{"gene":"PPME1","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":1999,"finding":"PME-1 (protein phosphatase methylesterase-1) was identified as a novel protein that stably associates with catalytically inactive mutants of PP2A C subunit. Bacterially expressed PME-1 demethylated the PP2A C subunit in vitro, and okadaic acid inhibited this reaction. PME-1 contains a lipase-like motif with a catalytic triad-activated serine as its active site nucleophile.","method":"Co-purification with inactive PP2A mutants, microsequencing, cDNA cloning, in vitro demethylation assay with bacterially expressed protein, inhibitor studies","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution of enzymatic activity, active site characterization, replicated by multiple subsequent studies","pmids":["10318862"],"is_preprint":false},{"year":2008,"finding":"Targeted disruption of the PME-1 gene in mice causes perinatal lethality and a virtually complete loss of demethylated PP2A in the nervous system and peripheral tissues. PME-1 knockout tissues also showed dramatically reduced PP2A catalytic activity over a peptide substrate and alterations in phosphoproteome content.","method":"Genetic knockout (targeted disruption), biochemical assay of PP2A activity, phosphoproteome analysis","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean KO with defined in vivo phenotype plus biochemical validation of PP2A activity","pmids":["18596935"],"is_preprint":false},{"year":2009,"finding":"PME-1-mediated inhibition of PP2A promotes basal ERK pathway activity in malignant glioma cells; PME-1 supports ERK pathway signaling upstream of Raf but downstream of growth factor receptors and protein kinase C.","method":"siRNA knockdown, epistasis analysis with pathway modulators, cell-based signaling assays","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic loss-of-function with defined pathway placement, single lab","pmids":["19293187"],"is_preprint":false},{"year":2010,"finding":"Expression of PME-1 or the methylation-site mutant PP2A C subunit (L309Δ), which decrease intracellular methylated PP2A-C and Bα levels, block N2a cell differentiation and LCMT1-mediated neurite formation, establishing a mechanistic link between PP2A demethylation by PME-1 and regulation of neuronal process outgrowth.","method":"Overexpression, knockdown (inducible and non-inducible), methylation-site mutant expression, neurite outgrowth assay","journal":"Journal of neurochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — overexpression and KD with defined cellular phenotype, single lab with multiple constructs","pmids":["21044074"],"is_preprint":false},{"year":2012,"finding":"GSK-3β regulates demethylation of PP2A at leucine-309 by upregulating PME-1 and inhibiting PPMT1; knockdown of PME-1 or PPMT1 eliminated GSK-3β effects on PP2A-C demethylation.","method":"siRNA knockdown, Western blot for PP2A methylation status, epistasis via double knockdown","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis by double knockdown, single lab","pmids":["22732552"],"is_preprint":false},{"year":2014,"finding":"PME-1 can bind and regulate protein phosphatase 4 (PP4) catalytic subunit but not the related protein phosphatase 6 (PP6), demonstrating substrate selectivity among type 2A phosphatases.","method":"Co-immunoprecipitation, overexpression, functional assays in endometrial cancer cells","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP binding assay with functional context, single lab","pmids":["24928782"],"is_preprint":false},{"year":2014,"finding":"Carnosic acid promotes PME-1-mediated demethylation of the PP2A catalytic subunit, leading to suppressed PP2A activity and alleviation of PP2A-mediated repression of PKB/Akt, thereby stimulating glucose uptake via GLUT4 translocation in skeletal muscle cells.","method":"siRNA knockdown of PME-1, PP2A activity assay, GLUT4 translocation assay, PKB phosphorylation measurements","journal":"Cellular signalling","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined pathway placement and multiple readouts, single lab","pmids":["25038454"],"is_preprint":false},{"year":2015,"finding":"PME-1 methylesterase activity protects the PP2A catalytic subunit from ubiquitin/proteasome degradation; loss of PME-1 enhanced poly-ubiquitination of PP2Ac and shortened its half-life, leading to reduced PP2Ac levels and paradoxically lower PP2A activity.","method":"PME-1 knockout MEFs, chemical inhibition of PME-1, rescue experiments with wild-type and catalytic mutant PME-1, ubiquitination assays, protein half-life measurement","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Strong — KO cells plus chemical inhibition plus rescue with catalytic mutant, multiple orthogonal methods","pmids":["26678046"],"is_preprint":false},{"year":2015,"finding":"Depletion of PME-1 or pharmacological inhibition of PME-1, or overexpression of LCMT1, leads to short mitotic spindles, while depletion of LCMT1 or overexpression of PME-1 leads to long spindles; perturbation of the LCMT1-PME-1 methylation equilibrium causes mitotic arrest, spindle assembly checkpoint activation, defective cell divisions, and apoptosis.","method":"siRNA knockdown, overexpression, pharmacological inhibition, immunofluorescence microscopy of spindle size","journal":"Cell cycle (Georgetown, Tex.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function and gain-of-function with defined mitotic phenotype, single lab","pmids":["25839665"],"is_preprint":false},{"year":2016,"finding":"PME-1-mediated PP2A inhibition drives resistance of glioma cells to multikinase inhibitors; this resistance is dependent on specific PP2A complexes and is mediated by a decrease in cytoplasmic HDAC4 activity, with synthetic lethality requiring coexpression of proapoptotic BAD.","method":"PME-1 overexpression/knockdown, drug sensitivity assays, genetic epistasis with HDAC4 and BAD","journal":"Cancer research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — epistasis analysis with pathway components, single lab, multiple orthogonal approaches","pmids":["27671680"],"is_preprint":false},{"year":2018,"finding":"PME-1 demethylates PP2Ac in cell extracts even at 0°C unless prevented by a PME-1 methylesterase inhibitor, promoting dissociation of PP2A heterotrimers containing B55 or PR72 subunits but not those with B56 subunits, revealing differential sensitivity of PP2A holoenzyme families to methylation status.","method":"In vitro demethylation assay, pharmacological PME-1 inhibition, immunoprecipitation of PP2A subcomplexes","journal":"FEBS open bio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — biochemical assay with pharmacological inhibitor and multiple PP2A subcomplex readouts, single lab","pmids":["30186749"],"is_preprint":false},{"year":2018,"finding":"USP36 deubiquitinase stabilizes PME-1 through its deubiquitinating enzyme activity; depletion of USP36 decreases PME-1 expression level, and USP36 promotes ERK and Akt signaling pathways through PME-1.","method":"Co-immunoprecipitation, siRNA knockdown, ubiquitination assay, Western blot for PME-1 stability","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP plus knockdown with functional readout, single lab","pmids":["29577269"],"is_preprint":false},{"year":2020,"finding":"Systematic phosphoproteomics revealed that PME-1 depletion (to reactivate PP2A) modulates phosphorylation of targets in kinase signaling, cytoskeleton, RNA splicing, DNA repair, and nuclear lamina pathways, and that PME-1, CIP2A, and SET are non-redundant in phosphotarget regulation.","method":"siRNA depletion, mass spectrometry-based phosphoproteomics in HeLa cells","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — large-scale phosphoproteomics with siRNA depletion, single study","pmids":["32071079"],"is_preprint":false},{"year":2022,"finding":"Cryo-EM structure of a PP2A-B56 holoenzyme–PME-1 complex revealed that PME-1 disordered regions, including a substrate-mimicking motif, tether to the B56 regulatory subunit at remote sites, occupy the holoenzyme substrate-binding groove, and allow large structural shifts in both holoenzyme and PME-1 to activate the methylesterase. B56 interface mutations selectively block PME-1 activity toward PP2A-B56 holoenzymes and affect cellular PP2A methylation and p53 signaling.","method":"High-resolution cryo-EM structure, in vitro demethylation assay, B56 interface mutagenesis, cellular p53 signaling assay","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1 / Strong — high-resolution cryo-EM structure with functional mutagenesis validation and in vitro activity assays and cell-based readouts","pmids":["35924897"],"is_preprint":false},{"year":2023,"finding":"PME-1 sensitizes glioblastoma cells to oxidative stress-induced cell death via nuclear PP2A-B55α activity; oxidative stress increases nuclear localization of PP2A-B55α, binding of PP2A-B55α to PME-1, and B55α-bound PP2A-C demethylation. PME-1 overexpression increases stress-induced phosphorylation and activity of MAPKAPK2 and RIPK1, causing sensitization. The methylesterase function, PP2A binding capacity, and nuclear localization of PME-1 are all required for this effect.","method":"Pharmacological PME-1 inhibition (AMZ30), PME-1 mutants (methylesterase-dead, PP2A binding-dead, nuclear localization mutants), subcellular fractionation, co-immunoprecipitation, kinase activity assays","journal":"Cell death discovery","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods including pharmacological and genetic perturbations with defined mechanistic pathway placement in two cell lines","pmids":["37500619"],"is_preprint":false},{"year":2023,"finding":"Transcriptome analysis of PME-1 knockout mouse embryonic fibroblasts showed that PME-1 suppresses inflammatory signaling, activates PI3K/Akt signaling, and promotes epithelial-mesenchymal transition at the transcriptional level.","method":"PME-1 knockout MEFs, RNA-seq transcriptome analysis","journal":"Biochemical and biophysical research communications","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single KO study with transcriptome readout only, no direct mechanistic validation","pmids":["38043157"],"is_preprint":false},{"year":2024,"finding":"CHK1 directly phosphorylates the PP2A catalytic subunit (including Thr219) to promote PME-1 association with PP2Ac; CHK1 inhibitors block PME-1/PP2Ac association without affecting PP2Ac methylation levels. Reciprocally, PME-1 binding to PP2Ac hinders PP2A-mediated dephosphorylation of CHK1.","method":"NanoBiT bioluminescence protein-protein interaction assay, compound screening, in vitro kinase/phosphatase assays, phospho-mass spectrometry, anti-phospho-Thr219 antibody generation and validation","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution of kinase/phosphatase reactions, phospho-site identification by mass spectrometry, bioluminescence PPI assay with cell-based validation","pmids":["38588804"],"is_preprint":false},{"year":2025,"finding":"Two distinct mechanisms of PME-1 are both essential for mouse development: (1) methylesterase activity (abolished by S156A knock-in) is required to prevent systemic apoptosis, brain atrophy with cerebellar layer collapse, increased inflammation, and elevated reactive oxygen species in mitochondria; (2) PP2A inhibitory binding activity (abolished by M335D knock-in) is required for olfactory epithelium integrity and survival for ~2 days postnatally. Both phenotypes differ from the perinatal lethality of PME-1 null mice, demonstrating non-redundancy of the two mechanisms in vivo.","method":"Knock-in mouse models (S156A and M335D point mutants), histological and gene expression analysis, primary embryonic fibroblast assays (mitochondrial number, oxygen consumption rate, ROS levels)","journal":"FASEB journal","confidence":"High","confidence_rationale":"Tier 1 / Strong — separation-of-function knock-in mice with distinct phenotypes, multiple orthogonal readouts including cellular metabolism and histology","pmids":["40326231"],"is_preprint":false},{"year":2023,"finding":"PME-1 overexpression suppresses anoikis in PTEN-deficient prostate cancer cells; PME-1 inhibition increased apoptosis in in ovo PCa tumor xenografts and attenuated PCa cell survival in zebrafish circulation. PME-1-deficient PC3 cells display increased trimethylation at H3K9 and H3K27, correlating with increased apoptosis sensitivity.","method":"PME-1 overexpression, siRNA knockdown, in ovo xenograft, zebrafish circulation assay, histone modification analysis (ChIP/Western)","journal":"Molecular oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple in vitro and in vivo models, defined epigenetic phenotype, single lab","pmids":["36461911"],"is_preprint":false}],"current_model":"PPME1/PME-1 is a serine-active-site methylesterase that specifically demethylates the C-terminal Leu309 residue of the PP2A (and PP4) catalytic subunit via a lipase-like catalytic triad, thereby controlling holoenzyme composition (favoring dissociation of B55/PR72 but not B56 subcomplexes), protecting PP2Ac from ubiquitin-proteasome degradation, and acting as a direct PP2A inhibitory binding partner; structural and mechanistic studies reveal that PME-1 uses substrate-mimicking disordered motifs to engage the B56 regulatory subunit's substrate groove, while CHK1-mediated phosphorylation of PP2Ac at Thr219 promotes PME-1 association, and in vivo knock-in mice demonstrate that both the methylesterase activity and the direct PP2A-inhibitory binding activity are independently essential for development and tissue homeostasis."},"narrative":{"mechanistic_narrative":"PPME1/PME-1 is a serine-hydrolase methylesterase that controls the methylation status, composition, and activity of PP2A-family phosphatases, thereby tuning kinase signaling, mitosis, neuronal differentiation, and cell-death decisions [PMID:10318862, PMID:18596935]. It was identified through stable association with catalytically inactive PP2A C subunit and demethylates PP2Ac via a lipase-like catalytic triad whose nucleophilic serine is required for activity, a reaction blocked by okadaic acid [PMID:10318862]. Genetic ablation in mice eliminates demethylated PP2A and paradoxically lowers PP2A catalytic activity, because PME-1 methylesterase activity protects PP2Ac from poly-ubiquitination and proteasomal degradation, stabilizing the catalytic subunit while also acting as a direct PP2A inhibitory binding partner [PMID:18596935, PMID:26678046]. Demethylation by PME-1 selectively drives dissociation of B55- and PR72-containing holoenzymes but not B56 complexes [PMID:30186749], and a cryo-EM structure of the PP2A-B56–PME-1 complex shows that PME-1 disordered regions, including a substrate-mimicking motif, tether to the B56 regulatory subunit and occupy the holoenzyme substrate groove to activate the methylesterase [PMID:35924897]. CHK1-mediated phosphorylation of PP2Ac at Thr219 promotes PME-1 association independent of methylation, and PME-1 binding reciprocally shields CHK1 from PP2A-mediated dephosphorylation [PMID:38588804]. Through these activities PME-1 supports basal ERK and Akt signaling, controls mitotic spindle length via the LCMT1–PME-1 methylation equilibrium, and modulates apoptosis and stress responses in tumor cells [PMID:19293187, PMID:25839665, PMID:37500619]. Separation-of-function knock-in mice establish that the methylesterase activity and the PP2A-inhibitory binding activity are independently essential for development and tissue homeostasis, with distinct phenotypes in apoptosis/ROS control versus olfactory epithelium integrity [PMID:40326231].","teleology":[{"year":1999,"claim":"Established the molecular identity and catalytic mechanism of PME-1, answering what enzyme removes the methyl group from PP2A and how it acts.","evidence":"Co-purification with inactive PP2A mutants, cDNA cloning, and in vitro demethylation by bacterially expressed protein with active-site characterization","pmids":["10318862"],"confidence":"High","gaps":["Did not resolve the in vivo consequences of demethylation","Structural basis of substrate engagement not determined"]},{"year":2008,"claim":"Defined the organismal requirement for PME-1 and revealed the counterintuitive coupling between demethylation and PP2A activity.","evidence":"Targeted gene knockout in mice with PP2A activity assay and phosphoproteome analysis","pmids":["18596935"],"confidence":"High","gaps":["Mechanism behind reduced PP2A activity in KO tissues not yet explained","Did not separate methylesterase from binding functions"]},{"year":2009,"claim":"Placed PME-1-mediated PP2A inhibition within growth-factor/ERK signaling, linking it to malignant phenotypes.","evidence":"siRNA knockdown and epistasis analysis in malignant glioma cells","pmids":["19293187"],"confidence":"Medium","gaps":["Direct PP2A substrate in the ERK pathway not identified","Single cell-type context"]},{"year":2010,"claim":"Connected PP2A demethylation to a specific developmental output, neuronal process outgrowth.","evidence":"Overexpression, knockdown, and methylation-site mutant (L309Δ) in N2a neurite outgrowth assays","pmids":["21044074"],"confidence":"Medium","gaps":["Downstream phospho-substrates governing outgrowth not defined","Cell-line model only"]},{"year":2012,"claim":"Identified upstream regulation of the methylation equilibrium, showing GSK-3β tunes PP2A demethylation via PME-1 and PPMT1.","evidence":"siRNA knockdown and double-knockdown epistasis with methylation Western blots","pmids":["22732552"],"confidence":"Medium","gaps":["Direct vs indirect regulation of PME-1 by GSK-3β unresolved","Single lab"]},{"year":2014,"claim":"Defined substrate selectivity among type 2A phosphatases, showing PME-1 acts on PP4 but not PP6.","evidence":"Co-immunoprecipitation and functional assays in endometrial cancer cells","pmids":["24928782"],"confidence":"Medium","gaps":["Structural basis for PP4-versus-PP6 discrimination unknown","Demethylation of PP4 not directly demonstrated"]},{"year":2014,"claim":"Linked PME-1 to metabolic signaling, showing pharmacological promotion of demethylation relieves PP2A repression of Akt and enhances glucose uptake.","evidence":"siRNA knockdown, PP2A activity, GLUT4 translocation and PKB phosphorylation assays in skeletal muscle cells","pmids":["25038454"],"confidence":"Medium","gaps":["Mechanism of carnosic acid action on PME-1 not defined","Single lab"]},{"year":2015,"claim":"Resolved the paradox of the KO phenotype by showing methylesterase activity protects PP2Ac from ubiquitin-proteasome degradation.","evidence":"PME-1 KO MEFs, chemical inhibition, rescue with WT versus catalytic-mutant PME-1, ubiquitination and half-life measurements","pmids":["26678046"],"confidence":"High","gaps":["E3 ligase targeting PP2Ac not identified","How methylation status couples to ubiquitination not mechanistically detailed"]},{"year":2015,"claim":"Established that the LCMT1–PME-1 methylation balance controls mitotic spindle length and faithful division.","evidence":"siRNA, overexpression, pharmacological inhibition, and spindle immunofluorescence","pmids":["25839665"],"confidence":"Medium","gaps":["Relevant PP2A holoenzyme and spindle substrates not identified","Single lab"]},{"year":2016,"claim":"Showed PME-1-mediated PP2A inhibition confers drug resistance through HDAC4 and BAD, defining a synthetic-lethal vulnerability.","evidence":"Overexpression/knockdown with genetic epistasis to HDAC4 and BAD in glioma cells","pmids":["27671680"],"confidence":"Medium","gaps":["Direct PP2A complex responsible not fully defined","Single tumor context"]},{"year":2018,"claim":"Revealed holoenzyme-family selectivity, showing demethylation dissociates B55/PR72 but not B56 complexes.","evidence":"In vitro demethylation with pharmacological inhibition and immunoprecipitation of PP2A subcomplexes","pmids":["30186749"],"confidence":"Medium","gaps":["Mechanistic basis for B56 resistance not yet structurally explained","Single lab"]},{"year":2018,"claim":"Identified post-translational control of PME-1 abundance via USP36 deubiquitination, linking it to ERK and Akt signaling.","evidence":"Co-IP, siRNA knockdown, ubiquitination assay and stability Western blots","pmids":["29577269"],"confidence":"Medium","gaps":["E3 ligase opposing USP36 unknown","Single lab Co-IP without reciprocal structural mapping"]},{"year":2020,"claim":"Mapped the global phosphotarget landscape controlled by PME-1 and showed non-redundancy with CIP2A and SET.","evidence":"siRNA depletion with mass spectrometry phosphoproteomics in HeLa cells","pmids":["32071079"],"confidence":"Medium","gaps":["Direct versus indirect targets not distinguished","Single study"]},{"year":2022,"claim":"Provided the structural mechanism by which PME-1 engages the B56 holoenzyme using substrate-mimicking disordered motifs to access the active site.","evidence":"Cryo-EM structure plus B56 interface mutagenesis, in vitro activity, and cellular p53 signaling readouts","pmids":["35924897"],"confidence":"High","gaps":["Structures of other holoenzyme-family complexes not solved","Dynamics of the activating conformational shift in cells not captured"]},{"year":2023,"claim":"Demonstrated nuclear PME-1 sensitizes glioblastoma cells to oxidative-stress death via PP2A-B55α, requiring methylesterase, binding, and nuclear localization activities.","evidence":"Pharmacological inhibition, separation-of-function mutants, fractionation, Co-IP and kinase assays in two cell lines","pmids":["37500619"],"confidence":"High","gaps":["Determinants of PME-1 nuclear targeting not defined","Generality beyond glioblastoma unknown"]},{"year":2023,"claim":"Linked PME-1 to anoikis suppression and histone methylation in PTEN-deficient prostate cancer.","evidence":"Overexpression/knockdown, in ovo xenograft, zebrafish circulation and histone modification assays","pmids":["36461911"],"confidence":"Medium","gaps":["Mechanism connecting PP2A activity to H3K9/H3K27 trimethylation not established","Single lab"]},{"year":2023,"claim":"Provided transcriptome-level associations of PME-1 with inflammatory, PI3K/Akt, and EMT programs.","evidence":"RNA-seq of PME-1 knockout MEFs","pmids":["38043157"],"confidence":"Low","gaps":["No direct mechanistic validation beyond transcriptome","Causality versus secondary adaptation not resolved"]},{"year":2024,"claim":"Identified CHK1 as a kinase that primes PP2Ac (Thr219) for PME-1 binding and revealed a reciprocal CHK1-protective loop.","evidence":"NanoBiT PPI assay, compound screening, in vitro kinase/phosphatase reactions, phospho-MS, and phospho-Thr219 antibody validation","pmids":["38588804"],"confidence":"High","gaps":["Physiological contexts where CHK1-PME-1 axis operates not fully mapped","Effect on holoenzyme assembly downstream of Thr219 phosphorylation unresolved"]},{"year":2025,"claim":"Genetically separated the two essential PME-1 activities in vivo, showing methylesterase and PP2A-inhibitory binding functions are non-redundant for distinct developmental outcomes.","evidence":"S156A and M335D knock-in mice with histology, gene expression, and mitochondrial/ROS assays in primary fibroblasts","pmids":["40326231"],"confidence":"High","gaps":["Molecular basis of tissue-specific phenotype divergence not defined","Direct downstream substrates driving apoptosis and ROS not identified"]},{"year":null,"claim":"How PME-1 selects among PP2A/PP4 holoenzyme families in vivo and which specific phospho-substrates mediate its distinct developmental, mitotic, and stress phenotypes remain unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["Substrate-level wiring of PME-1-controlled PP2A to specific phenotypes incomplete","E3 ligase that degrades PP2Ac upon PME-1 loss unknown","Structural basis of B55/PR72 versus B56 selectivity not fully explained"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,7,10,13]},{"term_id":"GO:0016787","term_label":"hydrolase activity","supporting_discovery_ids":[0,7]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,7,14,16,17]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[14]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[2,6,9]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[8,16]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[14,18]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[7]}],"complexes":["PP2A holoenzyme (catalytic subunit complex)"],"partners":["PPP2CA","PPP4C","LCMT1","USP36","CHEK1","PPP2R5 (B56)","PPP2R2A (B55)"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y570","full_name":"Protein phosphatase methylesterase 1","aliases":[],"length_aa":386,"mass_kda":42.3,"function":"Demethylates proteins that have been reversibly carboxymethylated. Demethylates PPP2CB (in vitro) and PPP2CA. Binding to PPP2CA displaces the manganese ion and inactivates the enzyme","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q9Y570/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/PPME1","classification":"Not Classified","n_dependent_lines":279,"n_total_lines":1208,"dependency_fraction":0.23096026490066227},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"PAIP1","stoichiometry":0.2},{"gene":"PPP2CA","stoichiometry":0.2},{"gene":"PPP2CB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/PPME1","total_profiled":1310},"omim":[{"mim_id":"611117","title":"PROTEIN PHOSPHATASE METHYLESTERASE 1; PPME1","url":"https://www.omim.org/entry/611117"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nuclear bodies","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/PPME1"},"hgnc":{"alias_symbol":["PME-1","ABDH19"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y570","domains":[{"cath_id":"3.40.50.1820","chopping":"42-201_296-374","consensus_level":"high","plddt":95.5097,"start":42,"end":374}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y570","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y570-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y570-F1-predicted_aligned_error_v6.png","plddt_mean":82.62},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=PPME1","jax_strain_url":"https://www.jax.org/strain/search?query=PPME1"},"sequence":{"accession":"Q9Y570","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y570.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y570/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y570"}},"corpus_meta":[{"pmid":"10318862","id":"PMC_10318862","title":"A protein phosphatase methylesterase (PME-1) is one of several novel proteins stably associating with two inactive mutants of protein phosphatase 2A.","date":"1999","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10318862","citation_count":164,"is_preprint":false},{"pmid":"19293187","id":"PMC_19293187","title":"PME-1 protects extracellular signal-regulated kinase pathway activity from protein phosphatase 2A-mediated inactivation in human malignant glioma.","date":"2009","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/19293187","citation_count":81,"is_preprint":false},{"pmid":"24928782","id":"PMC_24928782","title":"PME-1 modulates protein phosphatase 2A activity to promote the malignant phenotype of endometrial cancer cells.","date":"2014","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/24928782","citation_count":54,"is_preprint":false},{"pmid":"22610346","id":"PMC_22610346","title":"A functional pectin methylesterase inhibitor protein (SolyPMEI) is expressed during tomato fruit ripening and interacts with PME-1.","date":"2012","source":"Plant molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/22610346","citation_count":53,"is_preprint":false},{"pmid":"32071079","id":"PMC_32071079","title":"Phosphoproteome and drug-response effects mediated by the three protein phosphatase 2A inhibitor proteins CIP2A, SET, and PME-1.","date":"2020","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/32071079","citation_count":51,"is_preprint":false},{"pmid":"27913678","id":"PMC_27913678","title":"Regulation of protein phosphatase 2A (PP2A) tumor suppressor function by PME-1.","date":"2016","source":"Biochemical Society transactions","url":"https://pubmed.ncbi.nlm.nih.gov/27913678","citation_count":45,"is_preprint":false},{"pmid":"21044074","id":"PMC_21044074","title":"Regulation of protein phosphatase 2A methylation by LCMT1 and PME-1 plays a critical role in differentiation of neuroblastoma cells.","date":"2010","source":"Journal of neurochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/21044074","citation_count":45,"is_preprint":false},{"pmid":"27671680","id":"PMC_27671680","title":"PP2A Inhibitor PME-1 Drives Kinase Inhibitor Resistance in Glioma Cells.","date":"2016","source":"Cancer research","url":"https://pubmed.ncbi.nlm.nih.gov/27671680","citation_count":40,"is_preprint":false},{"pmid":"29281045","id":"PMC_29281045","title":"Protein Phosphatase 2A and Its Methylation Modulating Enzymes LCMT-1 and PME-1 Are Dysregulated in Tauopathies of Progressive Supranuclear Palsy and Alzheimer Disease.","date":"2018","source":"Journal of neuropathology and experimental neurology","url":"https://pubmed.ncbi.nlm.nih.gov/29281045","citation_count":40,"is_preprint":false},{"pmid":"18596935","id":"PMC_18596935","title":"Targeted disruption of the PME-1 gene causes loss of demethylated PP2A and perinatal lethality in mice.","date":"2008","source":"PloS 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chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/21402845","citation_count":23,"is_preprint":false},{"pmid":"12145714","id":"PMC_12145714","title":"The genes pme-1 and pme-2 encode two poly(ADP-ribose) polymerases in Caenorhabditis elegans.","date":"2002","source":"The Biochemical journal","url":"https://pubmed.ncbi.nlm.nih.gov/12145714","citation_count":22,"is_preprint":false},{"pmid":"30186749","id":"PMC_30186749","title":"A stable association with PME-1 may be dispensable for PP2A demethylation - implications for the detection of PP2A methylation and immunoprecipitation.","date":"2018","source":"FEBS open bio","url":"https://pubmed.ncbi.nlm.nih.gov/30186749","citation_count":22,"is_preprint":false},{"pmid":"23911878","id":"PMC_23911878","title":"IMP1 promotes choriocarcinoma cell migration and invasion through the novel effectors RSK2 and PPME1.","date":"2013","source":"Gynecologic 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Tex.)","url":"https://pubmed.ncbi.nlm.nih.gov/25839665","citation_count":12,"is_preprint":false},{"pmid":"35924897","id":"PMC_35924897","title":"Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition.","date":"2022","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/35924897","citation_count":12,"is_preprint":false},{"pmid":"34195365","id":"PMC_34195365","title":"Long non-coding RNA HOTAIR/microRNA-761 sponge regulates PPME1 and further influences cell biological functions in thyroid carcinoma.","date":"2021","source":"Laryngoscope investigative otolaryngology","url":"https://pubmed.ncbi.nlm.nih.gov/34195365","citation_count":11,"is_preprint":false},{"pmid":"35060203","id":"PMC_35060203","title":"Hsa_circ_0050102 regulates the pancreatic cancer development via miR-218-5p/PPME1 axis.","date":"2022","source":"Journal of clinical laboratory 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Society for Neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/32341098","citation_count":5,"is_preprint":false},{"pmid":"38588804","id":"PMC_38588804","title":"The luciferase-based in vivo protein-protein interaction assay revealed that CHK1 promotes PP2A and PME-1 interaction.","date":"2024","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/38588804","citation_count":4,"is_preprint":false},{"pmid":"39998246","id":"PMC_39998246","title":"Coexistence of tmexCD-toprJ, blaNDM-1, and blaPME-1 in multi-drug-resistant Pseudomonas juntendi isolates recovered from stool samples.","date":"2025","source":"Microbiology spectrum","url":"https://pubmed.ncbi.nlm.nih.gov/39998246","citation_count":4,"is_preprint":false},{"pmid":"41388803","id":"PMC_41388803","title":"PP2A methylesterase, PME-1, and PP2A methyltransferase, LCMT-1, control sensitivity to impairments caused by injury-related oligomeric tau.","date":"2025","source":"Alzheimer's & dementia : the journal of the Alzheimer's Association","url":"https://pubmed.ncbi.nlm.nih.gov/41388803","citation_count":2,"is_preprint":false},{"pmid":"38043157","id":"PMC_38043157","title":"Transcriptome analysis revealed that PME-1 suppresses inflammatory signaling, activates PI3K/Akt signaling, and promotes epithelial-mesenchymal transition.","date":"2023","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/38043157","citation_count":2,"is_preprint":false},{"pmid":"40326231","id":"PMC_40326231","title":"Two Distinct Mechanisms of PP2A Regulation by Methylesterase PME-1 Are Both Essential for Mouse Development.","date":"2025","source":"FASEB journal : official publication of the Federation of American Societies for Experimental Biology","url":"https://pubmed.ncbi.nlm.nih.gov/40326231","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":18237,"output_tokens":4599,"usd":0.061848,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":12710,"output_tokens":5092,"usd":0.095425,"stage2_stop_reason":"end_turn"},"total_usd":0.157273,"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\": 1999,\n      \"finding\": \"PME-1 (protein phosphatase methylesterase-1) was identified as a novel protein that stably associates with catalytically inactive mutants of PP2A C subunit. Bacterially expressed PME-1 demethylated the PP2A C subunit in vitro, and okadaic acid inhibited this reaction. PME-1 contains a lipase-like motif with a catalytic triad-activated serine as its active site nucleophile.\",\n      \"method\": \"Co-purification with inactive PP2A mutants, microsequencing, cDNA cloning, in vitro demethylation assay with bacterially expressed protein, inhibitor studies\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution of enzymatic activity, active site characterization, replicated by multiple subsequent studies\",\n      \"pmids\": [\"10318862\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Targeted disruption of the PME-1 gene in mice causes perinatal lethality and a virtually complete loss of demethylated PP2A in the nervous system and peripheral tissues. PME-1 knockout tissues also showed dramatically reduced PP2A catalytic activity over a peptide substrate and alterations in phosphoproteome content.\",\n      \"method\": \"Genetic knockout (targeted disruption), biochemical assay of PP2A activity, phosphoproteome analysis\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean KO with defined in vivo phenotype plus biochemical validation of PP2A activity\",\n      \"pmids\": [\"18596935\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"PME-1-mediated inhibition of PP2A promotes basal ERK pathway activity in malignant glioma cells; PME-1 supports ERK pathway signaling upstream of Raf but downstream of growth factor receptors and protein kinase C.\",\n      \"method\": \"siRNA knockdown, epistasis analysis with pathway modulators, cell-based signaling assays\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic loss-of-function with defined pathway placement, single lab\",\n      \"pmids\": [\"19293187\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Expression of PME-1 or the methylation-site mutant PP2A C subunit (L309Δ), which decrease intracellular methylated PP2A-C and Bα levels, block N2a cell differentiation and LCMT1-mediated neurite formation, establishing a mechanistic link between PP2A demethylation by PME-1 and regulation of neuronal process outgrowth.\",\n      \"method\": \"Overexpression, knockdown (inducible and non-inducible), methylation-site mutant expression, neurite outgrowth assay\",\n      \"journal\": \"Journal of neurochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — overexpression and KD with defined cellular phenotype, single lab with multiple constructs\",\n      \"pmids\": [\"21044074\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"GSK-3β regulates demethylation of PP2A at leucine-309 by upregulating PME-1 and inhibiting PPMT1; knockdown of PME-1 or PPMT1 eliminated GSK-3β effects on PP2A-C demethylation.\",\n      \"method\": \"siRNA knockdown, Western blot for PP2A methylation status, epistasis via double knockdown\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis by double knockdown, single lab\",\n      \"pmids\": [\"22732552\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"PME-1 can bind and regulate protein phosphatase 4 (PP4) catalytic subunit but not the related protein phosphatase 6 (PP6), demonstrating substrate selectivity among type 2A phosphatases.\",\n      \"method\": \"Co-immunoprecipitation, overexpression, functional assays in endometrial cancer cells\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP binding assay with functional context, single lab\",\n      \"pmids\": [\"24928782\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Carnosic acid promotes PME-1-mediated demethylation of the PP2A catalytic subunit, leading to suppressed PP2A activity and alleviation of PP2A-mediated repression of PKB/Akt, thereby stimulating glucose uptake via GLUT4 translocation in skeletal muscle cells.\",\n      \"method\": \"siRNA knockdown of PME-1, PP2A activity assay, GLUT4 translocation assay, PKB phosphorylation measurements\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined pathway placement and multiple readouts, single lab\",\n      \"pmids\": [\"25038454\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"PME-1 methylesterase activity protects the PP2A catalytic subunit from ubiquitin/proteasome degradation; loss of PME-1 enhanced poly-ubiquitination of PP2Ac and shortened its half-life, leading to reduced PP2Ac levels and paradoxically lower PP2A activity.\",\n      \"method\": \"PME-1 knockout MEFs, chemical inhibition of PME-1, rescue experiments with wild-type and catalytic mutant PME-1, ubiquitination assays, protein half-life measurement\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — KO cells plus chemical inhibition plus rescue with catalytic mutant, multiple orthogonal methods\",\n      \"pmids\": [\"26678046\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Depletion of PME-1 or pharmacological inhibition of PME-1, or overexpression of LCMT1, leads to short mitotic spindles, while depletion of LCMT1 or overexpression of PME-1 leads to long spindles; perturbation of the LCMT1-PME-1 methylation equilibrium causes mitotic arrest, spindle assembly checkpoint activation, defective cell divisions, and apoptosis.\",\n      \"method\": \"siRNA knockdown, overexpression, pharmacological inhibition, immunofluorescence microscopy of spindle size\",\n      \"journal\": \"Cell cycle (Georgetown, Tex.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function and gain-of-function with defined mitotic phenotype, single lab\",\n      \"pmids\": [\"25839665\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"PME-1-mediated PP2A inhibition drives resistance of glioma cells to multikinase inhibitors; this resistance is dependent on specific PP2A complexes and is mediated by a decrease in cytoplasmic HDAC4 activity, with synthetic lethality requiring coexpression of proapoptotic BAD.\",\n      \"method\": \"PME-1 overexpression/knockdown, drug sensitivity assays, genetic epistasis with HDAC4 and BAD\",\n      \"journal\": \"Cancer research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — epistasis analysis with pathway components, single lab, multiple orthogonal approaches\",\n      \"pmids\": [\"27671680\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"PME-1 demethylates PP2Ac in cell extracts even at 0°C unless prevented by a PME-1 methylesterase inhibitor, promoting dissociation of PP2A heterotrimers containing B55 or PR72 subunits but not those with B56 subunits, revealing differential sensitivity of PP2A holoenzyme families to methylation status.\",\n      \"method\": \"In vitro demethylation assay, pharmacological PME-1 inhibition, immunoprecipitation of PP2A subcomplexes\",\n      \"journal\": \"FEBS open bio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — biochemical assay with pharmacological inhibitor and multiple PP2A subcomplex readouts, single lab\",\n      \"pmids\": [\"30186749\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"USP36 deubiquitinase stabilizes PME-1 through its deubiquitinating enzyme activity; depletion of USP36 decreases PME-1 expression level, and USP36 promotes ERK and Akt signaling pathways through PME-1.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, ubiquitination assay, Western blot for PME-1 stability\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP plus knockdown with functional readout, single lab\",\n      \"pmids\": [\"29577269\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Systematic phosphoproteomics revealed that PME-1 depletion (to reactivate PP2A) modulates phosphorylation of targets in kinase signaling, cytoskeleton, RNA splicing, DNA repair, and nuclear lamina pathways, and that PME-1, CIP2A, and SET are non-redundant in phosphotarget regulation.\",\n      \"method\": \"siRNA depletion, mass spectrometry-based phosphoproteomics in HeLa cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — large-scale phosphoproteomics with siRNA depletion, single study\",\n      \"pmids\": [\"32071079\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Cryo-EM structure of a PP2A-B56 holoenzyme–PME-1 complex revealed that PME-1 disordered regions, including a substrate-mimicking motif, tether to the B56 regulatory subunit at remote sites, occupy the holoenzyme substrate-binding groove, and allow large structural shifts in both holoenzyme and PME-1 to activate the methylesterase. B56 interface mutations selectively block PME-1 activity toward PP2A-B56 holoenzymes and affect cellular PP2A methylation and p53 signaling.\",\n      \"method\": \"High-resolution cryo-EM structure, in vitro demethylation assay, B56 interface mutagenesis, cellular p53 signaling assay\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — high-resolution cryo-EM structure with functional mutagenesis validation and in vitro activity assays and cell-based readouts\",\n      \"pmids\": [\"35924897\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PME-1 sensitizes glioblastoma cells to oxidative stress-induced cell death via nuclear PP2A-B55α activity; oxidative stress increases nuclear localization of PP2A-B55α, binding of PP2A-B55α to PME-1, and B55α-bound PP2A-C demethylation. PME-1 overexpression increases stress-induced phosphorylation and activity of MAPKAPK2 and RIPK1, causing sensitization. The methylesterase function, PP2A binding capacity, and nuclear localization of PME-1 are all required for this effect.\",\n      \"method\": \"Pharmacological PME-1 inhibition (AMZ30), PME-1 mutants (methylesterase-dead, PP2A binding-dead, nuclear localization mutants), subcellular fractionation, co-immunoprecipitation, kinase activity assays\",\n      \"journal\": \"Cell death discovery\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods including pharmacological and genetic perturbations with defined mechanistic pathway placement in two cell lines\",\n      \"pmids\": [\"37500619\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Transcriptome analysis of PME-1 knockout mouse embryonic fibroblasts showed that PME-1 suppresses inflammatory signaling, activates PI3K/Akt signaling, and promotes epithelial-mesenchymal transition at the transcriptional level.\",\n      \"method\": \"PME-1 knockout MEFs, RNA-seq transcriptome analysis\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single KO study with transcriptome readout only, no direct mechanistic validation\",\n      \"pmids\": [\"38043157\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"CHK1 directly phosphorylates the PP2A catalytic subunit (including Thr219) to promote PME-1 association with PP2Ac; CHK1 inhibitors block PME-1/PP2Ac association without affecting PP2Ac methylation levels. Reciprocally, PME-1 binding to PP2Ac hinders PP2A-mediated dephosphorylation of CHK1.\",\n      \"method\": \"NanoBiT bioluminescence protein-protein interaction assay, compound screening, in vitro kinase/phosphatase assays, phospho-mass spectrometry, anti-phospho-Thr219 antibody generation and validation\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution of kinase/phosphatase reactions, phospho-site identification by mass spectrometry, bioluminescence PPI assay with cell-based validation\",\n      \"pmids\": [\"38588804\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Two distinct mechanisms of PME-1 are both essential for mouse development: (1) methylesterase activity (abolished by S156A knock-in) is required to prevent systemic apoptosis, brain atrophy with cerebellar layer collapse, increased inflammation, and elevated reactive oxygen species in mitochondria; (2) PP2A inhibitory binding activity (abolished by M335D knock-in) is required for olfactory epithelium integrity and survival for ~2 days postnatally. Both phenotypes differ from the perinatal lethality of PME-1 null mice, demonstrating non-redundancy of the two mechanisms in vivo.\",\n      \"method\": \"Knock-in mouse models (S156A and M335D point mutants), histological and gene expression analysis, primary embryonic fibroblast assays (mitochondrial number, oxygen consumption rate, ROS levels)\",\n      \"journal\": \"FASEB journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — separation-of-function knock-in mice with distinct phenotypes, multiple orthogonal readouts including cellular metabolism and histology\",\n      \"pmids\": [\"40326231\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PME-1 overexpression suppresses anoikis in PTEN-deficient prostate cancer cells; PME-1 inhibition increased apoptosis in in ovo PCa tumor xenografts and attenuated PCa cell survival in zebrafish circulation. PME-1-deficient PC3 cells display increased trimethylation at H3K9 and H3K27, correlating with increased apoptosis sensitivity.\",\n      \"method\": \"PME-1 overexpression, siRNA knockdown, in ovo xenograft, zebrafish circulation assay, histone modification analysis (ChIP/Western)\",\n      \"journal\": \"Molecular oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple in vitro and in vivo models, defined epigenetic phenotype, single lab\",\n      \"pmids\": [\"36461911\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"PPME1/PME-1 is a serine-active-site methylesterase that specifically demethylates the C-terminal Leu309 residue of the PP2A (and PP4) catalytic subunit via a lipase-like catalytic triad, thereby controlling holoenzyme composition (favoring dissociation of B55/PR72 but not B56 subcomplexes), protecting PP2Ac from ubiquitin-proteasome degradation, and acting as a direct PP2A inhibitory binding partner; structural and mechanistic studies reveal that PME-1 uses substrate-mimicking disordered motifs to engage the B56 regulatory subunit's substrate groove, while CHK1-mediated phosphorylation of PP2Ac at Thr219 promotes PME-1 association, and in vivo knock-in mice demonstrate that both the methylesterase activity and the direct PP2A-inhibitory binding activity are independently essential for development and tissue homeostasis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"PPME1/PME-1 is a serine-hydrolase methylesterase that controls the methylation status, composition, and activity of PP2A-family phosphatases, thereby tuning kinase signaling, mitosis, neuronal differentiation, and cell-death decisions [#0, #1]. It was identified through stable association with catalytically inactive PP2A C subunit and demethylates PP2Ac via a lipase-like catalytic triad whose nucleophilic serine is required for activity, a reaction blocked by okadaic acid [#0]. Genetic ablation in mice eliminates demethylated PP2A and paradoxically lowers PP2A catalytic activity, because PME-1 methylesterase activity protects PP2Ac from poly-ubiquitination and proteasomal degradation, stabilizing the catalytic subunit while also acting as a direct PP2A inhibitory binding partner [#1, #7]. Demethylation by PME-1 selectively drives dissociation of B55- and PR72-containing holoenzymes but not B56 complexes [#10], and a cryo-EM structure of the PP2A-B56–PME-1 complex shows that PME-1 disordered regions, including a substrate-mimicking motif, tether to the B56 regulatory subunit and occupy the holoenzyme substrate groove to activate the methylesterase [#13]. CHK1-mediated phosphorylation of PP2Ac at Thr219 promotes PME-1 association independent of methylation, and PME-1 binding reciprocally shields CHK1 from PP2A-mediated dephosphorylation [#16]. Through these activities PME-1 supports basal ERK and Akt signaling, controls mitotic spindle length via the LCMT1–PME-1 methylation equilibrium, and modulates apoptosis and stress responses in tumor cells [#2, #8, #14]. Separation-of-function knock-in mice establish that the methylesterase activity and the PP2A-inhibitory binding activity are independently essential for development and tissue homeostasis, with distinct phenotypes in apoptosis/ROS control versus olfactory epithelium integrity [#17].\",\n  \"teleology\": [\n    {\n      \"year\": 1999,\n      \"claim\": \"Established the molecular identity and catalytic mechanism of PME-1, answering what enzyme removes the methyl group from PP2A and how it acts.\",\n      \"evidence\": \"Co-purification with inactive PP2A mutants, cDNA cloning, and in vitro demethylation by bacterially expressed protein with active-site characterization\",\n      \"pmids\": [\"10318862\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not resolve the in vivo consequences of demethylation\", \"Structural basis of substrate engagement not determined\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Defined the organismal requirement for PME-1 and revealed the counterintuitive coupling between demethylation and PP2A activity.\",\n      \"evidence\": \"Targeted gene knockout in mice with PP2A activity assay and phosphoproteome analysis\",\n      \"pmids\": [\"18596935\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism behind reduced PP2A activity in KO tissues not yet explained\", \"Did not separate methylesterase from binding functions\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Placed PME-1-mediated PP2A inhibition within growth-factor/ERK signaling, linking it to malignant phenotypes.\",\n      \"evidence\": \"siRNA knockdown and epistasis analysis in malignant glioma cells\",\n      \"pmids\": [\"19293187\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct PP2A substrate in the ERK pathway not identified\", \"Single cell-type context\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Connected PP2A demethylation to a specific developmental output, neuronal process outgrowth.\",\n      \"evidence\": \"Overexpression, knockdown, and methylation-site mutant (L309Δ) in N2a neurite outgrowth assays\",\n      \"pmids\": [\"21044074\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Downstream phospho-substrates governing outgrowth not defined\", \"Cell-line model only\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identified upstream regulation of the methylation equilibrium, showing GSK-3β tunes PP2A demethylation via PME-1 and PPMT1.\",\n      \"evidence\": \"siRNA knockdown and double-knockdown epistasis with methylation Western blots\",\n      \"pmids\": [\"22732552\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs indirect regulation of PME-1 by GSK-3β unresolved\", \"Single lab\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Defined substrate selectivity among type 2A phosphatases, showing PME-1 acts on PP4 but not PP6.\",\n      \"evidence\": \"Co-immunoprecipitation and functional assays in endometrial cancer cells\",\n      \"pmids\": [\"24928782\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis for PP4-versus-PP6 discrimination unknown\", \"Demethylation of PP4 not directly demonstrated\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Linked PME-1 to metabolic signaling, showing pharmacological promotion of demethylation relieves PP2A repression of Akt and enhances glucose uptake.\",\n      \"evidence\": \"siRNA knockdown, PP2A activity, GLUT4 translocation and PKB phosphorylation assays in skeletal muscle cells\",\n      \"pmids\": [\"25038454\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of carnosic acid action on PME-1 not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Resolved the paradox of the KO phenotype by showing methylesterase activity protects PP2Ac from ubiquitin-proteasome degradation.\",\n      \"evidence\": \"PME-1 KO MEFs, chemical inhibition, rescue with WT versus catalytic-mutant PME-1, ubiquitination and half-life measurements\",\n      \"pmids\": [\"26678046\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"E3 ligase targeting PP2Ac not identified\", \"How methylation status couples to ubiquitination not mechanistically detailed\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Established that the LCMT1–PME-1 methylation balance controls mitotic spindle length and faithful division.\",\n      \"evidence\": \"siRNA, overexpression, pharmacological inhibition, and spindle immunofluorescence\",\n      \"pmids\": [\"25839665\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Relevant PP2A holoenzyme and spindle substrates not identified\", \"Single lab\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Showed PME-1-mediated PP2A inhibition confers drug resistance through HDAC4 and BAD, defining a synthetic-lethal vulnerability.\",\n      \"evidence\": \"Overexpression/knockdown with genetic epistasis to HDAC4 and BAD in glioma cells\",\n      \"pmids\": [\"27671680\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct PP2A complex responsible not fully defined\", \"Single tumor context\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Revealed holoenzyme-family selectivity, showing demethylation dissociates B55/PR72 but not B56 complexes.\",\n      \"evidence\": \"In vitro demethylation with pharmacological inhibition and immunoprecipitation of PP2A subcomplexes\",\n      \"pmids\": [\"30186749\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanistic basis for B56 resistance not yet structurally explained\", \"Single lab\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Identified post-translational control of PME-1 abundance via USP36 deubiquitination, linking it to ERK and Akt signaling.\",\n      \"evidence\": \"Co-IP, siRNA knockdown, ubiquitination assay and stability Western blots\",\n      \"pmids\": [\"29577269\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"E3 ligase opposing USP36 unknown\", \"Single lab Co-IP without reciprocal structural mapping\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Mapped the global phosphotarget landscape controlled by PME-1 and showed non-redundancy with CIP2A and SET.\",\n      \"evidence\": \"siRNA depletion with mass spectrometry phosphoproteomics in HeLa cells\",\n      \"pmids\": [\"32071079\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct versus indirect targets not distinguished\", \"Single study\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Provided the structural mechanism by which PME-1 engages the B56 holoenzyme using substrate-mimicking disordered motifs to access the active site.\",\n      \"evidence\": \"Cryo-EM structure plus B56 interface mutagenesis, in vitro activity, and cellular p53 signaling readouts\",\n      \"pmids\": [\"35924897\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structures of other holoenzyme-family complexes not solved\", \"Dynamics of the activating conformational shift in cells not captured\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrated nuclear PME-1 sensitizes glioblastoma cells to oxidative-stress death via PP2A-B55α, requiring methylesterase, binding, and nuclear localization activities.\",\n      \"evidence\": \"Pharmacological inhibition, separation-of-function mutants, fractionation, Co-IP and kinase assays in two cell lines\",\n      \"pmids\": [\"37500619\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Determinants of PME-1 nuclear targeting not defined\", \"Generality beyond glioblastoma unknown\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Linked PME-1 to anoikis suppression and histone methylation in PTEN-deficient prostate cancer.\",\n      \"evidence\": \"Overexpression/knockdown, in ovo xenograft, zebrafish circulation and histone modification assays\",\n      \"pmids\": [\"36461911\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism connecting PP2A activity to H3K9/H3K27 trimethylation not established\", \"Single lab\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Provided transcriptome-level associations of PME-1 with inflammatory, PI3K/Akt, and EMT programs.\",\n      \"evidence\": \"RNA-seq of PME-1 knockout MEFs\",\n      \"pmids\": [\"38043157\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct mechanistic validation beyond transcriptome\", \"Causality versus secondary adaptation not resolved\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Identified CHK1 as a kinase that primes PP2Ac (Thr219) for PME-1 binding and revealed a reciprocal CHK1-protective loop.\",\n      \"evidence\": \"NanoBiT PPI assay, compound screening, in vitro kinase/phosphatase reactions, phospho-MS, and phospho-Thr219 antibody validation\",\n      \"pmids\": [\"38588804\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Physiological contexts where CHK1-PME-1 axis operates not fully mapped\", \"Effect on holoenzyme assembly downstream of Thr219 phosphorylation unresolved\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Genetically separated the two essential PME-1 activities in vivo, showing methylesterase and PP2A-inhibitory binding functions are non-redundant for distinct developmental outcomes.\",\n      \"evidence\": \"S156A and M335D knock-in mice with histology, gene expression, and mitochondrial/ROS assays in primary fibroblasts\",\n      \"pmids\": [\"40326231\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular basis of tissue-specific phenotype divergence not defined\", \"Direct downstream substrates driving apoptosis and ROS not identified\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How PME-1 selects among PP2A/PP4 holoenzyme families in vivo and which specific phospho-substrates mediate its distinct developmental, mitotic, and stress phenotypes remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Substrate-level wiring of PME-1-controlled PP2A to specific phenotypes incomplete\", \"E3 ligase that degrades PP2Ac upon PME-1 loss unknown\", \"Structural basis of B55/PR72 versus B56 selectivity not fully explained\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 7, 10, 13]},\n      {\"term_id\": \"GO:0016787\", \"supporting_discovery_ids\": [0, 7]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 7, 14, 16, 17]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [14]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [2, 6, 9]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [8, 16]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [14, 18]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"complexes\": [\n      \"PP2A holoenzyme (catalytic subunit complex)\"\n    ],\n    \"partners\": [\n      \"PPP2CA\",\n      \"PPP4C\",\n      \"LCMT1\",\n      \"USP36\",\n      \"CHEK1\",\n      \"PPP2R5 (B56)\",\n      \"PPP2R2A (B55)\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}