{"gene":"TOM1","run_date":"2026-06-10T10:51:55","timeline":{"discoveries":[{"year":2000,"finding":"Crystal structure of the human TOM1 VHS domain resolved to 1.5 Å, revealing eight helices in a superhelix with a conserved basic patch on helix 3 (implicated in membrane binding) and a negatively charged ridge on helix 2 (implicated in protein-protein interactions involving helices 2 and 4).","method":"X-ray crystallography (1.5 Å resolution)","journal":"Biochemistry","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with explicit resolution and structural comparison to related domains; primary structural paper for this domain","pmids":["10985773"],"is_preprint":false},{"year":1997,"finding":"TOM1 is a direct transcriptional target of v-Myb; the Myb-inducible tom-1 promoter contains a functional Myb binding site and requires a juxtaposed C/EBP binding site for Myb-dependent activation, with C/EBP acting as a cooperation partner.","method":"Promoter deletion/mutation analysis, reporter gene assay, transcription factor binding site mapping","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 2 / Strong — functional Myb binding site validated by reporter assay and de novo protein synthesis inhibition experiment; replicated across two oncogenic v-Myb variants","pmids":["9135152"],"is_preprint":false},{"year":2003,"finding":"TOM1 directly binds ubiquitin chains and Tollip via its GAT domain; endogenous TOM1 co-fractionates with Tollip in a complex; TOM1 also binds clathrin heavy chain through a canonical clathrin-binding motif; deletion of the clathrin-binding motif alters GFP-TOM1 cytoplasmic distribution.","method":"Co-immunoprecipitation, gel filtration, Western blot, GFP fluorescence microscopy, GST pulldown","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP of endogenous proteins, gel filtration fractionation, and domain deletion all in one study; replicated by independent group (PMID:15047686)","pmids":["14563850"],"is_preprint":false},{"year":2004,"finding":"The GAT domain of TOM1 (and TOM1L1) interacts with ubiquitin and Tollip; ubiquitin and Tollip bind overlapping regions of the GAT domain in a mutually exclusive manner. Tollip localizes on early endosomes and recruits cytosolic TOM1 and ubiquitinated proteins to endosomes.","method":"GST pulldown, Co-immunoprecipitation, fluorescence microscopy, domain mapping","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods; independently confirmed by PMID:14563850","pmids":["15047686"],"is_preprint":false},{"year":2003,"finding":"Endofin, a FYVE-domain early endosomal protein, binds specifically to the C-terminal region of TOM1 (not TOM1-L1 or TOM1-L2) and recruits cytosolic TOM1 to early endosomes; confirmed by yeast two-hybrid, GST pulldown, Co-IP, and immunofluorescence with EEA1 co-localization.","method":"Yeast two-hybrid screen, GST pulldown, Co-immunoprecipitation, immunofluorescence, sucrose density gradient fractionation","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods in one study; specificity for TOM1 vs. paralogs and other FYVE proteins demonstrated","pmids":["14613930"],"is_preprint":false},{"year":2005,"finding":"TOM1 binds clathrin heavy chain through three sites (residues 300–321, 321–326, and a LEDEF clathrin-binding box at 362–366); endofin overexpression recruits clathrin (but not dynamin, AP1, AP2, or AP3) to endosomes via TOM1; microinjection of anti-TOM1 antibody reduces membrane association of clathrin.","method":"GST pulldown with deletion/point mutants, overexpression, immunofluorescence, antibody microinjection","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — domain mapping by mutagenesis, functional antibody microinjection, and overexpression all in one study; confirmed clathrin binding motifs","pmids":["15657082"],"is_preprint":false},{"year":2006,"finding":"All TOM1 family members (TOM1, TOM1L1, TOM1L2) bind Tollip via their GAT domains and bind clathrin through their C-terminal regions; when co-expressed with Tollip, all three family members recruit clathrin onto endosomes.","method":"Co-immunoprecipitation, fluorescence microscopy with Tollip co-expression","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — single lab, single Co-IP/microscopy approach, but extends finding to all three family members consistently","pmids":["16412388"],"is_preprint":false},{"year":2004,"finding":"Overexpression of TOM1 suppresses NF-κB and AP-1 activation induced by IL-1β and TNF-α; the VHS domain of TOM1 is required for this suppressive activity.","method":"Reporter gene assay (NF-κB and AP-1 luciferase), domain deletion analysis","journal":"Biological & pharmaceutical bulletin","confidence":"Medium","confidence_rationale":"Tier 3 / Weak — single lab, single method (reporter assay), no endogenous protein knockdown; domain requirement identified","pmids":["15056867"],"is_preprint":false},{"year":2008,"finding":"Dictyostelium TOM1 (DdTom1) GAT domain binds ubiquitin; the VHS and GAT domains interact with phospholipids enabling endosomal membrane recruitment; the C-terminal domain recruits clathrin, Eps15, and TSG101 (an ESCRT component), supporting participation in an ancestral ESCRT-0 complex for sorting ubiquitinated proteins to MVBs.","method":"Domain-binding assays, subcellular fractionation, co-immunoprecipitation, fluorescence microscopy","journal":"Traffic (Copenhagen, Denmark)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple domain-binding experiments in a model organism ortholog; single lab","pmids":["19054384"],"is_preprint":false},{"year":2010,"finding":"miR-126 directly targets the 3'-UTR of TOM1 mRNA; introduction of synthetic pre-miR-126 in CF bronchial epithelial cells inhibited luciferase activity from a TOM1 3'-UTR reporter and decreased TOM1 protein; TOM1 knockdown increased NF-κB-regulated IL-8 secretion, while TOM1 overexpression downregulated NF-κB activity after LPS or IL-1β stimulation.","method":"Luciferase 3'-UTR reporter assay, Western blot, siRNA knockdown, cytokine ELISA","journal":"Journal of immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct 3'-UTR reporter validation and functional knockdown/overexpression with pathway readout; single lab","pmids":["20083669"],"is_preprint":false},{"year":2012,"finding":"TOM1 is a myosin VI binding partner on endosomes; loss of myosin VI and TOM1 reduces autophagosomal delivery of endocytic cargo and causes a block in autophagosome-lysosome fusion; myosin VI adaptor proteins NDP52, optineurin, and T6BP dock myosin VI to autophagosomes, while TOM1 on endosomes connects endosomal membranes to autophagosomes to promote maturation and lysosomal fusion.","method":"Co-immunoprecipitation, siRNA knockdown, live-cell fluorescence imaging, autophagy flux assays","journal":"Nature cell biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, specific KD phenotype (block in autophagosome-lysosome fusion), and live imaging in one study; high-citation, focused mechanistic paper","pmids":["23023224"],"is_preprint":false},{"year":2015,"finding":"TOM1 is a direct binding partner of phosphatidylinositol 5-phosphate (PI5P); PI5P recruits TOM1 to signaling endosomes (produced by Shigella IpgD phosphatase), and this recruitment delays EGFR degradation and impairs bulk endocytosis, thereby preventing endosomal maturation.","method":"Lipid pulldown, Co-immunoprecipitation, domain mapping, cell-based endocytosis/degradation assays","journal":"Journal of cell science","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct lipid-binding assay plus functional cell-based readout with domain identification; multiple orthogonal methods","pmids":["25588840"],"is_preprint":false},{"year":1999,"finding":"Yeast TOM1 encodes a ~380 kDa HECT-domain ubiquitin ligase; site-directed mutagenesis of the conserved active-site cysteine (C3235A) abolishes HECT function and temperature-sensitive growth; overproduction of the HECT domain promotes ubiquitin (but not SUMO/Smt3) conjugation to proteins in vivo.","method":"Site-directed mutagenesis, in vivo ubiquitin conjugation assay with GST-HECT overproduction, genetic complementation","journal":"Gene","confidence":"High","confidence_rationale":"Tier 1 / Strong — active-site mutagenesis of catalytic cysteine combined with in vivo ubiquitination assay; foundational paper establishing E3 ligase activity","pmids":["10395901"],"is_preprint":false},{"year":2012,"finding":"Yeast HECT E3 ligase Tom1 and F-box protein Dia2 independently control Cdc6 degradation in G1 phase; both Tom1 and Dia2 immunoprecipitate Cdc6 (binding its C-terminal region) and are required for Cdc6 ubiquitination; Cdc6 and Mcm4 chromatin association is aberrant in tom1Δ cells in G1.","method":"Co-immunoprecipitation, ubiquitination assay, chromatin fractionation, genetic deletion","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP of substrate, ubiquitination assay, and chromatin phenotype all in one study","pmids":["23129771"],"is_preprint":false},{"year":2012,"finding":"Yeast HECT E3 ligase Tom1 ubiquitinates the F-box protein Dia2 for its cell-cycle-dependent degradation in G1 and G2/M (stabilized in S phase); Tom1 binding to Dia2 is enhanced in G1 and reduced in S phase; Tom1 recognizes specific positively charged residues in the Dia2 degradation/NLS domain; loss of Dia2 partially suppresses tom1 temperature-sensitive phenotype; Dia2 degradation is required for G1-to-S phase progression.","method":"Genetic deletion, Co-immunoprecipitation, ubiquitination assay, cell cycle analysis, domain point mutagenesis","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — substrate identification with Co-IP, ubiquitination assay, mutagenesis of recognition motif, and genetic epistasis all in one study","pmids":["22933573"],"is_preprint":false},{"year":2016,"finding":"Solution NMR structure of the TOM1 GAT domain determined, showing a bundle of three helical elements; structural comparison with Tollip TBD-bound and ubiquitin-bound states reveals conformational differences at the binding interface.","method":"Solution NMR structural determination","journal":"Data in brief","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — NMR structure reported; functional validation of structural states is limited within this data article","pmids":["26977434"],"is_preprint":false},{"year":2017,"finding":"Yeast Tom1 E3 ubiquitin ligase interacts with aberrant nascent peptides escorted by the ribosome-bound quality control (RQC) complex to the proteasome; Tom1 limits accumulation and aggregation of stalled peptides in rqc1Δ cells; notably, Tom1's E3 ubiquitin ligase activity is not required for this aggregate-prevention function.","method":"Co-immunoprecipitation, genetic deletion, protein aggregation assay","journal":"Molecular biology of the cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and genetic KO with aggregation phenotype; single lab; ligase-dead mutant experiment reveals mechanistic distinction","pmids":["28298488"],"is_preprint":false},{"year":2018,"finding":"Yeast HECT E3 ligase Tom1 physically interacts with Spo12 (a FEAR network component) and mediates its ubiquitin-dependent turnover in G2/M phase; overexpression of Spo12 is cytotoxic in tom1Δ; Spo12 is still degraded in S phase in the absence of Tom1 and Cdh1, indicating additional E3 ligase(s).","method":"Co-immunoprecipitation, genetic deletion, protein stability assay","journal":"FEBS letters","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and genetic deletion with stability assay; single lab, modest follow-up","pmids":["29683484"],"is_preprint":false},{"year":2018,"finding":"TOM1 binds FcγRIIb2 (a variant Fc receptor) and attenuates its recycling, thereby suppressing neuronal uptake of oligomeric Aβ1-42; TOM1 expression is downregulated in the hippocampus of 3xTg-AD mice and AD patients; lentiviral TOM1 restoration rescues memory deficits in 3xTg-AD mice.","method":"Co-immunoprecipitation, Fcgr2b knockout neurons, lentiviral gene delivery, behavioral testing","journal":"The Journal of neuroscience","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP for binding, KO for functional readout, in vivo gene delivery; single lab","pmids":["30185465"],"is_preprint":false},{"year":2019,"finding":"TOM1 VHS domain preferentially binds PI5P over other phosphoinositides; PI5P binding destabilizes the VHS domain structure (reduced thermostability, interhelical contacts, and conformational compaction) and binding is endothermic with two non-cooperative binding sites; acyl chains of PI5P contribute to interaction; this structural change may alter downstream effector interactions under Shigella infection.","method":"Thermal denaturation (DSF), isothermal calorimetry (ITC), NMR spectroscopy","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — multiple biophysical methods (ITC, thermal denaturation, NMR) characterizing the binding mechanism in one study; single lab","pmids":["31350523"],"is_preprint":false},{"year":2019,"finding":"The TOM1 p.G307D missense variant fails to interact with TOLLIP; patient-derived cells show impaired autophagy and enhanced apoptosis susceptibility; these functional defects are consistent with TOM1's established role in TOLLIP-dependent IL-1 recycling and autophagosome maturation.","method":"Whole-exome sequencing, Co-immunoprecipitation (mutant vs. WT), autophagy flux assays in patient cells, signaling assays (STAT, ERK1/2)","journal":"NPJ genomic medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP demonstrating interaction loss and patient cell functional assays; single lab, disease variant paper","pmids":["31263572"],"is_preprint":false},{"year":2023,"finding":"SENP1 de-SUMOylates TOM1, promoting its stability and function; CIH induces SUMOylation of TOM1 leading to its destabilization; SENP1 overexpression reduces TOM1 SUMOylation, enhances TOM1 levels and microglial migration, and reduces neuroinflammation; TOM1 knockdown suppresses these SENP1-driven effects, placing TOM1 downstream of SENP1 in this pathway.","method":"Co-immunoprecipitation, siRNA knockdown, SENP1 overexpression/knockout, SUMO immunoprecipitation, in vitro and in vivo CIH model","journal":"International immunopharmacology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — SUMOylation pulldown, genetic epistasis by siRNA rescue; single lab","pmids":["37137262"],"is_preprint":false},{"year":2024,"finding":"SIRT5 directly interacts with TOM1 and desuccinylates it at the K48 site, stabilizing TOM1 protein; TOM1 knockdown reverses the pro-autophagy and anti-apoptotic effects of SIRT5 overexpression in an H/R-induced MIRI cell model, placing TOM1 downstream of SIRT5 in regulating autophagy-related cell death.","method":"Co-immunoprecipitation, succinylation immunoprecipitation, siRNA knockdown rescue assay, overexpression, in vivo MI model","journal":"BMC cardiovascular disorders","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct protein interaction shown by Co-IP, site-specific PTM identified, epistasis by knockdown rescue; single lab","pmids":["39210272"],"is_preprint":false},{"year":2024,"finding":"TOM1 contains a DXXLL motif-adjacent region that enhances VHS domain affinity for ubiquitin and is modulated by phosphorylation; TOM1 PI5P binding is pH-dependent—under acidic conditions TOM1 retains TOLLIP complex formation but cannot bind ubiquitin; acidic endosomal pH promotes TOM1 and TOLLIP accumulation at endosomes through this pH-sensing mechanism.","method":"Biophysical binding assays, phosphorylation analysis, pH-dependent binding assays, Co-immunoprecipitation","journal":"Structure (London, England : 1993)","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — multiple biophysical experiments characterizing binding mechanisms; single lab","pmids":["39208792"],"is_preprint":false},{"year":2025,"finding":"Cryo-EM structures of yeast Tom1 during an active ubiquitination cycle reveal that its extended solenoid domain architecture harbors a non-canonical ubiquitin-binding site that coordinates a structural ubiquitin; this structural ubiquitin contributes to the fidelity of K48-linked poly-ubiquitin chain assembly by the HECT domain.","method":"Cryo-electron microscopy (cryo-EM), in vitro ubiquitination assay, mutagenesis of ubiquitin-binding site","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 / Strong — cryo-EM structure during active ubiquitination cycle plus mutagenesis of the identified site, multiple orthogonal methods in one study","pmids":["40359109"],"is_preprint":false},{"year":2025,"finding":"The TOM1 G307D variant impairs TOM1-TOLLIP interaction and reduces TOM1's ability to inhibit TOLLIP binding to PI(3)P; patient cells show autophagosome accumulation due to impaired autophagosome-lysosome fusion and excessive activation of inflammatory pathways.","method":"Biophysical binding assays, Co-immunoprecipitation, patient cell autophagy/lysosome fusion assays, inflammatory signaling assays","journal":"Disease models & mechanisms","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple biochemical and cell-based methods; single lab; extends PMID:31263572 with mechanistic detail on PI(3)P regulation","pmids":["40936361"],"is_preprint":false},{"year":2026,"finding":"TOM1 binds the NTF2L domain of the stress granule scaffold protein G3BP1 and promotes stress granule disassembly; TOM1 upregulation during chronic colitis drives SG disassembly, enabling nuclear translocation of FUBP1 and upregulation of c-Myc, thereby contributing to tumorigenesis.","method":"Co-immunoprecipitation, overexpression, nuclear fractionation, cell-based SG assembly/disassembly assays","journal":"Redox biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and functional SG assay with downstream transcription factor readout; single lab, novel function","pmids":["42127552"],"is_preprint":false}],"current_model":"Human TOM1 is a VHS- and GAT-domain adaptor protein that functions as an ESCRT-0 component on early endosomes: its GAT domain binds ubiquitin and Tollip (mutually exclusively) to sort ubiquitinated cargo toward lysosomal degradation; Tollip and endofin recruit cytosolic TOM1 to endosomal membranes, where TOM1 in turn recruits clathrin heavy chain via C-terminal binding motifs; TOM1 also acts as a pH-sensitive effector of phosphatidylinositol 5-phosphate—enriched on signaling endosomes during Shigella infection—which destabilizes its VHS domain and diverts it from ubiquitin binding, impairing endosomal maturation; in autophagy, TOM1 connects endosomes to autophagosomes through myosin VI, driving autophagosome-lysosome fusion; TOM1 negatively regulates IL-1β/TNF-α-induced NF-κB and AP-1 signaling; it is subject to SUMOylation (reversed by SENP1) and succinylation at K48 (reversed by SIRT5), both post-translational modifications regulating its stability and function; in yeast, the orthologous Tom1 is a HECT-domain E3 ubiquitin ligase whose solenoid architecture coordinates a structural ubiquitin to enforce K48 poly-ubiquitin chain specificity, and which ubiquitinates substrates including Cdc6, Dia2, and Spo12 to control cell cycle progression and protein quality control."},"narrative":{"mechanistic_narrative":"Human TOM1 is a VHS- and GAT-domain endosomal adaptor that sorts ubiquitinated cargo and couples endosomal membranes to downstream degradative machinery [PMID:14563850, PMID:15047686]. Its GAT domain binds ubiquitin chains and Tollip through overlapping, mutually exclusive interfaces, and Tollip — together with the FYVE-domain protein endofin, which binds TOM1's C-terminal region — recruits cytosolic TOM1 onto early endosomes [PMID:15047686, PMID:14613930]. Once membrane-bound, TOM1 engages clathrin heavy chain through three C-terminal binding sites including a LEDEF clathrin box, recruiting clathrin (but not AP1/AP2/AP3 or dynamin) to endosomes [PMID:14563850, PMID:15657082]. TOM1 also binds myosin VI on endosomes, connecting endosomal membranes to autophagosomes and driving autophagosome–lysosome fusion [PMID:23023224]. Phosphatidylinositol 5-phosphate is a direct TOM1 ligand: PI5P binding by the VHS domain — exploited during Shigella infection — destabilizes the VHS fold and, in a pH-dependent manner, diverts TOM1 from ubiquitin binding while preserving Tollip complex formation, delaying endosomal maturation and cargo degradation [PMID:25588840, PMID:31350523, PMID:39208792]. TOM1 negatively regulates IL-1β/TNF-α-induced NF-κB and AP-1 signaling via its VHS domain [PMID:15056867], and its abundance is controlled post-translationally by SUMOylation reversed by SENP1 [PMID:37137262] and by K48 succinylation reversed by SIRT5 [PMID:39210272]. A TOM1 p.G307D missense variant abolishes the TOLLIP interaction, impairs autophagosome–lysosome fusion, and causes excessive inflammatory signaling in patient cells, linking TOM1 dysfunction to human disease [PMID:31263572, PMID:40936361]. The yeast ortholog Tom1 is a mechanistically distinct ~380 kDa HECT-domain E3 ubiquitin ligase whose solenoid architecture coordinates a structural ubiquitin to enforce K48-linked chain specificity and which ubiquitinates Cdc6, Dia2, and Spo12 to govern cell-cycle progression and protein quality control [PMID:10395901, PMID:40359109, PMID:23129771, PMID:22933573].","teleology":[{"year":1997,"claim":"Established how TOM1 expression is driven, identifying it as a transcriptional output of an oncogenic transcription factor rather than a constitutive housekeeping gene.","evidence":"Promoter deletion/mutation and reporter assays mapping a functional Myb site cooperating with C/EBP","pmids":["9135152"],"confidence":"High","gaps":["Does not address TOM1 protein function","Physiological contexts of Myb-driven induction not defined"]},{"year":1999,"claim":"Defined the yeast ortholog as a catalytically active HECT E3 ubiquitin ligase, establishing an enzymatic identity entirely distinct from the human adaptor.","evidence":"Active-site cysteine mutagenesis (C3235A) and in vivo ubiquitin conjugation assay with GST-HECT overproduction in yeast","pmids":["10395901"],"confidence":"High","gaps":["Substrates not yet identified","No structural basis for chain specificity"]},{"year":2000,"claim":"Provided the first atomic view of the TOM1 VHS domain, distinguishing membrane-binding and protein-interaction surfaces that later work would tie to function.","evidence":"X-ray crystallography at 1.5 Å","pmids":["10985773"],"confidence":"High","gaps":["No bound ligand in the structure","Functional roles of the basic patch and charged ridge inferred, not tested here"]},{"year":2004,"claim":"Resolved how TOM1 recognizes cargo and is recruited to membranes, showing GAT-domain binding of ubiquitin and Tollip is mutually exclusive and that Tollip and endofin deliver cytosolic TOM1 to early endosomes.","evidence":"GST pulldown, reciprocal Co-IP, gel filtration, domain mapping and EEA1 co-localization microscopy across multiple studies","pmids":["14563850","15047686","14613930"],"confidence":"High","gaps":["Stoichiometry of the TOM1–Tollip–ubiquitin switch unresolved","Spatial regulation of mutual exclusivity in vivo not defined"]},{"year":2005,"claim":"Mapped the clathrin-recruitment activity of TOM1 to defined C-terminal motifs and showed it selectively brings clathrin (not adaptor complexes or dynamin) to endosomes.","evidence":"GST pulldown with deletion/point mutants, overexpression, immunofluorescence and anti-TOM1 antibody microinjection; family-wide confirmation by Co-IP","pmids":["15657082","16412388"],"confidence":"High","gaps":["Functional consequence of endosomal clathrin recruitment not fully defined","Family member redundancy in vivo untested"]},{"year":2004,"claim":"Linked TOM1 to inflammatory signaling control, showing it dampens cytokine-induced NF-κB/AP-1 activation through its VHS domain.","evidence":"NF-κB and AP-1 luciferase reporter assays with domain deletion in overexpression","pmids":["15056867"],"confidence":"Medium","gaps":["No endogenous knockdown in original study","Molecular target of VHS-mediated suppression not identified"]},{"year":2010,"claim":"Identified post-transcriptional control of TOM1 by miR-126 and tied TOM1 levels causally to NF-κB-driven cytokine output.","evidence":"3'-UTR luciferase reporter, siRNA knockdown, overexpression and IL-8 ELISA in bronchial epithelial cells","pmids":["20083669"],"confidence":"Medium","gaps":["Single cell-type context","Direct molecular mechanism linking TOM1 to NF-κB not resolved"]},{"year":2012,"claim":"Placed TOM1 at the endosome–autophagosome interface, showing myosin VI binding is required for autophagosome maturation and lysosomal fusion.","evidence":"Reciprocal Co-IP, siRNA knockdown, live-cell imaging and autophagy flux assays","pmids":["23023224"],"confidence":"High","gaps":["How TOM1 physically bridges the two membranes mechanistically unresolved","Regulation of this step not defined"]},{"year":2012,"claim":"Defined yeast Tom1 substrates and its role in cell-cycle control, showing ubiquitination of Cdc6 and Dia2 governs G1-to-S progression and replication licensing.","evidence":"Co-IP of substrates, in vitro/in vivo ubiquitination assays, chromatin fractionation, recognition-motif mutagenesis and genetic epistasis","pmids":["23129771","22933573"],"confidence":"High","gaps":["Full substrate repertoire incomplete","Redundant E3s for these substrates exist"]},{"year":2015,"claim":"Identified PI5P as a direct TOM1 ligand exploited by Shigella, showing lipid-driven recruitment to signaling endosomes blocks cargo degradation and maturation.","evidence":"Lipid pulldown, Co-IP, domain mapping and cell-based EGFR degradation/endocytosis assays","pmids":["25588840"],"confidence":"High","gaps":["Endogenous physiological role of PI5P sensing beyond infection unclear","Downstream effectors diverted by PI5P not enumerated"]},{"year":2016,"claim":"Provided a solution structure of the GAT domain, revealing conformational differences between Tollip-bound and ubiquitin-bound states underlying the mutually exclusive switch.","evidence":"Solution NMR structural determination","pmids":["26977434"],"confidence":"Medium","gaps":["Limited functional validation in this data article","Switch dynamics in a membrane context untested"]},{"year":2017,"claim":"Extended yeast Tom1 into protein quality control, showing it limits aggregation of stalled RQC peptides through a ligase-independent function.","evidence":"Co-IP, genetic deletion, aggregation assays and a ligase-dead mutant","pmids":["28298488"],"confidence":"Medium","gaps":["Mechanism of catalysis-independent aggregate prevention unknown","Single-lab observation"]},{"year":2018,"claim":"Added Spo12 as a yeast Tom1 substrate in G2/M and broadened TOM1's reach to mammalian receptor handling and Alzheimer-relevant amyloid uptake.","evidence":"Co-IP, genetic deletion and stability assays in yeast; Co-IP, Fcgr2b-knockout neurons, lentiviral rescue and behavior in mouse AD models","pmids":["29683484","30185465"],"confidence":"Medium","gaps":["Additional Spo12 E3 ligases remain active","Mechanistic link between FcγRIIb2 binding and Aβ uptake incompletely defined"]},{"year":2019,"claim":"Characterized the biophysics of PI5P sensing and linked a human disease variant to loss of the TOLLIP interaction, autophagy defects and apoptosis susceptibility.","evidence":"ITC, thermal denaturation and NMR for PI5P-induced VHS destabilization; whole-exome sequencing, Co-IP and patient-cell autophagy/signaling assays for the G307D variant","pmids":["31350523","31263572"],"confidence":"High","gaps":["Causality of the disease variant in a defined Mendelian syndrome not fully established","Effectors altered by VHS destabilization unidentified"]},{"year":2023,"claim":"Defined SUMOylation, reversed by SENP1, as a stability switch placing TOM1 downstream of SENP1 in controlling microglial migration and neuroinflammation.","evidence":"SUMO-IP, siRNA knockdown rescue, SENP1 gain/loss in CIH cell and animal models","pmids":["37137262"],"confidence":"Medium","gaps":["SUMO acceptor site(s) not mapped","Single disease-model context"]},{"year":2024,"claim":"Established succinylation at K48 (reversed by SIRT5) as a second stability-regulating modification and refined the pH-dependent logic separating TOM1 ubiquitin binding from TOLLIP binding.","evidence":"SIRT5 Co-IP and succinylation-IP with knockdown rescue in MIRI models; biophysical, phosphorylation and pH-dependent binding assays plus Co-IP","pmids":["39210272","39208792"],"confidence":"Medium","gaps":["Interplay between SUMOylation and succinylation unknown","Physiological pH ranges driving the ubiquitin/TOLLIP switch in vivo not defined"]},{"year":2025,"claim":"Delivered a structural mechanism for yeast Tom1 chain fidelity and a refined mechanism for the human disease variant's autophagy and inflammatory defects.","evidence":"Cryo-EM of an active ubiquitination cycle with ubiquitin-binding-site mutagenesis (yeast); biophysical binding, Co-IP and patient-cell autophagy/inflammation assays for G307D and PI(3)P regulation","pmids":["40359109","40936361"],"confidence":"High","gaps":["Whether a structural ubiquitin contributes to other HECT ligases untested here","How G307D-driven PI(3)P dysregulation feeds into inflammation mechanistically incomplete"]},{"year":2026,"claim":"Uncovered a new TOM1 function in stress granule dynamics, showing G3BP1 binding promotes SG disassembly and drives an oncogenic transcriptional program in colitis-associated tumorigenesis.","evidence":"Co-IP, overexpression, nuclear fractionation and SG assembly/disassembly assays with FUBP1/c-Myc readouts","pmids":["42127552"],"confidence":"Medium","gaps":["Direct vs. indirect effect on SG disassembly not fully separated","How this function integrates with endosomal/autophagy roles unknown"]},{"year":null,"claim":"It remains unresolved how TOM1's distinct activities — endosomal cargo sorting, autophagosome maturation, inflammatory suppression, stress granule disassembly — are coordinated and switched by its PI5P/pH sensing and competing post-translational modifications within a single cell.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No integrated model linking PTM state to functional partitioning","Physiological triggers selecting between TOM1 functions undefined","Stoichiometry and dynamics of competing partner interactions in vivo unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,3,4,5]},{"term_id":"GO:0008289","term_label":"lipid binding","supporting_discovery_ids":[11,19,23]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[12,13,14,24]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[7]}],"localization":[{"term_id":"GO:0005768","term_label":"endosome","supporting_discovery_ids":[3,4,5,11]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[3,4]}],"pathway":[{"term_id":"R-HSA-9612973","term_label":"Autophagy","supporting_discovery_ids":[10,20,25]},{"term_id":"R-HSA-5653656","term_label":"Vesicle-mediated transport","supporting_discovery_ids":[2,5,11]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[7,9]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[13,14,17]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[12,24,16]}],"complexes":["ESCRT-0 (TOM1–Tollip)"],"partners":["TOLLIP","ZFYVE16","CLTC","MYO6","G3BP1","FCGR2B","DIA2","CDC6"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O60784","full_name":"Target of Myb1 membrane trafficking protein","aliases":["Target of Myb protein 1"],"length_aa":492,"mass_kda":53.8,"function":"Adapter protein that plays a role in the intracellular membrane trafficking of ubiquitinated proteins, thereby participating in autophagy, ubiquitination-dependent signaling and receptor recycling pathways (PubMed:14563850, PubMed:15047686, PubMed:23023224, PubMed:25588840, PubMed:26320582, PubMed:31371777). Acts as a MYO6/Myosin VI adapter protein that targets MYO6 to endocytic structures (PubMed:23023224). Together with MYO6, required for autophagosomal delivery of endocytic cargo, the maturation of autophagosomes and their fusion with lysosomes (PubMed:23023224). MYO6 links TOM1 with autophagy receptors, such as TAX1BP1; CALCOCO2/NDP52 and OPTN (PubMed:31371777). Binds to polyubiquitinated proteins via its GAT domain (PubMed:14563850). In a complex with TOLLIP, recruits ubiquitin-conjugated proteins onto early endosomes (PubMed:15047686). The Tom1-Tollip complex may regulate endosomal trafficking by linking polyubiquitinated proteins to clathrin (PubMed:14563850, PubMed:15047686). Mediates clathrin recruitment to early endosomes by ZFYVE16 (PubMed:15657082). Modulates binding of TOLLIP to phosphatidylinositol 3-phosphate (PtdIns(3)P) via binding competition; the association with TOLLIP may favor the release of TOLLIP from endosomal membranes, allowing TOLLIP to commit to cargo trafficking (PubMed:26320582). Acts as a phosphatidylinositol 5-phosphate (PtdIns(5)P) effector by binding to PtdIns(5)P, thereby regulating endosomal maturation (PubMed:25588840). PtdIns(5)P-dependent recruitment to signaling endosomes may block endosomal maturation (PubMed:25588840). Also inhibits Toll-like receptor (TLR) signaling and participates in immune receptor recycling (PubMed:15047686, PubMed:26320582)","subcellular_location":"Cytoplasm; Endosome membrane; Early endosome membrane","url":"https://www.uniprot.org/uniprotkb/O60784/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TOM1","classification":"Not Classified","n_dependent_lines":20,"n_total_lines":1208,"dependency_fraction":0.016556291390728478},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"MYO6","stoichiometry":4.0},{"gene":"TOLLIP","stoichiometry":4.0},{"gene":"CALM1","stoichiometry":0.2},{"gene":"CALM2","stoichiometry":0.2},{"gene":"CALM3","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/TOM1","total_profiled":1310},"omim":[{"mim_id":"619510","title":"IMMUNODEFICIENCY 85 AND AUTOIMMUNITY; IMD85","url":"https://www.omim.org/entry/619510"},{"mim_id":"615519","title":"TARGET OF MYB1-LIKE 2 MEMBRANE TRAFFICKING PROTEIN; TOM1L2","url":"https://www.omim.org/entry/615519"},{"mim_id":"608880","title":"ZINC FINGER FYVE DOMAIN-CONTAINING PROTEIN 16; ZFYVE16","url":"https://www.omim.org/entry/608880"},{"mim_id":"606277","title":"TOLL-INTERACTING PROTEIN; TOLLIP","url":"https://www.omim.org/entry/606277"},{"mim_id":"604702","title":"HMG BOX DOMAIN-CONTAINING 4; HMGXB4","url":"https://www.omim.org/entry/604702"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Golgi apparatus","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal muscle","ntpm":212.6}],"url":"https://www.proteinatlas.org/search/TOM1"},"hgnc":{"alias_symbol":[],"prev_symbol":[]},"alphafold":{"accession":"O60784","domains":[{"cath_id":"1.25.40.90","chopping":"13-159","consensus_level":"high","plddt":94.512,"start":13,"end":159},{"cath_id":"1.20.58.160","chopping":"215-307","consensus_level":"high","plddt":93.7367,"start":215,"end":307}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O60784","model_url":"https://alphafold.ebi.ac.uk/files/AF-O60784-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O60784-F1-predicted_aligned_error_v6.png","plddt_mean":70.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TOM1","jax_strain_url":"https://www.jax.org/strain/search?query=TOM1"},"sequence":{"accession":"O60784","fasta_url":"https://rest.uniprot.org/uniprotkb/O60784.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O60784/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O60784"}},"corpus_meta":[{"pmid":"23023224","id":"PMC_23023224","title":"Autophagy 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Neuroinflammation","date":"2024-07-03","source":"bioRxiv","url":"https://doi.org/10.1101/2024.07.01.601612","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":25219,"output_tokens":6616,"usd":0.087448,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":15585,"output_tokens":5581,"usd":0.108725,"stage2_stop_reason":"end_turn"},"total_usd":0.196173,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2000,\n      \"finding\": \"Crystal structure of the human TOM1 VHS domain resolved to 1.5 Å, revealing eight helices in a superhelix with a conserved basic patch on helix 3 (implicated in membrane binding) and a negatively charged ridge on helix 2 (implicated in protein-protein interactions involving helices 2 and 4).\",\n      \"method\": \"X-ray crystallography (1.5 Å resolution)\",\n      \"journal\": \"Biochemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with explicit resolution and structural comparison to related domains; primary structural paper for this domain\",\n      \"pmids\": [\"10985773\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"TOM1 is a direct transcriptional target of v-Myb; the Myb-inducible tom-1 promoter contains a functional Myb binding site and requires a juxtaposed C/EBP binding site for Myb-dependent activation, with C/EBP acting as a cooperation partner.\",\n      \"method\": \"Promoter deletion/mutation analysis, reporter gene assay, transcription factor binding site mapping\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — functional Myb binding site validated by reporter assay and de novo protein synthesis inhibition experiment; replicated across two oncogenic v-Myb variants\",\n      \"pmids\": [\"9135152\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"TOM1 directly binds ubiquitin chains and Tollip via its GAT domain; endogenous TOM1 co-fractionates with Tollip in a complex; TOM1 also binds clathrin heavy chain through a canonical clathrin-binding motif; deletion of the clathrin-binding motif alters GFP-TOM1 cytoplasmic distribution.\",\n      \"method\": \"Co-immunoprecipitation, gel filtration, Western blot, GFP fluorescence microscopy, GST pulldown\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP of endogenous proteins, gel filtration fractionation, and domain deletion all in one study; replicated by independent group (PMID:15047686)\",\n      \"pmids\": [\"14563850\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"The GAT domain of TOM1 (and TOM1L1) interacts with ubiquitin and Tollip; ubiquitin and Tollip bind overlapping regions of the GAT domain in a mutually exclusive manner. Tollip localizes on early endosomes and recruits cytosolic TOM1 and ubiquitinated proteins to endosomes.\",\n      \"method\": \"GST pulldown, Co-immunoprecipitation, fluorescence microscopy, domain mapping\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods; independently confirmed by PMID:14563850\",\n      \"pmids\": [\"15047686\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"Endofin, a FYVE-domain early endosomal protein, binds specifically to the C-terminal region of TOM1 (not TOM1-L1 or TOM1-L2) and recruits cytosolic TOM1 to early endosomes; confirmed by yeast two-hybrid, GST pulldown, Co-IP, and immunofluorescence with EEA1 co-localization.\",\n      \"method\": \"Yeast two-hybrid screen, GST pulldown, Co-immunoprecipitation, immunofluorescence, sucrose density gradient fractionation\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods in one study; specificity for TOM1 vs. paralogs and other FYVE proteins demonstrated\",\n      \"pmids\": [\"14613930\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"TOM1 binds clathrin heavy chain through three sites (residues 300–321, 321–326, and a LEDEF clathrin-binding box at 362–366); endofin overexpression recruits clathrin (but not dynamin, AP1, AP2, or AP3) to endosomes via TOM1; microinjection of anti-TOM1 antibody reduces membrane association of clathrin.\",\n      \"method\": \"GST pulldown with deletion/point mutants, overexpression, immunofluorescence, antibody microinjection\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — domain mapping by mutagenesis, functional antibody microinjection, and overexpression all in one study; confirmed clathrin binding motifs\",\n      \"pmids\": [\"15657082\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"All TOM1 family members (TOM1, TOM1L1, TOM1L2) bind Tollip via their GAT domains and bind clathrin through their C-terminal regions; when co-expressed with Tollip, all three family members recruit clathrin onto endosomes.\",\n      \"method\": \"Co-immunoprecipitation, fluorescence microscopy with Tollip co-expression\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — single lab, single Co-IP/microscopy approach, but extends finding to all three family members consistently\",\n      \"pmids\": [\"16412388\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Overexpression of TOM1 suppresses NF-κB and AP-1 activation induced by IL-1β and TNF-α; the VHS domain of TOM1 is required for this suppressive activity.\",\n      \"method\": \"Reporter gene assay (NF-κB and AP-1 luciferase), domain deletion analysis\",\n      \"journal\": \"Biological & pharmaceutical bulletin\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single method (reporter assay), no endogenous protein knockdown; domain requirement identified\",\n      \"pmids\": [\"15056867\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Dictyostelium TOM1 (DdTom1) GAT domain binds ubiquitin; the VHS and GAT domains interact with phospholipids enabling endosomal membrane recruitment; the C-terminal domain recruits clathrin, Eps15, and TSG101 (an ESCRT component), supporting participation in an ancestral ESCRT-0 complex for sorting ubiquitinated proteins to MVBs.\",\n      \"method\": \"Domain-binding assays, subcellular fractionation, co-immunoprecipitation, fluorescence microscopy\",\n      \"journal\": \"Traffic (Copenhagen, Denmark)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple domain-binding experiments in a model organism ortholog; single lab\",\n      \"pmids\": [\"19054384\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"miR-126 directly targets the 3'-UTR of TOM1 mRNA; introduction of synthetic pre-miR-126 in CF bronchial epithelial cells inhibited luciferase activity from a TOM1 3'-UTR reporter and decreased TOM1 protein; TOM1 knockdown increased NF-κB-regulated IL-8 secretion, while TOM1 overexpression downregulated NF-κB activity after LPS or IL-1β stimulation.\",\n      \"method\": \"Luciferase 3'-UTR reporter assay, Western blot, siRNA knockdown, cytokine ELISA\",\n      \"journal\": \"Journal of immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct 3'-UTR reporter validation and functional knockdown/overexpression with pathway readout; single lab\",\n      \"pmids\": [\"20083669\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"TOM1 is a myosin VI binding partner on endosomes; loss of myosin VI and TOM1 reduces autophagosomal delivery of endocytic cargo and causes a block in autophagosome-lysosome fusion; myosin VI adaptor proteins NDP52, optineurin, and T6BP dock myosin VI to autophagosomes, while TOM1 on endosomes connects endosomal membranes to autophagosomes to promote maturation and lysosomal fusion.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, live-cell fluorescence imaging, autophagy flux assays\",\n      \"journal\": \"Nature cell biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, specific KD phenotype (block in autophagosome-lysosome fusion), and live imaging in one study; high-citation, focused mechanistic paper\",\n      \"pmids\": [\"23023224\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"TOM1 is a direct binding partner of phosphatidylinositol 5-phosphate (PI5P); PI5P recruits TOM1 to signaling endosomes (produced by Shigella IpgD phosphatase), and this recruitment delays EGFR degradation and impairs bulk endocytosis, thereby preventing endosomal maturation.\",\n      \"method\": \"Lipid pulldown, Co-immunoprecipitation, domain mapping, cell-based endocytosis/degradation assays\",\n      \"journal\": \"Journal of cell science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct lipid-binding assay plus functional cell-based readout with domain identification; multiple orthogonal methods\",\n      \"pmids\": [\"25588840\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1999,\n      \"finding\": \"Yeast TOM1 encodes a ~380 kDa HECT-domain ubiquitin ligase; site-directed mutagenesis of the conserved active-site cysteine (C3235A) abolishes HECT function and temperature-sensitive growth; overproduction of the HECT domain promotes ubiquitin (but not SUMO/Smt3) conjugation to proteins in vivo.\",\n      \"method\": \"Site-directed mutagenesis, in vivo ubiquitin conjugation assay with GST-HECT overproduction, genetic complementation\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — active-site mutagenesis of catalytic cysteine combined with in vivo ubiquitination assay; foundational paper establishing E3 ligase activity\",\n      \"pmids\": [\"10395901\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Yeast HECT E3 ligase Tom1 and F-box protein Dia2 independently control Cdc6 degradation in G1 phase; both Tom1 and Dia2 immunoprecipitate Cdc6 (binding its C-terminal region) and are required for Cdc6 ubiquitination; Cdc6 and Mcm4 chromatin association is aberrant in tom1Δ cells in G1.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, chromatin fractionation, genetic deletion\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP of substrate, ubiquitination assay, and chromatin phenotype all in one study\",\n      \"pmids\": [\"23129771\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Yeast HECT E3 ligase Tom1 ubiquitinates the F-box protein Dia2 for its cell-cycle-dependent degradation in G1 and G2/M (stabilized in S phase); Tom1 binding to Dia2 is enhanced in G1 and reduced in S phase; Tom1 recognizes specific positively charged residues in the Dia2 degradation/NLS domain; loss of Dia2 partially suppresses tom1 temperature-sensitive phenotype; Dia2 degradation is required for G1-to-S phase progression.\",\n      \"method\": \"Genetic deletion, Co-immunoprecipitation, ubiquitination assay, cell cycle analysis, domain point mutagenesis\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — substrate identification with Co-IP, ubiquitination assay, mutagenesis of recognition motif, and genetic epistasis all in one study\",\n      \"pmids\": [\"22933573\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"Solution NMR structure of the TOM1 GAT domain determined, showing a bundle of three helical elements; structural comparison with Tollip TBD-bound and ubiquitin-bound states reveals conformational differences at the binding interface.\",\n      \"method\": \"Solution NMR structural determination\",\n      \"journal\": \"Data in brief\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — NMR structure reported; functional validation of structural states is limited within this data article\",\n      \"pmids\": [\"26977434\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Yeast Tom1 E3 ubiquitin ligase interacts with aberrant nascent peptides escorted by the ribosome-bound quality control (RQC) complex to the proteasome; Tom1 limits accumulation and aggregation of stalled peptides in rqc1Δ cells; notably, Tom1's E3 ubiquitin ligase activity is not required for this aggregate-prevention function.\",\n      \"method\": \"Co-immunoprecipitation, genetic deletion, protein aggregation assay\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and genetic KO with aggregation phenotype; single lab; ligase-dead mutant experiment reveals mechanistic distinction\",\n      \"pmids\": [\"28298488\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"Yeast HECT E3 ligase Tom1 physically interacts with Spo12 (a FEAR network component) and mediates its ubiquitin-dependent turnover in G2/M phase; overexpression of Spo12 is cytotoxic in tom1Δ; Spo12 is still degraded in S phase in the absence of Tom1 and Cdh1, indicating additional E3 ligase(s).\",\n      \"method\": \"Co-immunoprecipitation, genetic deletion, protein stability assay\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and genetic deletion with stability assay; single lab, modest follow-up\",\n      \"pmids\": [\"29683484\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TOM1 binds FcγRIIb2 (a variant Fc receptor) and attenuates its recycling, thereby suppressing neuronal uptake of oligomeric Aβ1-42; TOM1 expression is downregulated in the hippocampus of 3xTg-AD mice and AD patients; lentiviral TOM1 restoration rescues memory deficits in 3xTg-AD mice.\",\n      \"method\": \"Co-immunoprecipitation, Fcgr2b knockout neurons, lentiviral gene delivery, behavioral testing\",\n      \"journal\": \"The Journal of neuroscience\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP for binding, KO for functional readout, in vivo gene delivery; single lab\",\n      \"pmids\": [\"30185465\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TOM1 VHS domain preferentially binds PI5P over other phosphoinositides; PI5P binding destabilizes the VHS domain structure (reduced thermostability, interhelical contacts, and conformational compaction) and binding is endothermic with two non-cooperative binding sites; acyl chains of PI5P contribute to interaction; this structural change may alter downstream effector interactions under Shigella infection.\",\n      \"method\": \"Thermal denaturation (DSF), isothermal calorimetry (ITC), NMR spectroscopy\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — multiple biophysical methods (ITC, thermal denaturation, NMR) characterizing the binding mechanism in one study; single lab\",\n      \"pmids\": [\"31350523\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"The TOM1 p.G307D missense variant fails to interact with TOLLIP; patient-derived cells show impaired autophagy and enhanced apoptosis susceptibility; these functional defects are consistent with TOM1's established role in TOLLIP-dependent IL-1 recycling and autophagosome maturation.\",\n      \"method\": \"Whole-exome sequencing, Co-immunoprecipitation (mutant vs. WT), autophagy flux assays in patient cells, signaling assays (STAT, ERK1/2)\",\n      \"journal\": \"NPJ genomic medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP demonstrating interaction loss and patient cell functional assays; single lab, disease variant paper\",\n      \"pmids\": [\"31263572\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"SENP1 de-SUMOylates TOM1, promoting its stability and function; CIH induces SUMOylation of TOM1 leading to its destabilization; SENP1 overexpression reduces TOM1 SUMOylation, enhances TOM1 levels and microglial migration, and reduces neuroinflammation; TOM1 knockdown suppresses these SENP1-driven effects, placing TOM1 downstream of SENP1 in this pathway.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, SENP1 overexpression/knockout, SUMO immunoprecipitation, in vitro and in vivo CIH model\",\n      \"journal\": \"International immunopharmacology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — SUMOylation pulldown, genetic epistasis by siRNA rescue; single lab\",\n      \"pmids\": [\"37137262\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"SIRT5 directly interacts with TOM1 and desuccinylates it at the K48 site, stabilizing TOM1 protein; TOM1 knockdown reverses the pro-autophagy and anti-apoptotic effects of SIRT5 overexpression in an H/R-induced MIRI cell model, placing TOM1 downstream of SIRT5 in regulating autophagy-related cell death.\",\n      \"method\": \"Co-immunoprecipitation, succinylation immunoprecipitation, siRNA knockdown rescue assay, overexpression, in vivo MI model\",\n      \"journal\": \"BMC cardiovascular disorders\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct protein interaction shown by Co-IP, site-specific PTM identified, epistasis by knockdown rescue; single lab\",\n      \"pmids\": [\"39210272\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"TOM1 contains a DXXLL motif-adjacent region that enhances VHS domain affinity for ubiquitin and is modulated by phosphorylation; TOM1 PI5P binding is pH-dependent—under acidic conditions TOM1 retains TOLLIP complex formation but cannot bind ubiquitin; acidic endosomal pH promotes TOM1 and TOLLIP accumulation at endosomes through this pH-sensing mechanism.\",\n      \"method\": \"Biophysical binding assays, phosphorylation analysis, pH-dependent binding assays, Co-immunoprecipitation\",\n      \"journal\": \"Structure (London, England : 1993)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — multiple biophysical experiments characterizing binding mechanisms; single lab\",\n      \"pmids\": [\"39208792\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Cryo-EM structures of yeast Tom1 during an active ubiquitination cycle reveal that its extended solenoid domain architecture harbors a non-canonical ubiquitin-binding site that coordinates a structural ubiquitin; this structural ubiquitin contributes to the fidelity of K48-linked poly-ubiquitin chain assembly by the HECT domain.\",\n      \"method\": \"Cryo-electron microscopy (cryo-EM), in vitro ubiquitination assay, mutagenesis of ubiquitin-binding site\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — cryo-EM structure during active ubiquitination cycle plus mutagenesis of the identified site, multiple orthogonal methods in one study\",\n      \"pmids\": [\"40359109\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The TOM1 G307D variant impairs TOM1-TOLLIP interaction and reduces TOM1's ability to inhibit TOLLIP binding to PI(3)P; patient cells show autophagosome accumulation due to impaired autophagosome-lysosome fusion and excessive activation of inflammatory pathways.\",\n      \"method\": \"Biophysical binding assays, Co-immunoprecipitation, patient cell autophagy/lysosome fusion assays, inflammatory signaling assays\",\n      \"journal\": \"Disease models & mechanisms\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple biochemical and cell-based methods; single lab; extends PMID:31263572 with mechanistic detail on PI(3)P regulation\",\n      \"pmids\": [\"40936361\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"TOM1 binds the NTF2L domain of the stress granule scaffold protein G3BP1 and promotes stress granule disassembly; TOM1 upregulation during chronic colitis drives SG disassembly, enabling nuclear translocation of FUBP1 and upregulation of c-Myc, thereby contributing to tumorigenesis.\",\n      \"method\": \"Co-immunoprecipitation, overexpression, nuclear fractionation, cell-based SG assembly/disassembly assays\",\n      \"journal\": \"Redox biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and functional SG assay with downstream transcription factor readout; single lab, novel function\",\n      \"pmids\": [\"42127552\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"Human TOM1 is a VHS- and GAT-domain adaptor protein that functions as an ESCRT-0 component on early endosomes: its GAT domain binds ubiquitin and Tollip (mutually exclusively) to sort ubiquitinated cargo toward lysosomal degradation; Tollip and endofin recruit cytosolic TOM1 to endosomal membranes, where TOM1 in turn recruits clathrin heavy chain via C-terminal binding motifs; TOM1 also acts as a pH-sensitive effector of phosphatidylinositol 5-phosphate—enriched on signaling endosomes during Shigella infection—which destabilizes its VHS domain and diverts it from ubiquitin binding, impairing endosomal maturation; in autophagy, TOM1 connects endosomes to autophagosomes through myosin VI, driving autophagosome-lysosome fusion; TOM1 negatively regulates IL-1β/TNF-α-induced NF-κB and AP-1 signaling; it is subject to SUMOylation (reversed by SENP1) and succinylation at K48 (reversed by SIRT5), both post-translational modifications regulating its stability and function; in yeast, the orthologous Tom1 is a HECT-domain E3 ubiquitin ligase whose solenoid architecture coordinates a structural ubiquitin to enforce K48 poly-ubiquitin chain specificity, and which ubiquitinates substrates including Cdc6, Dia2, and Spo12 to control cell cycle progression and protein quality control.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"Human TOM1 is a VHS- and GAT-domain endosomal adaptor that sorts ubiquitinated cargo and couples endosomal membranes to downstream degradative machinery [#2, #3]. Its GAT domain binds ubiquitin chains and Tollip through overlapping, mutually exclusive interfaces, and Tollip — together with the FYVE-domain protein endofin, which binds TOM1's C-terminal region — recruits cytosolic TOM1 onto early endosomes [#3, #4]. Once membrane-bound, TOM1 engages clathrin heavy chain through three C-terminal binding sites including a LEDEF clathrin box, recruiting clathrin (but not AP1/AP2/AP3 or dynamin) to endosomes [#2, #5]. TOM1 also binds myosin VI on endosomes, connecting endosomal membranes to autophagosomes and driving autophagosome–lysosome fusion [#10]. Phosphatidylinositol 5-phosphate is a direct TOM1 ligand: PI5P binding by the VHS domain — exploited during Shigella infection — destabilizes the VHS fold and, in a pH-dependent manner, diverts TOM1 from ubiquitin binding while preserving Tollip complex formation, delaying endosomal maturation and cargo degradation [#11, #19, #23]. TOM1 negatively regulates IL-1\\u03b2/TNF-\\u03b1-induced NF-\\u03baB and AP-1 signaling via its VHS domain [#7], and its abundance is controlled post-translationally by SUMOylation reversed by SENP1 [#21] and by K48 succinylation reversed by SIRT5 [#22]. A TOM1 p.G307D missense variant abolishes the TOLLIP interaction, impairs autophagosome–lysosome fusion, and causes excessive inflammatory signaling in patient cells, linking TOM1 dysfunction to human disease [#20, #25]. The yeast ortholog Tom1 is a mechanistically distinct ~380 kDa HECT-domain E3 ubiquitin ligase whose solenoid architecture coordinates a structural ubiquitin to enforce K48-linked chain specificity and which ubiquitinates Cdc6, Dia2, and Spo12 to govern cell-cycle progression and protein quality control [#12, #24, #13, #14].\",\n  \"teleology\": [\n    {\n      \"year\": 1997,\n      \"claim\": \"Established how TOM1 expression is driven, identifying it as a transcriptional output of an oncogenic transcription factor rather than a constitutive housekeeping gene.\",\n      \"evidence\": \"Promoter deletion/mutation and reporter assays mapping a functional Myb site cooperating with C/EBP\",\n      \"pmids\": [\"9135152\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not address TOM1 protein function\", \"Physiological contexts of Myb-driven induction not defined\"]\n    },\n    {\n      \"year\": 1999,\n      \"claim\": \"Defined the yeast ortholog as a catalytically active HECT E3 ubiquitin ligase, establishing an enzymatic identity entirely distinct from the human adaptor.\",\n      \"evidence\": \"Active-site cysteine mutagenesis (C3235A) and in vivo ubiquitin conjugation assay with GST-HECT overproduction in yeast\",\n      \"pmids\": [\"10395901\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Substrates not yet identified\", \"No structural basis for chain specificity\"]\n    },\n    {\n      \"year\": 2000,\n      \"claim\": \"Provided the first atomic view of the TOM1 VHS domain, distinguishing membrane-binding and protein-interaction surfaces that later work would tie to function.\",\n      \"evidence\": \"X-ray crystallography at 1.5 \\u00c5\",\n      \"pmids\": [\"10985773\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"No bound ligand in the structure\", \"Functional roles of the basic patch and charged ridge inferred, not tested here\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Resolved how TOM1 recognizes cargo and is recruited to membranes, showing GAT-domain binding of ubiquitin and Tollip is mutually exclusive and that Tollip and endofin deliver cytosolic TOM1 to early endosomes.\",\n      \"evidence\": \"GST pulldown, reciprocal Co-IP, gel filtration, domain mapping and EEA1 co-localization microscopy across multiple studies\",\n      \"pmids\": [\"14563850\", \"15047686\", \"14613930\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Stoichiometry of the TOM1\\u2013Tollip\\u2013ubiquitin switch unresolved\", \"Spatial regulation of mutual exclusivity in vivo not defined\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Mapped the clathrin-recruitment activity of TOM1 to defined C-terminal motifs and showed it selectively brings clathrin (not adaptor complexes or dynamin) to endosomes.\",\n      \"evidence\": \"GST pulldown with deletion/point mutants, overexpression, immunofluorescence and anti-TOM1 antibody microinjection; family-wide confirmation by Co-IP\",\n      \"pmids\": [\"15657082\", \"16412388\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Functional consequence of endosomal clathrin recruitment not fully defined\", \"Family member redundancy in vivo untested\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Linked TOM1 to inflammatory signaling control, showing it dampens cytokine-induced NF-\\u03baB/AP-1 activation through its VHS domain.\",\n      \"evidence\": \"NF-\\u03baB and AP-1 luciferase reporter assays with domain deletion in overexpression\",\n      \"pmids\": [\"15056867\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No endogenous knockdown in original study\", \"Molecular target of VHS-mediated suppression not identified\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Identified post-transcriptional control of TOM1 by miR-126 and tied TOM1 levels causally to NF-\\u03baB-driven cytokine output.\",\n      \"evidence\": \"3'-UTR luciferase reporter, siRNA knockdown, overexpression and IL-8 ELISA in bronchial epithelial cells\",\n      \"pmids\": [\"20083669\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single cell-type context\", \"Direct molecular mechanism linking TOM1 to NF-\\u03baB not resolved\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Placed TOM1 at the endosome\\u2013autophagosome interface, showing myosin VI binding is required for autophagosome maturation and lysosomal fusion.\",\n      \"evidence\": \"Reciprocal Co-IP, siRNA knockdown, live-cell imaging and autophagy flux assays\",\n      \"pmids\": [\"23023224\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How TOM1 physically bridges the two membranes mechanistically unresolved\", \"Regulation of this step not defined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Defined yeast Tom1 substrates and its role in cell-cycle control, showing ubiquitination of Cdc6 and Dia2 governs G1-to-S progression and replication licensing.\",\n      \"evidence\": \"Co-IP of substrates, in vitro/in vivo ubiquitination assays, chromatin fractionation, recognition-motif mutagenesis and genetic epistasis\",\n      \"pmids\": [\"23129771\", \"22933573\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full substrate repertoire incomplete\", \"Redundant E3s for these substrates exist\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Identified PI5P as a direct TOM1 ligand exploited by Shigella, showing lipid-driven recruitment to signaling endosomes blocks cargo degradation and maturation.\",\n      \"evidence\": \"Lipid pulldown, Co-IP, domain mapping and cell-based EGFR degradation/endocytosis assays\",\n      \"pmids\": [\"25588840\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Endogenous physiological role of PI5P sensing beyond infection unclear\", \"Downstream effectors diverted by PI5P not enumerated\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Provided a solution structure of the GAT domain, revealing conformational differences between Tollip-bound and ubiquitin-bound states underlying the mutually exclusive switch.\",\n      \"evidence\": \"Solution NMR structural determination\",\n      \"pmids\": [\"26977434\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Limited functional validation in this data article\", \"Switch dynamics in a membrane context untested\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Extended yeast Tom1 into protein quality control, showing it limits aggregation of stalled RQC peptides through a ligase-independent function.\",\n      \"evidence\": \"Co-IP, genetic deletion, aggregation assays and a ligase-dead mutant\",\n      \"pmids\": [\"28298488\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of catalysis-independent aggregate prevention unknown\", \"Single-lab observation\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Added Spo12 as a yeast Tom1 substrate in G2/M and broadened TOM1's reach to mammalian receptor handling and Alzheimer-relevant amyloid uptake.\",\n      \"evidence\": \"Co-IP, genetic deletion and stability assays in yeast; Co-IP, Fcgr2b-knockout neurons, lentiviral rescue and behavior in mouse AD models\",\n      \"pmids\": [\"29683484\", \"30185465\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Additional Spo12 E3 ligases remain active\", \"Mechanistic link between Fc\\u03b3RIIb2 binding and A\\u03b2 uptake incompletely defined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Characterized the biophysics of PI5P sensing and linked a human disease variant to loss of the TOLLIP interaction, autophagy defects and apoptosis susceptibility.\",\n      \"evidence\": \"ITC, thermal denaturation and NMR for PI5P-induced VHS destabilization; whole-exome sequencing, Co-IP and patient-cell autophagy/signaling assays for the G307D variant\",\n      \"pmids\": [\"31350523\", \"31263572\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Causality of the disease variant in a defined Mendelian syndrome not fully established\", \"Effectors altered by VHS destabilization unidentified\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined SUMOylation, reversed by SENP1, as a stability switch placing TOM1 downstream of SENP1 in controlling microglial migration and neuroinflammation.\",\n      \"evidence\": \"SUMO-IP, siRNA knockdown rescue, SENP1 gain/loss in CIH cell and animal models\",\n      \"pmids\": [\"37137262\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"SUMO acceptor site(s) not mapped\", \"Single disease-model context\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Established succinylation at K48 (reversed by SIRT5) as a second stability-regulating modification and refined the pH-dependent logic separating TOM1 ubiquitin binding from TOLLIP binding.\",\n      \"evidence\": \"SIRT5 Co-IP and succinylation-IP with knockdown rescue in MIRI models; biophysical, phosphorylation and pH-dependent binding assays plus Co-IP\",\n      \"pmids\": [\"39210272\", \"39208792\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Interplay between SUMOylation and succinylation unknown\", \"Physiological pH ranges driving the ubiquitin/TOLLIP switch in vivo not defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Delivered a structural mechanism for yeast Tom1 chain fidelity and a refined mechanism for the human disease variant's autophagy and inflammatory defects.\",\n      \"evidence\": \"Cryo-EM of an active ubiquitination cycle with ubiquitin-binding-site mutagenesis (yeast); biophysical binding, Co-IP and patient-cell autophagy/inflammation assays for G307D and PI(3)P regulation\",\n      \"pmids\": [\"40359109\", \"40936361\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether a structural ubiquitin contributes to other HECT ligases untested here\", \"How G307D-driven PI(3)P dysregulation feeds into inflammation mechanistically incomplete\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Uncovered a new TOM1 function in stress granule dynamics, showing G3BP1 binding promotes SG disassembly and drives an oncogenic transcriptional program in colitis-associated tumorigenesis.\",\n      \"evidence\": \"Co-IP, overexpression, nuclear fractionation and SG assembly/disassembly assays with FUBP1/c-Myc readouts\",\n      \"pmids\": [\"42127552\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct vs. indirect effect on SG disassembly not fully separated\", \"How this function integrates with endosomal/autophagy roles unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how TOM1's distinct activities — endosomal cargo sorting, autophagosome maturation, inflammatory suppression, stress granule disassembly — are coordinated and switched by its PI5P/pH sensing and competing post-translational modifications within a single cell.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No integrated model linking PTM state to functional partitioning\", \"Physiological triggers selecting between TOM1 functions undefined\", \"Stoichiometry and dynamics of competing partner interactions in vivo unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 3, 4, 5]},\n      {\"term_id\": \"GO:0008289\", \"supporting_discovery_ids\": [11, 19, 23]},\n      {\"term_id\": \"GO:0016874\", \"supporting_discovery_ids\": [12, 13, 14, 24]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [7]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005768\", \"supporting_discovery_ids\": [3, 4, 5, 11]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-9612973\", \"supporting_discovery_ids\": [10, 20, 25]},\n      {\"term_id\": \"R-HSA-5653656\", \"supporting_discovery_ids\": [2, 5, 11]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [7, 9]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [13, 14, 17]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [12, 24, 16]}\n    ],\n    \"complexes\": [\"ESCRT-0 (TOM1\\u2013Tollip)\"],\n    \"partners\": [\"TOLLIP\", \"ZFYVE16\", \"CLTC\", \"MYO6\", \"G3BP1\", \"FCGR2B\", \"DIA2\", \"CDC6\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":8,"faith_total":8,"faith_pct":100.0}}