{"gene":"TMUB1","run_date":"2026-06-10T10:51:55","timeline":{"discoveries":[{"year":2022,"finding":"TMUB1 competes with the E3 ubiquitin ligase HUWE1 to interact with PD-L1 at the endoplasmic reticulum, inhibiting PD-L1 polyubiquitination at K281, while also recruiting STT3A to enhance PD-L1 N-glycosylation and stability, thereby promoting PD-L1 maturation and tumor immune evasion.","method":"Co-immunoprecipitation, site-directed mutagenesis (K281), competition binding assays, glycosylation assays, in vivo tumor models with synthetic competing peptide","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, mutagenesis of specific ubiquitination site, multiple orthogonal functional assays, in vivo validation","pmids":["36376293"],"is_preprint":false},{"year":2022,"finding":"TMUB1 is an ER-resident escortase that interacts with transmembrane domains (TMDs) of client proteins undergoing ERAD retrotranslocation, shielding ~10–14 hydrophobic residues exposed out of the membrane via its transmembrane and cytosolic regions, and recruits p97 via its ubiquitin-like domain to pull client TMDs into the cytosol for proteasomal degradation.","method":"In vitro reconstitution, biochemical retrotranslocation assays, domain mutagenesis, trapping of retrotranslocation intermediates, co-immunoprecipitation with p97","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstitution of escortase activity, domain mutagenesis, multiple orthogonal biochemical assays in a single rigorous study","pmids":["35961308"],"is_preprint":false},{"year":2019,"finding":"HOPS/TMUB1 binds p53 in the cytoplasm, inhibits its proteasomal degradation, interferes with importin α to increase cytoplasmic p53 levels, and promotes p53 recruitment to mitochondria to induce the intrinsic apoptosis pathway; Hops−/− mice show significantly reduced apoptosis after chemotherapy.","method":"Co-immunoprecipitation (HOPS–p53 and HOPS–importin α), Hops knockout mouse model, apoptosis assays, mitochondrial fractionation","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP, in vivo knockout mouse, multiple orthogonal assays across multiple cell types","pmids":["31867855"],"is_preprint":false},{"year":2008,"finding":"Tmub1/HOPS facilitates recycling of GluR2-containing AMPA receptors to the synaptic surface by forming a complex with GluR2 and GRIP; RNAi knockdown of Tmub1 reduces AMPAR currents and synaptic surface GluR2, while overexpression increases surface GluR2.","method":"Co-immunoprecipitation from mouse brain (Tmub1–GluR2–GRIP complex), RNAi knockdown in neurons, electrophysiology (AMPAR current), surface recycling assay, EGFP-Tmub1 overexpression","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP from native tissue, loss- and gain-of-function with electrophysiological and biochemical readouts, recycling assay","pmids":["18665261"],"is_preprint":false},{"year":2020,"finding":"HOPS/TMUB1 directly binds the E3 ubiquitin ligase TRAF6, reducing TRAF6 stability and thereby increasing IKK complex activation, which destabilizes IκBα and enhances NF-κB (p65/RelA) transcriptional activity; Hops−/− cells show impaired pro-inflammatory responses.","method":"Co-immunoprecipitation (HOPS–TRAF6), Hops knockout cells, IκBα stability assays, NF-κB transcriptional reporter assays, inflammatory cytokine measurements","journal":"Cell death & disease","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct binding demonstrated by Co-IP, KO cells with multiple downstream readouts, multiple orthogonal methods","pmids":["33060567"],"is_preprint":false},{"year":2010,"finding":"Tmub1 binds to CAMLG (calcium-modulating cyclophilin ligand) as confirmed by yeast two-hybrid screen and co-immunoprecipitation in HEK cells; the two proteins co-localize in the cytoplasm; Tmub1 knockout mice exhibit increased wakefulness and locomotor activity during the dark phase.","method":"Yeast two-hybrid screen, co-immunoprecipitation in HEK cells, co-localization (fluorescence microscopy), Tmub1 knockout mouse with EEG/telemetric locomotor recording","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Strong — yeast two-hybrid confirmed by reciprocal Co-IP, in vivo KO mouse with EEG and telemetric readouts","pmids":["20582322"],"is_preprint":false},{"year":2019,"finding":"Tmub1 inhibits STAT3 phosphorylation and STAT3 signaling in hepatocytes; co-immunoprecipitation demonstrates direct interaction between Tmub1 and STAT3; chromatin immunoprecipitation and luciferase assays show STAT3 binds the Tmub1 promoter, suggesting a negative feedback loop.","method":"Co-immunoprecipitation (Tmub1–STAT3), loss- and gain-of-function in Lo2 cells, partial hepatectomy mouse model, chromatin immunoprecipitation, luciferase reporter assay","journal":"Cellular signalling","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP, in vivo mouse model, ChIP, reporter assay — multiple orthogonal methods in one study","pmids":["30610893"],"is_preprint":false},{"year":2020,"finding":"Tmub1 forms a protein complex with ΔNp63 isoforms (ΔNp63α, β, γ) and promotes their ubiquitination and proteasomal degradation, thereby inducing apoptosis in hepatocellular carcinoma cells.","method":"Co-immunoprecipitation (Tmub1–ΔNp63), ubiquitination assay, loss- and gain-of-function (Hep3B and MHCC-LM3 cells), xenograft growth assay, rescue experiments with ΔNp63 overexpression","journal":"Molecular therapy oncolytics","confidence":"High","confidence_rationale":"Tier 2 / Strong — Co-IP, ubiquitination assay, in vivo xenograft, rescue experiments provide multiple orthogonal lines of evidence","pmids":["32671188"],"is_preprint":false},{"year":2018,"finding":"TMUB1 interacts with CAML via its TM1 hydrophobic domain; overexpression of TMUB1 abolishes the interaction between CAML and cyclophilin B, reducing intracellular Ca2+ influx and inhibiting hepatocyte proliferation; deletion of TM1 abolishes these effects.","method":"Co-immunoprecipitation in BRL-3A cells, TM1 domain deletion mutant, Ca2+ influx assay (fluorescence microscopy), hepatocyte proliferation assay","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 2 / Strong — domain mutagenesis combined with Co-IP, Ca2+ imaging, and functional proliferation assays in a single study","pmids":["29967478"],"is_preprint":false},{"year":2024,"finding":"ERLIN1/2 scaffolds mediate the interaction between the full-length isoform of TMUB1 and RNF170; a luminal N-terminal conserved region in TMUB1 (and RNF170) is required for binding to the SPFH domain of adjacent ERLIN subunits; disruption of this interaction is linked to hereditary spastic paraplegia.","method":"Co-immunoprecipitation, domain deletion/mutation analysis, 3D structural modelling, proteomics (omics-based), HeLa ERLIN double-knockout phenotypic characterization","journal":"Life science alliance","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with domain mapping and structural modelling, single lab, functional consequences shown in ERLIN KO rather than direct TMUB1 KO","pmids":["38782601"],"is_preprint":false},{"year":2012,"finding":"Tmub1 co-localizes with CAML in the hepatocellular cytoplasm; Tmub1 knockdown upregulates CAML protein expression and alters Ca2+ influx; Tmub1 plays a negative role in IL-6-induced hepatocyte proliferation through its interaction with CAML.","method":"Co-immunoprecipitation, laser scanning confocal microscopy (co-localization), shRNA knockdown, Ca2+ influx assay, [3H]-thymidine incorporation proliferation assay","journal":"International journal of molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP confirmed interaction, multiple assays but single lab and partial mechanistic follow-up","pmids":["22426572"],"is_preprint":false},{"year":2024,"finding":"NNK promotes TMUB1 upregulation via METTL14/YTHDF2-mediated m6A modification; elevated TMUB1 interacts with AMFR to promote K63-linked ubiquitination of AKT, leading to malignant proliferation and metastasis in colorectal cancer cells.","method":"Methylated RNA immunoprecipitation sequencing, co-immunoprecipitation (TMUB1–AMFR–AKT), ubiquitination assay (K63-linkage), in vivo and in vitro functional assays","journal":"Journal of hazardous materials","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and ubiquitination assay demonstrate mechanism, but single lab with limited orthogonal validation of the specific AKT K63-ubiquitination claim","pmids":["38341886"],"is_preprint":false},{"year":2019,"finding":"TMUB1 promotes STAT1 expression in hepatocellular carcinoma cells and suppresses CCND1, negatively regulating HCC cell proliferation; TMUB1 expression is positively correlated with STAT1 in HCC tissues.","method":"Loss- and gain-of-function in HCC cell lines, qPCR, western blotting, CCK-8 and EdU proliferation assays","journal":"Medical science monitor","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, no direct binding assay between TMUB1 and STAT1 shown, only expression-level correlation and loss/gain-of-function without pathway placement","pmids":["31827061"],"is_preprint":false},{"year":2021,"finding":"HOPS/TMUB1 shuttles between nucleus and cytoplasm during the cell cycle in lens cells; it localizes mainly to the nucleus of central epithelial cells and moves to cytoplasm during mitosis, returning to nucleus post-mitosis; in differentiating fiber cells it associates with crystallin proteins, possibly acting in the ubiquitin-proteasome system.","method":"Immunofluorescence localization in mouse lens tissue across cell cycle stages and differentiation zones","journal":"Bioscience reports","confidence":"Low","confidence_rationale":"Tier 3 / Weak — localization by immunofluorescence without direct functional consequence testing, single descriptive study","pmids":["33543240"],"is_preprint":false},{"year":2021,"finding":"Hops heterozygous mice and mouse embryonic fibroblasts show impaired apoptotic response to etoposide-induced DNA damage, with reduced p53 protein levels and reduced percentage of apoptotic cells, demonstrating haploinsufficiency of HOPS in supporting p53-dependent DNA damage responses.","method":"Hops heterozygous mouse model, etoposide treatment, p53 protein quantification (western blot), apoptosis assay, p53-target gene expression profiling","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — in vivo haploinsufficiency model with defined molecular and cellular readouts, single lab","pmids":["34281239"],"is_preprint":false},{"year":2023,"finding":"TMUB1 deficiency in LPS-stimulated trophoblast cells suppresses phosphorylation of IKKα/β and blocks cytoplasmic-to-nuclear translocation of NF-κB p65, inhibiting apoptosis and NF-κB-mediated inflammation.","method":"TMUB1 knockdown in human chorionic trophoblast cells, LPS-induced mouse abortion model, IKKα/β phosphorylation assay, NF-κB p65 nuclear translocation (immunofluorescence), apoptosis assay","journal":"Immunity, inflammation and disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KO/KD with defined molecular pathway readout (IKK phosphorylation, p65 translocation), in vivo corroboration, single lab","pmids":["37249279"],"is_preprint":false},{"year":2024,"finding":"HOPS/TMUB1 binds mutant p53 forms (R175H, R248W, R273H) by immunoprecipitation and promotes apoptosis in p53-mutant cancer cells; the interaction with p53-mutants modulates apoptosis in a context-dependent gain- or loss-of-function manner involving TP63-dependent pathways.","method":"Immunoprecipitation (HOPS–mutant p53), apoptosis assays in SKBR3/MIA PaCa2/H1975 cells, gene expression analysis (MYC, TP63)","journal":"International journal of molecular sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP confirmed binding to mutant p53 isoforms with functional apoptosis readout, single lab","pmids":["38731819"],"is_preprint":false},{"year":2025,"finding":"PBX1 transcription factor binds the TMUB1 promoter and represses TMUB1 transcription; restoration of TMUB1 expression abolishes PBX1-mediated suppression of apoptosis, inflammation, and NF-κB signaling in LPS-treated trophoblast cells.","method":"Luciferase reporter assay (PBX1 binding to TMUB1 promoter), PBX1 overexpression, exogenous TMUB1 rescue experiment, NF-κB pathway assays","journal":"Journal of molecular histology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — luciferase reporter directly validates promoter binding, rescue experiment confirms epistasis, single lab","pmids":["39961876"],"is_preprint":false}],"current_model":"TMUB1/HOPS is an ER-resident transmembrane ubiquitin-like domain protein that functions as a multi-context regulator: in the ER it acts as a TMD-escortase that shields hydrophobic client sequences during retrotranslocation and recruits p97 for ERAD, competes with HUWE1 to protect PD-L1 from ubiquitination while recruiting STT3A to promote PD-L1 glycosylation and stability, and interacts with ERLIN1/2 scaffolds to associate with RNF170; in the cytoplasm it stabilises p53, blocks importin-α-mediated nuclear import of p53, and directs p53 to mitochondria for intrinsic apoptosis; it modulates NF-κB signalling by binding and destabilising TRAF6; in neurons it forms a complex with GluR2 and GRIP to facilitate AMPA receptor recycling to the synaptic surface; and in hepatocytes it suppresses proliferation by interacting with CAML through its TM1 domain to interrupt the CAML–cyclophilin B interaction and reduce Ca²⁺ influx, while also inhibiting STAT3 phosphorylation."},"narrative":{"mechanistic_narrative":"TMUB1 (HOPS) is an endoplasmic reticulum-resident transmembrane ubiquitin-like protein that operates at the interface of protein quality control, apoptosis, and inflammatory signalling [PMID:35961308, PMID:31867855]. In the ER membrane it functions as a transmembrane-domain escortase: it engages the exposed hydrophobic TMDs of client proteins undergoing ERAD retrotranslocation, shielding ~10–14 residues through its transmembrane and cytosolic regions, and uses its ubiquitin-like domain to recruit the p97 ATPase that extracts clients into the cytosol for proteasomal degradation [PMID:35961308]. Acting on specific ER substrates, it competes with the E3 ligase HUWE1 to protect PD-L1 from K281 polyubiquitination while recruiting STT3A to promote PD-L1 N-glycosylation and maturation, thereby supporting tumour immune evasion [PMID:36376293], and it is organized within ER ERLIN1/2 SPFH-domain scaffolds that mediate its association with RNF170, an interaction linked to hereditary spastic paraplegia [PMID:38782601]. TMUB1 also governs apoptosis through p53: it binds cytoplasmic p53, blocks importin-α-mediated nuclear import to raise cytoplasmic p53, inhibits p53 proteasomal turnover, and directs p53 to mitochondria to trigger intrinsic apoptosis, with Hops-null and haploinsufficient mice showing blunted chemotherapy- and DNA-damage-induced apoptosis [PMID:31867855, PMID:34281239]. It additionally regulates NF-κB signalling by binding and destabilising the E3 ligase TRAF6 to enhance IKK activation and p65 transcriptional output [PMID:33060567], and as a synaptic factor it complexes with GluR2 and GRIP to promote AMPA-receptor recycling to the neuronal surface [PMID:18665261]. In hepatocytes it acts as a proliferation suppressor, interacting with CAML via its TM1 domain to disrupt the CAML–cyclophilin B interaction and reduce Ca²⁺ influx, and inhibiting STAT3 phosphorylation within a STAT3-driven negative feedback loop [PMID:29967478, PMID:30610893].","teleology":[{"year":2008,"claim":"Established the first molecular function for TMUB1 outside the ER, showing it acts as a trafficking adaptor that controls synaptic receptor availability.","evidence":"Co-IP of a Tmub1–GluR2–GRIP complex from mouse brain with RNAi/overexpression, electrophysiology, and surface recycling assays","pmids":["18665261"],"confidence":"High","gaps":["Does not define which TMUB1 domain mediates GluR2/GRIP binding","Relationship to TMUB1's ER escortase role not addressed"]},{"year":2010,"claim":"Identified CAMLG as a TMUB1 partner and linked the protein to organismal physiology, opening a Ca2+-related signalling axis.","evidence":"Yeast two-hybrid screen confirmed by reciprocal Co-IP and co-localization in HEK cells, plus Tmub1 knockout mouse EEG/locomotor recordings","pmids":["20582322"],"confidence":"High","gaps":["Mechanism connecting CAML binding to the behavioral phenotype unresolved","No downstream Ca2+ effector defined here"]},{"year":2012,"claim":"Connected the TMUB1–CAML interaction to a cellular outcome, showing TMUB1 negatively controls hepatocyte proliferation.","evidence":"Co-IP, confocal co-localization, shRNA knockdown, Ca2+ influx and thymidine incorporation assays in hepatocytes","pmids":["22426572"],"confidence":"Medium","gaps":["Single lab","Domain requirement for CAML binding not yet mapped","Molecular link from CAML to proliferation incomplete"]},{"year":2018,"claim":"Mapped the structural basis of TMUB1's anti-proliferative effect to its TM1 domain and a defined biochemical mechanism.","evidence":"Co-IP with TM1 deletion mutant, Ca2+ imaging, and proliferation assays in BRL-3A cells showing TMUB1 disrupts CAML–cyclophilin B","pmids":["29967478"],"confidence":"High","gaps":["Does not show how reduced Ca2+ influx mechanistically halts the cell cycle","In vivo relevance in liver regeneration not tested here"]},{"year":2019,"claim":"Defined a major apoptotic function for TMUB1 by showing it stabilizes and relocalizes p53 to mitochondria, with in vivo confirmation.","evidence":"Reciprocal Co-IP (HOPS–p53, HOPS–importin α), mitochondrial fractionation, apoptosis assays, and Hops-/- mouse","pmids":["31867855"],"confidence":"High","gaps":["Does not resolve how a transmembrane ER protein accesses cytoplasmic p53","Whether p53 stabilization is direct or via blocked degradation not fully separated"]},{"year":2019,"claim":"Established TMUB1 as a STAT3-pathway regulator embedded in a transcriptional negative-feedback loop in hepatocytes.","evidence":"Co-IP (Tmub1–STAT3), loss/gain-of-function in Lo2 cells, partial hepatectomy model, ChIP and luciferase reporter assays","pmids":["30610893"],"confidence":"High","gaps":["Does not show how TMUB1 binding inhibits STAT3 phosphorylation mechanistically","Relationship to the CAML/Ca2+ proliferation axis unclear"]},{"year":2019,"claim":"Proposed a STAT1/CCND1 transcriptional axis for TMUB1's growth-suppressive role in hepatocellular carcinoma.","evidence":"Loss/gain-of-function in HCC cell lines with qPCR, western blot, proliferation assays, and tissue correlation","pmids":["31827061"],"confidence":"Low","gaps":["No direct TMUB1–STAT1 binding demonstrated; only expression correlation","Pathway placement relative to STAT3 regulation unresolved"]},{"year":2020,"claim":"Revealed that TMUB1 amplifies NF-κB inflammatory signalling by destabilizing the E3 ligase TRAF6.","evidence":"Co-IP (HOPS–TRAF6), Hops-/- cells, IκBα stability, NF-κB reporter assays, and cytokine measurements","pmids":["33060567"],"confidence":"High","gaps":["Mechanism of TRAF6 destabilization (ligase recruitment vs sequestration) not defined","Reconciliation with TMUB1's pro-apoptotic role left open"]},{"year":2020,"claim":"Extended TMUB1's pro-apoptotic activity in HCC by showing it drives ubiquitin-dependent degradation of ΔNp63 isoforms.","evidence":"Co-IP (Tmub1–ΔNp63), ubiquitination assay, loss/gain-of-function, xenograft, and ΔNp63 rescue experiments","pmids":["32671188"],"confidence":"High","gaps":["E3 ligase that TMUB1 recruits to ΔNp63 not identified","Link to the p53 axis not directly tested"]},{"year":2022,"claim":"Provided the defining biochemical mechanism of TMUB1 as an ER escortase coupling client TMD shielding to p97-driven retrotranslocation in ERAD.","evidence":"In vitro reconstitution, retrotranslocation intermediate trapping, domain mutagenesis, and Co-IP with p97","pmids":["35961308"],"confidence":"High","gaps":["Full client repertoire not enumerated","Selectivity rules for which TMDs are escorted not defined"]},{"year":2022,"claim":"Demonstrated a substrate-protective ER role for TMUB1, shielding PD-L1 from ubiquitination while promoting its glycosylation to enable immune evasion.","evidence":"Reciprocal Co-IP, K281 mutagenesis, competition binding, glycosylation assays, and in vivo tumor models with competing peptide","pmids":["36376293"],"confidence":"High","gaps":["How TMUB1 reconciles substrate protection here with escortase-mediated degradation elsewhere unresolved","STT3A recruitment mechanism not structurally defined"]},{"year":2021,"claim":"Confirmed gene-dosage dependence of TMUB1's p53-apoptosis function via haploinsufficiency.","evidence":"Hops heterozygous mice and MEFs with etoposide, p53 quantification, apoptosis and p53-target profiling","pmids":["34281239"],"confidence":"Medium","gaps":["Single lab","Does not address tissue specificity of haploinsufficiency"]},{"year":2021,"claim":"Described cell-cycle-dependent nucleocytoplasmic shuttling and crystallin association of TMUB1 in lens, hinting at a UPS role in differentiation.","evidence":"Immunofluorescence localization in mouse lens across cell cycle and differentiation zones","pmids":["33543240"],"confidence":"Low","gaps":["Descriptive localization without functional perturbation","Crystallin association not validated biochemically"]},{"year":2023,"claim":"Showed TMUB1 is required for IKK/NF-κB activation and inflammation in trophoblasts, consistent with its TRAF6/NF-κB role.","evidence":"TMUB1 knockdown in trophoblast cells, LPS abortion model, IKKα/β phosphorylation and p65 translocation assays","pmids":["37249279"],"confidence":"Medium","gaps":["Single lab","Does not confirm TRAF6 dependence in this cell type"]},{"year":2024,"claim":"Placed TMUB1 in an oncogenic m6A-regulated AKT ubiquitination circuit in colorectal cancer, contrasting with its tumor-suppressive liver roles.","evidence":"MeRIP-seq, Co-IP (TMUB1–AMFR–AKT), K63-ubiquitination assay, and in vivo/in vitro functional assays","pmids":["38341886"],"confidence":"Medium","gaps":["Single lab with limited orthogonal validation of K63-AKT ubiquitination","Reconciliation with growth-suppressive functions unclear"]},{"year":2024,"claim":"Defined the ER ERLIN1/2 scaffold and N-terminal luminal region that organize TMUB1–RNF170 assembly, linking the complex to hereditary spastic paraplegia.","evidence":"Co-IP, domain deletion/mutation, 3D structural modelling, proteomics, and ERLIN double-knockout phenotyping in HeLa","pmids":["38782601"],"confidence":"Medium","gaps":["Functional consequences shown in ERLIN KO rather than direct TMUB1 KO","Disease causality from TMUB1 mutation not directly demonstrated"]},{"year":2024,"claim":"Extended TMUB1's apoptotic function to mutant p53 forms, indicating context-dependent regulation through TP63 pathways.","evidence":"IP (HOPS–mutant p53 R175H/R248W/R273H), apoptosis assays, and MYC/TP63 expression analysis","pmids":["38731819"],"confidence":"Medium","gaps":["Single lab","Determinants of gain- vs loss-of-function context not defined"]},{"year":2025,"claim":"Identified PBX1 as an upstream repressor of TMUB1 transcription controlling its inflammatory/apoptotic output.","evidence":"Luciferase reporter for PBX1 binding to the TMUB1 promoter, PBX1 overexpression, and TMUB1 rescue in LPS-treated trophoblasts","pmids":["39961876"],"confidence":"Medium","gaps":["Single lab","Direct PBX1 promoter occupancy by ChIP not shown"]},{"year":null,"claim":"How TMUB1's single biochemical identity as an ER transmembrane Ub-like escortase mechanistically gives rise to its diverse cytoplasmic, mitochondrial, synaptic, and transcription-coupled functions remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model unifying the escortase, p53, and TRAF6 roles","Topology allowing an ER protein to act on cytosolic/mitochondrial p53 unexplained","Determinants of context-dependent tumor-suppressive vs oncogenic behavior unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[0,4,7,11]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,3,9]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,8,6]}],"localization":[{"term_id":"GO:0005783","term_label":"endoplasmic reticulum","supporting_discovery_ids":[0,1,9]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[2,5,10]},{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[2]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[1,0]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[2,7,14]},{"term_id":"R-HSA-162582","term_label":"Signal Transduction","supporting_discovery_ids":[4,6,15]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[0,4,15]}],"complexes":["ERLIN1/2-RNF170 ER scaffold complex","GluR2-GRIP AMPA receptor recycling complex"],"partners":["HUWE1","STT3A","P97/VCP","TP53","TRAF6","CAMLG","STAT3","ERLIN1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9BVT8","full_name":"Transmembrane and ubiquitin-like domain-containing protein 1","aliases":["Dendritic cell-derived ubiquitin-like protein","DULP","Hepatocyte odd protein shuttling protein","Ubiquitin-like protein SB144"],"length_aa":246,"mass_kda":26.3,"function":"Involved in sterol-regulated ubiquitination and degradation of HMG-CoA reductase HMGCR (PubMed:21343306). Involved in positive regulation of AMPA-selective glutamate receptor GRIA2 recycling to the cell surface (By similarity). Acts as a negative regulator of hepatocyte growth during regeneration (By similarity) May contribute to the regulation of translation during cell-cycle progression. May contribute to the regulation of cell proliferation (By similarity). May be involved in centrosome assembly. Modulates stabilization and nucleolar localization of tumor suppressor CDKN2A and enhances association between CDKN2A and NPM1 (By similarity)","subcellular_location":"Cytoplasm; Cytoplasm, cytoskeleton, microtubule organizing center, centrosome; Nucleus, nucleolus; Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9BVT8/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TMUB1","classification":"Not Classified","n_dependent_lines":0,"n_total_lines":1208,"dependency_fraction":0.0},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CCDC47","stoichiometry":4.0},{"gene":"CANX","stoichiometry":0.2},{"gene":"NECAP1","stoichiometry":0.2},{"gene":"VAPA","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/TMUB1","total_profiled":1310},"omim":[{"mim_id":"620096","title":"RING FINGER PROTEIN 185; RNF185","url":"https://www.omim.org/entry/620096"},{"mim_id":"614792","title":"TRANSMEMBRANE AND UBIQUITIN-LIKE DOMAIN-CONTAINING PROTEIN 1; TMUB1","url":"https://www.omim.org/entry/614792"},{"mim_id":"604611","title":"RECQ PROTEIN-LIKE 2; RECQL2","url":"https://www.omim.org/entry/604611"},{"mim_id":"277700","title":"WERNER SYNDROME; WRN","url":"https://www.omim.org/entry/277700"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoplasm","reliability":"Approved"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TMUB1"},"hgnc":{"alias_symbol":["SB144","HOPS"],"prev_symbol":["C7orf21"]},"alphafold":{"accession":"Q9BVT8","domains":[{"cath_id":"3.10.20.90","chopping":"102-170","consensus_level":"high","plddt":86.7899,"start":102,"end":170},{"cath_id":"1.10.12","chopping":"202-240_242-246","consensus_level":"medium","plddt":75.3514,"start":202,"end":246}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BVT8","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BVT8-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9BVT8-F1-predicted_aligned_error_v6.png","plddt_mean":65.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TMUB1","jax_strain_url":"https://www.jax.org/strain/search?query=TMUB1"},"sequence":{"accession":"Q9BVT8","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9BVT8.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9BVT8/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9BVT8"}},"corpus_meta":[{"pmid":"36376293","id":"PMC_36376293","title":"Promoting anti-tumor immunity by targeting TMUB1 to modulate PD-L1 polyubiquitination and glycosylation.","date":"2022","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/36376293","citation_count":82,"is_preprint":false},{"pmid":"31867855","id":"PMC_31867855","title":"HOPS/TMUB1 retains p53 in the cytoplasm and sustains p53-dependent mitochondrial apoptosis.","date":"2019","source":"EMBO reports","url":"https://pubmed.ncbi.nlm.nih.gov/31867855","citation_count":29,"is_preprint":false},{"pmid":"18665261","id":"PMC_18665261","title":"Transmembrane and ubiquitin-like domain-containing protein 1 (Tmub1/HOPS) facilitates surface expression of GluR2-containing AMPA receptors.","date":"2008","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/18665261","citation_count":24,"is_preprint":false},{"pmid":"35961308","id":"PMC_35961308","title":"TMUB1 is an endoplasmic reticulum-resident escortase that promotes the p97-mediated extraction of membrane proteins for degradation.","date":"2022","source":"Molecular cell","url":"https://pubmed.ncbi.nlm.nih.gov/35961308","citation_count":20,"is_preprint":false},{"pmid":"22426572","id":"PMC_22426572","title":"IL-6 induction of hepatocyte proliferation through the Tmub1-regulated gene pathway.","date":"2012","source":"International journal of molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/22426572","citation_count":18,"is_preprint":false},{"pmid":"20582322","id":"PMC_20582322","title":"Transmembrane and ubiquitin-like domain containing 1 (Tmub1) regulates locomotor activity and wakefulness in mice and interacts with CAMLG.","date":"2010","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/20582322","citation_count":17,"is_preprint":false},{"pmid":"33060567","id":"PMC_33060567","title":"HOPS/Tmub1 involvement in the NF-kB-mediated inflammatory response through the modulation of TRAF6.","date":"2020","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/33060567","citation_count":16,"is_preprint":false},{"pmid":"38341886","id":"PMC_38341886","title":"Nicotine-derived NNK promotes CRC progression through activating TMUB1/AKT pathway in METTL14/YTHDF2-mediated m6A manner.","date":"2024","source":"Journal of hazardous materials","url":"https://pubmed.ncbi.nlm.nih.gov/38341886","citation_count":15,"is_preprint":false},{"pmid":"30610893","id":"PMC_30610893","title":"Tmub1 negatively regulates liver regeneration via inhibiting STAT3 phosphorylation.","date":"2019","source":"Cellular signalling","url":"https://pubmed.ncbi.nlm.nih.gov/30610893","citation_count":14,"is_preprint":false},{"pmid":"31827061","id":"PMC_31827061","title":"Transmembrane and Ubiquitin-Like Domain Containing 1 Protein (TMUB1) Negatively Regulates Hepatocellular Carcinoma Proliferation via Regulating Signal Transducer and Activator of Transcription 1 (STAT1).","date":"2019","source":"Medical science monitor : international medical journal of experimental and clinical research","url":"https://pubmed.ncbi.nlm.nih.gov/31827061","citation_count":14,"is_preprint":false},{"pmid":"37249279","id":"PMC_37249279","title":"Inhibition of TMUB1 blocks apoptosis and NF-κB pathway-mediated inflammation in recurrent spontaneous abortion.","date":"2023","source":"Immunity, inflammation and disease","url":"https://pubmed.ncbi.nlm.nih.gov/37249279","citation_count":13,"is_preprint":false},{"pmid":"32860479","id":"PMC_32860479","title":"The Ins and Outs of HOPS/TMUB1 in biology and pathology.","date":"2020","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/32860479","citation_count":12,"is_preprint":false},{"pmid":"29777440","id":"PMC_29777440","title":"MiR-27a/b Regulates Liver Regeneration by Posttranscriptional Modification of Tmub1.","date":"2018","source":"Digestive diseases and sciences","url":"https://pubmed.ncbi.nlm.nih.gov/29777440","citation_count":12,"is_preprint":false},{"pmid":"32671188","id":"PMC_32671188","title":"Tmub1 Suppresses Hepatocellular Carcinoma by Promoting the Ubiquitination of ΔNp63 Isoforms.","date":"2020","source":"Molecular therapy oncolytics","url":"https://pubmed.ncbi.nlm.nih.gov/32671188","citation_count":12,"is_preprint":false},{"pmid":"38782601","id":"PMC_38782601","title":"ERLIN1/2 scaffolds bridge TMUB1 and RNF170 and restrict cholesterol esterification to regulate the secretory pathway.","date":"2024","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/38782601","citation_count":6,"is_preprint":false},{"pmid":"34281239","id":"PMC_34281239","title":"Hops/Tmub1 Heterozygous Mouse Shows Haploinsufficiency Effect in Influencing p53-Mediated Apoptosis.","date":"2021","source":"International journal of molecular 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competition binding assays, glycosylation assays, in vivo tumor models with synthetic competing peptide\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, mutagenesis of specific ubiquitination site, multiple orthogonal functional assays, in vivo validation\",\n      \"pmids\": [\"36376293\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"TMUB1 is an ER-resident escortase that interacts with transmembrane domains (TMDs) of client proteins undergoing ERAD retrotranslocation, shielding ~10–14 hydrophobic residues exposed out of the membrane via its transmembrane and cytosolic regions, and recruits p97 via its ubiquitin-like domain to pull client TMDs into the cytosol for proteasomal degradation.\",\n      \"method\": \"In vitro reconstitution, biochemical retrotranslocation assays, domain mutagenesis, trapping of retrotranslocation intermediates, co-immunoprecipitation with p97\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstitution of escortase activity, domain mutagenesis, multiple orthogonal biochemical assays in a single rigorous study\",\n      \"pmids\": [\"35961308\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"HOPS/TMUB1 binds p53 in the cytoplasm, inhibits its proteasomal degradation, interferes with importin α to increase cytoplasmic p53 levels, and promotes p53 recruitment to mitochondria to induce the intrinsic apoptosis pathway; Hops−/− mice show significantly reduced apoptosis after chemotherapy.\",\n      \"method\": \"Co-immunoprecipitation (HOPS–p53 and HOPS–importin α), Hops knockout mouse model, apoptosis assays, mitochondrial fractionation\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP, in vivo knockout mouse, multiple orthogonal assays across multiple cell types\",\n      \"pmids\": [\"31867855\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Tmub1/HOPS facilitates recycling of GluR2-containing AMPA receptors to the synaptic surface by forming a complex with GluR2 and GRIP; RNAi knockdown of Tmub1 reduces AMPAR currents and synaptic surface GluR2, while overexpression increases surface GluR2.\",\n      \"method\": \"Co-immunoprecipitation from mouse brain (Tmub1–GluR2–GRIP complex), RNAi knockdown in neurons, electrophysiology (AMPAR current), surface recycling assay, EGFP-Tmub1 overexpression\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP from native tissue, loss- and gain-of-function with electrophysiological and biochemical readouts, recycling assay\",\n      \"pmids\": [\"18665261\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"HOPS/TMUB1 directly binds the E3 ubiquitin ligase TRAF6, reducing TRAF6 stability and thereby increasing IKK complex activation, which destabilizes IκBα and enhances NF-κB (p65/RelA) transcriptional activity; Hops−/− cells show impaired pro-inflammatory responses.\",\n      \"method\": \"Co-immunoprecipitation (HOPS–TRAF6), Hops knockout cells, IκBα stability assays, NF-κB transcriptional reporter assays, inflammatory cytokine measurements\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct binding demonstrated by Co-IP, KO cells with multiple downstream readouts, multiple orthogonal methods\",\n      \"pmids\": [\"33060567\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"Tmub1 binds to CAMLG (calcium-modulating cyclophilin ligand) as confirmed by yeast two-hybrid screen and co-immunoprecipitation in HEK cells; the two proteins co-localize in the cytoplasm; Tmub1 knockout mice exhibit increased wakefulness and locomotor activity during the dark phase.\",\n      \"method\": \"Yeast two-hybrid screen, co-immunoprecipitation in HEK cells, co-localization (fluorescence microscopy), Tmub1 knockout mouse with EEG/telemetric locomotor recording\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — yeast two-hybrid confirmed by reciprocal Co-IP, in vivo KO mouse with EEG and telemetric readouts\",\n      \"pmids\": [\"20582322\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Tmub1 inhibits STAT3 phosphorylation and STAT3 signaling in hepatocytes; co-immunoprecipitation demonstrates direct interaction between Tmub1 and STAT3; chromatin immunoprecipitation and luciferase assays show STAT3 binds the Tmub1 promoter, suggesting a negative feedback loop.\",\n      \"method\": \"Co-immunoprecipitation (Tmub1–STAT3), loss- and gain-of-function in Lo2 cells, partial hepatectomy mouse model, chromatin immunoprecipitation, luciferase reporter assay\",\n      \"journal\": \"Cellular signalling\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP, in vivo mouse model, ChIP, reporter assay — multiple orthogonal methods in one study\",\n      \"pmids\": [\"30610893\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Tmub1 forms a protein complex with ΔNp63 isoforms (ΔNp63α, β, γ) and promotes their ubiquitination and proteasomal degradation, thereby inducing apoptosis in hepatocellular carcinoma cells.\",\n      \"method\": \"Co-immunoprecipitation (Tmub1–ΔNp63), ubiquitination assay, loss- and gain-of-function (Hep3B and MHCC-LM3 cells), xenograft growth assay, rescue experiments with ΔNp63 overexpression\",\n      \"journal\": \"Molecular therapy oncolytics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — Co-IP, ubiquitination assay, in vivo xenograft, rescue experiments provide multiple orthogonal lines of evidence\",\n      \"pmids\": [\"32671188\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"TMUB1 interacts with CAML via its TM1 hydrophobic domain; overexpression of TMUB1 abolishes the interaction between CAML and cyclophilin B, reducing intracellular Ca2+ influx and inhibiting hepatocyte proliferation; deletion of TM1 abolishes these effects.\",\n      \"method\": \"Co-immunoprecipitation in BRL-3A cells, TM1 domain deletion mutant, Ca2+ influx assay (fluorescence microscopy), hepatocyte proliferation assay\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — domain mutagenesis combined with Co-IP, Ca2+ imaging, and functional proliferation assays in a single study\",\n      \"pmids\": [\"29967478\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"ERLIN1/2 scaffolds mediate the interaction between the full-length isoform of TMUB1 and RNF170; a luminal N-terminal conserved region in TMUB1 (and RNF170) is required for binding to the SPFH domain of adjacent ERLIN subunits; disruption of this interaction is linked to hereditary spastic paraplegia.\",\n      \"method\": \"Co-immunoprecipitation, domain deletion/mutation analysis, 3D structural modelling, proteomics (omics-based), HeLa ERLIN double-knockout phenotypic characterization\",\n      \"journal\": \"Life science alliance\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with domain mapping and structural modelling, single lab, functional consequences shown in ERLIN KO rather than direct TMUB1 KO\",\n      \"pmids\": [\"38782601\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Tmub1 co-localizes with CAML in the hepatocellular cytoplasm; Tmub1 knockdown upregulates CAML protein expression and alters Ca2+ influx; Tmub1 plays a negative role in IL-6-induced hepatocyte proliferation through its interaction with CAML.\",\n      \"method\": \"Co-immunoprecipitation, laser scanning confocal microscopy (co-localization), shRNA knockdown, Ca2+ influx assay, [3H]-thymidine incorporation proliferation assay\",\n      \"journal\": \"International journal of molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP confirmed interaction, multiple assays but single lab and partial mechanistic follow-up\",\n      \"pmids\": [\"22426572\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NNK promotes TMUB1 upregulation via METTL14/YTHDF2-mediated m6A modification; elevated TMUB1 interacts with AMFR to promote K63-linked ubiquitination of AKT, leading to malignant proliferation and metastasis in colorectal cancer cells.\",\n      \"method\": \"Methylated RNA immunoprecipitation sequencing, co-immunoprecipitation (TMUB1–AMFR–AKT), ubiquitination assay (K63-linkage), in vivo and in vitro functional assays\",\n      \"journal\": \"Journal of hazardous materials\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and ubiquitination assay demonstrate mechanism, but single lab with limited orthogonal validation of the specific AKT K63-ubiquitination claim\",\n      \"pmids\": [\"38341886\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TMUB1 promotes STAT1 expression in hepatocellular carcinoma cells and suppresses CCND1, negatively regulating HCC cell proliferation; TMUB1 expression is positively correlated with STAT1 in HCC tissues.\",\n      \"method\": \"Loss- and gain-of-function in HCC cell lines, qPCR, western blotting, CCK-8 and EdU proliferation assays\",\n      \"journal\": \"Medical science monitor\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, no direct binding assay between TMUB1 and STAT1 shown, only expression-level correlation and loss/gain-of-function without pathway placement\",\n      \"pmids\": [\"31827061\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"HOPS/TMUB1 shuttles between nucleus and cytoplasm during the cell cycle in lens cells; it localizes mainly to the nucleus of central epithelial cells and moves to cytoplasm during mitosis, returning to nucleus post-mitosis; in differentiating fiber cells it associates with crystallin proteins, possibly acting in the ubiquitin-proteasome system.\",\n      \"method\": \"Immunofluorescence localization in mouse lens tissue across cell cycle stages and differentiation zones\",\n      \"journal\": \"Bioscience reports\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — localization by immunofluorescence without direct functional consequence testing, single descriptive study\",\n      \"pmids\": [\"33543240\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Hops heterozygous mice and mouse embryonic fibroblasts show impaired apoptotic response to etoposide-induced DNA damage, with reduced p53 protein levels and reduced percentage of apoptotic cells, demonstrating haploinsufficiency of HOPS in supporting p53-dependent DNA damage responses.\",\n      \"method\": \"Hops heterozygous mouse model, etoposide treatment, p53 protein quantification (western blot), apoptosis assay, p53-target gene expression profiling\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — in vivo haploinsufficiency model with defined molecular and cellular readouts, single lab\",\n      \"pmids\": [\"34281239\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"TMUB1 deficiency in LPS-stimulated trophoblast cells suppresses phosphorylation of IKKα/β and blocks cytoplasmic-to-nuclear translocation of NF-κB p65, inhibiting apoptosis and NF-κB-mediated inflammation.\",\n      \"method\": \"TMUB1 knockdown in human chorionic trophoblast cells, LPS-induced mouse abortion model, IKKα/β phosphorylation assay, NF-κB p65 nuclear translocation (immunofluorescence), apoptosis assay\",\n      \"journal\": \"Immunity, inflammation and disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KO/KD with defined molecular pathway readout (IKK phosphorylation, p65 translocation), in vivo corroboration, single lab\",\n      \"pmids\": [\"37249279\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"HOPS/TMUB1 binds mutant p53 forms (R175H, R248W, R273H) by immunoprecipitation and promotes apoptosis in p53-mutant cancer cells; the interaction with p53-mutants modulates apoptosis in a context-dependent gain- or loss-of-function manner involving TP63-dependent pathways.\",\n      \"method\": \"Immunoprecipitation (HOPS–mutant p53), apoptosis assays in SKBR3/MIA PaCa2/H1975 cells, gene expression analysis (MYC, TP63)\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP confirmed binding to mutant p53 isoforms with functional apoptosis readout, single lab\",\n      \"pmids\": [\"38731819\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"PBX1 transcription factor binds the TMUB1 promoter and represses TMUB1 transcription; restoration of TMUB1 expression abolishes PBX1-mediated suppression of apoptosis, inflammation, and NF-κB signaling in LPS-treated trophoblast cells.\",\n      \"method\": \"Luciferase reporter assay (PBX1 binding to TMUB1 promoter), PBX1 overexpression, exogenous TMUB1 rescue experiment, NF-κB pathway assays\",\n      \"journal\": \"Journal of molecular histology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — luciferase reporter directly validates promoter binding, rescue experiment confirms epistasis, single lab\",\n      \"pmids\": [\"39961876\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TMUB1/HOPS is an ER-resident transmembrane ubiquitin-like domain protein that functions as a multi-context regulator: in the ER it acts as a TMD-escortase that shields hydrophobic client sequences during retrotranslocation and recruits p97 for ERAD, competes with HUWE1 to protect PD-L1 from ubiquitination while recruiting STT3A to promote PD-L1 glycosylation and stability, and interacts with ERLIN1/2 scaffolds to associate with RNF170; in the cytoplasm it stabilises p53, blocks importin-α-mediated nuclear import of p53, and directs p53 to mitochondria for intrinsic apoptosis; it modulates NF-κB signalling by binding and destabilising TRAF6; in neurons it forms a complex with GluR2 and GRIP to facilitate AMPA receptor recycling to the synaptic surface; and in hepatocytes it suppresses proliferation by interacting with CAML through its TM1 domain to interrupt the CAML–cyclophilin B interaction and reduce Ca²⁺ influx, while also inhibiting STAT3 phosphorylation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TMUB1 (HOPS) is an endoplasmic reticulum-resident transmembrane ubiquitin-like protein that operates at the interface of protein quality control, apoptosis, and inflammatory signalling [#1, #2]. In the ER membrane it functions as a transmembrane-domain escortase: it engages the exposed hydrophobic TMDs of client proteins undergoing ERAD retrotranslocation, shielding ~10\\u201314 residues through its transmembrane and cytosolic regions, and uses its ubiquitin-like domain to recruit the p97 ATPase that extracts clients into the cytosol for proteasomal degradation [#1]. Acting on specific ER substrates, it competes with the E3 ligase HUWE1 to protect PD-L1 from K281 polyubiquitination while recruiting STT3A to promote PD-L1 N-glycosylation and maturation, thereby supporting tumour immune evasion [#0], and it is organized within ER ERLIN1/2 SPFH-domain scaffolds that mediate its association with RNF170, an interaction linked to hereditary spastic paraplegia [#9]. TMUB1 also governs apoptosis through p53: it binds cytoplasmic p53, blocks importin-\\u03b1-mediated nuclear import to raise cytoplasmic p53, inhibits p53 proteasomal turnover, and directs p53 to mitochondria to trigger intrinsic apoptosis, with Hops-null and haploinsufficient mice showing blunted chemotherapy- and DNA-damage-induced apoptosis [#2, #14]. It additionally regulates NF-\\u03baB signalling by binding and destabilising the E3 ligase TRAF6 to enhance IKK activation and p65 transcriptional output [#4], and as a synaptic factor it complexes with GluR2 and GRIP to promote AMPA-receptor recycling to the neuronal surface [#3]. In hepatocytes it acts as a proliferation suppressor, interacting with CAML via its TM1 domain to disrupt the CAML\\u2013cyclophilin B interaction and reduce Ca\\u00b2\\u207a influx, and inhibiting STAT3 phosphorylation within a STAT3-driven negative feedback loop [#8, #6].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Established the first molecular function for TMUB1 outside the ER, showing it acts as a trafficking adaptor that controls synaptic receptor availability.\",\n      \"evidence\": \"Co-IP of a Tmub1\\u2013GluR2\\u2013GRIP complex from mouse brain with RNAi/overexpression, electrophysiology, and surface recycling assays\",\n      \"pmids\": [\"18665261\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not define which TMUB1 domain mediates GluR2/GRIP binding\", \"Relationship to TMUB1's ER escortase role not addressed\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Identified CAMLG as a TMUB1 partner and linked the protein to organismal physiology, opening a Ca2+-related signalling axis.\",\n      \"evidence\": \"Yeast two-hybrid screen confirmed by reciprocal Co-IP and co-localization in HEK cells, plus Tmub1 knockout mouse EEG/locomotor recordings\",\n      \"pmids\": [\"20582322\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism connecting CAML binding to the behavioral phenotype unresolved\", \"No downstream Ca2+ effector defined here\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Connected the TMUB1\\u2013CAML interaction to a cellular outcome, showing TMUB1 negatively controls hepatocyte proliferation.\",\n      \"evidence\": \"Co-IP, confocal co-localization, shRNA knockdown, Ca2+ influx and thymidine incorporation assays in hepatocytes\",\n      \"pmids\": [\"22426572\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Domain requirement for CAML binding not yet mapped\", \"Molecular link from CAML to proliferation incomplete\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Mapped the structural basis of TMUB1's anti-proliferative effect to its TM1 domain and a defined biochemical mechanism.\",\n      \"evidence\": \"Co-IP with TM1 deletion mutant, Ca2+ imaging, and proliferation assays in BRL-3A cells showing TMUB1 disrupts CAML\\u2013cyclophilin B\",\n      \"pmids\": [\"29967478\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not show how reduced Ca2+ influx mechanistically halts the cell cycle\", \"In vivo relevance in liver regeneration not tested here\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined a major apoptotic function for TMUB1 by showing it stabilizes and relocalizes p53 to mitochondria, with in vivo confirmation.\",\n      \"evidence\": \"Reciprocal Co-IP (HOPS\\u2013p53, HOPS\\u2013importin \\u03b1), mitochondrial fractionation, apoptosis assays, and Hops-/- mouse\",\n      \"pmids\": [\"31867855\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not resolve how a transmembrane ER protein accesses cytoplasmic p53\", \"Whether p53 stabilization is direct or via blocked degradation not fully separated\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Established TMUB1 as a STAT3-pathway regulator embedded in a transcriptional negative-feedback loop in hepatocytes.\",\n      \"evidence\": \"Co-IP (Tmub1\\u2013STAT3), loss/gain-of-function in Lo2 cells, partial hepatectomy model, ChIP and luciferase reporter assays\",\n      \"pmids\": [\"30610893\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Does not show how TMUB1 binding inhibits STAT3 phosphorylation mechanistically\", \"Relationship to the CAML/Ca2+ proliferation axis unclear\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Proposed a STAT1/CCND1 transcriptional axis for TMUB1's growth-suppressive role in hepatocellular carcinoma.\",\n      \"evidence\": \"Loss/gain-of-function in HCC cell lines with qPCR, western blot, proliferation assays, and tissue correlation\",\n      \"pmids\": [\"31827061\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct TMUB1\\u2013STAT1 binding demonstrated; only expression correlation\", \"Pathway placement relative to STAT3 regulation unresolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Revealed that TMUB1 amplifies NF-\\u03baB inflammatory signalling by destabilizing the E3 ligase TRAF6.\",\n      \"evidence\": \"Co-IP (HOPS\\u2013TRAF6), Hops-/- cells, I\\u03baB\\u03b1 stability, NF-\\u03baB reporter assays, and cytokine measurements\",\n      \"pmids\": [\"33060567\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of TRAF6 destabilization (ligase recruitment vs sequestration) not defined\", \"Reconciliation with TMUB1's pro-apoptotic role left open\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Extended TMUB1's pro-apoptotic activity in HCC by showing it drives ubiquitin-dependent degradation of \\u0394Np63 isoforms.\",\n      \"evidence\": \"Co-IP (Tmub1\\u2013\\u0394Np63), ubiquitination assay, loss/gain-of-function, xenograft, and \\u0394Np63 rescue experiments\",\n      \"pmids\": [\"32671188\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"E3 ligase that TMUB1 recruits to \\u0394Np63 not identified\", \"Link to the p53 axis not directly tested\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Provided the defining biochemical mechanism of TMUB1 as an ER escortase coupling client TMD shielding to p97-driven retrotranslocation in ERAD.\",\n      \"evidence\": \"In vitro reconstitution, retrotranslocation intermediate trapping, domain mutagenesis, and Co-IP with p97\",\n      \"pmids\": [\"35961308\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full client repertoire not enumerated\", \"Selectivity rules for which TMDs are escorted not defined\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Demonstrated a substrate-protective ER role for TMUB1, shielding PD-L1 from ubiquitination while promoting its glycosylation to enable immune evasion.\",\n      \"evidence\": \"Reciprocal Co-IP, K281 mutagenesis, competition binding, glycosylation assays, and in vivo tumor models with competing peptide\",\n      \"pmids\": [\"36376293\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How TMUB1 reconciles substrate protection here with escortase-mediated degradation elsewhere unresolved\", \"STT3A recruitment mechanism not structurally defined\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Confirmed gene-dosage dependence of TMUB1's p53-apoptosis function via haploinsufficiency.\",\n      \"evidence\": \"Hops heterozygous mice and MEFs with etoposide, p53 quantification, apoptosis and p53-target profiling\",\n      \"pmids\": [\"34281239\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Does not address tissue specificity of haploinsufficiency\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Described cell-cycle-dependent nucleocytoplasmic shuttling and crystallin association of TMUB1 in lens, hinting at a UPS role in differentiation.\",\n      \"evidence\": \"Immunofluorescence localization in mouse lens across cell cycle and differentiation zones\",\n      \"pmids\": [\"33543240\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Descriptive localization without functional perturbation\", \"Crystallin association not validated biochemically\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Showed TMUB1 is required for IKK/NF-\\u03baB activation and inflammation in trophoblasts, consistent with its TRAF6/NF-\\u03baB role.\",\n      \"evidence\": \"TMUB1 knockdown in trophoblast cells, LPS abortion model, IKK\\u03b1/\\u03b2 phosphorylation and p65 translocation assays\",\n      \"pmids\": [\"37249279\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Does not confirm TRAF6 dependence in this cell type\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Placed TMUB1 in an oncogenic m6A-regulated AKT ubiquitination circuit in colorectal cancer, contrasting with its tumor-suppressive liver roles.\",\n      \"evidence\": \"MeRIP-seq, Co-IP (TMUB1\\u2013AMFR\\u2013AKT), K63-ubiquitination assay, and in vivo/in vitro functional assays\",\n      \"pmids\": [\"38341886\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab with limited orthogonal validation of K63-AKT ubiquitination\", \"Reconciliation with growth-suppressive functions unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Defined the ER ERLIN1/2 scaffold and N-terminal luminal region that organize TMUB1\\u2013RNF170 assembly, linking the complex to hereditary spastic paraplegia.\",\n      \"evidence\": \"Co-IP, domain deletion/mutation, 3D structural modelling, proteomics, and ERLIN double-knockout phenotyping in HeLa\",\n      \"pmids\": [\"38782601\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequences shown in ERLIN KO rather than direct TMUB1 KO\", \"Disease causality from TMUB1 mutation not directly demonstrated\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Extended TMUB1's apoptotic function to mutant p53 forms, indicating context-dependent regulation through TP63 pathways.\",\n      \"evidence\": \"IP (HOPS\\u2013mutant p53 R175H/R248W/R273H), apoptosis assays, and MYC/TP63 expression analysis\",\n      \"pmids\": [\"38731819\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Determinants of gain- vs loss-of-function context not defined\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Identified PBX1 as an upstream repressor of TMUB1 transcription controlling its inflammatory/apoptotic output.\",\n      \"evidence\": \"Luciferase reporter for PBX1 binding to the TMUB1 promoter, PBX1 overexpression, and TMUB1 rescue in LPS-treated trophoblasts\",\n      \"pmids\": [\"39961876\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab\", \"Direct PBX1 promoter occupancy by ChIP not shown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TMUB1's single biochemical identity as an ER transmembrane Ub-like escortase mechanistically gives rise to its diverse cytoplasmic, mitochondrial, synaptic, and transcription-coupled functions remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model unifying the escortase, p53, and TRAF6 roles\", \"Topology allowing an ER protein to act on cytosolic/mitochondrial p53 unexplained\", \"Determinants of context-dependent tumor-suppressive vs oncogenic behavior unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [0, 4, 7, 11]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 3, 9]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 8, 6]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005783\", \"supporting_discovery_ids\": [0, 1, 9]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [2, 5, 10]},\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [1, 0]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [2, 7, 14]},\n      {\"term_id\": \"R-HSA-162582\", \"supporting_discovery_ids\": [4, 6, 15]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [0, 4, 15]}\n    ],\n    \"complexes\": [\"ERLIN1/2-RNF170 ER scaffold complex\", \"GluR2-GRIP AMPA receptor recycling complex\"],\n    \"partners\": [\"HUWE1\", \"STT3A\", \"p97/VCP\", \"TP53\", \"TRAF6\", \"CAMLG\", \"STAT3\", \"ERLIN1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}