{"gene":"WDR59","run_date":"2026-04-28T23:00:23","timeline":{"discoveries":[{"year":2013,"finding":"WDR59 is a subunit of the GATOR2 complex, which negatively regulates GATOR1 (a GAP for RagA/B GTPases) upstream of mTORC1. Inhibition of WDR59 (a GATOR2 subunit) suppresses mTORC1 signaling, and epistasis analysis places GATOR2 as a negative regulator of DEPDC5 (GATOR1 subunit), establishing WDR59 within the amino acid-sensing pathway controlling mTORC1 lysosomal activation.","method":"RNAi knockdown, epistasis analysis, Co-immunoprecipitation, mTORC1 activity assays (phospho-S6K1)","journal":"Science","confidence":"High","confidence_rationale":"Tier 2 — reciprocal Co-IP and genetic epistasis, foundational paper with >800 citations replicated by multiple labs","pmids":["23723238"],"is_preprint":false},{"year":2017,"finding":"Lysosome-targeted WDR59 (GATOR2 component) suppresses mTORC1 signaling in SZT2-deficient cells and contributes to lysosomal localization of the SOG (SZT2-orchestrated GATOR) complex; WDR59 overexpression partially rescues constitutive mTORC1 activation caused by SZT2 deficiency, placing GATOR2/WDR59 in a lysosome-localized nutrient-sensing complex.","method":"Overexpression rescue experiments, lysosome-targeting constructs, mTORC1 activity assays, Co-immunoprecipitation","journal":"Nature","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (rescue, localization, activity assays), published in Nature with 158 citations","pmids":["28199315"],"is_preprint":false},{"year":2020,"finding":"WDR59 is the GATOR2 component essential for the GATOR2-mTORC2 interaction; silencing or deletion of WDR59 completely ablates Sestrin2-induced AKT activation, establishing WDR59 as the molecular bridge between the GATOR2 complex and mTORC2 in the Sestrin2-AKT signaling axis.","method":"siRNA knockdown, CRISPR knockout, in vitro kinase assay, Co-immunoprecipitation, AKT phosphorylation assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 — multiple orthogonal methods (KO, KD, in vitro kinase assay, Co-IP) in a single study","pmids":["31915252"],"is_preprint":false},{"year":2022,"finding":"Cryo-EM structure of human GATOR2 at ~1.1 MDa reveals WDR59 (two copies per complex) contributes to the octagonal scaffold circularized via non-catalytic RING domains and α-solenoids; WDR59 WD40 β-propeller dimers mediate interactions with SESN2, CASTOR1, and GATOR1, providing structural basis for WDR59's role in nutrient sensing.","method":"Cryo-electron microscopy (cryo-EM) structure determination with functional validation of subunit interactions","journal":"Nature","confidence":"High","confidence_rationale":"Tier 1 — cryo-EM structure with biochemical validation, published in Nature","pmids":["35831510"],"is_preprint":false},{"year":2022,"finding":"In Drosophila ovary and eye imaginal disc, Wdr59 inhibits TORC1 activity by opposing GATOR2-dependent inhibition of GATOR1 (context-dependent TORC1 inhibition). In the fat body, Wdr59 promotes accumulation of GATOR2 component Mio and is required for TORC1 activation. In mammalian HeLa cells, WDR59 prevents proteasomal degradation of GATOR2 proteins Mio and Wdr24; WDR59 knockout leads to reduced TORC1 activity restored by proteasome inhibition.","method":"Drosophila genetics (tissue-specific knockouts), CRISPR knockout in HeLa cells, proteasome inhibitor rescue, Western blotting for TORC1 activity","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 — genetic loss-of-function in multiple tissues/contexts with orthogonal rescue experiments, replicated across Drosophila and mammalian cells","pmids":["36577058"],"is_preprint":false},{"year":2021,"finding":"In fission yeast, the WDR59 ortholog Sea3 physically and functionally associates with GATOR1 (rather than GATOR2) to attenuate TORC1 activity; genetic and biochemical analysis shows Sea3/WDR59 is proximal to GATOR1 in fission yeast, revealing an evolutionarily divergent role compared to metazoans.","method":"Genetic epistasis, Co-immunoprecipitation, TORC1 activity assays in fission yeast","journal":"eLife","confidence":"Medium","confidence_rationale":"Tier 2 — epistasis and Co-IP in yeast ortholog, but functionally divergent from mammalian context","pmids":["33534698"],"is_preprint":false},{"year":2025,"finding":"Cryo-EM structures of GATOR2 bound to amino acid sensors (CASTOR1 and/or Sestrin2) reveal that CASTOR1 engages Mios WD40 β-propellers while Sestrin2 interacts with the WDR24-Seh1L subcomplex; HDX-MS reveals dynamic conformational changes in WDR59-containing GATOR2 upon sensor binding and amino acid supplementation, defining the structural mechanism of GATOR2 inhibition by amino acid sensors.","method":"Cryo-EM structure determination, hydrogen-deuterium exchange mass spectrometry (HDX-MS)","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 — cryo-EM structures with HDX-MS conformational validation","pmids":["40742811"],"is_preprint":false},{"year":2022,"finding":"Endogenous GFP-tagging of WDR59 in HeLa cells demonstrates that the fusion protein does not affect GATOR2 complex association or downstream mTORC1 signaling, validating WDR59's role in metabolically regulated protein-protein interactions within the GATOR2 complex under physiological expression conditions.","method":"CRISPR/Cas9 endogenous tagging, Co-immunoprecipitation, mTORC1 signaling assays","journal":"MethodsX","confidence":"Medium","confidence_rationale":"Tier 3 — single lab, Co-IP validation of complex integrity with endogenous tag","pmids":["36444289"],"is_preprint":false},{"year":2024,"finding":"AlphaFold2 modeling combined with biochemical experiments and FRET analysis shows GATOR2 undergoes structural transitions in response to amino acid signals; deletion of Mios β-propeller impedes these conformational changes at distinct arginine levels, and mutagenesis of interface residues (including WDR59-containing scaffold) reduces mTORC1 signaling capacity.","method":"AlphaFold2 structural prediction, biochemical mutagenesis, FRET analysis, molecular dynamics simulations","journal":"Bioscience reports","confidence":"Medium","confidence_rationale":"Tier 3 — computational modeling with biochemical and FRET validation, single lab","pmids":["38372438"],"is_preprint":false},{"year":2026,"finding":"Homozygous and compound heterozygous loss-of-function variants in WDR59 cause autosomal recessive syndromic dilated cardiomyopathy in humans, implicating dysregulated GATOR2-mTORC1 signaling in cardiomyocyte homeostasis; splicing defects confirmed by RNA-seq.","method":"Human genetics (variant identification), RNA-seq splicing validation, clinical phenotyping","journal":"Clinical genetics","confidence":"Medium","confidence_rationale":"Tier 2 — human loss-of-function with RNA-seq validation, but mechanistic pathway link inferred rather than directly tested","pmids":["41715954"],"is_preprint":false}],"current_model":"WDR59 is a core structural subunit of the pentameric GATOR2 complex (with WDR24, MIOS, SEH1L, SEC13) that adopts a 1.1 MDa cage-like architecture; within this complex, WDR59 forms part of the octagonal scaffold and orients WD40 β-propeller domains that mediate interactions with amino acid sensors (SESN2, CASTOR1) and GATOR1, thereby inhibiting GATOR1's GAP activity toward RagA/B GTPases to promote mTORC1 activation at the lysosome; additionally, WDR59 serves as the GATOR2 subunit essential for GATOR2-mTORC2 interaction and protects other GATOR2 subunits from proteasomal degradation, while in specific cellular contexts (Drosophila ovary/eye disc) it can paradoxically inhibit TORC1 by opposing GATOR2 function."},"narrative":{"teleology":[{"year":2013,"claim":"The discovery that WDR59 resides in a five-member GATOR2 complex that negatively regulates GATOR1 established the first direct placement of WDR59 in the amino acid–mTORC1 signaling cascade.","evidence":"RNAi knockdown, epistasis analysis, and co-immunoprecipitation in mammalian cells with phospho-S6K1 readouts","pmids":["23723238"],"confidence":"High","gaps":["No structural information on how GATOR2 inhibits GATOR1","Individual contributions of each GATOR2 subunit unresolved","No connection to mTORC2 signaling"]},{"year":2017,"claim":"Lysosome-targeted WDR59 overexpression rescued constitutive mTORC1 activation in SZT2-deficient cells, establishing that WDR59/GATOR2 operates at the lysosomal surface within the SZT2-orchestrated nutrient-sensing supercomplex.","evidence":"Lysosome-targeting constructs, overexpression rescue, co-immunoprecipitation, mTORC1 activity assays","pmids":["28199315"],"confidence":"High","gaps":["Endogenous WDR59 lysosomal dynamics not directly visualized","Whether WDR59 is recruited independently of other GATOR2 subunits unknown"]},{"year":2020,"claim":"Identifying WDR59 as the specific GATOR2 subunit essential for the GATOR2–mTORC2 interaction broadened its role beyond mTORC1, revealing it bridges Sestrin2-dependent AKT activation through mTORC2.","evidence":"siRNA, CRISPR knockout, in vitro kinase assay, co-immunoprecipitation, AKT phosphorylation assays","pmids":["31915252"],"confidence":"High","gaps":["Direct binding interface between WDR59 and mTORC2 not mapped","Whether WDR59–mTORC2 interaction is constitutive or amino acid-regulated unknown"]},{"year":2021,"claim":"In fission yeast, the WDR59 ortholog Sea3 associates with GATOR1 rather than GATOR2 to attenuate TORC1, revealing evolutionary divergence in WDR59's complex membership and raising questions about ancestral function.","evidence":"Genetic epistasis, co-immunoprecipitation, TORC1 activity assays in Schizosaccharomyces pombe","pmids":["33534698"],"confidence":"Medium","gaps":["Whether yeast Sea3 retains any GATOR2-like scaffolding role not tested","Structural basis for the divergent complex association unknown"]},{"year":2022,"claim":"Cryo-EM resolution of the full GATOR2 complex revealed WDR59 as a duplicated scaffold component whose WD40 β-propeller dimers mediate contacts with Sestrin2, CASTOR1, and GATOR1, providing the first atomic framework for WDR59's multivalent role in nutrient sensing.","evidence":"Cryo-EM structure determination at near-atomic resolution with biochemical validation of subunit interactions","pmids":["35831510"],"confidence":"High","gaps":["Conformational dynamics upon amino acid stimulation not captured in static structure","How WDR59 scaffold rearrangements relay sensor binding to GATOR1 inhibition unclear"]},{"year":2022,"claim":"Context-dependent roles of WDR59 were uncovered: in Drosophila ovary/eye disc WDR59 paradoxically inhibits TORC1, while in fat body and mammalian cells it stabilizes GATOR2 subunits against proteasomal degradation and promotes TORC1 activation.","evidence":"Drosophila tissue-specific knockouts, CRISPR knockout in HeLa cells, proteasome inhibitor rescue, Western blotting","pmids":["36577058"],"confidence":"High","gaps":["Molecular basis for tissue-specific opposing effects unresolved","Whether WDR59 directly interacts with proteasome components or acts indirectly unknown"]},{"year":2024,"claim":"Computational and FRET-based analyses demonstrated that the GATOR2 scaffold including WDR59 undergoes conformational transitions in response to arginine levels, and mutagenesis of interface residues reduced mTORC1 signaling capacity.","evidence":"AlphaFold2 modeling, biochemical mutagenesis, FRET analysis, molecular dynamics simulations","pmids":["38372438"],"confidence":"Medium","gaps":["In vivo validation of predicted conformational states not performed","Specific WDR59 residues critical for conformational relay not individually mapped"]},{"year":2025,"claim":"Cryo-EM structures of GATOR2 bound to CASTOR1 and/or Sestrin2 combined with HDX-MS showed that amino acid sensor engagement induces dynamic conformational changes across the WDR59-containing scaffold, defining the allosteric mechanism of GATOR2 inhibition.","evidence":"Cryo-EM structure determination of sensor-bound complexes, hydrogen-deuterium exchange mass spectrometry","pmids":["40742811"],"confidence":"High","gaps":["How conformational changes in WDR59 translate to altered GATOR1 GAP regulation not fully resolved","Whether WDR59 conformational changes also affect mTORC2 interaction untested"]},{"year":2026,"claim":"Human genetics linked homozygous WDR59 loss-of-function to autosomal recessive syndromic dilated cardiomyopathy, providing the first Mendelian disease association and implicating GATOR2–mTORC1 signaling in cardiomyocyte homeostasis.","evidence":"Human variant identification, RNA-seq splicing validation, clinical phenotyping","pmids":["41715954"],"confidence":"Medium","gaps":["Mechanistic pathway from WDR59 loss to cardiomyopathy not directly tested in model systems","Whether mTORC1, mTORC2, or both pathways are disrupted in patient cardiomyocytes unknown","No rescue experiments performed"]},{"year":null,"claim":"How WDR59-mediated conformational changes in GATOR2 are transduced to GATOR1 GAP inhibition, what determines tissue-specific opposing effects on TORC1, and the precise mechanism linking WDR59 loss to dilated cardiomyopathy remain unresolved.","evidence":"","pmids":[],"confidence":"High","gaps":["No reconstituted system demonstrating direct allosteric relay from WDR59 to GATOR1 GAP activity","Tissue-specific regulatory partners or post-translational modifications of WDR59 not identified","No animal model recapitulating the human cardiomyopathy phenotype"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[3,6]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,2,4]}],"localization":[{"term_id":"GO:0005764","term_label":"lysosome","supporting_discovery_ids":[1]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[0,3]}],"pathway":[{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[0,1,2,4]},{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[0,1]}],"complexes":["GATOR2"],"partners":["WDR24","MIOS","SEH1L","SEC13","SESN2","CASTOR1","SZT2"],"other_free_text":[]},"mechanistic_narrative":"WDR59 is a core structural subunit of the pentameric GATOR2 complex that functions as a central regulatory node in the amino acid–sensing pathway controlling mTORC1 and mTORC2 signaling. Within the ~1.1 MDa GATOR2 cage-like architecture, two copies of WDR59 contribute WD40 β-propeller domains and α-solenoid/RING-mediated scaffold contacts that orient the complex for interactions with amino acid sensors (Sestrin2, CASTOR1) and the GATOR1 GAP complex, thereby inhibiting GATOR1 and permitting Rag GTPase–dependent mTORC1 activation at the lysosome [PMID:23723238, PMID:35831510, PMID:40742811]. WDR59 is uniquely required among GATOR2 subunits for the GATOR2–mTORC2 interaction and Sestrin2-induced AKT activation, and it protects other GATOR2 subunits (MIOS, WDR24) from proteasomal degradation, such that WDR59 loss destabilizes the entire complex and reduces mTORC1 activity [PMID:31915252, PMID:36577058]. Homozygous loss-of-function variants in WDR59 cause autosomal recessive syndromic dilated cardiomyopathy in humans [PMID:41715954]."},"prefetch_data":{"uniprot":{"accession":"Q6PJI9","full_name":"GATOR2 complex protein WDR59","aliases":["WD repeat-containing protein 59"],"length_aa":974,"mass_kda":109.8,"function":"As a component of the GATOR2 complex, functions as an activator of the amino acid-sensing branch of the mTORC1 signaling pathway (PubMed:23723238, PubMed:25457612, PubMed:27487210, PubMed:35831510, PubMed:36528027, PubMed:36577058). The GATOR2 complex indirectly activates mTORC1 through the inhibition of the GATOR1 subcomplex (PubMed:23723238, PubMed:27487210, PubMed:35831510, PubMed:36528027). GATOR2 probably acts as an E3 ubiquitin-protein ligase toward GATOR1 (PubMed:36528027). In the presence of abundant amino acids, the GATOR2 complex mediates ubiquitination of the NPRL2 core component of the GATOR1 complex, leading to GATOR1 inactivation (PubMed:36528027). In the absence of amino acids, GATOR2 is inhibited, activating the GATOR1 complex (PubMed:25457612, PubMed:27487210)","subcellular_location":"Lysosome membrane","url":"https://www.uniprot.org/uniprotkb/Q6PJI9/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/WDR59","classification":"Not Classified","n_dependent_lines":327,"n_total_lines":1208,"dependency_fraction":0.2706953642384106},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"HSP90B1","stoichiometry":0.2},{"gene":"SEC13","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/WDR59","total_profiled":1310},"omim":[{"mim_id":"620307","title":"WD REPEAT-CONTAINING PROTEIN 24; WDR24","url":"https://www.omim.org/entry/620307"},{"mim_id":"617418","title":"WD REPEAT-CONTAINING PROTEIN 59; WDR59","url":"https://www.omim.org/entry/617418"},{"mim_id":"617034","title":"CELLULAR ARGININE SENSOR FOR MTORC1 PROTEIN 1; CASTOR1","url":"https://www.omim.org/entry/617034"},{"mim_id":"615359","title":"MEIOSIS REGULATOR FOR OOCYTE DEVELOPMENT; MIOS","url":"https://www.omim.org/entry/615359"},{"mim_id":"614191","title":"DEP DOMAIN-CONTAINING PROTEIN 5; DEPDC5","url":"https://www.omim.org/entry/614191"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Vesicles","reliability":"Approved"},{"location":"Cytosol","reliability":"Approved"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/WDR59"},"hgnc":{"alias_symbol":["FLJ12270"],"prev_symbol":[]},"alphafold":{"accession":"Q6PJI9","domains":[{"cath_id":"3.10.110.10","chopping":"395-497","consensus_level":"high","plddt":83.9756,"start":395,"end":497},{"cath_id":"-","chopping":"658-757_858-885","consensus_level":"high","plddt":87.723,"start":658,"end":885},{"cath_id":"3.30.40","chopping":"901-974","consensus_level":"medium","plddt":82.523,"start":901,"end":974}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6PJI9","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q6PJI9-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q6PJI9-F1-predicted_aligned_error_v6.png","plddt_mean":72.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=WDR59","jax_strain_url":"https://www.jax.org/strain/search?query=WDR59"},"sequence":{"accession":"Q6PJI9","fasta_url":"https://rest.uniprot.org/uniprotkb/Q6PJI9.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q6PJI9/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q6PJI9"}},"corpus_meta":[{"pmid":"23723238","id":"PMC_23723238","title":"A Tumor suppressor complex with GAP activity for the Rag GTPases that signal amino acid sufficiency to mTORC1.","date":"2013","source":"Science (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/23723238","citation_count":882,"is_preprint":false},{"pmid":"28199315","id":"PMC_28199315","title":"SZT2 dictates GATOR control of mTORC1 signalling.","date":"2017","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/28199315","citation_count":158,"is_preprint":false},{"pmid":"27173016","id":"PMC_27173016","title":"Involvement of GATOR complex genes in familial focal epilepsies and focal cortical dysplasia.","date":"2016","source":"Epilepsia","url":"https://pubmed.ncbi.nlm.nih.gov/27173016","citation_count":139,"is_preprint":false},{"pmid":"31917448","id":"PMC_31917448","title":"A Transcriptome-Wide Association Study Identifies Novel Candidate Susceptibility Genes for Pancreatic Cancer.","date":"2020","source":"Journal of the National Cancer Institute","url":"https://pubmed.ncbi.nlm.nih.gov/31917448","citation_count":70,"is_preprint":false},{"pmid":"35831510","id":"PMC_35831510","title":"Structure of the nutrient-sensing hub GATOR2.","date":"2022","source":"Nature","url":"https://pubmed.ncbi.nlm.nih.gov/35831510","citation_count":66,"is_preprint":false},{"pmid":"31915252","id":"PMC_31915252","title":"The GATOR2-mTORC2 axis mediates Sestrin2-induced AKT Ser/Thr kinase activation.","date":"2020","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/31915252","citation_count":51,"is_preprint":false},{"pmid":"33534698","id":"PMC_33534698","title":"Tripartite suppression of fission yeast TORC1 signaling by the GATOR1-Sea3 complex, the TSC complex, and Gcn2 kinase.","date":"2021","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/33534698","citation_count":28,"is_preprint":false},{"pmid":"35230915","id":"PMC_35230915","title":"The FACT complex facilitates expression of lysosomal and antioxidant genes through binding to TFEB and TFE3.","date":"2022","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/35230915","citation_count":22,"is_preprint":false},{"pmid":"34085593","id":"PMC_34085593","title":"Multiplexed suppression of TOR complex 1 induces autophagy during starvation.","date":"2021","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/34085593","citation_count":8,"is_preprint":false},{"pmid":"36577058","id":"PMC_36577058","title":"Wdr59 promotes or inhibits TORC1 activity depending on cellular context.","date":"2022","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/36577058","citation_count":7,"is_preprint":false},{"pmid":"40742811","id":"PMC_40742811","title":"Cryo-EM structures of amino acid sensors bound to the human GATOR2 complex.","date":"2025","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/40742811","citation_count":7,"is_preprint":false},{"pmid":"38372438","id":"PMC_38372438","title":"New insights into GATOR2-dependent interactions and its conformational changes in amino acid sensing.","date":"2024","source":"Bioscience reports","url":"https://pubmed.ncbi.nlm.nih.gov/38372438","citation_count":6,"is_preprint":false},{"pmid":"37194451","id":"PMC_37194451","title":"Integration of GWAS and eGWAS to screen candidate genes underlying green head traits in male ducks.","date":"2023","source":"Animal genetics","url":"https://pubmed.ncbi.nlm.nih.gov/37194451","citation_count":4,"is_preprint":false},{"pmid":"37040585","id":"PMC_37040585","title":"Interactions between genetic variants and environmental risk factors are associated with the severity of pelvic organ prolapse.","date":"2023","source":"Menopause (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/37040585","citation_count":3,"is_preprint":false},{"pmid":"39513902","id":"PMC_39513902","title":"Unveiling GATOR2 Function: Novel Insights from Drosophila Research.","date":"2024","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/39513902","citation_count":2,"is_preprint":false},{"pmid":"41715954","id":"PMC_41715954","title":"WDR59 Is Mutated in Individuals With Autosomal Recessive Syndromic Dilated Cardiomyopathy.","date":"2026","source":"Clinical genetics","url":"https://pubmed.ncbi.nlm.nih.gov/41715954","citation_count":0,"is_preprint":false},{"pmid":"36444289","id":"PMC_36444289","title":"Selection-free endogenous tagging of cell lines by bicistronic co-expression of the surface antigen NGFR.","date":"2022","source":"MethodsX","url":"https://pubmed.ncbi.nlm.nih.gov/36444289","citation_count":0,"is_preprint":false},{"pmid":"40887617","id":"PMC_40887617","title":"Comparative genomics of two closely related Acropora coral species with different spawning seasons reveals genomic regions possibly associated with gametogenesis.","date":"2025","source":"BMC ecology and evolution","url":"https://pubmed.ncbi.nlm.nih.gov/40887617","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":11391,"output_tokens":2659,"usd":0.037029},"stage2":{"model":"claude-opus-4-6","input_tokens":5986,"output_tokens":2674,"usd":0.14517},"total_usd":0.182199,"stage1_batch_id":"msgbatch_01BparvgRZ9S2LMidvaoo86K","stage2_batch_id":"msgbatch_01NkBfv9SVZWthhS7j6mU6G3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2013,\n      \"finding\": \"WDR59 is a subunit of the GATOR2 complex, which negatively regulates GATOR1 (a GAP for RagA/B GTPases) upstream of mTORC1. Inhibition of WDR59 (a GATOR2 subunit) suppresses mTORC1 signaling, and epistasis analysis places GATOR2 as a negative regulator of DEPDC5 (GATOR1 subunit), establishing WDR59 within the amino acid-sensing pathway controlling mTORC1 lysosomal activation.\",\n      \"method\": \"RNAi knockdown, epistasis analysis, Co-immunoprecipitation, mTORC1 activity assays (phospho-S6K1)\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — reciprocal Co-IP and genetic epistasis, foundational paper with >800 citations replicated by multiple labs\",\n      \"pmids\": [\"23723238\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Lysosome-targeted WDR59 (GATOR2 component) suppresses mTORC1 signaling in SZT2-deficient cells and contributes to lysosomal localization of the SOG (SZT2-orchestrated GATOR) complex; WDR59 overexpression partially rescues constitutive mTORC1 activation caused by SZT2 deficiency, placing GATOR2/WDR59 in a lysosome-localized nutrient-sensing complex.\",\n      \"method\": \"Overexpression rescue experiments, lysosome-targeting constructs, mTORC1 activity assays, Co-immunoprecipitation\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (rescue, localization, activity assays), published in Nature with 158 citations\",\n      \"pmids\": [\"28199315\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"WDR59 is the GATOR2 component essential for the GATOR2-mTORC2 interaction; silencing or deletion of WDR59 completely ablates Sestrin2-induced AKT activation, establishing WDR59 as the molecular bridge between the GATOR2 complex and mTORC2 in the Sestrin2-AKT signaling axis.\",\n      \"method\": \"siRNA knockdown, CRISPR knockout, in vitro kinase assay, Co-immunoprecipitation, AKT phosphorylation assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — multiple orthogonal methods (KO, KD, in vitro kinase assay, Co-IP) in a single study\",\n      \"pmids\": [\"31915252\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Cryo-EM structure of human GATOR2 at ~1.1 MDa reveals WDR59 (two copies per complex) contributes to the octagonal scaffold circularized via non-catalytic RING domains and α-solenoids; WDR59 WD40 β-propeller dimers mediate interactions with SESN2, CASTOR1, and GATOR1, providing structural basis for WDR59's role in nutrient sensing.\",\n      \"method\": \"Cryo-electron microscopy (cryo-EM) structure determination with functional validation of subunit interactions\",\n      \"journal\": \"Nature\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structure with biochemical validation, published in Nature\",\n      \"pmids\": [\"35831510\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"In Drosophila ovary and eye imaginal disc, Wdr59 inhibits TORC1 activity by opposing GATOR2-dependent inhibition of GATOR1 (context-dependent TORC1 inhibition). In the fat body, Wdr59 promotes accumulation of GATOR2 component Mio and is required for TORC1 activation. In mammalian HeLa cells, WDR59 prevents proteasomal degradation of GATOR2 proteins Mio and Wdr24; WDR59 knockout leads to reduced TORC1 activity restored by proteasome inhibition.\",\n      \"method\": \"Drosophila genetics (tissue-specific knockouts), CRISPR knockout in HeLa cells, proteasome inhibitor rescue, Western blotting for TORC1 activity\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 — genetic loss-of-function in multiple tissues/contexts with orthogonal rescue experiments, replicated across Drosophila and mammalian cells\",\n      \"pmids\": [\"36577058\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"In fission yeast, the WDR59 ortholog Sea3 physically and functionally associates with GATOR1 (rather than GATOR2) to attenuate TORC1 activity; genetic and biochemical analysis shows Sea3/WDR59 is proximal to GATOR1 in fission yeast, revealing an evolutionarily divergent role compared to metazoans.\",\n      \"method\": \"Genetic epistasis, Co-immunoprecipitation, TORC1 activity assays in fission yeast\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — epistasis and Co-IP in yeast ortholog, but functionally divergent from mammalian context\",\n      \"pmids\": [\"33534698\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-EM structures of GATOR2 bound to amino acid sensors (CASTOR1 and/or Sestrin2) reveal that CASTOR1 engages Mios WD40 β-propellers while Sestrin2 interacts with the WDR24-Seh1L subcomplex; HDX-MS reveals dynamic conformational changes in WDR59-containing GATOR2 upon sensor binding and amino acid supplementation, defining the structural mechanism of GATOR2 inhibition by amino acid sensors.\",\n      \"method\": \"Cryo-EM structure determination, hydrogen-deuterium exchange mass spectrometry (HDX-MS)\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 — cryo-EM structures with HDX-MS conformational validation\",\n      \"pmids\": [\"40742811\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"Endogenous GFP-tagging of WDR59 in HeLa cells demonstrates that the fusion protein does not affect GATOR2 complex association or downstream mTORC1 signaling, validating WDR59's role in metabolically regulated protein-protein interactions within the GATOR2 complex under physiological expression conditions.\",\n      \"method\": \"CRISPR/Cas9 endogenous tagging, Co-immunoprecipitation, mTORC1 signaling assays\",\n      \"journal\": \"MethodsX\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — single lab, Co-IP validation of complex integrity with endogenous tag\",\n      \"pmids\": [\"36444289\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"AlphaFold2 modeling combined with biochemical experiments and FRET analysis shows GATOR2 undergoes structural transitions in response to amino acid signals; deletion of Mios β-propeller impedes these conformational changes at distinct arginine levels, and mutagenesis of interface residues (including WDR59-containing scaffold) reduces mTORC1 signaling capacity.\",\n      \"method\": \"AlphaFold2 structural prediction, biochemical mutagenesis, FRET analysis, molecular dynamics simulations\",\n      \"journal\": \"Bioscience reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 — computational modeling with biochemical and FRET validation, single lab\",\n      \"pmids\": [\"38372438\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Homozygous and compound heterozygous loss-of-function variants in WDR59 cause autosomal recessive syndromic dilated cardiomyopathy in humans, implicating dysregulated GATOR2-mTORC1 signaling in cardiomyocyte homeostasis; splicing defects confirmed by RNA-seq.\",\n      \"method\": \"Human genetics (variant identification), RNA-seq splicing validation, clinical phenotyping\",\n      \"journal\": \"Clinical genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 — human loss-of-function with RNA-seq validation, but mechanistic pathway link inferred rather than directly tested\",\n      \"pmids\": [\"41715954\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"WDR59 is a core structural subunit of the pentameric GATOR2 complex (with WDR24, MIOS, SEH1L, SEC13) that adopts a 1.1 MDa cage-like architecture; within this complex, WDR59 forms part of the octagonal scaffold and orients WD40 β-propeller domains that mediate interactions with amino acid sensors (SESN2, CASTOR1) and GATOR1, thereby inhibiting GATOR1's GAP activity toward RagA/B GTPases to promote mTORC1 activation at the lysosome; additionally, WDR59 serves as the GATOR2 subunit essential for GATOR2-mTORC2 interaction and protects other GATOR2 subunits from proteasomal degradation, while in specific cellular contexts (Drosophila ovary/eye disc) it can paradoxically inhibit TORC1 by opposing GATOR2 function.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"WDR59 is a core structural subunit of the pentameric GATOR2 complex that functions as a central regulatory node in the amino acid–sensing pathway controlling mTORC1 and mTORC2 signaling. Within the ~1.1 MDa GATOR2 cage-like architecture, two copies of WDR59 contribute WD40 β-propeller domains and α-solenoid/RING-mediated scaffold contacts that orient the complex for interactions with amino acid sensors (Sestrin2, CASTOR1) and the GATOR1 GAP complex, thereby inhibiting GATOR1 and permitting Rag GTPase–dependent mTORC1 activation at the lysosome [PMID:23723238, PMID:35831510, PMID:40742811]. WDR59 is uniquely required among GATOR2 subunits for the GATOR2–mTORC2 interaction and Sestrin2-induced AKT activation, and it protects other GATOR2 subunits (MIOS, WDR24) from proteasomal degradation, such that WDR59 loss destabilizes the entire complex and reduces mTORC1 activity [PMID:31915252, PMID:36577058]. Homozygous loss-of-function variants in WDR59 cause autosomal recessive syndromic dilated cardiomyopathy in humans [PMID:41715954].\",\n  \"teleology\": [\n    {\n      \"year\": 2013,\n      \"claim\": \"The discovery that WDR59 resides in a five-member GATOR2 complex that negatively regulates GATOR1 established the first direct placement of WDR59 in the amino acid–mTORC1 signaling cascade.\",\n      \"evidence\": \"RNAi knockdown, epistasis analysis, and co-immunoprecipitation in mammalian cells with phospho-S6K1 readouts\",\n      \"pmids\": [\"23723238\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No structural information on how GATOR2 inhibits GATOR1\",\n        \"Individual contributions of each GATOR2 subunit unresolved\",\n        \"No connection to mTORC2 signaling\"\n      ]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Lysosome-targeted WDR59 overexpression rescued constitutive mTORC1 activation in SZT2-deficient cells, establishing that WDR59/GATOR2 operates at the lysosomal surface within the SZT2-orchestrated nutrient-sensing supercomplex.\",\n      \"evidence\": \"Lysosome-targeting constructs, overexpression rescue, co-immunoprecipitation, mTORC1 activity assays\",\n      \"pmids\": [\"28199315\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Endogenous WDR59 lysosomal dynamics not directly visualized\",\n        \"Whether WDR59 is recruited independently of other GATOR2 subunits unknown\"\n      ]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Identifying WDR59 as the specific GATOR2 subunit essential for the GATOR2–mTORC2 interaction broadened its role beyond mTORC1, revealing it bridges Sestrin2-dependent AKT activation through mTORC2.\",\n      \"evidence\": \"siRNA, CRISPR knockout, in vitro kinase assay, co-immunoprecipitation, AKT phosphorylation assays\",\n      \"pmids\": [\"31915252\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct binding interface between WDR59 and mTORC2 not mapped\",\n        \"Whether WDR59–mTORC2 interaction is constitutive or amino acid-regulated unknown\"\n      ]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"In fission yeast, the WDR59 ortholog Sea3 associates with GATOR1 rather than GATOR2 to attenuate TORC1, revealing evolutionary divergence in WDR59's complex membership and raising questions about ancestral function.\",\n      \"evidence\": \"Genetic epistasis, co-immunoprecipitation, TORC1 activity assays in Schizosaccharomyces pombe\",\n      \"pmids\": [\"33534698\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Whether yeast Sea3 retains any GATOR2-like scaffolding role not tested\",\n        \"Structural basis for the divergent complex association unknown\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Cryo-EM resolution of the full GATOR2 complex revealed WDR59 as a duplicated scaffold component whose WD40 β-propeller dimers mediate contacts with Sestrin2, CASTOR1, and GATOR1, providing the first atomic framework for WDR59's multivalent role in nutrient sensing.\",\n      \"evidence\": \"Cryo-EM structure determination at near-atomic resolution with biochemical validation of subunit interactions\",\n      \"pmids\": [\"35831510\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Conformational dynamics upon amino acid stimulation not captured in static structure\",\n        \"How WDR59 scaffold rearrangements relay sensor binding to GATOR1 inhibition unclear\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Context-dependent roles of WDR59 were uncovered: in Drosophila ovary/eye disc WDR59 paradoxically inhibits TORC1, while in fat body and mammalian cells it stabilizes GATOR2 subunits against proteasomal degradation and promotes TORC1 activation.\",\n      \"evidence\": \"Drosophila tissue-specific knockouts, CRISPR knockout in HeLa cells, proteasome inhibitor rescue, Western blotting\",\n      \"pmids\": [\"36577058\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Molecular basis for tissue-specific opposing effects unresolved\",\n        \"Whether WDR59 directly interacts with proteasome components or acts indirectly unknown\"\n      ]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Computational and FRET-based analyses demonstrated that the GATOR2 scaffold including WDR59 undergoes conformational transitions in response to arginine levels, and mutagenesis of interface residues reduced mTORC1 signaling capacity.\",\n      \"evidence\": \"AlphaFold2 modeling, biochemical mutagenesis, FRET analysis, molecular dynamics simulations\",\n      \"pmids\": [\"38372438\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"In vivo validation of predicted conformational states not performed\",\n        \"Specific WDR59 residues critical for conformational relay not individually mapped\"\n      ]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Cryo-EM structures of GATOR2 bound to CASTOR1 and/or Sestrin2 combined with HDX-MS showed that amino acid sensor engagement induces dynamic conformational changes across the WDR59-containing scaffold, defining the allosteric mechanism of GATOR2 inhibition.\",\n      \"evidence\": \"Cryo-EM structure determination of sensor-bound complexes, hydrogen-deuterium exchange mass spectrometry\",\n      \"pmids\": [\"40742811\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"How conformational changes in WDR59 translate to altered GATOR1 GAP regulation not fully resolved\",\n        \"Whether WDR59 conformational changes also affect mTORC2 interaction untested\"\n      ]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Human genetics linked homozygous WDR59 loss-of-function to autosomal recessive syndromic dilated cardiomyopathy, providing the first Mendelian disease association and implicating GATOR2–mTORC1 signaling in cardiomyocyte homeostasis.\",\n      \"evidence\": \"Human variant identification, RNA-seq splicing validation, clinical phenotyping\",\n      \"pmids\": [\"41715954\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"Mechanistic pathway from WDR59 loss to cardiomyopathy not directly tested in model systems\",\n        \"Whether mTORC1, mTORC2, or both pathways are disrupted in patient cardiomyocytes unknown\",\n        \"No rescue experiments performed\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How WDR59-mediated conformational changes in GATOR2 are transduced to GATOR1 GAP inhibition, what determines tissue-specific opposing effects on TORC1, and the precise mechanism linking WDR59 loss to dilated cardiomyopathy remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"No reconstituted system demonstrating direct allosteric relay from WDR59 to GATOR1 GAP activity\",\n        \"Tissue-specific regulatory partners or post-translational modifications of WDR59 not identified\",\n        \"No animal model recapitulating the human cardiomyopathy phenotype\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [3, 6]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 2, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005764\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [0, 3]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [0, 1, 2, 4]},\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"complexes\": [\n      \"GATOR2\"\n    ],\n    \"partners\": [\n      \"WDR24\",\n      \"MIOS\",\n      \"SEH1L\",\n      \"SEC13\",\n      \"SESN2\",\n      \"CASTOR1\",\n      \"SZT2\"\n    ],\n    \"other_free_text\": []\n  }\n}\n```"}