps1 sorting assay; synthetic growth defect in doa1Δ vps27Δ double mutant; ubiquitin overexpression epistasis","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal binding assays, structure-guided mutagenesis, in vivo sorting readout, and genetic epistasis in a single study","pmids":["18508771"],"is_preprint":false},{"year":2014,"finding":"Solution structure of the Doa1/PFU:Hse1/SH3 complex determined by SAXS combined with molecular docking; Asn-438 of Doa1/PFU and Trp-254 of Hse1/SH3 are critical residues for the interaction (hydrogen bonding), whereas Phe-434, implicated in ubiquitin binding, is not required for this interaction.","method":"Small-angle X-ray scattering (SAXS); molecular docking; mutagenesis; biochemical binding assays","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — SAXS structure with mutagenesis, single lab, single study","pmids":["24607902"],"is_preprint":false},{"year":2016,"finding":"Upon lysosomal damage, p97 translocates to lysosomes and cooperates with cofactors UBXD1, PLAA, and the deubiquitylase YOD1 (termed ELDR components) to selectively remove K48-linked ubiquitin conjugates from a subpopulation of damaged lysosomes and promote autophagosome formation. This complex acts downstream of K63-linked ubiquitination and p62 recruitment.","method":"Co-immunoprecipitation of p97 with PLAA, UBXD1, YOD1; lysosomal damage assay (LLOMe); immunofluorescence localization; analysis of p97 disease-mutant MEFs and patient tissue; tau fibril endocytosis model","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, direct localization with functional consequence, genetic disease-mutant validation, replicated across multiple damage models","pmids":["27753622"],"is_preprint":false},{"year":2016,"finding":"Yeast Doa1 (PLAA ortholog) forms a functional complex with Cdc48-Ufd1-Npl4 to mediate mitochondria-associated degradation (MAD) of ubiquitinated outer-membrane proteins. Doa1 directly interacts with ubiquitinated substrates and facilitates their recruitment to the Cdc48 complex. Loss of DOA1 causes accumulation and mislocalization of substrates on mitochondria, and is critical for cell survival under mitochondrial oxidative stress.","method":"Genetic screen for MAD regulators; Co-immunoprecipitation of Doa1 with Cdc48-Ufd1-Npl4; ubiquitinated substrate binding assay; doa1Δ phenotypic analysis under oxidative and ER stress","journal":"The Journal of cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, substrate binding assay, genetic screen, and stress-phenotype readout in single rigorous study","pmids":["27044889"],"is_preprint":false},{"year":2015,"finding":"Yeast Doa1 forms a SUMO-specific ternary complex with Cdc48 and Wss1 metalloprotease. Upon DNA damage, this Wss1/Cdc48/Doa1 complex is recruited to sumoylated targets and the Wss1 protease catalyzes SUMO chain extension (SUMO ligase activity) and subsequent self-cleavage and proteolysis. Doa1 acts as the adaptor in this complex. Upon genotoxic stress, Wss1 (and by extension the complex) is vacuolar.","method":"Co-immunoprecipitation (Wss1/Cdc48/Doa1 complex); in vitro SUMO ligase assay; genetic analysis (smt3-331, Camptothecin, UV); localization by fluorescence microscopy","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — complex reconstitution, in vitro enzymatic assay, genetic epistasis, localization, multiple orthogonal methods","pmids":["26349035"],"is_preprint":false},{"year":2006,"finding":"Yeast Doa1 channels ubiquitin from the proteasomal degradation pathway into pathways mediating DNA damage-induced ubiquitination of PCNA (monoubiquitination) and histone H2B monoubiquitination. In doa1Δ cells, damage-induced PCNA ubiquitination is absent; H2B ubiquitination is reduced basally and absent after DNA damage. The PCNA defect is rescued by ubiquitin overexpression but H2B monoubiquitination is not, indicating an additional specific role for Doa1 in H2B ubiquitination beyond simply supplying ubiquitin.","method":"Genetic interactions (doa1Δ with rad6, rad18, rad5, ubc13, mms2, bre1, lge1, cdc73, ubp8, ubp10, htb2); Western blot for PCNA-Ub and H2B-Ub; ubiquitin overexpression rescue experiments","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with multiple pathway members, biochemical readout of ubiquitin marks, rescue experiments — replicated across multiple damage conditions","pmids":["16705165"],"is_preprint":false},{"year":2017,"finding":"Hypomorphic mutations in PLAA in humans and mice cause infantile-lethal neurodysfunction with seizures. PLAA functions as a ubiquitin adaptor protein for endolysosomal degradation; Plaa mutant neurons accumulate K63-polyubiquitylated proteins and synaptic membrane proteins, disrupting synaptic vesicle recycling and neurotransmission.","method":"Human genetics (biallelic PLAA mutations); mouse Plaa mutant model; immunofluorescence for K63-ubiquitylated proteins; synaptic vesicle recycling assays; electrophysiology of neurotransmission","journal":"American journal of human genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function in both human patients and mouse model with defined molecular (K63-Ub accumulation) and cellular (synaptic vesicle recycling) phenotypes","pmids":["28413018"],"is_preprint":false},{"year":2024,"finding":"De novo missense variants affecting conserved residues within the PUL domain of PLAA reduce PLAA–p97/VCP interaction, as shown by in vitro studies, and are associated with perturbed vesicle recycling. Computational modeling showed abnormal chain arrangements at the C-terminal PUL domain.","method":"Exome/genome sequencing; in vitro PLAA–p97 interaction assay with patient variants; computational structural modeling","journal":"Frontiers in molecular neuroscience","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — in vitro binding assay with patient variants, single lab, limited functional follow-up described in abstract","pmids":["38650658"],"is_preprint":false},{"year":2005,"finding":"PLAA (phospholipase A2-activating protein) is required for 1α,25(OH)2D3-dependent PKCα activation in rat growth plate chondrocytes. PLAA peptide increases arachidonic acid release and PLA2-specific activity in plasma membranes and matrix vesicles; its effect on PKC is blocked by PLA2 inhibitors (quinacrine, AACOCF3) and cyclooxygenase inhibitor indomethacin, indicating PLAA activates PLA2 leading to prostaglandin production acting via EP1 receptor. PLAA peptide also activates PLC-β1 and PLC-β3 via lysophospholipid.","method":"PLAA peptide treatment of primary chondrocytes; arachidonic acid release assay; PLA2 activity assay; PKC isoform activity measurement; pharmacological inhibitor studies; PLC isoform assays","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal biochemical assays with peptide and pharmacological inhibitors, single lab","pmids":["15368540"],"is_preprint":false},{"year":2014,"finding":"PLAA and its membrane receptor partner Pdia3 are required for rapid 1α,25(OH)2D3-mediated activation of CaMKII in growth zone chondrocytes. Caveolae disruption abolishes CaMKII activation by 1α,25(OH)2D3 or PLAA peptide. Immunoprecipitation shows increased CaM binding to PLAA in response to 1α,25(OH)2D3, suggesting CaM links PLAA to CaMKII.","method":"Antibody blocking of PLAA and Pdia3; PLAA peptide treatment; caveolae disruption; CaMKII activity assay; co-immunoprecipitation of PLAA with calmodulin","journal":"Connective tissue research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, peptide activation, and antibody blocking with defined signaling readout, single lab, multiple methods","pmids":["25158196"],"is_preprint":false},{"year":2008,"finding":"PLAA overexpression in HeLa cells increases PGE2, IL-6, activated cytosolic PLA2, COX-2, and NF-κB in response to TNF-α. PLAA promotes annexin A4 downregulation (annexin A4 acts as a PLA2 inhibitor) and clusterin downregulation, thereby amplifying PLA2-dependent inflammation. The plaa promoter contains a stimulatory Sp1-binding element in exon 1 that maintains basal expression and an inhibitory element.","method":"plaa(high)/plaa(low) HeLa Tet-off cell system; ELISA for PGE2, IL-6; Western blot for COX-2, NF-κB; microarray followed by functional assays; luciferase reporter assay; Sp1 decoy oligonucleotides and competitive binding assays","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — overexpression system with multiple downstream readouts, single lab, pathway placement established but no direct enzyme assay for PLAA itself","pmids":["18291623"],"is_preprint":false},{"year":2009,"finding":"PLAA overexpression enhances cisplatin-induced apoptosis in HeLa cells through: (1) accumulation of arachidonic acid causing mitochondrial cytochrome c leakage (blocked by siRNA-PLAA, rescued by exogenous arachidonic acid); (2) downregulation of cytoprotective clusterin; (3) upregulation of pro-apoptotic IL-32; (4) activation of JNK/c-Jun and FasL. PLAA induction by cisplatin also activates PLA2.","method":"plaa(high)/plaa(low) HeLa Tet-off cell system; siRNA-PLAA knockdown; caspase 3/8/9 activity assay; cytochrome c release assay; arachidonic acid rescue; proteomics for phospho-JNK/c-Jun and FasL","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — overexpression and knockdown with multiple functional readouts, arachidonic acid rescue experiment, single lab","pmids":["19258036"],"is_preprint":false},{"year":2022,"finding":"PLAA inhibits the stability of METTL3 protein via ubiquitin-mediated degradation, reducing METTL3 expression, which in turn decreases TRPC3 mRNA stability (via m6A modification). Loss of PLAA leads to elevated METTL3, increased TRPC3, and enhanced intracellular Ca2+ signaling promoting ovarian cancer cell migration and invasion.","method":"PLAA overexpression/knockdown in ovarian cancer cell lines; ubiquitin-mediated METTL3 degradation assay; m6A-seq/MeRIP for TRPC3 mRNA; TRPC3 Ca2+ channel activity measurement; orthotopic xenograft mouse model","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ubiquitin-degradation assay, m6A profiling, in vivo xenograft, single lab with multiple orthogonal methods","pmids":["35869392"],"is_preprint":false},{"year":2025,"finding":"The C. elegans PLAA ortholog UFD-3 directly interacts with the mRNA decapping complex regulatory subunit DCAP-1, and UFD-3's intrinsic disordered region (IDR) is required for recruitment of DCAP-1 to P-bodies. Loss of the IDR does not affect UFD-3's role in sorting ubiquitinated proteins through the MVB pathway, demonstrating that PLAA/UFD-3 regulates P-bodies through a pathway distinct from ubiquitin-dependent protein degradation.","method":"C. elegans genetics; unbiased proteomics (neuronal interactome); in vitro biochemical interaction assay (UFD-3–DCAP-1 direct binding); fluorescence imaging of P-bodies in C. elegans; IDR deletion mutant analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding assay, in vivo imaging, domain deletion with two orthogonal functional readouts, single lab","pmids":["40560612"],"is_preprint":false}],"current_model":"PLAA (phospholipase A2-activating protein) is a multi-domain ubiquitin adaptor protein whose C-terminal PUL domain binds p97/VCP (Cdc48 in yeast) via a positively charged Armadillo-repeat ridge, while its PFU domain binds ubiquitin and ESCRT component Hse1/HRS; acting as part of the p97-UBXD1-PLAA-YOD1 (ELDR) complex, it removes K48-linked ubiquitin conjugates from damaged lysosomes to promote selective autophagy, and as a Cdc48 adaptor (Doa1) it recruits ubiquitinated substrates for mitochondria-associated degradation, MVB sorting, and genotoxic SUMO-conjugate clearance; at synapses, PLAA-dependent K63-ubiquitin-mediated endolysosomal trafficking is essential for synaptic vesicle recycling and neurotransmission, with loss-of-function mutations causing infantile-lethal epileptic encephalopathy; additionally, PLAA activates PLA2 downstream of the Pdia3 membrane receptor in a caveolae-dependent manner to drive arachidonic acid/prostaglandin/PKC/CaMKII signaling in chondrocytes, and its intrinsic disordered region independently regulates cytoplasmic P-body assembly through direct interaction with the mRNA decapping regulator DCAP-1."},"narrative":{"mechanistic_narrative":"PLAA (yeast Doa1/Ufd3, C. elegans UFD-3) is a multi-domain ubiquitin adaptor that links ubiquitinated cargo to the p97/Cdc48 AAA-ATPase to direct protein fate across endolysosomal sorting, organelle-associated degradation, and DNA-damage responses [PMID:27044889, PMID:16705165]. Its C-terminal PUL domain forms a six-helix Armadillo-repeat fold whose positively charged inner ridge engages the acidic C-terminus of p97/Cdc48, while the adjacent PFU domain provides a ubiquitin- and Hse1-binding surface [PMID:19887378, PMID:21063153]. Through the PFU–Hse1/SH3 interaction PLAA couples ubiquitinated membrane cargo to the ESCRT machinery for MVB sorting [PMID:18508771, PMID:24607902], and as an adaptor within the Cdc48-Ufd1-Npl4 complex it recruits ubiquitinated outer-membrane substrates for mitochondria-associated degradation and forms a SUMO-specific complex with Cdc48 and the Wss1 metalloprotease that clears sumoylated targets after genotoxic stress [PMID:27044889, PMID:26349035]. In human cells PLAA, together with p97, UBXD1, and the deubiquitylase YOD1, strips K48-linked ubiquitin conjugates from damaged lysosomes to promote selective autophagy [PMID:27753622]. Biallelic and de novo PUL-domain mutations that weaken the PLAA–p97 interaction cause infantile-lethal epileptic encephalopathy, with mutant neurons accumulating K63-polyubiquitylated and synaptic membrane proteins and failing in synaptic vesicle recycling and neurotransmission [PMID:28413018, PMID:38650658]. Independent of its ubiquitin-degradation role, PLAA's intrinsic disordered region directly binds the decapping regulator DCAP-1 to recruit it to cytoplasmic P-bodies [PMID:40560612]. A separate body of work assigns PLAA a signaling function as an activator of phospholipase A2 downstream of the Pdia3 membrane receptor, driving arachidonic acid release, prostaglandin production, and PKC/CaMKII activation in chondrocytes [PMID:15368540, PMID:25158196].","teleology":[{"year":2006,"claim":"Established that yeast Doa1/PLAA does more than maintain free ubiquitin pools, channeling ubiquitin into specific damage-induced modifications and acting as a dedicated factor for H2B monoubiquitination.","evidence":"Genetic epistasis with DNA-damage ubiquitination machinery plus Western blots for PCNA-Ub and H2B-Ub and ubiquitin-overexpression rescue in yeast","pmids":["16705165"],"confidence":"High","gaps":["Did not define the direct physical mechanism by which Doa1 promotes H2B ubiquitination","No structural basis for substrate selection"]},{"year":2008,"claim":"Identified the PFU domain as the module coupling Doa1 to ESCRT-mediated endosomal sorting, separating this function from ubiquitin homeostasis.","evidence":"Direct PFU–Hse1/SH3 binding assay, structure-guided mutagenesis, GFP-Cps1 MVB sorting readout and genetic epistasis in yeast","pmids":["18508771"],"confidence":"High","gaps":["Atomic detail of the PFU–SH3 interface not resolved","Human ortholog interaction not tested here"]},{"year":2009,"claim":"Resolved how the PUL domain recognizes p97/Cdc48, providing the structural basis for PLAA as a p97 cofactor and showing this interaction supports only a subset of PLAA functions.","evidence":"Crystal structure of the PUL domain–p97 C-terminal peptide complex with structure-guided mutagenesis and complementation in doa1Δ yeast","pmids":["19887378"],"confidence":"High","gaps":["Which downstream processes require the p97 interaction versus not was only partially mapped","Role of p97 Tyr805 phosphorylation in regulation not functionally demonstrated"]},{"year":2010,"claim":"Provided a combined PFU-PUL structural view and proposed competition between Doa1 and Ufd2 for Cdc48 as a determinant of ubiquitinated-protein fate.","evidence":"1.9 Å crystal structure of the yeast Doa1 PFU-PUL domain pair with structural comparison to Ufd2","pmids":["21063153"],"confidence":"Medium","gaps":["Competition model not validated functionally","Single lab structural study with limited in vivo follow-up"]},{"year":2014,"claim":"Defined the solution architecture and critical residues of the Doa1/PFU:Hse1/SH3 complex, distinguishing the SH3-binding surface from the ubiquitin-binding surface.","evidence":"SAXS plus molecular docking and mutagenesis of the yeast Doa1–Hse1 interface","pmids":["24607902"],"confidence":"Medium","gaps":["Low-resolution envelope rather than atomic structure","Not extended to human PLAA"]},{"year":2015,"claim":"Revealed an adaptor role for Doa1 in a Cdc48-Wss1 SUMO-targeted protease complex acting on sumoylated substrates during DNA damage.","evidence":"Co-IP of the Wss1/Cdc48/Doa1 complex, in vitro SUMO ligase assay, genetic analysis and fluorescence localization in yeast","pmids":["26349035"],"confidence":"High","gaps":["Whether the human PLAA participates in an analogous SUMO-clearance complex unknown","Substrate range of the complex not defined"]},{"year":2016,"claim":"Showed Doa1/PLAA functions as a substrate-recruiting adaptor for Cdc48-Ufd1-Npl4 in mitochondria-associated degradation under oxidative stress.","evidence":"Genetic screen, reciprocal Co-IP with Cdc48-Ufd1-Npl4, ubiquitinated substrate binding assay and stress phenotyping in yeast","pmids":["27044889"],"confidence":"High","gaps":["Conservation of MAD role in mammalian PLAA not established","Identity of physiological mitochondrial substrates limited"]},{"year":2016,"claim":"Placed human PLAA in the p97-UBXD1-PLAA-YOD1 (ELDR) machinery that removes K48-linked ubiquitin from damaged lysosomes to drive selective autophagy.","evidence":"Reciprocal Co-IP, lysosomal damage (LLOMe) assays, immunofluorescence localization, and disease-mutant MEF/patient tissue analysis in mammalian cells","pmids":["27753622"],"confidence":"High","gaps":["How the complex selects the damaged-lysosome subpopulation not defined","Order of cofactor recruitment incompletely mapped"]},{"year":2017,"claim":"Connected PLAA loss-of-function to human disease, defining its essential role in K63-ubiquitin-mediated endolysosomal trafficking for synaptic vesicle recycling.","evidence":"Biallelic human mutations, mouse Plaa mutant model, K63-ubiquitin immunofluorescence, synaptic vesicle recycling assays and electrophysiology","pmids":["28413018"],"confidence":"High","gaps":["Direct substrates accumulating at synapses not enumerated","Link between K63 accumulation and vesicle defect mechanistically incomplete"]},{"year":2022,"claim":"Implicated PLAA in cancer by showing it destabilizes METTL3 via ubiquitin-mediated degradation, modulating m6A-dependent TRPC3 mRNA stability and Ca2+ signaling.","evidence":"PLAA overexpression/knockdown in ovarian cancer lines, ubiquitin-degradation assay, MeRIP profiling, channel activity measurement and xenograft model","pmids":["35869392"],"confidence":"Medium","gaps":["Whether PLAA acts directly or via an associated E3 on METTL3 unclear","Single lab; mechanism of METTL3 selection undefined"]},{"year":2024,"claim":"Provided patient-derived evidence that de novo PUL-domain missense variants weaken the PLAA–p97 interaction and perturb vesicle recycling, extending the genotype-phenotype link.","evidence":"Exome/genome sequencing with in vitro PLAA–p97 binding assays of patient variants and computational structural modeling","pmids":["38650658"],"confidence":"Medium","gaps":["Functional consequences shown in vitro only","Limited cellular follow-up"]},{"year":2025,"claim":"Uncovered a degradation-independent PLAA function, with its intrinsic disordered region recruiting the decapping regulator DCAP-1 to P-bodies.","evidence":"C. elegans genetics, neuronal interactome proteomics, in vitro UFD-3–DCAP-1 binding, P-body imaging and IDR deletion analysis","pmids":["40560612"],"confidence":"Medium","gaps":["Mammalian PLAA P-body role not tested","Functional output of P-body regulation on mRNA fate undefined"]},{"year":null,"claim":"How PLAA's distinct activities — p97-coupled ubiquitin clearance, ESCRT-mediated sorting, P-body assembly, and Pdia3-dependent PLA2/lipid signaling — are integrated or partitioned within a single protein in mammalian cells remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unified model reconciling the ubiquitin-adaptor and PLA2-activating functions","Tissue- and cargo-specific selection mechanisms unknown","Direct mammalian substrate repertoire largely uncharacterized"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,4,5,6]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[4,5,7]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[4]},{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[2]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[15]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[4]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[5,7]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[2,8]}],"complexes":["p97-UBXD1-PLAA-YOD1 (ELDR) complex","Cdc48-Ufd1-Npl4 complex","Wss1/Cdc48/Doa1 SUMO complex"],"partners":["VCP","UBXD1","YOD1","HGS","WSS1","PDIA3","METTL3","DCAP-1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y263","full_name":"Phospholipase A-2-activating protein","aliases":[],"length_aa":795,"mass_kda":87.2,"function":"Plays a role in protein ubiquitination, sorting and degradation through its association with VCP (PubMed:27753622). Involved in ubiquitin-mediated membrane proteins trafficking to late endosomes in an ESCRT-dependent manner, and hence plays a role in synaptic vesicle recycling (By similarity). May play a role in macroautophagy, regulating for instance the clearance of damaged lysosomes (PubMed:27753622). Plays a role in cerebellar Purkinje cell development (By similarity). Positively regulates cytosolic and calcium-independent phospholipase A2 activities in a tumor necrosis factor alpha (TNF)- or lipopolysaccharide (LPS)-dependent manner, and hence prostaglandin E2 biosynthesis (PubMed:18291623, PubMed:28007986)","subcellular_location":"Nucleus; Cytoplasm; Synapse","url":"https://www.uniprot.org/uniprotkb/Q9Y263/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PLAA","classification":"Not Classified","n_dependent_lines":25,"n_total_lines":1208,"dependency_fraction":0.020695364238410598},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"EMC9","stoichiometry":0.2},{"gene":"NCAPH","stoichiometry":0.2},{"gene":"VCP","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/PLAA","total_profiled":1310},"omim":[{"mim_id":"617527","title":"NEURODEVELOPMENTAL DISORDER WITH PROGRESSIVE MICROCEPHALY, SPASTICITY, AND BRAIN ANOMALIES; NDMSBA","url":"https://www.omim.org/entry/617527"},{"mim_id":"603873","title":"PHOSPHOLIPASE A2-ACTIVATING PROTEIN; PLAA","url":"https://www.omim.org/entry/603873"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Plasma membrane","reliability":"Supported"},{"location":"Cytosol","reliability":"Supported"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PLAA"},"hgnc":{"alias_symbol":["PLAP","PLA2P","FLJ11281","FLJ12699","DOA1"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y263","domains":[{"cath_id":"2.130.10.10","chopping":"10-320","consensus_level":"medium","plddt":93.7396,"start":10,"end":320},{"cath_id":"-","chopping":"321-384_392-402","consensus_level":"medium","plddt":76.766,"start":321,"end":402},{"cath_id":"3.10.20.870","chopping":"404-456","consensus_level":"medium","plddt":80.8391,"start":404,"end":456},{"cath_id":"1.25.10.10","chopping":"549-795","consensus_level":"medium","plddt":92.0652,"start":549,"end":795}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y263","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y263-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y263-F1-predicted_aligned_error_v6.png","plddt_mean":84.0},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PLAA","jax_strain_url":"https://www.jax.org/strain/search?query=PLAA"},"sequence":{"accession":"Q9Y263","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y263.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y263/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y263"}},"corpus_meta":[{"pmid":"27753622","id":"PMC_27753622","title":"VCP/p97 cooperates with YOD1, UBXD1 and PLAA to drive clearance of ruptured lysosomes by autophagy.","date":"2016","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/27753622","citation_count":289,"is_preprint":false},{"pmid":"17293526","id":"PMC_17293526","title":"Weissellicin 110, a newly discovered bacteriocin from Weissella cibaria 110, isolated from plaa-som, a fermented fish product from Thailand.","date":"2007","source":"Applied and environmental microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/17293526","citation_count":78,"is_preprint":false},{"pmid":"27044889","id":"PMC_27044889","title":"Doa1 targets ubiquitinated substrates for mitochondria-associated degradation.","date":"2016","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/27044889","citation_count":77,"is_preprint":false},{"pmid":"17399831","id":"PMC_17399831","title":"Expression of the mucus adhesion genes Mub and MapA, adhesion-like factor EF-Tu and bacteriocin gene plaA of Lactobacillus plantarum 423, monitored with real-time PCR.","date":"2007","source":"International journal of food microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/17399831","citation_count":71,"is_preprint":false},{"pmid":"26349035","id":"PMC_26349035","title":"Wss1 metalloprotease partners with Cdc48/Doa1 in processing genotoxic SUMO conjugates.","date":"2015","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/26349035","citation_count":66,"is_preprint":false},{"pmid":"11883675","id":"PMC_11883675","title":"Fermentation and microflora of plaa-som, a thai fermented fish product prepared with different salt concentrations.","date":"2002","source":"International journal of food microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/11883675","citation_count":47,"is_preprint":false},{"pmid":"18508771","id":"PMC_18508771","title":"DOA1/UFD3 plays a role in sorting ubiquitinated membrane proteins into multivesicular bodies.","date":"2008","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/18508771","citation_count":40,"is_preprint":false},{"pmid":"28413018","id":"PMC_28413018","title":"PLAA Mutations Cause a Lethal Infantile Epileptic Encephalopathy by Disrupting Ubiquitin-Mediated Endolysosomal Degradation of Synaptic Proteins.","date":"2017","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/28413018","citation_count":37,"is_preprint":false},{"pmid":"19887378","id":"PMC_19887378","title":"Structure and function of the PLAA/Ufd3-p97/Cdc48 complex.","date":"2009","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/19887378","citation_count":34,"is_preprint":false},{"pmid":"35869392","id":"PMC_35869392","title":"PLAA suppresses ovarian cancer metastasis via METTL3-mediated m6A modification of TRPC3 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microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/20167386","citation_count":26,"is_preprint":false},{"pmid":"19258036","id":"PMC_19258036","title":"Phospholipase A2-activating protein (PLAA) enhances cisplatin-induced apoptosis in HeLa cells.","date":"2009","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/19258036","citation_count":25,"is_preprint":false},{"pmid":"10380373","id":"PMC_10380373","title":"HLA DOA1 and DOB1 loci in Honduran women with cervical dysplasia and invasive cervical carcinoma and their relationship to human papillomavirus infection.","date":"1999","source":"Human biology","url":"https://pubmed.ncbi.nlm.nih.gov/10380373","citation_count":25,"is_preprint":false},{"pmid":"18291623","id":"PMC_18291623","title":"Alteration in the activation state of new inflammation-associated targets by phospholipase A2-activating protein (PLAA).","date":"2008","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/18291623","citation_count":19,"is_preprint":false},{"pmid":"8144461","id":"PMC_8144461","title":"Expression of the Prevotella loescheii adhesin gene (plaA) is mediated by a programmed frameshifting hop.","date":"1994","source":"Journal of bacteriology","url":"https://pubmed.ncbi.nlm.nih.gov/8144461","citation_count":15,"is_preprint":false},{"pmid":"17379712","id":"PMC_17379712","title":"Multiple functions of DOA1 in Candida albicans.","date":"2007","source":"Microbiology (Reading, England)","url":"https://pubmed.ncbi.nlm.nih.gov/17379712","citation_count":13,"is_preprint":false},{"pmid":"9841777","id":"PMC_9841777","title":"The translational hop junction and the 5' transcriptional start site for the Prevotella loescheii adhesin encoded by plaA.","date":"1999","source":"Current microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/9841777","citation_count":13,"is_preprint":false},{"pmid":"25158196","id":"PMC_25158196","title":"Rapid 1α,25(OH)₂D ₃ membrane-mediated activation of Ca²⁺/calmodulin-dependent protein kinase II in growth plate chondrocytes requires Pdia3, PLAA and caveolae.","date":"2014","source":"Connective tissue research","url":"https://pubmed.ncbi.nlm.nih.gov/25158196","citation_count":11,"is_preprint":false},{"pmid":"29176577","id":"PMC_29176577","title":"Disulfide loop cleavage of Legionella pneumophila PlaA boosts lysophospholipase A activity.","date":"2017","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/29176577","citation_count":10,"is_preprint":false},{"pmid":"16051517","id":"PMC_16051517","title":"Identification and molecular cloning of a gene encoding Phospholipase A2 (plaA) from Aspergillus nidulans.","date":"2005","source":"Biochimica et biophysica acta","url":"https://pubmed.ncbi.nlm.nih.gov/16051517","citation_count":10,"is_preprint":false},{"pmid":"36294595","id":"PMC_36294595","title":"Distribution of Kazachstania Yeast in Thai Traditional Fermented Fish (Plaa-Som) in Northeastern Thailand.","date":"2022","source":"Journal of fungi (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/36294595","citation_count":9,"is_preprint":false},{"pmid":"37486296","id":"PMC_37486296","title":"Degradation of α-Subunits, Doa1 and Doa4, are Critical for Growth, Development, Programmed Cell Death Events, Stress Responses, and Pathogenicity in the Watermelon Fusarium Wilt Fungus Fusarium oxysporum f. sp. niveum.","date":"2023","source":"Journal of agricultural and food chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/37486296","citation_count":7,"is_preprint":false},{"pmid":"21063153","id":"PMC_21063153","title":"Crystal structure of a PFU-PUL domain pair of Saccharomyces cerevisiae Doa1/Ufd3.","date":"2010","source":"The Kobe journal of medical sciences","url":"https://pubmed.ncbi.nlm.nih.gov/21063153","citation_count":6,"is_preprint":false},{"pmid":"27044894","id":"PMC_27044894","title":"Doa1 is a MAD adaptor for Cdc48.","date":"2016","source":"The Journal of cell biology","url":"https://pubmed.ncbi.nlm.nih.gov/27044894","citation_count":5,"is_preprint":false},{"pmid":"38130174","id":"PMC_38130174","title":"Structure-function relationships underpin disulfide loop cleavage-dependent activation of Legionella pneumophila lysophospholipase A PlaA.","date":"2023","source":"Molecular microbiology","url":"https://pubmed.ncbi.nlm.nih.gov/38130174","citation_count":4,"is_preprint":false},{"pmid":"21482087","id":"PMC_21482087","title":"Identification and molecular cloning Moplaa gene, a homologue of Homo sapiens PLAA, in Magnaporthe oryzae.","date":"2011","source":"Microbiological research","url":"https://pubmed.ncbi.nlm.nih.gov/21482087","citation_count":4,"is_preprint":false},{"pmid":"38650658","id":"PMC_38650658","title":"Allelic heterogeneity and abnormal vesicle recycling in PLAA-related neurodevelopmental disorders.","date":"2024","source":"Frontiers in molecular neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/38650658","citation_count":2,"is_preprint":false},{"pmid":"24607902","id":"PMC_24607902","title":"Molecular determinants of the interaction between Doa1 and Hse1 involved in endosomal sorting.","date":"2014","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/24607902","citation_count":2,"is_preprint":false},{"pmid":"32133999","id":"PMC_32133999","title":"The phospholipase A effector PlaA from Legionella pneumophila: expression, purification and crystallization.","date":"2020","source":"Acta crystallographica. Section F, Structural biology communications","url":"https://pubmed.ncbi.nlm.nih.gov/32133999","citation_count":1,"is_preprint":false},{"pmid":"40560612","id":"PMC_40560612","title":"PLAA/UFD-3 regulates P-bodies through its intrinsic disordered domain.","date":"2025","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/40560612","citation_count":1,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":17129,"output_tokens":5045,"usd":0.063531,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":13213,"output_tokens":4312,"usd":0.086932,"stage2_stop_reason":"end_turn"},"total_usd":0.150463,"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\": 2009,\n      \"finding\": \"The C-terminal PUL domain of PLAA (human ortholog of yeast Doa1/Ufd3) forms a 6-mer Armadillo-containing domain whose positively charged inner ridge binds the C-terminus of p97/Cdc48; Tyr805 of p97 is buried in this ridge and implicated in phosphorylation-dependent regulation. Point mutants disrupting this interaction display only partial loss-of-function phenotypes, indicating the p97-PLAA interaction is required for a subset of PLAA-dependent processes.\",\n      \"method\": \"Crystal structure of PUL domain–p97 C-terminal peptide complex; structure-guided mutagenesis of yeast Doa1; functional complementation assays in doa1Δ cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution crystal structure combined with mutagenesis and in vivo functional validation in a single rigorous study\",\n      \"pmids\": [\"19887378\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Crystal structure of the PFU-PUL domain pair of yeast Doa1 at 1.9 Å reveals that the PUL domain adopts an Armadillo-like repeat fold with a positively charged concave surface that binds the negatively charged C-terminus of Cdc48; the PFU domain conserved surface is implicated in binding ubiquitin and Hse1. Structural comparison with Ufd2 suggests Doa1 and Ufd2 compete for Cdc48 binding to dictate fate of ubiquitinated proteins.\",\n      \"method\": \"X-ray crystallography at 1.9 Å resolution; structural comparison\",\n      \"journal\": \"The Kobe journal of medical sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — high-quality structural data but single lab, limited functional validation reported in abstract\",\n      \"pmids\": [\"21063153\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"The PFU domain of yeast Doa1 binds directly to the SH3 domain of Hse1 (component of the ESCRT machinery), mediating Doa1's role in endosomal sorting. Loss of Doa1 causes missorting of MVB cargo GFP-Cps1 and reduces flux of ubiquitinated membrane proteins through the MVB pathway. This function is genetically separable from Doa1's role in maintaining ubiquitin levels.\",\n      \"method\": \"Direct binding assay (Hse1-SH3 pulldown of Doa1-PFU); site-directed mutations blocking PFU–SH3 interaction; GFP-Cps1 sorting assay; synthetic growth defect in doa1Δ vps27Δ double mutant; ubiquitin overexpression epistasis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal binding assays, structure-guided mutagenesis, in vivo sorting readout, and genetic epistasis in a single study\",\n      \"pmids\": [\"18508771\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Solution structure of the Doa1/PFU:Hse1/SH3 complex determined by SAXS combined with molecular docking; Asn-438 of Doa1/PFU and Trp-254 of Hse1/SH3 are critical residues for the interaction (hydrogen bonding), whereas Phe-434, implicated in ubiquitin binding, is not required for this interaction.\",\n      \"method\": \"Small-angle X-ray scattering (SAXS); molecular docking; mutagenesis; biochemical binding assays\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — SAXS structure with mutagenesis, single lab, single study\",\n      \"pmids\": [\"24607902\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Upon lysosomal damage, p97 translocates to lysosomes and cooperates with cofactors UBXD1, PLAA, and the deubiquitylase YOD1 (termed ELDR components) to selectively remove K48-linked ubiquitin conjugates from a subpopulation of damaged lysosomes and promote autophagosome formation. This complex acts downstream of K63-linked ubiquitination and p62 recruitment.\",\n      \"method\": \"Co-immunoprecipitation of p97 with PLAA, UBXD1, YOD1; lysosomal damage assay (LLOMe); immunofluorescence localization; analysis of p97 disease-mutant MEFs and patient tissue; tau fibril endocytosis model\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, direct localization with functional consequence, genetic disease-mutant validation, replicated across multiple damage models\",\n      \"pmids\": [\"27753622\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Yeast Doa1 (PLAA ortholog) forms a functional complex with Cdc48-Ufd1-Npl4 to mediate mitochondria-associated degradation (MAD) of ubiquitinated outer-membrane proteins. Doa1 directly interacts with ubiquitinated substrates and facilitates their recruitment to the Cdc48 complex. Loss of DOA1 causes accumulation and mislocalization of substrates on mitochondria, and is critical for cell survival under mitochondrial oxidative stress.\",\n      \"method\": \"Genetic screen for MAD regulators; Co-immunoprecipitation of Doa1 with Cdc48-Ufd1-Npl4; ubiquitinated substrate binding assay; doa1Δ phenotypic analysis under oxidative and ER stress\",\n      \"journal\": \"The Journal of cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, substrate binding assay, genetic screen, and stress-phenotype readout in single rigorous study\",\n      \"pmids\": [\"27044889\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Yeast Doa1 forms a SUMO-specific ternary complex with Cdc48 and Wss1 metalloprotease. Upon DNA damage, this Wss1/Cdc48/Doa1 complex is recruited to sumoylated targets and the Wss1 protease catalyzes SUMO chain extension (SUMO ligase activity) and subsequent self-cleavage and proteolysis. Doa1 acts as the adaptor in this complex. Upon genotoxic stress, Wss1 (and by extension the complex) is vacuolar.\",\n      \"method\": \"Co-immunoprecipitation (Wss1/Cdc48/Doa1 complex); in vitro SUMO ligase assay; genetic analysis (smt3-331, Camptothecin, UV); localization by fluorescence microscopy\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — complex reconstitution, in vitro enzymatic assay, genetic epistasis, localization, multiple orthogonal methods\",\n      \"pmids\": [\"26349035\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Yeast Doa1 channels ubiquitin from the proteasomal degradation pathway into pathways mediating DNA damage-induced ubiquitination of PCNA (monoubiquitination) and histone H2B monoubiquitination. In doa1Δ cells, damage-induced PCNA ubiquitination is absent; H2B ubiquitination is reduced basally and absent after DNA damage. The PCNA defect is rescued by ubiquitin overexpression but H2B monoubiquitination is not, indicating an additional specific role for Doa1 in H2B ubiquitination beyond simply supplying ubiquitin.\",\n      \"method\": \"Genetic interactions (doa1Δ with rad6, rad18, rad5, ubc13, mms2, bre1, lge1, cdc73, ubp8, ubp10, htb2); Western blot for PCNA-Ub and H2B-Ub; ubiquitin overexpression rescue experiments\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with multiple pathway members, biochemical readout of ubiquitin marks, rescue experiments — replicated across multiple damage conditions\",\n      \"pmids\": [\"16705165\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Hypomorphic mutations in PLAA in humans and mice cause infantile-lethal neurodysfunction with seizures. PLAA functions as a ubiquitin adaptor protein for endolysosomal degradation; Plaa mutant neurons accumulate K63-polyubiquitylated proteins and synaptic membrane proteins, disrupting synaptic vesicle recycling and neurotransmission.\",\n      \"method\": \"Human genetics (biallelic PLAA mutations); mouse Plaa mutant model; immunofluorescence for K63-ubiquitylated proteins; synaptic vesicle recycling assays; electrophysiology of neurotransmission\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function in both human patients and mouse model with defined molecular (K63-Ub accumulation) and cellular (synaptic vesicle recycling) phenotypes\",\n      \"pmids\": [\"28413018\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"De novo missense variants affecting conserved residues within the PUL domain of PLAA reduce PLAA–p97/VCP interaction, as shown by in vitro studies, and are associated with perturbed vesicle recycling. Computational modeling showed abnormal chain arrangements at the C-terminal PUL domain.\",\n      \"method\": \"Exome/genome sequencing; in vitro PLAA–p97 interaction assay with patient variants; computational structural modeling\",\n      \"journal\": \"Frontiers in molecular neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — in vitro binding assay with patient variants, single lab, limited functional follow-up described in abstract\",\n      \"pmids\": [\"38650658\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"PLAA (phospholipase A2-activating protein) is required for 1α,25(OH)2D3-dependent PKCα activation in rat growth plate chondrocytes. PLAA peptide increases arachidonic acid release and PLA2-specific activity in plasma membranes and matrix vesicles; its effect on PKC is blocked by PLA2 inhibitors (quinacrine, AACOCF3) and cyclooxygenase inhibitor indomethacin, indicating PLAA activates PLA2 leading to prostaglandin production acting via EP1 receptor. PLAA peptide also activates PLC-β1 and PLC-β3 via lysophospholipid.\",\n      \"method\": \"PLAA peptide treatment of primary chondrocytes; arachidonic acid release assay; PLA2 activity assay; PKC isoform activity measurement; pharmacological inhibitor studies; PLC isoform assays\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal biochemical assays with peptide and pharmacological inhibitors, single lab\",\n      \"pmids\": [\"15368540\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"PLAA and its membrane receptor partner Pdia3 are required for rapid 1α,25(OH)2D3-mediated activation of CaMKII in growth zone chondrocytes. Caveolae disruption abolishes CaMKII activation by 1α,25(OH)2D3 or PLAA peptide. Immunoprecipitation shows increased CaM binding to PLAA in response to 1α,25(OH)2D3, suggesting CaM links PLAA to CaMKII.\",\n      \"method\": \"Antibody blocking of PLAA and Pdia3; PLAA peptide treatment; caveolae disruption; CaMKII activity assay; co-immunoprecipitation of PLAA with calmodulin\",\n      \"journal\": \"Connective tissue research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, peptide activation, and antibody blocking with defined signaling readout, single lab, multiple methods\",\n      \"pmids\": [\"25158196\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"PLAA overexpression in HeLa cells increases PGE2, IL-6, activated cytosolic PLA2, COX-2, and NF-κB in response to TNF-α. PLAA promotes annexin A4 downregulation (annexin A4 acts as a PLA2 inhibitor) and clusterin downregulation, thereby amplifying PLA2-dependent inflammation. The plaa promoter contains a stimulatory Sp1-binding element in exon 1 that maintains basal expression and an inhibitory element.\",\n      \"method\": \"plaa(high)/plaa(low) HeLa Tet-off cell system; ELISA for PGE2, IL-6; Western blot for COX-2, NF-κB; microarray followed by functional assays; luciferase reporter assay; Sp1 decoy oligonucleotides and competitive binding assays\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — overexpression system with multiple downstream readouts, single lab, pathway placement established but no direct enzyme assay for PLAA itself\",\n      \"pmids\": [\"18291623\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"PLAA overexpression enhances cisplatin-induced apoptosis in HeLa cells through: (1) accumulation of arachidonic acid causing mitochondrial cytochrome c leakage (blocked by siRNA-PLAA, rescued by exogenous arachidonic acid); (2) downregulation of cytoprotective clusterin; (3) upregulation of pro-apoptotic IL-32; (4) activation of JNK/c-Jun and FasL. PLAA induction by cisplatin also activates PLA2.\",\n      \"method\": \"plaa(high)/plaa(low) HeLa Tet-off cell system; siRNA-PLAA knockdown; caspase 3/8/9 activity assay; cytochrome c release assay; arachidonic acid rescue; proteomics for phospho-JNK/c-Jun and FasL\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — overexpression and knockdown with multiple functional readouts, arachidonic acid rescue experiment, single lab\",\n      \"pmids\": [\"19258036\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"PLAA inhibits the stability of METTL3 protein via ubiquitin-mediated degradation, reducing METTL3 expression, which in turn decreases TRPC3 mRNA stability (via m6A modification). Loss of PLAA leads to elevated METTL3, increased TRPC3, and enhanced intracellular Ca2+ signaling promoting ovarian cancer cell migration and invasion.\",\n      \"method\": \"PLAA overexpression/knockdown in ovarian cancer cell lines; ubiquitin-mediated METTL3 degradation assay; m6A-seq/MeRIP for TRPC3 mRNA; TRPC3 Ca2+ channel activity measurement; orthotopic xenograft mouse model\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ubiquitin-degradation assay, m6A profiling, in vivo xenograft, single lab with multiple orthogonal methods\",\n      \"pmids\": [\"35869392\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The C. elegans PLAA ortholog UFD-3 directly interacts with the mRNA decapping complex regulatory subunit DCAP-1, and UFD-3's intrinsic disordered region (IDR) is required for recruitment of DCAP-1 to P-bodies. Loss of the IDR does not affect UFD-3's role in sorting ubiquitinated proteins through the MVB pathway, demonstrating that PLAA/UFD-3 regulates P-bodies through a pathway distinct from ubiquitin-dependent protein degradation.\",\n      \"method\": \"C. elegans genetics; unbiased proteomics (neuronal interactome); in vitro biochemical interaction assay (UFD-3–DCAP-1 direct binding); fluorescence imaging of P-bodies in C. elegans; IDR deletion mutant analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding assay, in vivo imaging, domain deletion with two orthogonal functional readouts, single lab\",\n      \"pmids\": [\"40560612\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PLAA (phospholipase A2-activating protein) is a multi-domain ubiquitin adaptor protein whose C-terminal PUL domain binds p97/VCP (Cdc48 in yeast) via a positively charged Armadillo-repeat ridge, while its PFU domain binds ubiquitin and ESCRT component Hse1/HRS; acting as part of the p97-UBXD1-PLAA-YOD1 (ELDR) complex, it removes K48-linked ubiquitin conjugates from damaged lysosomes to promote selective autophagy, and as a Cdc48 adaptor (Doa1) it recruits ubiquitinated substrates for mitochondria-associated degradation, MVB sorting, and genotoxic SUMO-conjugate clearance; at synapses, PLAA-dependent K63-ubiquitin-mediated endolysosomal trafficking is essential for synaptic vesicle recycling and neurotransmission, with loss-of-function mutations causing infantile-lethal epileptic encephalopathy; additionally, PLAA activates PLA2 downstream of the Pdia3 membrane receptor in a caveolae-dependent manner to drive arachidonic acid/prostaglandin/PKC/CaMKII signaling in chondrocytes, and its intrinsic disordered region independently regulates cytoplasmic P-body assembly through direct interaction with the mRNA decapping regulator DCAP-1.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PLAA (yeast Doa1/Ufd3, C. elegans UFD-3) is a multi-domain ubiquitin adaptor that links ubiquitinated cargo to the p97/Cdc48 AAA-ATPase to direct protein fate across endolysosomal sorting, organelle-associated degradation, and DNA-damage responses [#5, #7]. Its C-terminal PUL domain forms a six-helix Armadillo-repeat fold whose positively charged inner ridge engages the acidic C-terminus of p97/Cdc48, while the adjacent PFU domain provides a ubiquitin- and Hse1-binding surface [#0, #1]. Through the PFU\\u2013Hse1/SH3 interaction PLAA couples ubiquitinated membrane cargo to the ESCRT machinery for MVB sorting [#2, #3], and as an adaptor within the Cdc48-Ufd1-Npl4 complex it recruits ubiquitinated outer-membrane substrates for mitochondria-associated degradation and forms a SUMO-specific complex with Cdc48 and the Wss1 metalloprotease that clears sumoylated targets after genotoxic stress [#5, #6]. In human cells PLAA, together with p97, UBXD1, and the deubiquitylase YOD1, strips K48-linked ubiquitin conjugates from damaged lysosomes to promote selective autophagy [#4]. Biallelic and de novo PUL-domain mutations that weaken the PLAA\\u2013p97 interaction cause infantile-lethal epileptic encephalopathy, with mutant neurons accumulating K63-polyubiquitylated and synaptic membrane proteins and failing in synaptic vesicle recycling and neurotransmission [#8, #9]. Independent of its ubiquitin-degradation role, PLAA's intrinsic disordered region directly binds the decapping regulator DCAP-1 to recruit it to cytoplasmic P-bodies [#15]. A separate body of work assigns PLAA a signaling function as an activator of phospholipase A2 downstream of the Pdia3 membrane receptor, driving arachidonic acid release, prostaglandin production, and PKC/CaMKII activation in chondrocytes [#10, #11].\",\n  \"teleology\": [\n    {\n      \"year\": 2006,\n      \"claim\": \"Established that yeast Doa1/PLAA does more than maintain free ubiquitin pools, channeling ubiquitin into specific damage-induced modifications and acting as a dedicated factor for H2B monoubiquitination.\",\n      \"evidence\": \"Genetic epistasis with DNA-damage ubiquitination machinery plus Western blots for PCNA-Ub and H2B-Ub and ubiquitin-overexpression rescue in yeast\",\n      \"pmids\": [\"16705165\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the direct physical mechanism by which Doa1 promotes H2B ubiquitination\", \"No structural basis for substrate selection\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Identified the PFU domain as the module coupling Doa1 to ESCRT-mediated endosomal sorting, separating this function from ubiquitin homeostasis.\",\n      \"evidence\": \"Direct PFU\\u2013Hse1/SH3 binding assay, structure-guided mutagenesis, GFP-Cps1 MVB sorting readout and genetic epistasis in yeast\",\n      \"pmids\": [\"18508771\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atomic detail of the PFU\\u2013SH3 interface not resolved\", \"Human ortholog interaction not tested here\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Resolved how the PUL domain recognizes p97/Cdc48, providing the structural basis for PLAA as a p97 cofactor and showing this interaction supports only a subset of PLAA functions.\",\n      \"evidence\": \"Crystal structure of the PUL domain\\u2013p97 C-terminal peptide complex with structure-guided mutagenesis and complementation in doa1\\u0394 yeast\",\n      \"pmids\": [\"19887378\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which downstream processes require the p97 interaction versus not was only partially mapped\", \"Role of p97 Tyr805 phosphorylation in regulation not functionally demonstrated\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Provided a combined PFU-PUL structural view and proposed competition between Doa1 and Ufd2 for Cdc48 as a determinant of ubiquitinated-protein fate.\",\n      \"evidence\": \"1.9 \\u00c5 crystal structure of the yeast Doa1 PFU-PUL domain pair with structural comparison to Ufd2\",\n      \"pmids\": [\"21063153\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Competition model not validated functionally\", \"Single lab structural study with limited in vivo follow-up\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Defined the solution architecture and critical residues of the Doa1/PFU:Hse1/SH3 complex, distinguishing the SH3-binding surface from the ubiquitin-binding surface.\",\n      \"evidence\": \"SAXS plus molecular docking and mutagenesis of the yeast Doa1\\u2013Hse1 interface\",\n      \"pmids\": [\"24607902\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Low-resolution envelope rather than atomic structure\", \"Not extended to human PLAA\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Revealed an adaptor role for Doa1 in a Cdc48-Wss1 SUMO-targeted protease complex acting on sumoylated substrates during DNA damage.\",\n      \"evidence\": \"Co-IP of the Wss1/Cdc48/Doa1 complex, in vitro SUMO ligase assay, genetic analysis and fluorescence localization in yeast\",\n      \"pmids\": [\"26349035\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the human PLAA participates in an analogous SUMO-clearance complex unknown\", \"Substrate range of the complex not defined\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showed Doa1/PLAA functions as a substrate-recruiting adaptor for Cdc48-Ufd1-Npl4 in mitochondria-associated degradation under oxidative stress.\",\n      \"evidence\": \"Genetic screen, reciprocal Co-IP with Cdc48-Ufd1-Npl4, ubiquitinated substrate binding assay and stress phenotyping in yeast\",\n      \"pmids\": [\"27044889\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Conservation of MAD role in mammalian PLAA not established\", \"Identity of physiological mitochondrial substrates limited\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Placed human PLAA in the p97-UBXD1-PLAA-YOD1 (ELDR) machinery that removes K48-linked ubiquitin from damaged lysosomes to drive selective autophagy.\",\n      \"evidence\": \"Reciprocal Co-IP, lysosomal damage (LLOMe) assays, immunofluorescence localization, and disease-mutant MEF/patient tissue analysis in mammalian cells\",\n      \"pmids\": [\"27753622\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How the complex selects the damaged-lysosome subpopulation not defined\", \"Order of cofactor recruitment incompletely mapped\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Connected PLAA loss-of-function to human disease, defining its essential role in K63-ubiquitin-mediated endolysosomal trafficking for synaptic vesicle recycling.\",\n      \"evidence\": \"Biallelic human mutations, mouse Plaa mutant model, K63-ubiquitin immunofluorescence, synaptic vesicle recycling assays and electrophysiology\",\n      \"pmids\": [\"28413018\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct substrates accumulating at synapses not enumerated\", \"Link between K63 accumulation and vesicle defect mechanistically incomplete\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Implicated PLAA in cancer by showing it destabilizes METTL3 via ubiquitin-mediated degradation, modulating m6A-dependent TRPC3 mRNA stability and Ca2+ signaling.\",\n      \"evidence\": \"PLAA overexpression/knockdown in ovarian cancer lines, ubiquitin-degradation assay, MeRIP profiling, channel activity measurement and xenograft model\",\n      \"pmids\": [\"35869392\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether PLAA acts directly or via an associated E3 on METTL3 unclear\", \"Single lab; mechanism of METTL3 selection undefined\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Provided patient-derived evidence that de novo PUL-domain missense variants weaken the PLAA\\u2013p97 interaction and perturb vesicle recycling, extending the genotype-phenotype link.\",\n      \"evidence\": \"Exome/genome sequencing with in vitro PLAA\\u2013p97 binding assays of patient variants and computational structural modeling\",\n      \"pmids\": [\"38650658\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequences shown in vitro only\", \"Limited cellular follow-up\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Uncovered a degradation-independent PLAA function, with its intrinsic disordered region recruiting the decapping regulator DCAP-1 to P-bodies.\",\n      \"evidence\": \"C. elegans genetics, neuronal interactome proteomics, in vitro UFD-3\\u2013DCAP-1 binding, P-body imaging and IDR deletion analysis\",\n      \"pmids\": [\"40560612\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mammalian PLAA P-body role not tested\", \"Functional output of P-body regulation on mRNA fate undefined\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PLAA's distinct activities — p97-coupled ubiquitin clearance, ESCRT-mediated sorting, P-body assembly, and Pdia3-dependent PLA2/lipid signaling — are integrated or partitioned within a single protein in mammalian cells remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unified model reconciling the ubiquitin-adaptor and PLA2-activating functions\", \"Tissue- and cargo-specific selection mechanisms unknown\", \"Direct mammalian substrate repertoire largely uncharacterized\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 4, 5, 6]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [4, 5, 7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [2]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [15]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [5, 7]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [2, 8]}\n    ],\n    \"complexes\": [\n      \"p97-UBXD1-PLAA-YOD1 (ELDR) complex\",\n      \"Cdc48-Ufd1-Npl4 complex\",\n      \"Wss1/Cdc48/Doa1 SUMO complex\"\n    ],\n    \"partners\": [\n      \"VCP\",\n      \"UBXD1\",\n      \"YOD1\",\n      \"HGS\",\n      \"WSS1\",\n      \"PDIA3\",\n      \"METTL3\",\n      \"DCAP-1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}