{"gene":"NUB1","run_date":"2026-06-10T05:19:52","timeline":{"discoveries":[{"year":2001,"finding":"NUB1 was identified as an interferon-inducible protein that interacts with NEDD8 (ubiquitin-like protein) via yeast two-hybrid screening and down-regulates NEDD8 expression through a post-transcriptional mechanism. NUB1 is predominantly localized in the nucleus and overexpression causes severe reduction of NEDD8 monomer and conjugates.","method":"Yeast two-hybrid screening, western blot, overexpression in U2OS cells","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — yeast two-hybrid plus biochemical overexpression assays in a single lab, two orthogonal methods","pmids":["11259415"],"is_preprint":false},{"year":2001,"finding":"NUB1 possesses a ubiquitin-like (UBL) domain at its N-terminus and binds to S5a (PSMD4) of the 19S proteasome (PA700). GST pull-down assays showed that NUB1 overexpression increases precipitation of NEDD8 conjugates with GST-S5a, and proteasome inhibitors block NUB1-mediated down-regulation of NEDD8 — indicating NUB1 acts as an adaptor that recruits NEDD8 and its conjugates to the proteasome for degradation.","method":"GST pull-down assay, proteasome inhibitor treatment, overexpression studies","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal pulldown plus inhibitor experiments, replicated across two papers from the same group with orthogonal methods","pmids":["11585840"],"is_preprint":false},{"year":2003,"finding":"A splicing variant of NUB1, NUB1L, possesses an additional 14-amino-acid insertion encoding a UBA domain, giving it an extra NEDD8-binding site. Mutational studies identified a conserved sequence A(X4)L(X10)L(X3)L in NEDD8-binding sites where at least three Leu residues are required for NEDD8 binding. The C-terminal NEDD8-binding site of both NUB1 and NUB1L is primarily responsible for down-regulation of NEDD8, while the UBA2 domain of NUB1L is minimally or not involved in this activity.","method":"Mutagenesis, structural/domain analysis, functional down-regulation assays","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1 / Moderate — mutagenesis with functional validation, single lab but multiple orthogonal approaches (binding assay + functional down-regulation)","pmids":["12816948"],"is_preprint":false},{"year":2002,"finding":"NUB1 physically interacts with AIPL1 (aryl hydrocarbon receptor-interacting protein-like 1), as demonstrated by yeast two-hybrid and co-immunoprecipitation in Y79 retinoblastoma cells.","method":"Yeast two-hybrid, co-immunoprecipitation in Y79 cells","journal":"Human molecular genetics","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP confirmed the yeast two-hybrid hit in a relevant cell line, single lab","pmids":["12374762"],"is_preprint":false},{"year":2004,"finding":"AIPL1 modulates the nuclear translocation of NUB1: co-transfection of AIPL1 with GFP-NUB1 shifted NUB1 distribution toward the cytoplasm. AIPL1 also suppressed inclusion formation by NUB1 fragments in a chaperone-like manner. C-terminal truncation of AIPL1 abolished this effect, and the interaction requires residues 181–330 of AIPL1.","method":"Co-transfection with GFP-fusion proteins, fluorescence imaging, domain deletion analysis","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — live imaging localization with functional consequence (inclusion suppression) and domain mapping, single lab","pmids":["15347646"],"is_preprint":false},{"year":2004,"finding":"Several LCA-associated mutations of AIPL1 located between residues 181–330 abolish interaction with NUB1 as demonstrated by three independent interaction assays, while other AIPL1 mutants retain NUB1 binding.","method":"Three independent interaction assays (yeast two-hybrid, co-IP, and in vitro binding)","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — three orthogonal interaction assays in a single study, single lab","pmids":["15081406"],"is_preprint":false},{"year":2005,"finding":"NUB1 directly interacts with the proteasome subunit S5a through its C-terminal region (residues 536–584), NOT through its UBL domain. The UBL domain is not an S5a-binding motif in NUB1 but is required for NUB1 function.","method":"In vitro GST pull-down assay, yeast two-hybrid assay, deletion mapping","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — in vitro GST pulldown plus yeast two-hybrid with deletion mapping, single lab, two orthogonal methods","pmids":["16171779"],"is_preprint":false},{"year":2006,"finding":"NUB1 physically interacts with synphilin-1 through its NEDD8-binding site and promotes proteasomal degradation of synphilin-1. Overexpression of NUB1 suppresses formation of synphilin-1-positive inclusions in HEK293 cells, and this effect is blocked by proteasome inhibitors.","method":"Co-transfection/co-immunoprecipitation, biochemical proteasome inhibitor assay, inclusion formation assay in HEK293 cells","journal":"The American journal of pathology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — co-IP plus functional proteasomal degradation assay with inhibitor validation, single lab, two orthogonal methods","pmids":["16877356"],"is_preprint":false},{"year":2009,"finding":"FAT10-mediated proteasomal degradation occurs independently of polyubiquitylation: purified 26S proteasome degraded FAT10-DHFR but not ubiquitin-DHFR in vitro. Critically, degradation of FAT10-DHFR by the 26S proteasome required NUB1L; knockdown of NUB1L attenuated FAT10-DHFR degradation in intact cells.","method":"In vitro reconstituted degradation assay with purified 26S proteasome, siRNA knockdown in cells","journal":"FEBS letters","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstituted in vitro degradation assay plus siRNA confirmation in cells, single lab but two orthogonal methods","pmids":["19166848"],"is_preprint":false},{"year":2010,"finding":"NUB1 controls the subcellular localization of p53: NUB1 expression leads to decreased NEDDylation of p53, stimulation of p53 ubiquitination by Mdm2, and cytoplasmic localization of p53 with inhibition of its transcriptional activity. This requires cooperation between NEDD8 and ubiquitin pathways.","method":"Overexpression, co-immunoprecipitation, subcellular fractionation/imaging, transcription reporter assays","journal":"Oncogene","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple methods (localization, ubiquitination assays, transcriptional readout) in a single lab","pmids":["20101219"],"is_preprint":false},{"year":2012,"finding":"NUB1L and FAT10 bind to the 26S proteasome via the VWA domain of hRpn10/S5a; NUB1L can also bind Rpn1/S2. Depletion of hRpn10 in human cells causes accumulation of FAT10-conjugates. Functional reconstitution in Rpn10-deficient yeast showed the VWA domain of hRpn10 suffices for FAT10 degradation.","method":"Co-IP, yeast functional complementation, siRNA knockdown, domain mapping","journal":"Nature communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, yeast complementation, and siRNA knockdown all in one study, multiple orthogonal methods","pmids":["22434192"],"is_preprint":false},{"year":2012,"finding":"NUB1 interacts with both tau and GSK3β, disrupts their interaction, abolishes recruitment of GSK3β to tau inclusions, reduces GSK3β-mediated phosphorylation of tau, and promotes GSK3β degradation. The UBL domain of NUB1 is required for GSK3β degradation but not for the interaction with tau/GSK3β. The UBA domain is required for NUB1 to interact with and degrade GSK3β and suppress tau aggregation. NUB1 silencing stabilizes endogenous GSK3β and exacerbates tau phosphorylation.","method":"Co-immunoprecipitation, domain deletion mutagenesis, siRNA silencing, tau aggregation assay, phosphorylation assays","journal":"Human molecular genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal co-IP, domain mutants, siRNA knockdown, multiple functional readouts in one study","pmids":["22965877"],"is_preprint":false},{"year":2013,"finding":"NUB1 overexpression reduces mutant huntingtin (mHTT) levels by enhancing polyubiquitination and proteasomal degradation of mHTT. This process requires CUL3 and NEDD8 (required for CUL3 activation). Interferon-β lowers mHTT and rescues neuronal toxicity through induction of NUB1.","method":"Genome-wide RNAi screen, Drosophila in vivo validation, proteasome inhibitor studies, ubiquitination assays in neuronal models","journal":"Nature neuroscience","confidence":"High","confidence_rationale":"Tier 2 / Strong — genome-wide screen followed by in vivo Drosophila validation and mechanistic biochemical assays, replicated across multiple model systems","pmids":["23525043"],"is_preprint":false},{"year":2013,"finding":"NUB1L promotes transfer of NEDD8 to the proteasome for degradation by directly recognizing NEDD8 at its key residue Asn-51 and interacting with P97/VCP via a positively charged VCP-binding motif. NUB1L coordinates with the P97-UFD1-NPL4 complex for NEDD8 delivery to the proteasome. NUB1L does not interact with ubiquitin.","method":"Co-immunoprecipitation, mutagenesis (Asn-51), in vitro binding assays","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — mutagenesis identifying a key residue plus co-IP validation, single lab, two orthogonal methods","pmids":["24019527"],"is_preprint":false},{"year":2015,"finding":"NUB1L suppresses atypical neddylation (ubiquitin enzyme-mediated NEDD8 conjugation) and promotes degradation of misfolded proteins by the proteasome. Loss of NUB1L exaggerates atypical neddylation; NUB1L overexpression represses it via promoting NEDD8 degradation. NUB1L depletion accumulates the cardiomyopathy-linked misfolded protein CryAB(R120G), and NUB1L overexpression promotes its degradation by suppressing neddylation of ubiquitinated proteins.","method":"siRNA knockdown, overexpression, GFPu degradation assay, western blotting in cardiomyocytes","journal":"The Journal of biological chemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function and gain-of-function with specific substrate readouts, single lab, multiple conditions tested","pmids":["26260793"],"is_preprint":false},{"year":2017,"finding":"Mdm2 E3 ubiquitin ligase is a NUB1-interacting protein that induces non-proteolytic di-ubiquitination of NUB1 specifically on lysine 159. This di-ubiquitination positively regulates NUB1 function: mutation of Lys-159 to Arg impairs NUB1's negative regulation of Nedd8 and neddylated proteins. Mdm2 thus acts as a positive regulator of NUB1.","method":"Co-immunoprecipitation, site-directed mutagenesis (K159R), ubiquitination assays","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — site-directed mutagenesis with functional readout plus co-IP, single lab, two orthogonal methods","pmids":["28099510"],"is_preprint":false},{"year":2019,"finding":"Phosphorylation of NUB1 at serine 46 (P-NUB46) creates a phosphomimetic mutant that more efficiently degrades aggregates in a cell-based assay. Antibodies specific to P-NUB46 react with Lewy bodies in PD/DLB but not with glial cytoplasmic inclusions in MSA, indicating phosphorylation modulates NUB1 activity during synucleinopathy pathology.","method":"Phosphomimetic mutagenesis, cell-based aggregate degradation assay, immunohistochemistry","journal":"Brain pathology (Zurich, Switzerland)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — mutagenesis with functional readout (aggregate degradation) and disease-relevant localization data, single lab","pmids":["31006160"],"is_preprint":false},{"year":2023,"finding":"FAT10 and NUB1L cooperate to activate the 26S proteasome: FAT10 binds to the UBA domains of NUB1L and interferes with NUB1L dimerization, which increases NUB1L's affinity for the proteasomal subunit RPN1. Together, FAT10 and NUB1L facilitate gate opening of the 20S proteasome and activate all peptidolytic activities of the 26S proteasome in a ubiquitin- and USP14-independent manner.","method":"In vitro proteasome activity assays, co-immunoprecipitation, domain interaction studies","journal":"Life science alliance","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution of proteasome activation plus co-IP interaction mapping, single lab, multiple orthogonal methods","pmids":["37188463"],"is_preprint":false},{"year":2024,"finding":"NUB1 reduction in hepatocellular carcinoma upregulates NEDD8, which promotes NEDDylation of PCNA at lysine 164. This NEDDylation antagonizes PCNA K48-linked polyubiquitination and thereby stabilizes PCNA protein, promoting tumor cell growth. The NEDDylation inhibitor TAS4464 reversed this by decreasing PCNA NEDDylation.","method":"Knockdown/overexpression experiments, site-specific mutagenesis (Lys164), in vitro and in vivo xenograft assays, western blotting","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with specific mechanistic readout (PCNA NEDDylation at defined site), in vitro and in vivo validation, single lab","pmids":["40164590"],"is_preprint":false},{"year":2025,"finding":"NUB1 traps the N-terminal ubiquitin-like domain of FAT10 in an unfolded state and delivers it to the 26S proteasome for engagement via the Rpn1 subunit, enabling ubiquitin-independent and p97-independent degradation of FAT10-ylated substrates. Cryo-EM revealed a highly dynamic NUB1 complex bound to Rpn1 during FAT10 delivery and early ATP-dependent degradation. Hydrogen-deuterium exchange and site-directed mutagenesis defined the FAT10-NUB1 interaction complex that activates NUB1 for proteasome docking.","method":"In vitro reconstitution with purified human components, hydrogen-deuterium exchange mass spectrometry, cryo-EM, site-directed mutagenesis, structural modeling","journal":"Nature structural & molecular biology","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstitution, cryo-EM structure, HDX-MS, and mutagenesis in a single rigorous study; peer-reviewed publication","pmids":["40217121"],"is_preprint":false},{"year":2024,"finding":"NUB1 overexpression decreases NF-κB nuclear translocation and IL-6 mRNA in IL-1β-stimulated rheumatoid arthritis fibroblast-like synoviocytes (FLS), placing NUB1 as a negative regulator of NF-κB-mediated inflammatory signaling through the neddylation/CUL1 axis.","method":"Overexpression vector transfection, NF-κB nuclear translocation assay, RT-PCR for IL-6 mRNA in RA FLS","journal":"Arthritis & rheumatology (Hoboken, N.J.)","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — gain-of-function with defined molecular readouts (NF-κB translocation, IL-6 mRNA) in primary disease-relevant cells, single lab","pmids":["38566346"],"is_preprint":false},{"year":2004,"finding":"NUB1 interacts with the ubiquitin precursor UbC1 (composed of nine tandem ubiquitin repeats linked by alpha-peptide bonds) through its UBA domain. The UBA domain binds alpha-peptide bond-linked polyubiquitin but not isopeptide bond-linked polyubiquitin. An unidentified ubiquitin C-terminal hydrolase co-immunoprecipitates with NUB1, suggesting NUB1 recruits UbC1 to this hydrolase complex for processing into ubiquitin monomers.","method":"Yeast two-hybrid, co-immunoprecipitation, domain-specific binding assays","journal":"European journal of biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — yeast two-hybrid confirmed by co-IP with domain specificity determination, single lab","pmids":["15009209"],"is_preprint":false}],"current_model":"NUB1/NUB1L is an adaptor protein that negatively regulates the NEDD8 conjugation system and ubiquitin-like modifier FAT10 by binding NEDD8 and FAT10 through its C-terminal NEDD8-binding site(s) and UBA domain, recruiting them and their conjugates to the 26S proteasome for degradation via direct interaction with proteasomal subunits S5a/Rpn10 (through a non-UBL C-terminal region) and Rpn1; mechanistically, NUB1L traps the N-terminal domain of FAT10 in an unfolded state to enable ubiquitin-independent and p97-independent substrate delivery to the proteasome, and together FAT10–NUB1L cooperate to activate proteasomal gate opening; NUB1 also modulates p53 localization via the NEDD8/ubiquitin/Mdm2 axis, reduces tau aggregation by promoting GSK3β degradation, and suppresses synphilin-1 inclusion formation and mutant huntingtin levels through proteasomal targeting; NUB1 activity itself is positively regulated by non-proteolytic di-ubiquitination at Lys-159 by Mdm2, by phosphorylation at Ser-46 which enhances aggregate clearance, and by cytoplasmic retention through interaction with AIPL1."},"narrative":{"mechanistic_narrative":"NUB1/NUB1L is an interferon-inducible adaptor that negatively regulates the ubiquitin-like modifiers NEDD8 and FAT10 by recruiting them and their conjugates to the 26S proteasome for degradation [PMID:11259415, PMID:11585840]. It engages substrates through a conserved C-terminal NEDD8-binding site and, in the NUB1L splice variant, an additional UBA domain conferring a second NEDD8-binding site, with the C-terminal site being chiefly responsible for NEDD8 down-regulation [PMID:12816948]. NUB1 docks onto the proteasome through a non-UBL C-terminal region (residues 536–584) that binds the VWA domain of S5a/Rpn10 and can also engage Rpn1 [PMID:16171779, PMID:22434192]. For FAT10-modified substrates, NUB1L enables proteasomal degradation independently of polyubiquitylation by trapping the FAT10 N-terminal ubiquitin-like domain in an unfolded state and delivering it to the proteasome via Rpn1, a ubiquitin- and p97-independent route resolved structurally by cryo-EM; FAT10 binding to the NUB1L UBA domains disrupts NUB1L dimerization, raising its affinity for Rpn1 and together activating 20S gate opening and all peptidolytic activities of the 26S proteasome [PMID:37188463, PMID:40217121]. Beyond modifier turnover, NUB1 acts as a protein quality-control factor: it promotes proteasomal clearance of synphilin-1, mutant huntingtin (via CUL3/NEDD8-dependent polyubiquitination), and GSK3β—thereby reducing tau phosphorylation and aggregation—and suppresses inclusion formation [PMID:16877356, PMID:22965877, PMID:23525043]. Through the NEDD8/ubiquitin/Mdm2 axis NUB1 reduces p53 NEDDylation, stimulates its Mdm2-dependent ubiquitination, and drives cytoplasmic p53 with loss of transcriptional activity [PMID:20101219]. NUB1 activity is itself positively regulated by non-proteolytic K159 di-ubiquitination by Mdm2 and by Ser-46 phosphorylation that enhances aggregate clearance [PMID:28099510, PMID:31006160], and its subcellular distribution is controlled by AIPL1, which retains NUB1 in the cytoplasm [PMID:12374762, PMID:15347646].","teleology":[{"year":2001,"claim":"Established NUB1 as an interferon-inducible NEDD8-interacting protein that suppresses NEDD8 levels, defining its core role as a negative regulator of a ubiquitin-like modifier.","evidence":"Yeast two-hybrid and overexpression/western blot in U2OS cells","pmids":["11259415"],"confidence":"Medium","gaps":["Mechanism of NEDD8 down-regulation not yet linked to the proteasome","Direct binding interface on NEDD8 undefined"]},{"year":2001,"claim":"Showed NUB1 functions as a proteasomal adaptor by binding S5a and recruiting NEDD8 conjugates for degradation, converting the regulatory observation into a delivery mechanism.","evidence":"GST pull-down with S5a, proteasome inhibitor blockade, overexpression","pmids":["11585840"],"confidence":"High","gaps":["Which NUB1 region binds S5a not yet mapped","UBL domain role unresolved"]},{"year":2003,"claim":"Defined the substrate-binding determinants by identifying the NUB1L UBA domain as a second NEDD8-binding site and a conserved Leu-rich motif required for NEDD8 binding, establishing how the adaptor recognizes its cargo.","evidence":"Mutagenesis and functional down-regulation assays","pmids":["12816948"],"confidence":"High","gaps":["Structural basis of the Leu-motif interaction not resolved","Functional distinction between NUB1 and NUB1L variants incomplete"]},{"year":2002,"claim":"Identified AIPL1 as a NUB1 partner, opening a route to understanding NUB1 spatial regulation.","evidence":"Yeast two-hybrid and co-IP in Y79 retinoblastoma cells","pmids":["12374762"],"confidence":"Medium","gaps":["Functional consequence of the interaction not yet shown","Interaction interface unmapped"]},{"year":2004,"claim":"Showed AIPL1 retains NUB1 in the cytoplasm and suppresses NUB1-fragment inclusions, and that LCA-associated AIPL1 mutations (residues 181–330) abolish NUB1 binding, linking NUB1 localization control to disease-relevant AIPL1 variants.","evidence":"GFP-fusion imaging, domain deletion, and three independent interaction assays with LCA mutants","pmids":["15347646","15081406"],"confidence":"Medium","gaps":["Whether disrupted NUB1 regulation contributes causally to LCA pathology untested","Chaperone-like mechanism of inclusion suppression undefined"]},{"year":2004,"claim":"Linked the UBA domain to alpha-linked polyubiquitin processing, suggesting NUB1 routes the ubiquitin precursor UbC1 to a hydrolase.","evidence":"Yeast two-hybrid, co-IP, and domain-specific binding assays","pmids":["15009209"],"confidence":"Medium","gaps":["The co-immunoprecipitating C-terminal hydrolase was never identified","Physiological relevance of UbC1 processing unconfirmed"]},{"year":2005,"claim":"Mapped the proteasome-docking site to a non-UBL C-terminal region (536–584), separating substrate binding from proteasome engagement and clarifying the UBL domain is required for function but not S5a binding.","evidence":"In vitro GST pull-down, yeast two-hybrid, deletion mapping","pmids":["16171779"],"confidence":"Medium","gaps":["Functional role of the UBL domain still unexplained","S5a residues contacted not defined"]},{"year":2006,"claim":"Extended NUB1 function to neurodegeneration-relevant substrates by showing it binds synphilin-1 via its NEDD8-binding site and promotes its proteasomal degradation and inclusion suppression.","evidence":"Co-IP, proteasome inhibitor assay, inclusion formation in HEK293","pmids":["16877356"],"confidence":"Medium","gaps":["Whether synphilin-1 is NEDD8/FAT10-modified prior to delivery unclear","In vivo relevance to Parkinson pathology untested"]},{"year":2009,"claim":"Demonstrated that FAT10-mediated proteasomal degradation is ubiquitin-independent and strictly requires NUB1L, establishing NUB1L as the essential delivery factor for the FAT10 pathway.","evidence":"In vitro reconstituted degradation with purified 26S proteasome and siRNA knockdown","pmids":["19166848"],"confidence":"High","gaps":["Proteasome receptor for the NUB1L-FAT10 complex not yet identified","Conformational mechanism of substrate engagement unknown"]},{"year":2010,"claim":"Connected NUB1 to tumor-suppressor regulation by showing it lowers p53 NEDDylation, enhances Mdm2-mediated ubiquitination, and drives cytoplasmic p53 with loss of transcriptional activity.","evidence":"Overexpression, co-IP, fractionation/imaging, reporter assays","pmids":["20101219"],"confidence":"Medium","gaps":["Direct versus indirect effect on p53 modification not fully separated","In vivo tumor relevance not addressed in this study"]},{"year":2012,"claim":"Resolved the proteasome receptor by showing NUB1L and FAT10 bind the hRpn10/S5a VWA domain (with Rpn1 as a secondary site), and that this receptor is required for FAT10-conjugate turnover.","evidence":"Co-IP, yeast complementation, siRNA knockdown, domain mapping","pmids":["22434192"],"confidence":"High","gaps":["Relative contributions of Rpn10 versus Rpn1 in vivo unresolved","Stoichiometry of the NUB1L-FAT10-proteasome assembly undefined"]},{"year":2012,"claim":"Defined a tau-protective mechanism whereby NUB1 disrupts the tau-GSK3β interaction and degrades GSK3β (UBL- and UBA-dependent), reducing tau phosphorylation and aggregation.","evidence":"Co-IP, domain mutants, siRNA silencing, aggregation and phosphorylation assays","pmids":["22965877"],"confidence":"High","gaps":["Whether GSK3β degradation is NEDD8/FAT10-dependent unclear","In vivo tauopathy effect not tested"]},{"year":2013,"claim":"Showed NUB1 lowers mutant huntingtin via CUL3/NEDD8-dependent polyubiquitination and that interferon-β rescues neuronal toxicity through NUB1 induction, linking the interferon-NUB1 axis to Huntington disease.","evidence":"Genome-wide RNAi screen, Drosophila validation, ubiquitination and inhibitor assays","pmids":["23525043"],"confidence":"High","gaps":["Direct NUB1 contact with mHTT versus indirect CUL3 effect not separated","Therapeutic window of interferon induction undefined"]},{"year":2013,"claim":"Identified NEDD8 residue Asn-51 recognition and a VCP-binding motif, showing NUB1L coordinates with the p97-UFD1-NPL4 complex for NEDD8 delivery and does not bind ubiquitin.","evidence":"Co-IP, Asn-51 mutagenesis, in vitro binding","pmids":["24019527"],"confidence":"Medium","gaps":["Reconciliation with later p97-independent FAT10 delivery unresolved","p97 dependence for NEDD8 versus FAT10 cargo differs"]},{"year":2015,"claim":"Showed NUB1L suppresses atypical neddylation and promotes misfolded-protein clearance, accumulating CryAB(R120G) on loss, broadening NUB1L to general proteostasis under stress.","evidence":"siRNA, overexpression, GFPu degradation assay in cardiomyocytes","pmids":["26260793"],"confidence":"Medium","gaps":["Direct enzymatic target of atypical neddylation suppression unclear","Cardiac phenotype in vivo not established"]},{"year":2017,"claim":"Revealed an activating modification: Mdm2 induces non-proteolytic K159 di-ubiquitination of NUB1 that is required for its repression of NEDD8, defining a positive feedback regulator of NUB1.","evidence":"Co-IP, K159R mutagenesis, ubiquitination assays","pmids":["28099510"],"confidence":"Medium","gaps":["How K159 di-ubiquitin alters NUB1 conformation/activity unknown","Ubiquitin chain linkage type at K159 not defined"]},{"year":2019,"claim":"Identified Ser-46 phosphorylation as an activating mark enhancing aggregate degradation, with disease-specific presence in Lewy bodies, linking NUB1 phospho-regulation to synucleinopathy pathology.","evidence":"Phosphomimetic mutant, aggregate degradation assay, immunohistochemistry","pmids":["31006160"],"confidence":"Medium","gaps":["Kinase responsible for Ser-46 phosphorylation unidentified","Causal versus correlative link to Lewy body pathology unresolved"]},{"year":2023,"claim":"Provided the mechanistic basis for proteasome activation by showing FAT10 binding to NUB1L UBA domains blocks NUB1L dimerization, raising Rpn1 affinity and triggering 20S gate opening independent of ubiquitin and USP14.","evidence":"In vitro proteasome activity assays, co-IP, domain interaction studies","pmids":["37188463"],"confidence":"High","gaps":["Structural state of the activated proteasome not yet visualized in this study","Whether NEDD8 cargo activates the proteasome similarly untested"]},{"year":2025,"claim":"Delivered a structural model showing NUB1 traps the FAT10 N-terminal UBL domain unfolded and docks onto Rpn1 for ubiquitin- and p97-independent degradation, integrating prior receptor and activation data into a delivery mechanism.","evidence":"In vitro reconstitution, HDX-MS, cryo-EM, site-directed mutagenesis","pmids":["40217121"],"confidence":"High","gaps":["Dynamics of the complex limit a single high-resolution snapshot","Whether NEDD8 cargo uses the same unfolding-trap mechanism not shown"]},{"year":2024,"claim":"Connected NUB1 loss to oncogenesis by showing reduced NUB1 elevates NEDD8, promoting PCNA K164 NEDDylation that antagonizes its K48 ubiquitination and stabilizes PCNA to drive hepatocellular carcinoma growth.","evidence":"Knockdown/overexpression, K164 mutagenesis, xenograft, western blot, NEDDylation inhibitor TAS4464","pmids":["40164590"],"confidence":"Medium","gaps":["Whether NUB1 directly controls PCNA modification or acts solely via NEDD8 levels unclear","Clinical correlation of NUB1 loss across tumor types not established"]},{"year":2024,"claim":"Implicated NUB1 in inflammatory signaling by showing its overexpression suppresses NF-κB nuclear translocation and IL-6 in stimulated rheumatoid arthritis synoviocytes via the neddylation/CUL1 axis.","evidence":"Overexpression, NF-κB translocation assay, RT-PCR in RA FLS","pmids":["38566346"],"confidence":"Medium","gaps":["Direct CUL1-substrate target mediating the effect not identified","In vivo arthritis model not tested"]},{"year":null,"claim":"Whether the unfolding-trap delivery mechanism defined for FAT10 also governs NUB1-mediated NEDD8 and misfolded-substrate turnover, and how the K159 di-ubiquitination and Ser-46 phosphorylation marks structurally activate NUB1, remain open.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural comparison of NEDD8 versus FAT10 cargo delivery","Kinase and conformational consequences of activating modifications undefined","Unified model reconciling p97-dependent NEDD8 and p97-independent FAT10 routes lacking"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[1,6,10,19]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[0,2,14,17]},{"term_id":"GO:0031386","term_label":"protein tag activity","supporting_discovery_ids":[1,2]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[0,4]},{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[1,8,10,17,19]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,2,13]}],"complexes":[],"partners":["NEDD8","FAT10","PSMD4","RPN1","AIPL1","GSK3B","MDM2","VCP"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9Y5A7","full_name":"NEDD8 ultimate buster 1","aliases":["Negative regulator of ubiquitin-like proteins 1","Renal carcinoma antigen NY-REN-18"],"length_aa":615,"mass_kda":70.5,"function":"Specific down-regulator of the NEDD8 conjugation system. Recruits NEDD8, UBD, and their conjugates to the proteasome for degradation. Isoform 1 promotes the degradation of NEDD8 more efficiently than isoform 2","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q9Y5A7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/NUB1","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":"PSMC5","stoichiometry":0.2},{"gene":"UBB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/NUB1","total_profiled":1310},"omim":[{"mim_id":"607981","title":"NEGATIVE REGULATOR OF UBIQUITIN-LIKE PROTEINS 1; NUB1","url":"https://www.omim.org/entry/607981"},{"mim_id":"604392","title":"ARYLHYDROCARBON-INTERACTING RECEPTOR PROTEIN-LIKE 1; AIPL1","url":"https://www.omim.org/entry/604392"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"},{"location":"Nucleoli","reliability":"Enhanced"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/NUB1"},"hgnc":{"alias_symbol":["BS4","NYREN18","NUB1L"],"prev_symbol":[]},"alphafold":{"accession":"Q9Y5A7","domains":[{"cath_id":"-","chopping":"2-75","consensus_level":"medium","plddt":91.2381,"start":2,"end":75},{"cath_id":"3.10.20.90","chopping":"82-158","consensus_level":"medium","plddt":87.8949,"start":82,"end":158},{"cath_id":"-","chopping":"181-326","consensus_level":"medium","plddt":82.8971,"start":181,"end":326},{"cath_id":"1.10.8","chopping":"489-537","consensus_level":"medium","plddt":84.941,"start":489,"end":537}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y5A7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y5A7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9Y5A7-F1-predicted_aligned_error_v6.png","plddt_mean":83.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=NUB1","jax_strain_url":"https://www.jax.org/strain/search?query=NUB1"},"sequence":{"accession":"Q9Y5A7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9Y5A7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9Y5A7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9Y5A7"}},"corpus_meta":[{"pmid":"14675431","id":"PMC_14675431","title":"The tomato resistance protein Bs4 is a predicted non-nuclear TIR-NB-LRR protein that mediates defense responses to severely truncated derivatives of AvrBs4 and overexpressed AvrBs3.","date":"2004","source":"The Plant journal : for cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/14675431","citation_count":141,"is_preprint":false},{"pmid":"11585840","id":"PMC_11585840","title":"Targeting of NEDD8 and its conjugates for proteasomal degradation by NUB1.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11585840","citation_count":125,"is_preprint":false},{"pmid":"11259415","id":"PMC_11259415","title":"NUB1, a NEDD8-interacting protein, is induced by interferon and down-regulates the NEDD8 expression.","date":"2001","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/11259415","citation_count":94,"is_preprint":false},{"pmid":"23525043","id":"PMC_23525043","title":"Identification of NUB1 as a suppressor of mutant Huntington toxicity via enhanced protein clearance.","date":"2013","source":"Nature neuroscience","url":"https://pubmed.ncbi.nlm.nih.gov/23525043","citation_count":81,"is_preprint":false},{"pmid":"22434192","id":"PMC_22434192","title":"FAT10 and NUB1L bind to the VWA domain of Rpn10 and Rpn1 to enable proteasome-mediated proteolysis.","date":"2012","source":"Nature communications","url":"https://pubmed.ncbi.nlm.nih.gov/22434192","citation_count":73,"is_preprint":false},{"pmid":"38103548","id":"PMC_38103548","title":"ClinGen guidance for use of the PP1/BS4 co-segregation and PP4 phenotype specificity criteria for sequence variant pathogenicity classification.","date":"2023","source":"American journal of human genetics","url":"https://pubmed.ncbi.nlm.nih.gov/38103548","citation_count":71,"is_preprint":false},{"pmid":"19166848","id":"PMC_19166848","title":"Degradation of FAT10 by the 26S proteasome is independent of ubiquitylation but relies on NUB1L.","date":"2009","source":"FEBS letters","url":"https://pubmed.ncbi.nlm.nih.gov/19166848","citation_count":68,"is_preprint":false},{"pmid":"11332727","id":"PMC_11332727","title":"Genetic mapping and functional analysis of the tomato Bs4 locus governing recognition of the Xanthomonas campestris pv. vesicatoria AvrBs4 protein.","date":"2001","source":"Molecular plant-microbe interactions : MPMI","url":"https://pubmed.ncbi.nlm.nih.gov/11332727","citation_count":62,"is_preprint":false},{"pmid":"12816948","id":"PMC_12816948","title":"Regulation of the NEDD8 conjugation system by a splicing variant, NUB1L.","date":"2003","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12816948","citation_count":62,"is_preprint":false},{"pmid":"20101219","id":"PMC_20101219","title":"NUB1 promotes cytoplasmic localization of p53 through cooperation of the NEDD8 and ubiquitin pathways.","date":"2010","source":"Oncogene","url":"https://pubmed.ncbi.nlm.nih.gov/20101219","citation_count":59,"is_preprint":false},{"pmid":"16877356","id":"PMC_16877356","title":"NUB1 suppresses the formation of Lewy body-like inclusions by proteasomal degradation of synphilin-1.","date":"2006","source":"The American journal of pathology","url":"https://pubmed.ncbi.nlm.nih.gov/16877356","citation_count":56,"is_preprint":false},{"pmid":"12374762","id":"PMC_12374762","title":"The inherited blindness associated protein AIPL1 interacts with the cell cycle regulator protein NUB1.","date":"2002","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/12374762","citation_count":51,"is_preprint":false},{"pmid":"26905687","id":"PMC_26905687","title":"Antibacterial Azaphilones from an Endophytic Fungus, Colletotrichum sp. BS4.","date":"2016","source":"Journal of natural products","url":"https://pubmed.ncbi.nlm.nih.gov/26905687","citation_count":49,"is_preprint":false},{"pmid":"23667807","id":"PMC_23667807","title":"Halomonas sp. BS4, A biosurfactant producing halophilic bacterium isolated from solar salt works in India and their biomedical importance.","date":"2013","source":"SpringerPlus","url":"https://pubmed.ncbi.nlm.nih.gov/23667807","citation_count":39,"is_preprint":false},{"pmid":"20160729","id":"PMC_20160729","title":"NUB1, an interferon-inducible protein, mediates anti-proliferative actions and apoptosis in renal cell carcinoma cells through cell-cycle regulation.","date":"2010","source":"British journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/20160729","citation_count":31,"is_preprint":false},{"pmid":"26260793","id":"PMC_26260793","title":"NEDD8 Ultimate Buster 1 Long (NUB1L) Protein Suppresses Atypical Neddylation and Promotes the Proteasomal Degradation of Misfolded Proteins.","date":"2015","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/26260793","citation_count":29,"is_preprint":false},{"pmid":"22965877","id":"PMC_22965877","title":"NUB1 modulation of GSK3β reduces tau aggregation.","date":"2012","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/22965877","citation_count":27,"is_preprint":false},{"pmid":"15347646","id":"PMC_15347646","title":"The Leber congenital amaurosis protein AIPL1 modulates the nuclear translocation of NUB1 and suppresses inclusion formation by NUB1 fragments.","date":"2004","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15347646","citation_count":27,"is_preprint":false},{"pmid":"16171779","id":"PMC_16171779","title":"Interaction of NUB1 with the proteasome subunit S5a.","date":"2005","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/16171779","citation_count":26,"is_preprint":false},{"pmid":"24019527","id":"PMC_24019527","title":"NEDD8 ultimate buster-1 long (NUB1L) protein promotes transfer of NEDD8 to proteasome for degradation through the P97UFD1/NPL4 complex.","date":"2013","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/24019527","citation_count":23,"is_preprint":false},{"pmid":"17549501","id":"PMC_17549501","title":"Immunohistochemical localization of NUB1, a synphilin-1-binding protein, in neurodegenerative disorders.","date":"2007","source":"Acta neuropathologica","url":"https://pubmed.ncbi.nlm.nih.gov/17549501","citation_count":23,"is_preprint":false},{"pmid":"15081406","id":"PMC_15081406","title":"Abolished interaction of NUB1 with mutant AIPL1 involved in Leber congenital amaurosis.","date":"2004","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/15081406","citation_count":16,"is_preprint":false},{"pmid":"38566346","id":"PMC_38566346","title":"Dysregulated NUB1 and Neddylation Enhances Rheumatoid Arthritis Fibroblast-Like Synoviocyte Inflammatory Responses.","date":"2024","source":"Arthritis & rheumatology (Hoboken, N.J.)","url":"https://pubmed.ncbi.nlm.nih.gov/38566346","citation_count":15,"is_preprint":false},{"pmid":"34571823","id":"PMC_34571823","title":"NUB1 and FAT10 Proteins as Potential Novel Biomarkers in Cancer: A Translational Perspective.","date":"2021","source":"Cells","url":"https://pubmed.ncbi.nlm.nih.gov/34571823","citation_count":14,"is_preprint":false},{"pmid":"15009209","id":"PMC_15009209","title":"NUB1-mediated targeting of the ubiquitin precursor UbC1 for its C-terminal hydrolysis.","date":"2004","source":"European journal of biochemistry","url":"https://pubmed.ncbi.nlm.nih.gov/15009209","citation_count":12,"is_preprint":false},{"pmid":"11810236","id":"PMC_11810236","title":"Chromosome landing at the tomato Bs4 locus.","date":"2001","source":"Molecular genetics and genomics : MGG","url":"https://pubmed.ncbi.nlm.nih.gov/11810236","citation_count":12,"is_preprint":false},{"pmid":"21937912","id":"PMC_21937912","title":"Synphilin-1-binding protein NUB1 is colocalized with nonfibrillar, proteinase K-resistant α-synuclein in presynapses in Lewy body disease.","date":"2011","source":"Journal of neuropathology and experimental neurology","url":"https://pubmed.ncbi.nlm.nih.gov/21937912","citation_count":12,"is_preprint":false},{"pmid":"32703484","id":"PMC_32703484","title":"Overexpression of negative regulator of ubiquitin-like proteins 1 (NUB1) inhibits proliferation and invasion of gastric cancer cells through upregulation of p27Kip1 and inhibition of epithelial-mesenchymal transition.","date":"2020","source":"Pathology, research and practice","url":"https://pubmed.ncbi.nlm.nih.gov/32703484","citation_count":11,"is_preprint":false},{"pmid":"34847450","id":"PMC_34847450","title":"SNHG12 regulates biological behaviors of ox-LDL-induced HA-VSMCs through upregulation of SPRY2 and NUB1.","date":"2021","source":"Atherosclerosis","url":"https://pubmed.ncbi.nlm.nih.gov/34847450","citation_count":11,"is_preprint":false},{"pmid":"28099510","id":"PMC_28099510","title":"Regulation of NUB1 Activity through Non-Proteolytic Mdm2-Mediated Ubiquitination.","date":"2017","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/28099510","citation_count":10,"is_preprint":false},{"pmid":"40217121","id":"PMC_40217121","title":"NUB1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome.","date":"2025","source":"Nature structural & molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/40217121","citation_count":9,"is_preprint":false},{"pmid":"31006160","id":"PMC_31006160","title":"Phosphorylated NUB1 distinguishes α-synuclein in Lewy bodies from that in glial cytoplasmic inclusions in multiple system atrophy.","date":"2019","source":"Brain pathology (Zurich, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/31006160","citation_count":9,"is_preprint":false},{"pmid":"37188463","id":"PMC_37188463","title":"FAT10 and NUB1L cooperate to activate the 26S proteasome.","date":"2023","source":"Life science alliance","url":"https://pubmed.ncbi.nlm.nih.gov/37188463","citation_count":8,"is_preprint":false},{"pmid":"38666980","id":"PMC_38666980","title":"Antimicrobial Activity of Bacillus amyloliquefaciens BS4 against Gram-Negative Pathogenic Bacteria.","date":"2024","source":"Antibiotics (Basel, Switzerland)","url":"https://pubmed.ncbi.nlm.nih.gov/38666980","citation_count":8,"is_preprint":false},{"pmid":"36056465","id":"PMC_36056465","title":"The tomato resistance gene Bs4 suppresses leaf watersoaking phenotypes induced by AvrHah1, a transcription activator-like effector from tomato-pathogenic xanthomonads.","date":"2022","source":"The New phytologist","url":"https://pubmed.ncbi.nlm.nih.gov/36056465","citation_count":7,"is_preprint":false},{"pmid":"9864031","id":"PMC_9864031","title":"Monoclonal antibody NU-B1 reacts with novel antigen on human B cells in mantle and marginal zones distinct from known CD molecules.","date":"1998","source":"Tissue antigens","url":"https://pubmed.ncbi.nlm.nih.gov/9864031","citation_count":5,"is_preprint":false},{"pmid":"27314618","id":"PMC_27314618","title":"Effects of Exogenous NUB1 Expression in the Striatum of HDQ175/Q7 Mice.","date":"2016","source":"Journal of Huntington's disease","url":"https://pubmed.ncbi.nlm.nih.gov/27314618","citation_count":4,"is_preprint":false},{"pmid":"24596939","id":"PMC_24596939","title":"Structural studies on AIPL1 and its functional interactions with NUB1 to identify key interacting residues in LCA4.","date":"2013","source":"Journal of ocular biology, diseases, and informatics","url":"https://pubmed.ncbi.nlm.nih.gov/24596939","citation_count":4,"is_preprint":false},{"pmid":"40164590","id":"PMC_40164590","title":"NUB1 reduction promotes PCNA-mediated tumor growth by disturbing the PCNA polyubiquitination/NEDDylation in hepatocellular carcinoma cells.","date":"2025","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/40164590","citation_count":3,"is_preprint":false},{"pmid":"39767703","id":"PMC_39767703","title":"Phosphorylated FAT10 Is More Efficiently Conjugated to Substrates, Does Not Bind to NUB1L, and Does Not Alter Degradation by the Proteasome.","date":"2024","source":"Biomedicines","url":"https://pubmed.ncbi.nlm.nih.gov/39767703","citation_count":2,"is_preprint":false},{"pmid":"40564026","id":"PMC_40564026","title":"Mechanism and Predictive Role of NUB1 Protein in Oestrogen Receptor Pathway of FEC-Treated Breast Cancer Patients.","date":"2025","source":"Biomedicines","url":"https://pubmed.ncbi.nlm.nih.gov/40564026","citation_count":1,"is_preprint":false},{"pmid":"38915702","id":"PMC_38915702","title":"Nub1 traps unfolded FAT10 for ubiquitin-independent degradation by the 26S proteasome.","date":"2024","source":"bioRxiv : the preprint server for biology","url":"https://pubmed.ncbi.nlm.nih.gov/38915702","citation_count":1,"is_preprint":false},{"pmid":"42159595","id":"PMC_42159595","title":"Intermolecular β-sheet Formation Guides the Interaction between Ubiquitin-like Modifier FAT10 and Adapter Protein NUB1L.","date":"2026","source":"Journal of the American Chemical Society","url":"https://pubmed.ncbi.nlm.nih.gov/42159595","citation_count":0,"is_preprint":false},{"pmid":"41667591","id":"PMC_41667591","title":"Altered fibroblast-like synoviocyte epigenetics is responsible for deficient NUB1 expression in rheumatoid arthritis.","date":"2026","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/41667591","citation_count":0,"is_preprint":false},{"pmid":"41866577","id":"PMC_41866577","title":"Complete NUB1 depletion in ER - negative breast cancer progression in paired primary-metastatic cases: a case series.","date":"2026","source":"Journal of medical case reports","url":"https://pubmed.ncbi.nlm.nih.gov/41866577","citation_count":0,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.08.25.25334371","title":"Multi-Platform Curation in the Development of ACMG/AMP Specifications for Von Hippel Lindau (VHL) Disease","date":"2025-08-27","source":"bioRxiv","url":"https://doi.org/10.1101/2025.08.25.25334371","citation_count":0,"is_preprint":true},{"pmid":null,"id":"bio_10.1101_2025.04.30.651500","title":"Custom-Built Electrodes Perform Comparably to a Discontinued Commercial Electrode for Neuromuscular Electrical Stimulation in Mice","date":"2025-05-01","source":"bioRxiv","url":"https://doi.org/10.1101/2025.04.30.651500","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":25753,"output_tokens":5812,"usd":0.08222,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":14231,"output_tokens":6098,"usd":0.111802,"stage2_stop_reason":"end_turn"},"total_usd":0.194022,"stage1_batch_id":"msgbatch_013a8chtv3AWyTqv4z4sEF4C","stage2_batch_id":"msgbatch_01AHsuW63vinsvuTgzmQ3n62","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2001,\n      \"finding\": \"NUB1 was identified as an interferon-inducible protein that interacts with NEDD8 (ubiquitin-like protein) via yeast two-hybrid screening and down-regulates NEDD8 expression through a post-transcriptional mechanism. NUB1 is predominantly localized in the nucleus and overexpression causes severe reduction of NEDD8 monomer and conjugates.\",\n      \"method\": \"Yeast two-hybrid screening, western blot, overexpression in U2OS cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — yeast two-hybrid plus biochemical overexpression assays in a single lab, two orthogonal methods\",\n      \"pmids\": [\"11259415\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"NUB1 possesses a ubiquitin-like (UBL) domain at its N-terminus and binds to S5a (PSMD4) of the 19S proteasome (PA700). GST pull-down assays showed that NUB1 overexpression increases precipitation of NEDD8 conjugates with GST-S5a, and proteasome inhibitors block NUB1-mediated down-regulation of NEDD8 — indicating NUB1 acts as an adaptor that recruits NEDD8 and its conjugates to the proteasome for degradation.\",\n      \"method\": \"GST pull-down assay, proteasome inhibitor treatment, overexpression studies\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal pulldown plus inhibitor experiments, replicated across two papers from the same group with orthogonal methods\",\n      \"pmids\": [\"11585840\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"A splicing variant of NUB1, NUB1L, possesses an additional 14-amino-acid insertion encoding a UBA domain, giving it an extra NEDD8-binding site. Mutational studies identified a conserved sequence A(X4)L(X10)L(X3)L in NEDD8-binding sites where at least three Leu residues are required for NEDD8 binding. The C-terminal NEDD8-binding site of both NUB1 and NUB1L is primarily responsible for down-regulation of NEDD8, while the UBA2 domain of NUB1L is minimally or not involved in this activity.\",\n      \"method\": \"Mutagenesis, structural/domain analysis, functional down-regulation assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — mutagenesis with functional validation, single lab but multiple orthogonal approaches (binding assay + functional down-regulation)\",\n      \"pmids\": [\"12816948\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"NUB1 physically interacts with AIPL1 (aryl hydrocarbon receptor-interacting protein-like 1), as demonstrated by yeast two-hybrid and co-immunoprecipitation in Y79 retinoblastoma cells.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation in Y79 cells\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP confirmed the yeast two-hybrid hit in a relevant cell line, single lab\",\n      \"pmids\": [\"12374762\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"AIPL1 modulates the nuclear translocation of NUB1: co-transfection of AIPL1 with GFP-NUB1 shifted NUB1 distribution toward the cytoplasm. AIPL1 also suppressed inclusion formation by NUB1 fragments in a chaperone-like manner. C-terminal truncation of AIPL1 abolished this effect, and the interaction requires residues 181–330 of AIPL1.\",\n      \"method\": \"Co-transfection with GFP-fusion proteins, fluorescence imaging, domain deletion analysis\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — live imaging localization with functional consequence (inclusion suppression) and domain mapping, single lab\",\n      \"pmids\": [\"15347646\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"Several LCA-associated mutations of AIPL1 located between residues 181–330 abolish interaction with NUB1 as demonstrated by three independent interaction assays, while other AIPL1 mutants retain NUB1 binding.\",\n      \"method\": \"Three independent interaction assays (yeast two-hybrid, co-IP, and in vitro binding)\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — three orthogonal interaction assays in a single study, single lab\",\n      \"pmids\": [\"15081406\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"NUB1 directly interacts with the proteasome subunit S5a through its C-terminal region (residues 536–584), NOT through its UBL domain. The UBL domain is not an S5a-binding motif in NUB1 but is required for NUB1 function.\",\n      \"method\": \"In vitro GST pull-down assay, yeast two-hybrid assay, deletion mapping\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro GST pulldown plus yeast two-hybrid with deletion mapping, single lab, two orthogonal methods\",\n      \"pmids\": [\"16171779\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"NUB1 physically interacts with synphilin-1 through its NEDD8-binding site and promotes proteasomal degradation of synphilin-1. Overexpression of NUB1 suppresses formation of synphilin-1-positive inclusions in HEK293 cells, and this effect is blocked by proteasome inhibitors.\",\n      \"method\": \"Co-transfection/co-immunoprecipitation, biochemical proteasome inhibitor assay, inclusion formation assay in HEK293 cells\",\n      \"journal\": \"The American journal of pathology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — co-IP plus functional proteasomal degradation assay with inhibitor validation, single lab, two orthogonal methods\",\n      \"pmids\": [\"16877356\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2009,\n      \"finding\": \"FAT10-mediated proteasomal degradation occurs independently of polyubiquitylation: purified 26S proteasome degraded FAT10-DHFR but not ubiquitin-DHFR in vitro. Critically, degradation of FAT10-DHFR by the 26S proteasome required NUB1L; knockdown of NUB1L attenuated FAT10-DHFR degradation in intact cells.\",\n      \"method\": \"In vitro reconstituted degradation assay with purified 26S proteasome, siRNA knockdown in cells\",\n      \"journal\": \"FEBS letters\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstituted in vitro degradation assay plus siRNA confirmation in cells, single lab but two orthogonal methods\",\n      \"pmids\": [\"19166848\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"NUB1 controls the subcellular localization of p53: NUB1 expression leads to decreased NEDDylation of p53, stimulation of p53 ubiquitination by Mdm2, and cytoplasmic localization of p53 with inhibition of its transcriptional activity. This requires cooperation between NEDD8 and ubiquitin pathways.\",\n      \"method\": \"Overexpression, co-immunoprecipitation, subcellular fractionation/imaging, transcription reporter assays\",\n      \"journal\": \"Oncogene\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple methods (localization, ubiquitination assays, transcriptional readout) in a single lab\",\n      \"pmids\": [\"20101219\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"NUB1L and FAT10 bind to the 26S proteasome via the VWA domain of hRpn10/S5a; NUB1L can also bind Rpn1/S2. Depletion of hRpn10 in human cells causes accumulation of FAT10-conjugates. Functional reconstitution in Rpn10-deficient yeast showed the VWA domain of hRpn10 suffices for FAT10 degradation.\",\n      \"method\": \"Co-IP, yeast functional complementation, siRNA knockdown, domain mapping\",\n      \"journal\": \"Nature communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, yeast complementation, and siRNA knockdown all in one study, multiple orthogonal methods\",\n      \"pmids\": [\"22434192\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"NUB1 interacts with both tau and GSK3β, disrupts their interaction, abolishes recruitment of GSK3β to tau inclusions, reduces GSK3β-mediated phosphorylation of tau, and promotes GSK3β degradation. The UBL domain of NUB1 is required for GSK3β degradation but not for the interaction with tau/GSK3β. The UBA domain is required for NUB1 to interact with and degrade GSK3β and suppress tau aggregation. NUB1 silencing stabilizes endogenous GSK3β and exacerbates tau phosphorylation.\",\n      \"method\": \"Co-immunoprecipitation, domain deletion mutagenesis, siRNA silencing, tau aggregation assay, phosphorylation assays\",\n      \"journal\": \"Human molecular genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal co-IP, domain mutants, siRNA knockdown, multiple functional readouts in one study\",\n      \"pmids\": [\"22965877\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"NUB1 overexpression reduces mutant huntingtin (mHTT) levels by enhancing polyubiquitination and proteasomal degradation of mHTT. This process requires CUL3 and NEDD8 (required for CUL3 activation). Interferon-β lowers mHTT and rescues neuronal toxicity through induction of NUB1.\",\n      \"method\": \"Genome-wide RNAi screen, Drosophila in vivo validation, proteasome inhibitor studies, ubiquitination assays in neuronal models\",\n      \"journal\": \"Nature neuroscience\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genome-wide screen followed by in vivo Drosophila validation and mechanistic biochemical assays, replicated across multiple model systems\",\n      \"pmids\": [\"23525043\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"NUB1L promotes transfer of NEDD8 to the proteasome for degradation by directly recognizing NEDD8 at its key residue Asn-51 and interacting with P97/VCP via a positively charged VCP-binding motif. NUB1L coordinates with the P97-UFD1-NPL4 complex for NEDD8 delivery to the proteasome. NUB1L does not interact with ubiquitin.\",\n      \"method\": \"Co-immunoprecipitation, mutagenesis (Asn-51), in vitro binding assays\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — mutagenesis identifying a key residue plus co-IP validation, single lab, two orthogonal methods\",\n      \"pmids\": [\"24019527\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"NUB1L suppresses atypical neddylation (ubiquitin enzyme-mediated NEDD8 conjugation) and promotes degradation of misfolded proteins by the proteasome. Loss of NUB1L exaggerates atypical neddylation; NUB1L overexpression represses it via promoting NEDD8 degradation. NUB1L depletion accumulates the cardiomyopathy-linked misfolded protein CryAB(R120G), and NUB1L overexpression promotes its degradation by suppressing neddylation of ubiquitinated proteins.\",\n      \"method\": \"siRNA knockdown, overexpression, GFPu degradation assay, western blotting in cardiomyocytes\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function and gain-of-function with specific substrate readouts, single lab, multiple conditions tested\",\n      \"pmids\": [\"26260793\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Mdm2 E3 ubiquitin ligase is a NUB1-interacting protein that induces non-proteolytic di-ubiquitination of NUB1 specifically on lysine 159. This di-ubiquitination positively regulates NUB1 function: mutation of Lys-159 to Arg impairs NUB1's negative regulation of Nedd8 and neddylated proteins. Mdm2 thus acts as a positive regulator of NUB1.\",\n      \"method\": \"Co-immunoprecipitation, site-directed mutagenesis (K159R), ubiquitination assays\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — site-directed mutagenesis with functional readout plus co-IP, single lab, two orthogonal methods\",\n      \"pmids\": [\"28099510\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Phosphorylation of NUB1 at serine 46 (P-NUB46) creates a phosphomimetic mutant that more efficiently degrades aggregates in a cell-based assay. Antibodies specific to P-NUB46 react with Lewy bodies in PD/DLB but not with glial cytoplasmic inclusions in MSA, indicating phosphorylation modulates NUB1 activity during synucleinopathy pathology.\",\n      \"method\": \"Phosphomimetic mutagenesis, cell-based aggregate degradation assay, immunohistochemistry\",\n      \"journal\": \"Brain pathology (Zurich, Switzerland)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — mutagenesis with functional readout (aggregate degradation) and disease-relevant localization data, single lab\",\n      \"pmids\": [\"31006160\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"FAT10 and NUB1L cooperate to activate the 26S proteasome: FAT10 binds to the UBA domains of NUB1L and interferes with NUB1L dimerization, which increases NUB1L's affinity for the proteasomal subunit RPN1. Together, FAT10 and NUB1L facilitate gate opening of the 20S proteasome and activate all peptidolytic activities of the 26S proteasome in a ubiquitin- and USP14-independent manner.\",\n      \"method\": \"In vitro proteasome activity assays, co-immunoprecipitation, domain interaction studies\",\n      \"journal\": \"Life science alliance\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution of proteasome activation plus co-IP interaction mapping, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"37188463\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NUB1 reduction in hepatocellular carcinoma upregulates NEDD8, which promotes NEDDylation of PCNA at lysine 164. This NEDDylation antagonizes PCNA K48-linked polyubiquitination and thereby stabilizes PCNA protein, promoting tumor cell growth. The NEDDylation inhibitor TAS4464 reversed this by decreasing PCNA NEDDylation.\",\n      \"method\": \"Knockdown/overexpression experiments, site-specific mutagenesis (Lys164), in vitro and in vivo xenograft assays, western blotting\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with specific mechanistic readout (PCNA NEDDylation at defined site), in vitro and in vivo validation, single lab\",\n      \"pmids\": [\"40164590\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"NUB1 traps the N-terminal ubiquitin-like domain of FAT10 in an unfolded state and delivers it to the 26S proteasome for engagement via the Rpn1 subunit, enabling ubiquitin-independent and p97-independent degradation of FAT10-ylated substrates. Cryo-EM revealed a highly dynamic NUB1 complex bound to Rpn1 during FAT10 delivery and early ATP-dependent degradation. Hydrogen-deuterium exchange and site-directed mutagenesis defined the FAT10-NUB1 interaction complex that activates NUB1 for proteasome docking.\",\n      \"method\": \"In vitro reconstitution with purified human components, hydrogen-deuterium exchange mass spectrometry, cryo-EM, site-directed mutagenesis, structural modeling\",\n      \"journal\": \"Nature structural & molecular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstitution, cryo-EM structure, HDX-MS, and mutagenesis in a single rigorous study; peer-reviewed publication\",\n      \"pmids\": [\"40217121\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"NUB1 overexpression decreases NF-κB nuclear translocation and IL-6 mRNA in IL-1β-stimulated rheumatoid arthritis fibroblast-like synoviocytes (FLS), placing NUB1 as a negative regulator of NF-κB-mediated inflammatory signaling through the neddylation/CUL1 axis.\",\n      \"method\": \"Overexpression vector transfection, NF-κB nuclear translocation assay, RT-PCR for IL-6 mRNA in RA FLS\",\n      \"journal\": \"Arthritis & rheumatology (Hoboken, N.J.)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — gain-of-function with defined molecular readouts (NF-κB translocation, IL-6 mRNA) in primary disease-relevant cells, single lab\",\n      \"pmids\": [\"38566346\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"NUB1 interacts with the ubiquitin precursor UbC1 (composed of nine tandem ubiquitin repeats linked by alpha-peptide bonds) through its UBA domain. The UBA domain binds alpha-peptide bond-linked polyubiquitin but not isopeptide bond-linked polyubiquitin. An unidentified ubiquitin C-terminal hydrolase co-immunoprecipitates with NUB1, suggesting NUB1 recruits UbC1 to this hydrolase complex for processing into ubiquitin monomers.\",\n      \"method\": \"Yeast two-hybrid, co-immunoprecipitation, domain-specific binding assays\",\n      \"journal\": \"European journal of biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — yeast two-hybrid confirmed by co-IP with domain specificity determination, single lab\",\n      \"pmids\": [\"15009209\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"NUB1/NUB1L is an adaptor protein that negatively regulates the NEDD8 conjugation system and ubiquitin-like modifier FAT10 by binding NEDD8 and FAT10 through its C-terminal NEDD8-binding site(s) and UBA domain, recruiting them and their conjugates to the 26S proteasome for degradation via direct interaction with proteasomal subunits S5a/Rpn10 (through a non-UBL C-terminal region) and Rpn1; mechanistically, NUB1L traps the N-terminal domain of FAT10 in an unfolded state to enable ubiquitin-independent and p97-independent substrate delivery to the proteasome, and together FAT10–NUB1L cooperate to activate proteasomal gate opening; NUB1 also modulates p53 localization via the NEDD8/ubiquitin/Mdm2 axis, reduces tau aggregation by promoting GSK3β degradation, and suppresses synphilin-1 inclusion formation and mutant huntingtin levels through proteasomal targeting; NUB1 activity itself is positively regulated by non-proteolytic di-ubiquitination at Lys-159 by Mdm2, by phosphorylation at Ser-46 which enhances aggregate clearance, and by cytoplasmic retention through interaction with AIPL1.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"NUB1/NUB1L is an interferon-inducible adaptor that negatively regulates the ubiquitin-like modifiers NEDD8 and FAT10 by recruiting them and their conjugates to the 26S proteasome for degradation [#0, #1]. It engages substrates through a conserved C-terminal NEDD8-binding site and, in the NUB1L splice variant, an additional UBA domain conferring a second NEDD8-binding site, with the C-terminal site being chiefly responsible for NEDD8 down-regulation [#2]. NUB1 docks onto the proteasome through a non-UBL C-terminal region (residues 536–584) that binds the VWA domain of S5a/Rpn10 and can also engage Rpn1 [#6, #10]. For FAT10-modified substrates, NUB1L enables proteasomal degradation independently of polyubiquitylation by trapping the FAT10 N-terminal ubiquitin-like domain in an unfolded state and delivering it to the proteasome via Rpn1, a ubiquitin- and p97-independent route resolved structurally by cryo-EM; FAT10 binding to the NUB1L UBA domains disrupts NUB1L dimerization, raising its affinity for Rpn1 and together activating 20S gate opening and all peptidolytic activities of the 26S proteasome [#17, #19]. Beyond modifier turnover, NUB1 acts as a protein quality-control factor: it promotes proteasomal clearance of synphilin-1, mutant huntingtin (via CUL3/NEDD8-dependent polyubiquitination), and GSK3β—thereby reducing tau phosphorylation and aggregation—and suppresses inclusion formation [#7, #11, #12]. Through the NEDD8/ubiquitin/Mdm2 axis NUB1 reduces p53 NEDDylation, stimulates its Mdm2-dependent ubiquitination, and drives cytoplasmic p53 with loss of transcriptional activity [#9]. NUB1 activity is itself positively regulated by non-proteolytic K159 di-ubiquitination by Mdm2 and by Ser-46 phosphorylation that enhances aggregate clearance [#15, #16], and its subcellular distribution is controlled by AIPL1, which retains NUB1 in the cytoplasm [#3, #4].\",\n  \"teleology\": [\n    {\n      \"year\": 2001,\n      \"claim\": \"Established NUB1 as an interferon-inducible NEDD8-interacting protein that suppresses NEDD8 levels, defining its core role as a negative regulator of a ubiquitin-like modifier.\",\n      \"evidence\": \"Yeast two-hybrid and overexpression/western blot in U2OS cells\",\n      \"pmids\": [\"11259415\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of NEDD8 down-regulation not yet linked to the proteasome\", \"Direct binding interface on NEDD8 undefined\"]\n    },\n    {\n      \"year\": 2001,\n      \"claim\": \"Showed NUB1 functions as a proteasomal adaptor by binding S5a and recruiting NEDD8 conjugates for degradation, converting the regulatory observation into a delivery mechanism.\",\n      \"evidence\": \"GST pull-down with S5a, proteasome inhibitor blockade, overexpression\",\n      \"pmids\": [\"11585840\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Which NUB1 region binds S5a not yet mapped\", \"UBL domain role unresolved\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Defined the substrate-binding determinants by identifying the NUB1L UBA domain as a second NEDD8-binding site and a conserved Leu-rich motif required for NEDD8 binding, establishing how the adaptor recognizes its cargo.\",\n      \"evidence\": \"Mutagenesis and functional down-regulation assays\",\n      \"pmids\": [\"12816948\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the Leu-motif interaction not resolved\", \"Functional distinction between NUB1 and NUB1L variants incomplete\"]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"Identified AIPL1 as a NUB1 partner, opening a route to understanding NUB1 spatial regulation.\",\n      \"evidence\": \"Yeast two-hybrid and co-IP in Y79 retinoblastoma cells\",\n      \"pmids\": [\"12374762\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of the interaction not yet shown\", \"Interaction interface unmapped\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Showed AIPL1 retains NUB1 in the cytoplasm and suppresses NUB1-fragment inclusions, and that LCA-associated AIPL1 mutations (residues 181–330) abolish NUB1 binding, linking NUB1 localization control to disease-relevant AIPL1 variants.\",\n      \"evidence\": \"GFP-fusion imaging, domain deletion, and three independent interaction assays with LCA mutants\",\n      \"pmids\": [\"15347646\", \"15081406\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether disrupted NUB1 regulation contributes causally to LCA pathology untested\", \"Chaperone-like mechanism of inclusion suppression undefined\"]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Linked the UBA domain to alpha-linked polyubiquitin processing, suggesting NUB1 routes the ubiquitin precursor UbC1 to a hydrolase.\",\n      \"evidence\": \"Yeast two-hybrid, co-IP, and domain-specific binding assays\",\n      \"pmids\": [\"15009209\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The co-immunoprecipitating C-terminal hydrolase was never identified\", \"Physiological relevance of UbC1 processing unconfirmed\"]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"Mapped the proteasome-docking site to a non-UBL C-terminal region (536–584), separating substrate binding from proteasome engagement and clarifying the UBL domain is required for function but not S5a binding.\",\n      \"evidence\": \"In vitro GST pull-down, yeast two-hybrid, deletion mapping\",\n      \"pmids\": [\"16171779\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional role of the UBL domain still unexplained\", \"S5a residues contacted not defined\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"Extended NUB1 function to neurodegeneration-relevant substrates by showing it binds synphilin-1 via its NEDD8-binding site and promotes its proteasomal degradation and inclusion suppression.\",\n      \"evidence\": \"Co-IP, proteasome inhibitor assay, inclusion formation in HEK293\",\n      \"pmids\": [\"16877356\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether synphilin-1 is NEDD8/FAT10-modified prior to delivery unclear\", \"In vivo relevance to Parkinson pathology untested\"]\n    },\n    {\n      \"year\": 2009,\n      \"claim\": \"Demonstrated that FAT10-mediated proteasomal degradation is ubiquitin-independent and strictly requires NUB1L, establishing NUB1L as the essential delivery factor for the FAT10 pathway.\",\n      \"evidence\": \"In vitro reconstituted degradation with purified 26S proteasome and siRNA knockdown\",\n      \"pmids\": [\"19166848\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Proteasome receptor for the NUB1L-FAT10 complex not yet identified\", \"Conformational mechanism of substrate engagement unknown\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"Connected NUB1 to tumor-suppressor regulation by showing it lowers p53 NEDDylation, enhances Mdm2-mediated ubiquitination, and drives cytoplasmic p53 with loss of transcriptional activity.\",\n      \"evidence\": \"Overexpression, co-IP, fractionation/imaging, reporter assays\",\n      \"pmids\": [\"20101219\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct versus indirect effect on p53 modification not fully separated\", \"In vivo tumor relevance not addressed in this study\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Resolved the proteasome receptor by showing NUB1L and FAT10 bind the hRpn10/S5a VWA domain (with Rpn1 as a secondary site), and that this receptor is required for FAT10-conjugate turnover.\",\n      \"evidence\": \"Co-IP, yeast complementation, siRNA knockdown, domain mapping\",\n      \"pmids\": [\"22434192\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative contributions of Rpn10 versus Rpn1 in vivo unresolved\", \"Stoichiometry of the NUB1L-FAT10-proteasome assembly undefined\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Defined a tau-protective mechanism whereby NUB1 disrupts the tau-GSK3β interaction and degrades GSK3β (UBL- and UBA-dependent), reducing tau phosphorylation and aggregation.\",\n      \"evidence\": \"Co-IP, domain mutants, siRNA silencing, aggregation and phosphorylation assays\",\n      \"pmids\": [\"22965877\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether GSK3β degradation is NEDD8/FAT10-dependent unclear\", \"In vivo tauopathy effect not tested\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Showed NUB1 lowers mutant huntingtin via CUL3/NEDD8-dependent polyubiquitination and that interferon-β rescues neuronal toxicity through NUB1 induction, linking the interferon-NUB1 axis to Huntington disease.\",\n      \"evidence\": \"Genome-wide RNAi screen, Drosophila validation, ubiquitination and inhibitor assays\",\n      \"pmids\": [\"23525043\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct NUB1 contact with mHTT versus indirect CUL3 effect not separated\", \"Therapeutic window of interferon induction undefined\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Identified NEDD8 residue Asn-51 recognition and a VCP-binding motif, showing NUB1L coordinates with the p97-UFD1-NPL4 complex for NEDD8 delivery and does not bind ubiquitin.\",\n      \"evidence\": \"Co-IP, Asn-51 mutagenesis, in vitro binding\",\n      \"pmids\": [\"24019527\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Reconciliation with later p97-independent FAT10 delivery unresolved\", \"p97 dependence for NEDD8 versus FAT10 cargo differs\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Showed NUB1L suppresses atypical neddylation and promotes misfolded-protein clearance, accumulating CryAB(R120G) on loss, broadening NUB1L to general proteostasis under stress.\",\n      \"evidence\": \"siRNA, overexpression, GFPu degradation assay in cardiomyocytes\",\n      \"pmids\": [\"26260793\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct enzymatic target of atypical neddylation suppression unclear\", \"Cardiac phenotype in vivo not established\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Revealed an activating modification: Mdm2 induces non-proteolytic K159 di-ubiquitination of NUB1 that is required for its repression of NEDD8, defining a positive feedback regulator of NUB1.\",\n      \"evidence\": \"Co-IP, K159R mutagenesis, ubiquitination assays\",\n      \"pmids\": [\"28099510\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How K159 di-ubiquitin alters NUB1 conformation/activity unknown\", \"Ubiquitin chain linkage type at K159 not defined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified Ser-46 phosphorylation as an activating mark enhancing aggregate degradation, with disease-specific presence in Lewy bodies, linking NUB1 phospho-regulation to synucleinopathy pathology.\",\n      \"evidence\": \"Phosphomimetic mutant, aggregate degradation assay, immunohistochemistry\",\n      \"pmids\": [\"31006160\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Kinase responsible for Ser-46 phosphorylation unidentified\", \"Causal versus correlative link to Lewy body pathology unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Provided the mechanistic basis for proteasome activation by showing FAT10 binding to NUB1L UBA domains blocks NUB1L dimerization, raising Rpn1 affinity and triggering 20S gate opening independent of ubiquitin and USP14.\",\n      \"evidence\": \"In vitro proteasome activity assays, co-IP, domain interaction studies\",\n      \"pmids\": [\"37188463\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural state of the activated proteasome not yet visualized in this study\", \"Whether NEDD8 cargo activates the proteasome similarly untested\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Delivered a structural model showing NUB1 traps the FAT10 N-terminal UBL domain unfolded and docks onto Rpn1 for ubiquitin- and p97-independent degradation, integrating prior receptor and activation data into a delivery mechanism.\",\n      \"evidence\": \"In vitro reconstitution, HDX-MS, cryo-EM, site-directed mutagenesis\",\n      \"pmids\": [\"40217121\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Dynamics of the complex limit a single high-resolution snapshot\", \"Whether NEDD8 cargo uses the same unfolding-trap mechanism not shown\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Connected NUB1 loss to oncogenesis by showing reduced NUB1 elevates NEDD8, promoting PCNA K164 NEDDylation that antagonizes its K48 ubiquitination and stabilizes PCNA to drive hepatocellular carcinoma growth.\",\n      \"evidence\": \"Knockdown/overexpression, K164 mutagenesis, xenograft, western blot, NEDDylation inhibitor TAS4464\",\n      \"pmids\": [\"40164590\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Whether NUB1 directly controls PCNA modification or acts solely via NEDD8 levels unclear\", \"Clinical correlation of NUB1 loss across tumor types not established\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Implicated NUB1 in inflammatory signaling by showing its overexpression suppresses NF-κB nuclear translocation and IL-6 in stimulated rheumatoid arthritis synoviocytes via the neddylation/CUL1 axis.\",\n      \"evidence\": \"Overexpression, NF-κB translocation assay, RT-PCR in RA FLS\",\n      \"pmids\": [\"38566346\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct CUL1-substrate target mediating the effect not identified\", \"In vivo arthritis model not tested\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether the unfolding-trap delivery mechanism defined for FAT10 also governs NUB1-mediated NEDD8 and misfolded-substrate turnover, and how the K159 di-ubiquitination and Ser-46 phosphorylation marks structurally activate NUB1, remain open.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural comparison of NEDD8 versus FAT10 cargo delivery\", \"Kinase and conformational consequences of activating modifications undefined\", \"Unified model reconciling p97-dependent NEDD8 and p97-independent FAT10 routes lacking\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [1, 6, 10, 19]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [0, 2, 14, 17]},\n      {\"term_id\": \"GO:0031386\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [0, 4]},\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [1, 8, 10, 17, 19]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 2, 13]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"NEDD8\", \"FAT10\", \"PSMD4\", \"RPN1\", \"AIPL1\", \"GSK3B\", \"MDM2\", \"VCP\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":7,"faith_total":7,"faith_pct":100.0}}