{"gene":"WDSUB1","run_date":"2026-04-28T23:00:23","timeline":{"discoveries":[{"year":2010,"finding":"WDSUB1 encodes a U-box domain-containing ubiquitin ligase (E3), representing one of seven main U-box ubiquitin ligase genes in humans, with phylogenetic analysis placing its origin in placozoans, cnidarians, and bilaterians.","method":"Phylogenetic and structural domain analysis","journal":"BMC evolutionary biology","confidence":"Low","confidence_rationale":"Tier 4 — computational/phylogenetic inference only, no direct enzymatic assay","pmids":["20979629"],"is_preprint":false},{"year":2023,"finding":"WDSUB1 was identified as an E3 ubiquitin ligase that binds to WHRN and regulates ubiquitination and stability of USH2A in a WHRN phosphorylation-dependent manner within the ankle-link complex (ALC) of hair cells.","method":"Yeast two-hybrid screening, NMR spectrometry, FlAsH-BRET assay, mutagenesis analysis","journal":"Advanced science","confidence":"High","confidence_rationale":"Tier 1–2 — multiple orthogonal methods (Y2H, NMR, BRET, mutagenesis) in a single study establishing direct binding and functional ubiquitination","pmids":["37066759"],"is_preprint":false},{"year":2023,"finding":"ADGRV1 inhibits WHRN phosphorylation via regional cAMP-PKA signaling, which in turn modulates WDSUB1 binding to WHRN and thereby controls USH2A ubiquitination and stability; the deafness-associated ADGRV1 Y6236fsX1 mutation abolishes this regulation.","method":"Adgrv1 mutant mouse model, biochemical interaction assays, NMR spectrometry, mutagenesis, FlAsH-BRET assay","journal":"Advanced science","confidence":"High","confidence_rationale":"Tier 1–2 — genetic mouse model combined with multiple orthogonal biochemical methods establishing pathway position","pmids":["37066759"],"is_preprint":false},{"year":2022,"finding":"WDSUB1 knockdown in a mouse colitis model reduced expression of inflammatory cytokines (IL-6, COX-2, TNF-α) and altered IκBα protein levels, suggesting WDSUB1 positively regulates NF-κB signaling in intestinal inflammation.","method":"siRNA knockdown in vivo (C57BL/6 mice, DSS-colitis model), Western blotting, RT-PCR","journal":"Journal of Southern Medical University","confidence":"Medium","confidence_rationale":"Tier 2–3 — clean in vivo KD with defined phenotypic and molecular readouts but no direct biochemical mechanism linking WDSUB1 E3 activity to NF-κB substrates","pmids":["36073209"],"is_preprint":false}],"current_model":"WDSUB1 is a U-box E3 ubiquitin ligase that binds phosphorylated WHRN within the ankle-link complex of hair cells to ubiquitinate and destabilize USH2A, a process regulated upstream by ADGRV1-dependent cAMP-PKA signaling; WDSUB1 also appears to promote NF-κB-mediated inflammatory signaling in intestinal epithelial contexts."},"narrative":{"teleology":[{"year":2010,"claim":"Computational identification of WDSUB1 as a U-box E3 ubiquitin ligase established its predicted enzymatic class, but left its substrates and biological roles unknown.","evidence":"Phylogenetic and structural domain analysis across metazoan genomes","pmids":["20979629"],"confidence":"Low","gaps":["No direct enzymatic assay confirming E3 ubiquitin ligase activity","No substrates or biological processes identified","Computational inference only, awaits biochemical reconstitution"]},{"year":2022,"claim":"In vivo knockdown in a colitis model showed that WDSUB1 promotes NF-κB-dependent inflammatory signaling in intestinal epithelium, revealing a biological function but not a direct E3 substrate.","evidence":"siRNA knockdown in DSS-induced colitis in C57BL/6 mice with Western blot and RT-PCR readouts","pmids":["36073209"],"confidence":"Medium","gaps":["No direct biochemical link between WDSUB1 E3 activity and IκBα or other NF-κB pathway substrates","siRNA specificity not independently validated by rescue or genetic knockout","Mechanism by which WDSUB1 regulates NF-κB signaling (direct ubiquitination target) remains unidentified"]},{"year":2023,"claim":"Identification of WHRN as a direct binding partner and USH2A as a ubiquitination target established the first complete substrate-pathway assignment for WDSUB1 within the hair-cell ankle-link complex, placing it downstream of ADGRV1-cAMP-PKA signaling.","evidence":"Yeast two-hybrid, NMR spectrometry, FlAsH-BRET, mutagenesis, and Adgrv1 mutant mouse model","pmids":["37066759"],"confidence":"High","gaps":["In vitro reconstitution of WDSUB1-catalyzed USH2A ubiquitination with purified components has not been reported","Structural basis for WDSUB1 U-box domain engagement with E2 enzymes is unknown","Whether WDSUB1 ubiquitinates additional substrates beyond USH2A in hair cells or other tissues is unresolved"]},{"year":null,"claim":"It remains unknown whether WDSUB1's E3 ligase activity directly ubiquitinates NF-κB pathway components, whether USH2A is the sole physiological substrate in hair cells, and what structural features govern WDSUB1 substrate selectivity.","evidence":"","pmids":[],"confidence":"Low","gaps":["No structural model of WDSUB1 U-box or WD-repeat domains exists","The relationship between the hair-cell and inflammatory signaling functions is unexplored","No in vivo hair-cell phenotype from WDSUB1 loss-of-function has been reported"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1,2]}],"localization":[],"pathway":[{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[1,2]},{"term_id":"R-HSA-168256","term_label":"Immune System","supporting_discovery_ids":[3]}],"complexes":["ankle-link complex"],"partners":["WHRN","USH2A","ADGRV1"],"other_free_text":[]},"mechanistic_narrative":"WDSUB1 is a U-box domain-containing E3 ubiquitin ligase that functions within the ankle-link complex (ALC) of inner-ear hair cells to regulate the stability of USH2A [PMID:37066759]. WDSUB1 binds phosphorylated WHRN and ubiquitinates USH2A, promoting its degradation; this interaction is controlled upstream by ADGRV1, which suppresses WHRN phosphorylation through regional cAMP-PKA signaling, and a deafness-associated ADGRV1 frameshift mutation abolishes this regulation [PMID:37066759]. In intestinal epithelial contexts, WDSUB1 positively regulates NF-κB-mediated inflammatory cytokine expression, as its knockdown in a mouse colitis model reduces IL-6, COX-2, and TNF-α levels and alters IκBα protein abundance [PMID:36073209]."},"prefetch_data":{"uniprot":{"accession":"Q8N9V3","full_name":"WD repeat, SAM and U-box domain-containing protein 1","aliases":[],"length_aa":476,"mass_kda":52.8,"function":"","subcellular_location":"","url":"https://www.uniprot.org/uniprotkb/Q8N9V3/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/WDSUB1","classification":"Not Classified","n_dependent_lines":3,"n_total_lines":1208,"dependency_fraction":0.0024834437086092716},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/WDSUB1","total_profiled":1310},"omim":[{"mim_id":"620802","title":"WD REPEAT-, STERILE ALPHA MOTIF-, AND U-BOX DOMAIN-CONTAINING PROTEIN 1; WDSUB1","url":"https://www.omim.org/entry/620802"},{"mim_id":"602851","title":"ADHESION G PROTEIN-COUPLED RECEPTOR V1; ADGRV1","url":"https://www.omim.org/entry/602851"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoli","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/WDSUB1"},"hgnc":{"alias_symbol":["UBOX6","FLJ36175"],"prev_symbol":["WDSAM1"]},"alphafold":{"accession":"Q8N9V3","domains":[{"cath_id":"2.130.10.10","chopping":"3-320","consensus_level":"high","plddt":91.8303,"start":3,"end":320},{"cath_id":"1.10.150.50","chopping":"330-402","consensus_level":"high","plddt":84.7242,"start":330,"end":402},{"cath_id":"3.30.40.10","chopping":"407-476","consensus_level":"high","plddt":86.5004,"start":407,"end":476}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N9V3","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N9V3-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q8N9V3-F1-predicted_aligned_error_v6.png","plddt_mean":88.88},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=WDSUB1","jax_strain_url":"https://www.jax.org/strain/search?query=WDSUB1"},"sequence":{"accession":"Q8N9V3","fasta_url":"https://rest.uniprot.org/uniprotkb/Q8N9V3.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q8N9V3/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q8N9V3"}},"corpus_meta":[{"pmid":"28077804","id":"PMC_28077804","title":"The complex genetics of gait speed: genome-wide meta-analysis approach.","date":"2017","source":"Aging","url":"https://pubmed.ncbi.nlm.nih.gov/28077804","citation_count":25,"is_preprint":false},{"pmid":"20979629","id":"PMC_20979629","title":"Ancient origin of animal U-box ubiquitin ligases.","date":"2010","source":"BMC evolutionary biology","url":"https://pubmed.ncbi.nlm.nih.gov/20979629","citation_count":25,"is_preprint":false},{"pmid":"37066759","id":"PMC_37066759","title":"Deafness-Associated ADGRV1 Mutation Impairs USH2A Stability through Improper Phosphorylation of WHRN and WDSUB1 Recruitment.","date":"2023","source":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/37066759","citation_count":13,"is_preprint":false},{"pmid":"33491795","id":"PMC_33491795","title":"Genetic determinants of ferritin, haemoglobin levels and haemoglobin trajectories: results from Donor InSight.","date":"2021","source":"Vox sanguinis","url":"https://pubmed.ncbi.nlm.nih.gov/33491795","citation_count":6,"is_preprint":false},{"pmid":"36073209","id":"PMC_36073209","title":"[WDSUB1 knockdown alleviates dextran sulfate sodium-induced colitis in mice by inhibiting nuclear factor-κB signaling pathway].","date":"2022","source":"Nan fang yi ke da xue xue bao = Journal of Southern Medical University","url":"https://pubmed.ncbi.nlm.nih.gov/36073209","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":3926,"output_tokens":965,"usd":0.013126},"stage2":{"model":"claude-opus-4-6","input_tokens":4192,"output_tokens":1249,"usd":0.078277},"total_usd":0.091403,"stage1_batch_id":"msgbatch_01BparvgRZ9S2LMidvaoo86K","stage2_batch_id":"msgbatch_01NkBfv9SVZWthhS7j6mU6G3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"WDSUB1 encodes a U-box domain-containing ubiquitin ligase (E3), representing one of seven main U-box ubiquitin ligase genes in humans, with phylogenetic analysis placing its origin in placozoans, cnidarians, and bilaterians.\",\n      \"method\": \"Phylogenetic and structural domain analysis\",\n      \"journal\": \"BMC evolutionary biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 — computational/phylogenetic inference only, no direct enzymatic assay\",\n      \"pmids\": [\"20979629\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"WDSUB1 was identified as an E3 ubiquitin ligase that binds to WHRN and regulates ubiquitination and stability of USH2A in a WHRN phosphorylation-dependent manner within the ankle-link complex (ALC) of hair cells.\",\n      \"method\": \"Yeast two-hybrid screening, NMR spectrometry, FlAsH-BRET assay, mutagenesis analysis\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — multiple orthogonal methods (Y2H, NMR, BRET, mutagenesis) in a single study establishing direct binding and functional ubiquitination\",\n      \"pmids\": [\"37066759\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"ADGRV1 inhibits WHRN phosphorylation via regional cAMP-PKA signaling, which in turn modulates WDSUB1 binding to WHRN and thereby controls USH2A ubiquitination and stability; the deafness-associated ADGRV1 Y6236fsX1 mutation abolishes this regulation.\",\n      \"method\": \"Adgrv1 mutant mouse model, biochemical interaction assays, NMR spectrometry, mutagenesis, FlAsH-BRET assay\",\n      \"journal\": \"Advanced science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 — genetic mouse model combined with multiple orthogonal biochemical methods establishing pathway position\",\n      \"pmids\": [\"37066759\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"WDSUB1 knockdown in a mouse colitis model reduced expression of inflammatory cytokines (IL-6, COX-2, TNF-α) and altered IκBα protein levels, suggesting WDSUB1 positively regulates NF-κB signaling in intestinal inflammation.\",\n      \"method\": \"siRNA knockdown in vivo (C57BL/6 mice, DSS-colitis model), Western blotting, RT-PCR\",\n      \"journal\": \"Journal of Southern Medical University\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 — clean in vivo KD with defined phenotypic and molecular readouts but no direct biochemical mechanism linking WDSUB1 E3 activity to NF-κB substrates\",\n      \"pmids\": [\"36073209\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"WDSUB1 is a U-box E3 ubiquitin ligase that binds phosphorylated WHRN within the ankle-link complex of hair cells to ubiquitinate and destabilize USH2A, a process regulated upstream by ADGRV1-dependent cAMP-PKA signaling; WDSUB1 also appears to promote NF-κB-mediated inflammatory signaling in intestinal epithelial contexts.\"\n}\n```","stage2_raw":"```json\n{\n  \"mechanistic_narrative\": \"WDSUB1 is a U-box domain-containing E3 ubiquitin ligase that functions within the ankle-link complex (ALC) of inner-ear hair cells to regulate the stability of USH2A [PMID:37066759]. WDSUB1 binds phosphorylated WHRN and ubiquitinates USH2A, promoting its degradation; this interaction is controlled upstream by ADGRV1, which suppresses WHRN phosphorylation through regional cAMP-PKA signaling, and a deafness-associated ADGRV1 frameshift mutation abolishes this regulation [PMID:37066759]. In intestinal epithelial contexts, WDSUB1 positively regulates NF-κB-mediated inflammatory cytokine expression, as its knockdown in a mouse colitis model reduces IL-6, COX-2, and TNF-α levels and alters IκBα protein abundance [PMID:36073209].\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Computational identification of WDSUB1 as a U-box E3 ubiquitin ligase established its predicted enzymatic class, but left its substrates and biological roles unknown.\",\n      \"evidence\": \"Phylogenetic and structural domain analysis across metazoan genomes\",\n      \"pmids\": [\"20979629\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No direct enzymatic assay confirming E3 ubiquitin ligase activity\",\n        \"No substrates or biological processes identified\",\n        \"Computational inference only, awaits biochemical reconstitution\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"In vivo knockdown in a colitis model showed that WDSUB1 promotes NF-κB-dependent inflammatory signaling in intestinal epithelium, revealing a biological function but not a direct E3 substrate.\",\n      \"evidence\": \"siRNA knockdown in DSS-induced colitis in C57BL/6 mice with Western blot and RT-PCR readouts\",\n      \"pmids\": [\"36073209\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\n        \"No direct biochemical link between WDSUB1 E3 activity and IκBα or other NF-κB pathway substrates\",\n        \"siRNA specificity not independently validated by rescue or genetic knockout\",\n        \"Mechanism by which WDSUB1 regulates NF-κB signaling (direct ubiquitination target) remains unidentified\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Identification of WHRN as a direct binding partner and USH2A as a ubiquitination target established the first complete substrate-pathway assignment for WDSUB1 within the hair-cell ankle-link complex, placing it downstream of ADGRV1-cAMP-PKA signaling.\",\n      \"evidence\": \"Yeast two-hybrid, NMR spectrometry, FlAsH-BRET, mutagenesis, and Adgrv1 mutant mouse model\",\n      \"pmids\": [\"37066759\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"In vitro reconstitution of WDSUB1-catalyzed USH2A ubiquitination with purified components has not been reported\",\n        \"Structural basis for WDSUB1 U-box domain engagement with E2 enzymes is unknown\",\n        \"Whether WDSUB1 ubiquitinates additional substrates beyond USH2A in hair cells or other tissues is unresolved\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown whether WDSUB1's E3 ligase activity directly ubiquitinates NF-κB pathway components, whether USH2A is the sole physiological substrate in hair cells, and what structural features govern WDSUB1 substrate selectivity.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No structural model of WDSUB1 U-box or WD-repeat domains exists\",\n        \"The relationship between the hair-cell and inflammatory signaling functions is unexplored\",\n        \"No in vivo hair-cell phenotype from WDSUB1 loss-of-function has been reported\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"localization\": [],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [1, 2]},\n      {\"term_id\": \"R-HSA-168256\", \"supporting_discovery_ids\": [3]}\n    ],\n    \"complexes\": [\"ankle-link complex\"],\n    \"partners\": [\"WHRN\", \"USH2A\", \"ADGRV1\"],\n    \"other_free_text\": []\n  }\n}\n```"}