{"gene":"WDSUB1","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":2010,"finding":"WDSUB1 encodes a U-box ubiquitin ligase (UUL), placing it in the U-box-containing E3 ligase family; phylogenetic analysis indicates it is present in placozoans, cnidarians, and bilaterians, representing the seventh main human UUL gene.","method":"Phylogenetic and structural/domain analysis of UUL gene families across metazoans","journal":"BMC evolutionary biology","confidence":"Low","confidence_rationale":"Tier 4 / Weak — computational/phylogenetic analysis only, no direct biochemical assay of WDSUB1 enzymatic activity","pmids":["20979629"],"is_preprint":false},{"year":2023,"finding":"WDSUB1 (an E3 ubiquitin ligase) binds directly to WHRN and regulates ubiquitination and stability of USH2A in a WHRN phosphorylation-dependent manner within the ankle-link complex (ALC) of hair cells; this interaction was disrupted when ADGRV1 Y6236fsX1 mutation prevents ADGRV1-mediated inhibition of WHRN phosphorylation via cAMP-PKA signaling.","method":"Yeast two-hybrid screening (identified WDSUB1–WHRN interaction), FlAsH-BRET assay, NMR spectrometry, mutagenesis analysis, in vivo mouse model (Adgrv1 Y6236fsX1 mutant)","journal":"Advanced science (Weinheim, Baden-Wurttemberg, Germany)","confidence":"High","confidence_rationale":"Tier 1–2 / Moderate — multiple orthogonal methods (yeast two-hybrid, BRET, NMR, mutagenesis, in vivo model) in a single rigorous study establishing binding partner, substrate, and regulatory mechanism","pmids":["37066759"],"is_preprint":false},{"year":2022,"finding":"WDSUB1 knockdown in a mouse DSS-induced colitis model reduced expression of inflammatory cytokines (IL-6, COX-2, TNF-α) and altered IκBα protein levels without changing P65 expression, suggesting WDSUB1 promotes NF-κB signaling in colonic inflammation.","method":"siRNA knockdown in mice (in vivo), Western blotting, RT-PCR for inflammatory markers","journal":"Nan fang yi ke da xue xue bao = Journal of Southern Medical University","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, in vivo knockdown with pathway marker readout but no direct biochemical substrate identification or pathway reconstitution","pmids":["36073209"],"is_preprint":false}],"current_model":"WDSUB1 is a U-box E3 ubiquitin ligase that binds WHRN (whirlin) in the hair-cell ankle-link complex and regulates USH2A ubiquitination and stability in a manner dependent on the phosphorylation state of WHRN, which is itself controlled by ADGRV1-mediated cAMP-PKA signaling; additionally, WDSUB1 appears to promote NF-κB-dependent inflammatory signaling in intestinal epithelial cells, as its knockdown attenuates colitis."},"narrative":{"mechanistic_narrative":"WDSUB1 is a U-box-containing E3 ubiquitin ligase that controls protein stability within the hair-cell ankle-link complex [PMID:37066759]. It binds directly to WHRN (whirlin) and, through this interaction, regulates the ubiquitination and stability of USH2A in a manner dependent on the phosphorylation state of WHRN; this regulatory coupling is disrupted by an ADGRV1 frameshift mutation that abrogates ADGRV1-mediated, cAMP-PKA-driven control of WHRN phosphorylation [PMID:37066759]. Beyond its role in the ankle-link complex, knockdown studies place WDSUB1 as a positive contributor to NF-κB-dependent inflammatory signaling in colonic epithelium [PMID:36073209]. Beyond these contexts, no further substrate repertoire or catalytic mechanism for WDSUB1 has been characterized in the available corpus.","teleology":[{"year":2010,"claim":"Established WDSUB1's molecular identity by classifying it within the U-box E3 ubiquitin ligase family, framing it as a candidate ubiquitination enzyme before any substrate was known.","evidence":"Phylogenetic and domain analysis of U-box ligase families across metazoans","pmids":["20979629"],"confidence":"Low","gaps":["Computational classification only; no direct biochemical demonstration of E3 ligase activity","No substrate or interacting partner identified at this stage","No subcellular localization established"]},{"year":2022,"claim":"Linked WDSUB1 to inflammatory signaling by showing its knockdown attenuates cytokine production and alters IκBα in colitis, implicating it as a positive regulator of NF-κB.","evidence":"siRNA knockdown in a mouse DSS-induced colitis model with Western blotting and RT-PCR readouts","pmids":["36073209"],"confidence":"Low","gaps":["No direct biochemical substrate identified; pathway readout is correlative","Mechanism connecting WDSUB1 to IκBα turnover not reconstituted","Single-lab in vivo study without orthogonal confirmation"]},{"year":2023,"claim":"Defined WDSUB1's first concrete molecular function by identifying WHRN as a direct binding partner and USH2A as a substrate whose ubiquitination and stability it controls, integrating it into ADGRV1-cAMP-PKA-regulated ankle-link biology.","evidence":"Yeast two-hybrid, FlAsH-BRET, NMR, mutagenesis, and an Adgrv1 Y6236fsX1 mutant mouse model","pmids":["37066759"],"confidence":"High","gaps":["Direct E3 ligase catalytic activity on USH2A not reconstituted in vitro with purified components","How WHRN phosphorylation state physically gates WDSUB1-mediated ubiquitination is not resolved","Relationship between the ankle-link role and the colitis/NF-κB phenotype is unknown"]},{"year":null,"claim":"Whether WDSUB1's reported inflammatory function and its hair-cell ankle-link function reflect a shared ubiquitination mechanism, and what its full substrate repertoire is, remains unresolved.","evidence":"No reconciling study present in the corpus","pmids":[],"confidence":"Low","gaps":["No unifying biochemical mechanism connecting the two contexts","Catalytic E3 activity not directly demonstrated in any system","Subcellular localization of WDSUB1 not directly established"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[1]},{"term_id":"GO:0016874","term_label":"ligase activity","supporting_discovery_ids":[1]}],"localization":[],"pathway":[],"complexes":["ankle-link complex"],"partners":["WHRN","USH2A"],"other_free_text":[]}},"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":14,"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":4698,"output_tokens":911,"usd":0.013879,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":7403,"output_tokens":1593,"usd":0.03842,"stage2_stop_reason":"end_turn"},"total_usd":0.052299,"stage1_batch_id":"msgbatch_01UT1AahFPCAyn2uVweS7A9z","stage2_batch_id":"msgbatch_01HuKWtKNT4Pqj1bc8eEP5RV","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"WDSUB1 encodes a U-box ubiquitin ligase (UUL), placing it in the U-box-containing E3 ligase family; phylogenetic analysis indicates it is present in placozoans, cnidarians, and bilaterians, representing the seventh main human UUL gene.\",\n      \"method\": \"Phylogenetic and structural/domain analysis of UUL gene families across metazoans\",\n      \"journal\": \"BMC evolutionary biology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — computational/phylogenetic analysis only, no direct biochemical assay of WDSUB1 enzymatic activity\",\n      \"pmids\": [\"20979629\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"WDSUB1 (an E3 ubiquitin ligase) binds directly to WHRN and regulates ubiquitination and stability of USH2A in a WHRN phosphorylation-dependent manner within the ankle-link complex (ALC) of hair cells; this interaction was disrupted when ADGRV1 Y6236fsX1 mutation prevents ADGRV1-mediated inhibition of WHRN phosphorylation via cAMP-PKA signaling.\",\n      \"method\": \"Yeast two-hybrid screening (identified WDSUB1–WHRN interaction), FlAsH-BRET assay, NMR spectrometry, mutagenesis analysis, in vivo mouse model (Adgrv1 Y6236fsX1 mutant)\",\n      \"journal\": \"Advanced science (Weinheim, Baden-Wurttemberg, Germany)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Moderate — multiple orthogonal methods (yeast two-hybrid, BRET, NMR, mutagenesis, in vivo model) in a single rigorous study establishing binding partner, substrate, and regulatory mechanism\",\n      \"pmids\": [\"37066759\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"WDSUB1 knockdown in a mouse DSS-induced colitis model reduced expression of inflammatory cytokines (IL-6, COX-2, TNF-α) and altered IκBα protein levels without changing P65 expression, suggesting WDSUB1 promotes NF-κB signaling in colonic inflammation.\",\n      \"method\": \"siRNA knockdown in mice (in vivo), Western blotting, RT-PCR for inflammatory markers\",\n      \"journal\": \"Nan fang yi ke da xue xue bao = Journal of Southern Medical University\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, in vivo knockdown with pathway marker readout but no direct biochemical substrate identification or pathway reconstitution\",\n      \"pmids\": [\"36073209\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"WDSUB1 is a U-box E3 ubiquitin ligase that binds WHRN (whirlin) in the hair-cell ankle-link complex and regulates USH2A ubiquitination and stability in a manner dependent on the phosphorylation state of WHRN, which is itself controlled by ADGRV1-mediated cAMP-PKA signaling; additionally, WDSUB1 appears to promote NF-κB-dependent inflammatory signaling in intestinal epithelial cells, as its knockdown attenuates colitis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"WDSUB1 is a U-box-containing E3 ubiquitin ligase that controls protein stability within the hair-cell ankle-link complex [#1]. It binds directly to WHRN (whirlin) and, through this interaction, regulates the ubiquitination and stability of USH2A in a manner dependent on the phosphorylation state of WHRN; this regulatory coupling is disrupted by an ADGRV1 frameshift mutation that abrogates ADGRV1-mediated, cAMP-PKA-driven control of WHRN phosphorylation [#1]. Beyond its role in the ankle-link complex, knockdown studies place WDSUB1 as a positive contributor to NF-\\u03baB-dependent inflammatory signaling in colonic epithelium [#2]. Beyond these contexts, no further substrate repertoire or catalytic mechanism for WDSUB1 has been characterized in the available corpus.\",\n  \"teleology\": [\n    {\n      \"year\": 2010,\n      \"claim\": \"Established WDSUB1's molecular identity by classifying it within the U-box E3 ubiquitin ligase family, framing it as a candidate ubiquitination enzyme before any substrate was known.\",\n      \"evidence\": \"Phylogenetic and domain analysis of U-box ligase families across metazoans\",\n      \"pmids\": [\n        \"20979629\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"Computational classification only; no direct biochemical demonstration of E3 ligase activity\",\n        \"No substrate or interacting partner identified at this stage\",\n        \"No subcellular localization established\"\n      ]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Linked WDSUB1 to inflammatory signaling by showing its knockdown attenuates cytokine production and alters I\\u03baB\\u03b1 in colitis, implicating it as a positive regulator of NF-\\u03baB.\",\n      \"evidence\": \"siRNA knockdown in a mouse DSS-induced colitis model with Western blotting and RT-PCR readouts\",\n      \"pmids\": [\n        \"36073209\"\n      ],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No direct biochemical substrate identified; pathway readout is correlative\",\n        \"Mechanism connecting WDSUB1 to I\\u03baB\\u03b1 turnover not reconstituted\",\n        \"Single-lab in vivo study without orthogonal confirmation\"\n      ]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Defined WDSUB1's first concrete molecular function by identifying WHRN as a direct binding partner and USH2A as a substrate whose ubiquitination and stability it controls, integrating it into ADGRV1-cAMP-PKA-regulated ankle-link biology.\",\n      \"evidence\": \"Yeast two-hybrid, FlAsH-BRET, NMR, mutagenesis, and an Adgrv1 Y6236fsX1 mutant mouse model\",\n      \"pmids\": [\n        \"37066759\"\n      ],\n      \"confidence\": \"High\",\n      \"gaps\": [\n        \"Direct E3 ligase catalytic activity on USH2A not reconstituted in vitro with purified components\",\n        \"How WHRN phosphorylation state physically gates WDSUB1-mediated ubiquitination is not resolved\",\n        \"Relationship between the ankle-link role and the colitis/NF-\\u03baB phenotype is unknown\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"Whether WDSUB1's reported inflammatory function and its hair-cell ankle-link function reflect a shared ubiquitination mechanism, and what its full substrate repertoire is, remains unresolved.\",\n      \"evidence\": \"No reconciling study present in the corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\n        \"No unifying biochemical mechanism connecting the two contexts\",\n        \"Catalytic E3 activity not directly demonstrated in any system\",\n        \"Subcellular localization of WDSUB1 not directly established\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\n        \"term_id\": \"GO:0140096\",\n        \"supporting_discovery_ids\": [\n          1\n        ]\n      },\n      {\n        \"term_id\": \"GO:0016874\",\n        \"supporting_discovery_ids\": [\n          1\n        ]\n      }\n    ],\n    \"localization\": [],\n    \"pathway\": [],\n    \"complexes\": [\n      \"ankle-link complex\"\n    ],\n    \"partners\": [\n      \"WHRN\",\n      \"USH2A\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"faith_supported":3,"faith_total":3,"faith_pct":100.0}}