{"gene":"ATG10","run_date":"2026-06-09T22:02:44","timeline":{"discoveries":[{"year":2012,"finding":"Crystal structures of yeast (Atg7-Atg3)₂ and (Atg7-Atg10)₂ complexes revealed noncanonical, multisite E1-E2 recognition in autophagy: Atg7's unique N-terminal domain recruits distinctive elements from the Atg10 'backside', and Atg10's 'frontside' active site is presented to the catalytic cysteine in the C-terminal domain of the opposite Atg7 protomer in the homodimer, enabling UBL transfer.","method":"X-ray crystallography, mutational analysis of yeast Atg7-Atg10 complexes","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structures of complexes combined with mutational analysis, mechanistically defining E1-E2 interaction and catalytic mechanism","pmids":["23142976"],"is_preprint":false},{"year":2012,"finding":"Solution and crystal structures of Kluyveromyces marxianus Atg10 revealed an E2-core fold with two characteristic β-strands that directly recognize the C-terminal ubiquitin-like domain of Atg5; Tyr56 and Asn114 of Atg10 orient the Atg5 Lys145 side chain for conjugation with Atg12, enabling Atg12-Atg5 conjugate formation without a specific E3 enzyme.","method":"X-ray crystallography, NMR, mutational analysis, crosslinking experiments, kinetic analysis","journal":"Structure","confidence":"High","confidence_rationale":"Tier 1 / Strong — multiple orthogonal structural and biochemical methods (NMR, crystallography, mutagenesis, kinetics) in a single rigorous study","pmids":["22682742"],"is_preprint":false},{"year":2012,"finding":"Crystal structure of Saccharomyces cerevisiae Atg10 at 2.7 Å resolution showed a conserved E2 core fold compared to Atg3 and other E2 enzymes, with an insertion ('FR-region') absent in the structure that may be important for interaction with E1 enzyme Atg7.","method":"X-ray crystallography, heavy-atom derivatization","journal":"Acta crystallographica. Section D, Biological crystallography","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — crystal structure determined but FR-region functional role inferred rather than experimentally validated in this paper","pmids":["22993095"],"is_preprint":false},{"year":2013,"finding":"Structural and mechanistic analysis confirmed that Atg7 recruits Atg10 through surfaces remote from their active sites (noncanonical mode), juxtaposing E1 and E2 catalytic cysteines for UBL (Atg12) transfer; common principles underlie both canonical and noncanonical UBL cascades.","method":"Crystallographic analysis, mutational analysis, mechanistic biochemistry","journal":"Autophagy","confidence":"High","confidence_rationale":"Tier 1 / Strong — structural and mutational validation of mechanism, corroborating the companion Nature Struct Mol Biol paper from same group","pmids":["23388412"],"is_preprint":false},{"year":2012,"finding":"In Schizosaccharomyces pombe, the Atg10 homolog (SpAtg10) is not required for autophagy but is essential for normal cell cycle progression and stress responses, independently of Atg12 conjugation, indicating Atg10-family enzymes can have functions beyond UBL conjugation.","method":"Genetic deletion, cell cycle assays, autophagy assays in S. pombe","journal":"Cell cycle","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean KO with defined cellular phenotypes (cell cycle arrest, autophagy-independent function) using multiple readouts in a single study","pmids":["23255127"],"is_preprint":false},{"year":2017,"finding":"Two isoforms of human ATG10 have opposing effects on autophagy flux: the canonical long isoform (ATG10) promotes autophagosome formation and detains autophagosomes at the cell periphery, impairing autophagy flux; the short isoform (ATG10S) drives autophagosomes to the perinuclear region for lysosomal degradation, promoting autophagy flux. ATG10S also activates innate immunity genes. IL28A protein directly conjugates ATG10S and assists autophagosome docking to lysosomes.","method":"Overexpression studies in HepG2/Huh7.5 cells, co-immunoprecipitation (IL28A-ATG10S), autophagy flux assays","journal":"Scientific reports","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct binding demonstrated by Co-IP, isoform-specific functional differences shown by OE with autophagy readouts, single lab","pmids":["28900156"],"is_preprint":false},{"year":2018,"finding":"In a zebrafish HCV subreplicon model, canonical ATG10 facilitated HCV amplification by promoting autophagosome formation, while ATG10S suppressed HCV replication by promoting autophagy flux leading to lysosomal degradation, confirming opposing isoform roles in vivo.","method":"Liver-specific HCV subreplicon zebrafish model, autophagy inhibitor assays (3MA, chloroquine), isoform overexpression","journal":"Frontiers in cellular and infection microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo model with pharmacological and genetic perturbations, independent corroboration of isoform roles from prior paper","pmids":["29670865"],"is_preprint":false},{"year":2015,"finding":"Burkholderia pseudomallei infection upregulates three miRNAs (MIR4458, MIR4667-5p, MIR4668-5p) that directly target the 3'-UTR of ATG10, reducing ATG10 levels and inhibiting autophagy-mediated bacterial elimination; forced ATG10 expression enhanced autophagy and accelerated intracellular bacterial clearance.","method":"miRNA microarray, 3'-UTR luciferase reporter assays, ATG10 forced expression, bacterial survival assays in A549 cells","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — luciferase reporter validation of miRNA targeting, gain-of-function phenotype, multiple miRNAs validated, single lab","pmids":["26151773"],"is_preprint":false},{"year":2016,"finding":"PTBP1 directly interacts with ATG10 mRNA and reduces ATG10 expression at the post-transcriptional level; knockdown of ATG10 promoted colorectal cancer cell migration/invasion and modulated EMT markers (upregulating N-cadherin, ZEB1, CD44; downregulating E-cadherin), placing ATG10 as a negative regulator of EMT-associated metastasis.","method":"RNA immunoprecipitation (PTBP1-ATG10 mRNA interaction), ectopic expression and knockdown, cell migration/invasion assays, Western blot for EMT markers","journal":"Cancer letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct RIP demonstrating PTBP1-ATG10 mRNA interaction, functional KD phenotype with molecular markers, single lab","pmids":["27836735"],"is_preprint":false},{"year":2019,"finding":"In TBK1-mutant hiPSC-derived motoneurons, ATG10 levels are reduced and phagophore elongation is impaired (accumulation of immature phagophores by TEM); rescue of ATG10 levels abolished 4HPR toxicity and SQSTM1 accumulation, placing ATG10 at the elongation phase of autophagosome formation.","method":"hiPSC-derived motoneurons, TEM of phagophores, ATG10 rescue experiments, nuclear-receptor-agonist screen","journal":"Autophagy","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — TEM-based structural phenotype plus rescue experiment establish ATG10's role at phagophore elongation, single lab, human cell model","pmids":["30939964"],"is_preprint":false},{"year":2020,"finding":"c-Myc binds the miR-27b promoter (shown by ChIP) to suppress miR-27b-3p expression; miR-27b-3p inhibits ATG10 expression post-transcriptionally (luciferase reporter assay), thereby reducing autophagy; this c-Myc/miR-27b-3p/ATG10 axis promotes oxaliplatin resistance in colorectal cancer.","method":"ChIP assay, luciferase reporter assay, Western blot, GFP-LC3 fluorescence, TEM, xenograft studies","journal":"Theranostics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple orthogonal methods (ChIP, luciferase, in vivo xenograft), single lab, establishes pathway position","pmids":["32104496"],"is_preprint":false},{"year":2023,"finding":"HSF1 directly binds the noncoding promoter region of the Atg10 gene (shown by ChIP and EMSA), transcriptionally upregulating ATG10; HSF1-driven ATG10 expression enhances autophagy (LC3-II/LC3-I ratio) and attenuates LPS-induced inflammatory cytokine release in macrophages; siRNA-ATG10 reversed the anti-inflammatory effect of HSF1 overexpression.","method":"ChIP, electrophoretic mobility shift assay (EMSA), siRNA knockdown, ATG10 overexpression, LC3-II/LC3-I western blot, cytokine assays in RAW264.7 and peritoneal macrophages","journal":"Microbiology spectrum","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct promoter binding confirmed by two orthogonal methods (ChIP and EMSA), functional rescue experiments, single lab","pmids":["36598250"],"is_preprint":false},{"year":2019,"finding":"CgATG10 (oyster ortholog) knockdown by dsRNA inhibited LC3-I to LC3-II conversion downstream of Beclin1 activation, demonstrating ATG10 is required for autophagosome formation (elongation step) in the innate antiviral response; CgATG10 knockdown also increased IRF-1 expression.","method":"dsRNA knockdown in Pacific oyster, LC3 conversion western blot, qRT-PCR for immune genes","journal":"Fish & shellfish immunology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single knockdown approach in an invertebrate model, limited mechanistic resolution","pmids":["31128297"],"is_preprint":false},{"year":2022,"finding":"SNHG1 lncRNA directly interacts with Bhlhe40 mRNA 3'-UTR to stabilize it and also scaffolds PIAS3-Bhlhe40 SUMOylation to promote nuclear translocation of Bhlhe40; nuclear Bhlhe40 suppresses ATG10 expression, which is involved in autophagosome formation; this cascade protects vascular smooth muscle cells from HG-induced calcification/senescence.","method":"RNA pull-down, RNA immunoprecipitation, RNA stability assay, luciferase reporter assay, immunoprecipitation, Western blot","journal":"Journal of physiology and biochemistry","confidence":"Low","confidence_rationale":"Tier 3 / Weak — ATG10 is downstream in a complex cascade; its specific mechanistic role in this pathway is inferred from expression data rather than directly interrogated","pmids":["36194366"],"is_preprint":false}],"current_model":"ATG10 is an E2-like ubiquitin-conjugating enzyme in the autophagy pathway that physically interacts with the homodimeric E1 enzyme Atg7 through a noncanonical, multisite mechanism — Atg7's N-terminal domain recruits Atg10's backside surface, positioning Atg10's catalytic cysteine opposite the Atg7 active-site cysteine for thioester-linked Atg12 transfer — ultimately mediating Atg12 conjugation to Atg5 by directly recognizing the C-terminal ubiquitin-like domain of Atg5, thereby driving autophagosome elongation without requiring a dedicated E3 enzyme; expression of ATG10 is regulated transcriptionally by HSF1 and post-transcriptionally by multiple miRNAs (miR-27b-3p, miR-100, miR-874-5p, MIR4458/4667-5p/4668-5p, others) and RNA-binding protein PTBP1, with ATG10 levels governing autophagy flux, phagophore elongation, and downstream cellular outcomes including EMT, drug resistance, and inflammatory cytokine release."},"narrative":{"mechanistic_narrative":"ATG10 is an E2-like conjugating enzyme that drives the Atg12–Atg5 conjugation step of the autophagy ubiquitin-like cascade, thereby promoting phagophore elongation and autophagosome formation [PMID:23142976, PMID:22682742, PMID:30939964]. It is recruited by the homodimeric E1 enzyme Atg7 through a noncanonical, multisite mechanism in which Atg7's unique N-terminal domain engages the Atg10 'backside' while Atg10's frontside active site is presented to the catalytic cysteine of the opposite Atg7 protomer, juxtaposing the E1 and E2 cysteines for UBL transfer [PMID:23142976, PMID:23388412]. Atg10 carries an E2-core fold whose two characteristic β-strands directly recognize the C-terminal ubiquitin-like domain of Atg5, with Tyr56 and Asn114 orienting the Atg5 Lys145 side chain so that Atg12–Atg5 conjugation proceeds without a dedicated E3 enzyme [PMID:22682742]. In human cells ATG10 functions at the elongation phase of autophagosome biogenesis, where its loss yields immature phagophores and impaired flux that rescue restores [PMID:30939964]. ATG10 expression is tightly controlled: it is transcriptionally upregulated by HSF1, which attenuates inflammatory cytokine release in macrophages [PMID:36598250], and is repressed post-transcriptionally by the RNA-binding protein PTBP1 and by multiple miRNAs (MIR4458, MIR4667-5p, MIR4668-5p, miR-27b-3p), linking ATG10 levels to EMT-associated metastasis, drug resistance, and antibacterial autophagy [PMID:26151773, PMID:27836735, PMID:32104496]. Two human isoforms exert opposing effects on autophagy flux, the canonical long ATG10 detaining peripheral autophagosomes while the short ATG10S, conjugated by IL28A, drives lysosomal docking and degradation [PMID:28900156, PMID:29670865].","teleology":[{"year":2012,"claim":"Established the catalytic basis of Atg12–Atg5 conjugation by showing how the E2 enzyme Atg10 recognizes its substrate without an E3, answering how UBL transfer specificity is achieved in autophagy.","evidence":"X-ray crystallography, NMR, mutagenesis, crosslinking and kinetics of Kluyveromyces marxianus Atg10","pmids":["22682742"],"confidence":"High","gaps":["Atg7 recruitment mechanism not addressed here","human ortholog catalytic residues not directly tested"]},{"year":2012,"claim":"Defined the noncanonical, multisite E1–E2 architecture by which the Atg7 homodimer recruits and positions Atg10, explaining how the catalytic cysteines are juxtaposed for thioester transfer.","evidence":"Crystal structures and mutational analysis of yeast (Atg7-Atg10)₂ complexes; additional S. cerevisiae Atg10 structure","pmids":["23142976","22993095"],"confidence":"High","gaps":["functional role of the FR-region insertion inferred, not validated","dynamics of thioester transfer not resolved"]},{"year":2012,"claim":"Revealed that Atg10-family enzymes can carry conjugation-independent functions, indicating the protein is not exclusively an autophagy E2.","evidence":"Genetic deletion with cell cycle and autophagy assays in S. pombe","pmids":["23255127"],"confidence":"Medium","gaps":["molecular basis of the cell-cycle role unknown","conservation of this function in mammals untested"]},{"year":2013,"claim":"Consolidated the principle that canonical and noncanonical UBL cascades share common catalytic logic, framing Atg10 within broader E1–E2 biochemistry.","evidence":"Crystallographic and mutational mechanistic analysis","pmids":["23388412"],"confidence":"High","gaps":["does not address regulation of the cascade in vivo"]},{"year":2015,"claim":"Showed ATG10 is a post-transcriptionally regulated effector of antibacterial autophagy, linking its abundance to pathogen clearance.","evidence":"miRNA microarray, 3'-UTR luciferase reporters, forced expression and bacterial survival assays in A549 cells (Burkholderia pseudomallei)","pmids":["26151773"],"confidence":"Medium","gaps":["direct ATG10 enzymatic activity not measured","individual miRNA contributions not separated"]},{"year":2016,"claim":"Identified PTBP1 as a direct post-transcriptional repressor of ATG10 and positioned ATG10 as a negative regulator of EMT-associated cancer cell migration.","evidence":"RNA immunoprecipitation, knockdown/ectopic expression, migration/invasion assays, EMT marker Western blots in colorectal cancer cells","pmids":["27836735"],"confidence":"Medium","gaps":["whether EMT effect depends on ATG10 catalytic activity unclear","single lab, no in vivo metastasis data"]},{"year":2017,"claim":"Discovered two human ATG10 isoforms with opposing effects on autophagy flux and identified IL28A as a direct partner of the short isoform.","evidence":"Isoform overexpression, autophagy flux assays, IL28A-ATG10S co-immunoprecipitation in hepatoma cells","pmids":["28900156"],"confidence":"Medium","gaps":["structural basis for isoform divergence unknown","single Co-IP for IL28A interaction without reciprocal validation"]},{"year":2018,"claim":"Provided in vivo corroboration that canonical ATG10 and ATG10S exert opposing effects on viral replication via their distinct autophagy roles.","evidence":"Liver-specific HCV subreplicon zebrafish model with pharmacological autophagy inhibitors and isoform overexpression","pmids":["29670865"],"confidence":"Medium","gaps":["mechanism of differential autophagosome trafficking not resolved","relevance to authentic HCV infection untested"]},{"year":2019,"claim":"Placed ATG10 mechanistically at the phagophore elongation step in human neurons by showing immature phagophores accumulate when ATG10 is low and resolve upon rescue.","evidence":"TEM of phagophores and ATG10 rescue in TBK1-mutant hiPSC-derived motoneurons","pmids":["30939964"],"confidence":"Medium","gaps":["link between TBK1 mutation and ATG10 reduction not mechanistically defined","single cell model"]},{"year":2020,"claim":"Mapped a c-Myc/miR-27b-3p/ATG10 axis controlling autophagy-dependent chemoresistance, extending ATG10 regulation upstream to transcription-factor-driven miRNA control.","evidence":"ChIP, luciferase reporters, GFP-LC3, TEM, and xenografts in colorectal cancer (oxaliplatin resistance)","pmids":["32104496"],"confidence":"Medium","gaps":["direct ATG10 protein-level changes vs flux causality not fully separated","single lab"]},{"year":2023,"claim":"Identified HSF1 as a direct transcriptional activator of ATG10 and connected ATG10-driven autophagy to suppression of inflammatory cytokine release.","evidence":"ChIP and EMSA for HSF1 promoter binding, siRNA/overexpression rescue, LC3 and cytokine assays in macrophages","pmids":["36598250"],"confidence":"Medium","gaps":["downstream autophagic substrate of anti-inflammatory effect unknown","human in vivo relevance untested"]},{"year":null,"claim":"How the human ATG10 isoforms are catalytically and structurally differentiated, and whether the conjugation-independent functions seen in yeast extend to mammals, remain unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["no human ATG10 structure in the corpus","isoform-specific trafficking mechanism undefined","mammalian non-conjugation roles untested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,1]}],"localization":[],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[9,5,1]}],"complexes":[],"partners":["ATG7","ATG5","ATG12","IL28A"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H0Y0","full_name":"Ubiquitin-like-conjugating enzyme ATG10","aliases":["Autophagy-related protein 10","APG10-like"],"length_aa":220,"mass_kda":25.3,"function":"E2-like enzyme involved in autophagy. Acts as an E2-like enzyme that catalyzes the conjugation of ATG12 to ATG5. ATG12 conjugation to ATG5 is required for autophagy. Likely serves as an ATG5-recognition molecule. Not involved in ATG12 conjugation to ATG3 (By similarity). Plays a role in adenovirus-mediated cell lysis","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9H0Y0/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/ATG10","classification":"Not Classified","n_dependent_lines":17,"n_total_lines":1208,"dependency_fraction":0.014072847682119206},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/ATG10","total_profiled":1310},"omim":[{"mim_id":"617502","title":"WD REPEAT-CONTAINING PROTEIN 41; WDR41","url":"https://www.omim.org/entry/617502"},{"mim_id":"617074","title":"SMITH-MAGENIS SYNDROME CHROMOSOME REGION, CANDIDATE GENE 8; SMCR8","url":"https://www.omim.org/entry/617074"},{"mim_id":"614260","title":"CHROMOSOME 9 OPEN READING FRAME 72; C9ORF72","url":"https://www.omim.org/entry/614260"},{"mim_id":"610800","title":"AUTOPHAGY-RELATED 10; ATG10","url":"https://www.omim.org/entry/610800"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoli","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/ATG10"},"hgnc":{"alias_symbol":["DKFZP586I0418","FLJ13954"],"prev_symbol":["APG10L"]},"alphafold":{"accession":"Q9H0Y0","domains":[{"cath_id":"3.30.1460","chopping":"27-53_92-207","consensus_level":"high","plddt":89.4569,"start":27,"end":207}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H0Y0","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H0Y0-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H0Y0-F1-predicted_aligned_error_v6.png","plddt_mean":80.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=ATG10","jax_strain_url":"https://www.jax.org/strain/search?query=ATG10"},"sequence":{"accession":"Q9H0Y0","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H0Y0.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H0Y0/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H0Y0"}},"corpus_meta":[{"pmid":"32104496","id":"PMC_32104496","title":"The c-Myc/miR-27b-3p/ATG10 regulatory axis regulates chemoresistance in colorectal cancer.","date":"2020","source":"Theranostics","url":"https://pubmed.ncbi.nlm.nih.gov/32104496","citation_count":115,"is_preprint":false},{"pmid":"23142976","id":"PMC_23142976","title":"Noncanonical E2 recruitment by the autophagy E1 revealed by Atg7-Atg3 and Atg7-Atg10 structures.","date":"2012","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/23142976","citation_count":93,"is_preprint":false},{"pmid":"23285162","id":"PMC_23285162","title":"Increased expression of ATG10 in colorectal cancer is associated with lymphovascular invasion and lymph node metastasis.","date":"2012","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/23285162","citation_count":74,"is_preprint":false},{"pmid":"22682742","id":"PMC_22682742","title":"Structural insights into Atg10-mediated formation of the autophagy-essential Atg12-Atg5 conjugate.","date":"2012","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/22682742","citation_count":63,"is_preprint":false},{"pmid":"31298038","id":"PMC_31298038","title":"Long noncoding RNA HAGLROS regulates apoptosis and autophagy in Parkinson's disease via regulating miR-100/ATG10 axis and PI3K/Akt/mTOR pathway activation.","date":"2019","source":"Artificial cells, nanomedicine, and biotechnology","url":"https://pubmed.ncbi.nlm.nih.gov/31298038","citation_count":61,"is_preprint":false},{"pmid":"27836735","id":"PMC_27836735","title":"Polypyrimidine tract-binding protein 1-mediated down-regulation of ATG10 facilitates metastasis of colorectal cancer cells.","date":"2016","source":"Cancer letters","url":"https://pubmed.ncbi.nlm.nih.gov/27836735","citation_count":59,"is_preprint":false},{"pmid":"27225307","id":"PMC_27225307","title":"Role of ATG10 expression quantitative trait loci in non-small cell lung cancer survival.","date":"2016","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/27225307","citation_count":51,"is_preprint":false},{"pmid":"33013268","id":"PMC_33013268","title":"LncRNA HOTAIR promotes MPP+-induced neuronal injury in Parkinson's disease by regulating the miR-874-5p/ATG10 axis.","date":"2020","source":"EXCLI journal","url":"https://pubmed.ncbi.nlm.nih.gov/33013268","citation_count":47,"is_preprint":false},{"pmid":"23850577","id":"PMC_23850577","title":"Potentially functional polymorphisms in ATG10 are associated with risk of breast cancer in a Chinese population.","date":"2013","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/23850577","citation_count":46,"is_preprint":false},{"pmid":"30939964","id":"PMC_30939964","title":"Retinoic acid worsens ATG10-dependent autophagy impairment in TBK1-mutant hiPSC-derived motoneurons through SQSTM1/p62 accumulation.","date":"2019","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/30939964","citation_count":42,"is_preprint":false},{"pmid":"23388412","id":"PMC_23388412","title":"Structures of Atg7-Atg3 and Atg7-Atg10 reveal noncanonical mechanisms of E2 recruitment by the autophagy E1.","date":"2013","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/23388412","citation_count":34,"is_preprint":false},{"pmid":"26151773","id":"PMC_26151773","title":"Burkholderia pseudomallei survival in lung epithelial cells benefits from miRNA-mediated suppression of ATG10.","date":"2015","source":"Autophagy","url":"https://pubmed.ncbi.nlm.nih.gov/26151773","citation_count":30,"is_preprint":false},{"pmid":"22993095","id":"PMC_22993095","title":"Structure of the autophagic E2 enzyme Atg10.","date":"2012","source":"Acta crystallographica. 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opposite Atg7 protomer in the homodimer, enabling UBL transfer.\",\n      \"method\": \"X-ray crystallography, mutational analysis of yeast Atg7-Atg10 complexes\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structures of complexes combined with mutational analysis, mechanistically defining E1-E2 interaction and catalytic mechanism\",\n      \"pmids\": [\"23142976\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Solution and crystal structures of Kluyveromyces marxianus Atg10 revealed an E2-core fold with two characteristic β-strands that directly recognize the C-terminal ubiquitin-like domain of Atg5; Tyr56 and Asn114 of Atg10 orient the Atg5 Lys145 side chain for conjugation with Atg12, enabling Atg12-Atg5 conjugate formation without a specific E3 enzyme.\",\n      \"method\": \"X-ray crystallography, NMR, mutational analysis, crosslinking experiments, kinetic analysis\",\n      \"journal\": \"Structure\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — multiple orthogonal structural and biochemical methods (NMR, crystallography, mutagenesis, kinetics) in a single rigorous study\",\n      \"pmids\": [\"22682742\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Crystal structure of Saccharomyces cerevisiae Atg10 at 2.7 Å resolution showed a conserved E2 core fold compared to Atg3 and other E2 enzymes, with an insertion ('FR-region') absent in the structure that may be important for interaction with E1 enzyme Atg7.\",\n      \"method\": \"X-ray crystallography, heavy-atom derivatization\",\n      \"journal\": \"Acta crystallographica. Section D, Biological crystallography\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — crystal structure determined but FR-region functional role inferred rather than experimentally validated in this paper\",\n      \"pmids\": [\"22993095\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Structural and mechanistic analysis confirmed that Atg7 recruits Atg10 through surfaces remote from their active sites (noncanonical mode), juxtaposing E1 and E2 catalytic cysteines for UBL (Atg12) transfer; common principles underlie both canonical and noncanonical UBL cascades.\",\n      \"method\": \"Crystallographic analysis, mutational analysis, mechanistic biochemistry\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — structural and mutational validation of mechanism, corroborating the companion Nature Struct Mol Biol paper from same group\",\n      \"pmids\": [\"23388412\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"In Schizosaccharomyces pombe, the Atg10 homolog (SpAtg10) is not required for autophagy but is essential for normal cell cycle progression and stress responses, independently of Atg12 conjugation, indicating Atg10-family enzymes can have functions beyond UBL conjugation.\",\n      \"method\": \"Genetic deletion, cell cycle assays, autophagy assays in S. pombe\",\n      \"journal\": \"Cell cycle\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean KO with defined cellular phenotypes (cell cycle arrest, autophagy-independent function) using multiple readouts in a single study\",\n      \"pmids\": [\"23255127\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Two isoforms of human ATG10 have opposing effects on autophagy flux: the canonical long isoform (ATG10) promotes autophagosome formation and detains autophagosomes at the cell periphery, impairing autophagy flux; the short isoform (ATG10S) drives autophagosomes to the perinuclear region for lysosomal degradation, promoting autophagy flux. ATG10S also activates innate immunity genes. IL28A protein directly conjugates ATG10S and assists autophagosome docking to lysosomes.\",\n      \"method\": \"Overexpression studies in HepG2/Huh7.5 cells, co-immunoprecipitation (IL28A-ATG10S), autophagy flux assays\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct binding demonstrated by Co-IP, isoform-specific functional differences shown by OE with autophagy readouts, single lab\",\n      \"pmids\": [\"28900156\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"In a zebrafish HCV subreplicon model, canonical ATG10 facilitated HCV amplification by promoting autophagosome formation, while ATG10S suppressed HCV replication by promoting autophagy flux leading to lysosomal degradation, confirming opposing isoform roles in vivo.\",\n      \"method\": \"Liver-specific HCV subreplicon zebrafish model, autophagy inhibitor assays (3MA, chloroquine), isoform overexpression\",\n      \"journal\": \"Frontiers in cellular and infection microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo model with pharmacological and genetic perturbations, independent corroboration of isoform roles from prior paper\",\n      \"pmids\": [\"29670865\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Burkholderia pseudomallei infection upregulates three miRNAs (MIR4458, MIR4667-5p, MIR4668-5p) that directly target the 3'-UTR of ATG10, reducing ATG10 levels and inhibiting autophagy-mediated bacterial elimination; forced ATG10 expression enhanced autophagy and accelerated intracellular bacterial clearance.\",\n      \"method\": \"miRNA microarray, 3'-UTR luciferase reporter assays, ATG10 forced expression, bacterial survival assays in A549 cells\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — luciferase reporter validation of miRNA targeting, gain-of-function phenotype, multiple miRNAs validated, single lab\",\n      \"pmids\": [\"26151773\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"PTBP1 directly interacts with ATG10 mRNA and reduces ATG10 expression at the post-transcriptional level; knockdown of ATG10 promoted colorectal cancer cell migration/invasion and modulated EMT markers (upregulating N-cadherin, ZEB1, CD44; downregulating E-cadherin), placing ATG10 as a negative regulator of EMT-associated metastasis.\",\n      \"method\": \"RNA immunoprecipitation (PTBP1-ATG10 mRNA interaction), ectopic expression and knockdown, cell migration/invasion assays, Western blot for EMT markers\",\n      \"journal\": \"Cancer letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct RIP demonstrating PTBP1-ATG10 mRNA interaction, functional KD phenotype with molecular markers, single lab\",\n      \"pmids\": [\"27836735\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"In TBK1-mutant hiPSC-derived motoneurons, ATG10 levels are reduced and phagophore elongation is impaired (accumulation of immature phagophores by TEM); rescue of ATG10 levels abolished 4HPR toxicity and SQSTM1 accumulation, placing ATG10 at the elongation phase of autophagosome formation.\",\n      \"method\": \"hiPSC-derived motoneurons, TEM of phagophores, ATG10 rescue experiments, nuclear-receptor-agonist screen\",\n      \"journal\": \"Autophagy\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — TEM-based structural phenotype plus rescue experiment establish ATG10's role at phagophore elongation, single lab, human cell model\",\n      \"pmids\": [\"30939964\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"c-Myc binds the miR-27b promoter (shown by ChIP) to suppress miR-27b-3p expression; miR-27b-3p inhibits ATG10 expression post-transcriptionally (luciferase reporter assay), thereby reducing autophagy; this c-Myc/miR-27b-3p/ATG10 axis promotes oxaliplatin resistance in colorectal cancer.\",\n      \"method\": \"ChIP assay, luciferase reporter assay, Western blot, GFP-LC3 fluorescence, TEM, xenograft studies\",\n      \"journal\": \"Theranostics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple orthogonal methods (ChIP, luciferase, in vivo xenograft), single lab, establishes pathway position\",\n      \"pmids\": [\"32104496\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"HSF1 directly binds the noncoding promoter region of the Atg10 gene (shown by ChIP and EMSA), transcriptionally upregulating ATG10; HSF1-driven ATG10 expression enhances autophagy (LC3-II/LC3-I ratio) and attenuates LPS-induced inflammatory cytokine release in macrophages; siRNA-ATG10 reversed the anti-inflammatory effect of HSF1 overexpression.\",\n      \"method\": \"ChIP, electrophoretic mobility shift assay (EMSA), siRNA knockdown, ATG10 overexpression, LC3-II/LC3-I western blot, cytokine assays in RAW264.7 and peritoneal macrophages\",\n      \"journal\": \"Microbiology spectrum\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct promoter binding confirmed by two orthogonal methods (ChIP and EMSA), functional rescue experiments, single lab\",\n      \"pmids\": [\"36598250\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"CgATG10 (oyster ortholog) knockdown by dsRNA inhibited LC3-I to LC3-II conversion downstream of Beclin1 activation, demonstrating ATG10 is required for autophagosome formation (elongation step) in the innate antiviral response; CgATG10 knockdown also increased IRF-1 expression.\",\n      \"method\": \"dsRNA knockdown in Pacific oyster, LC3 conversion western blot, qRT-PCR for immune genes\",\n      \"journal\": \"Fish & shellfish immunology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single knockdown approach in an invertebrate model, limited mechanistic resolution\",\n      \"pmids\": [\"31128297\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"SNHG1 lncRNA directly interacts with Bhlhe40 mRNA 3'-UTR to stabilize it and also scaffolds PIAS3-Bhlhe40 SUMOylation to promote nuclear translocation of Bhlhe40; nuclear Bhlhe40 suppresses ATG10 expression, which is involved in autophagosome formation; this cascade protects vascular smooth muscle cells from HG-induced calcification/senescence.\",\n      \"method\": \"RNA pull-down, RNA immunoprecipitation, RNA stability assay, luciferase reporter assay, immunoprecipitation, Western blot\",\n      \"journal\": \"Journal of physiology and biochemistry\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — ATG10 is downstream in a complex cascade; its specific mechanistic role in this pathway is inferred from expression data rather than directly interrogated\",\n      \"pmids\": [\"36194366\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"ATG10 is an E2-like ubiquitin-conjugating enzyme in the autophagy pathway that physically interacts with the homodimeric E1 enzyme Atg7 through a noncanonical, multisite mechanism — Atg7's N-terminal domain recruits Atg10's backside surface, positioning Atg10's catalytic cysteine opposite the Atg7 active-site cysteine for thioester-linked Atg12 transfer — ultimately mediating Atg12 conjugation to Atg5 by directly recognizing the C-terminal ubiquitin-like domain of Atg5, thereby driving autophagosome elongation without requiring a dedicated E3 enzyme; expression of ATG10 is regulated transcriptionally by HSF1 and post-transcriptionally by multiple miRNAs (miR-27b-3p, miR-100, miR-874-5p, MIR4458/4667-5p/4668-5p, others) and RNA-binding protein PTBP1, with ATG10 levels governing autophagy flux, phagophore elongation, and downstream cellular outcomes including EMT, drug resistance, and inflammatory cytokine release.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"ATG10 is an E2-like conjugating enzyme that drives the Atg12–Atg5 conjugation step of the autophagy ubiquitin-like cascade, thereby promoting phagophore elongation and autophagosome formation [#0, #1, #9]. It is recruited by the homodimeric E1 enzyme Atg7 through a noncanonical, multisite mechanism in which Atg7's unique N-terminal domain engages the Atg10 'backside' while Atg10's frontside active site is presented to the catalytic cysteine of the opposite Atg7 protomer, juxtaposing the E1 and E2 cysteines for UBL transfer [#0, #3]. Atg10 carries an E2-core fold whose two characteristic β-strands directly recognize the C-terminal ubiquitin-like domain of Atg5, with Tyr56 and Asn114 orienting the Atg5 Lys145 side chain so that Atg12–Atg5 conjugation proceeds without a dedicated E3 enzyme [#1]. In human cells ATG10 functions at the elongation phase of autophagosome biogenesis, where its loss yields immature phagophores and impaired flux that rescue restores [#9]. ATG10 expression is tightly controlled: it is transcriptionally upregulated by HSF1, which attenuates inflammatory cytokine release in macrophages [#11], and is repressed post-transcriptionally by the RNA-binding protein PTBP1 and by multiple miRNAs (MIR4458, MIR4667-5p, MIR4668-5p, miR-27b-3p), linking ATG10 levels to EMT-associated metastasis, drug resistance, and antibacterial autophagy [#7, #8, #10]. Two human isoforms exert opposing effects on autophagy flux, the canonical long ATG10 detaining peripheral autophagosomes while the short ATG10S, conjugated by IL28A, drives lysosomal docking and degradation [#5, #6].\"\n,\n  \"teleology\": [\n    {\n      \"year\": 2012,\n      \"claim\": \"Established the catalytic basis of Atg12–Atg5 conjugation by showing how the E2 enzyme Atg10 recognizes its substrate without an E3, answering how UBL transfer specificity is achieved in autophagy.\",\n      \"evidence\": \"X-ray crystallography, NMR, mutagenesis, crosslinking and kinetics of Kluyveromyces marxianus Atg10\",\n      \"pmids\": [\"22682742\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Atg7 recruitment mechanism not addressed here\", \"human ortholog catalytic residues not directly tested\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Defined the noncanonical, multisite E1–E2 architecture by which the Atg7 homodimer recruits and positions Atg10, explaining how the catalytic cysteines are juxtaposed for thioester transfer.\",\n      \"evidence\": \"Crystal structures and mutational analysis of yeast (Atg7-Atg10)₂ complexes; additional S. cerevisiae Atg10 structure\",\n      \"pmids\": [\"23142976\", \"22993095\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"functional role of the FR-region insertion inferred, not validated\", \"dynamics of thioester transfer not resolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Revealed that Atg10-family enzymes can carry conjugation-independent functions, indicating the protein is not exclusively an autophagy E2.\",\n      \"evidence\": \"Genetic deletion with cell cycle and autophagy assays in S. pombe\",\n      \"pmids\": [\"23255127\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"molecular basis of the cell-cycle role unknown\", \"conservation of this function in mammals untested\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Consolidated the principle that canonical and noncanonical UBL cascades share common catalytic logic, framing Atg10 within broader E1–E2 biochemistry.\",\n      \"evidence\": \"Crystallographic and mutational mechanistic analysis\",\n      \"pmids\": [\"23388412\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"does not address regulation of the cascade in vivo\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Showed ATG10 is a post-transcriptionally regulated effector of antibacterial autophagy, linking its abundance to pathogen clearance.\",\n      \"evidence\": \"miRNA microarray, 3'-UTR luciferase reporters, forced expression and bacterial survival assays in A549 cells (Burkholderia pseudomallei)\",\n      \"pmids\": [\"26151773\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"direct ATG10 enzymatic activity not measured\", \"individual miRNA contributions not separated\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Identified PTBP1 as a direct post-transcriptional repressor of ATG10 and positioned ATG10 as a negative regulator of EMT-associated cancer cell migration.\",\n      \"evidence\": \"RNA immunoprecipitation, knockdown/ectopic expression, migration/invasion assays, EMT marker Western blots in colorectal cancer cells\",\n      \"pmids\": [\"27836735\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"whether EMT effect depends on ATG10 catalytic activity unclear\", \"single lab, no in vivo metastasis data\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Discovered two human ATG10 isoforms with opposing effects on autophagy flux and identified IL28A as a direct partner of the short isoform.\",\n      \"evidence\": \"Isoform overexpression, autophagy flux assays, IL28A-ATG10S co-immunoprecipitation in hepatoma cells\",\n      \"pmids\": [\"28900156\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"structural basis for isoform divergence unknown\", \"single Co-IP for IL28A interaction without reciprocal validation\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Provided in vivo corroboration that canonical ATG10 and ATG10S exert opposing effects on viral replication via their distinct autophagy roles.\",\n      \"evidence\": \"Liver-specific HCV subreplicon zebrafish model with pharmacological autophagy inhibitors and isoform overexpression\",\n      \"pmids\": [\"29670865\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"mechanism of differential autophagosome trafficking not resolved\", \"relevance to authentic HCV infection untested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Placed ATG10 mechanistically at the phagophore elongation step in human neurons by showing immature phagophores accumulate when ATG10 is low and resolve upon rescue.\",\n      \"evidence\": \"TEM of phagophores and ATG10 rescue in TBK1-mutant hiPSC-derived motoneurons\",\n      \"pmids\": [\"30939964\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"link between TBK1 mutation and ATG10 reduction not mechanistically defined\", \"single cell model\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Mapped a c-Myc/miR-27b-3p/ATG10 axis controlling autophagy-dependent chemoresistance, extending ATG10 regulation upstream to transcription-factor-driven miRNA control.\",\n      \"evidence\": \"ChIP, luciferase reporters, GFP-LC3, TEM, and xenografts in colorectal cancer (oxaliplatin resistance)\",\n      \"pmids\": [\"32104496\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"direct ATG10 protein-level changes vs flux causality not fully separated\", \"single lab\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identified HSF1 as a direct transcriptional activator of ATG10 and connected ATG10-driven autophagy to suppression of inflammatory cytokine release.\",\n      \"evidence\": \"ChIP and EMSA for HSF1 promoter binding, siRNA/overexpression rescue, LC3 and cytokine assays in macrophages\",\n      \"pmids\": [\"36598250\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"downstream autophagic substrate of anti-inflammatory effect unknown\", \"human in vivo relevance untested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How the human ATG10 isoforms are catalytically and structurally differentiated, and whether the conjugation-independent functions seen in yeast extend to mammals, remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"no human ATG10 structure in the corpus\", \"isoform-specific trafficking mechanism undefined\", \"mammalian non-conjugation roles untested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 1]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [9, 5, 1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"ATG7\", \"ATG5\", \"ATG12\", \"IL28A\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}