{"gene":"WDR6","run_date":"2026-06-11T09:02:06","timeline":{"discoveries":[{"year":2020,"finding":"WDR6 is an interacting protein of FTSJ1 (human TRM7 ortholog), and the FTSJ1-WDR6 complex reconstituted in vitro catalyzes 2'-O-methylation at position 34 of specific tRNAs, with m1G37 as a prerequisite for this activity.","method":"Co-immunoprecipitation to identify interaction; in vitro reconstitution of methyltransferase activity; genetic knockout of ftsj1 to assess modification loss","journal":"EMBO reports","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution of enzymatic activity with identified binding partner, plus in vivo validation in knockout cells, single lab but multiple orthogonal methods","pmids":["32558197"],"is_preprint":false},{"year":2014,"finding":"Yeast Trm734 (WDR6 ortholog) forms a complex with Trm7 to specifically 2'-O-methylate position 34 (N34) of tRNA anticodon loop substrates including tRNAPhe, tRNATrp, and tRNALeu; this is distinct from the Trm7-Trm732 complex which methylates position 32.","method":"Genetic complementation assays in S. cerevisiae and S. pombe deletion mutants; tRNA modification analysis; growth phenotype rescue experiments","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 2 / Strong — replicated across two yeast species with genetic and biochemical evidence; consistent with multiple independent studies","pmids":["25404562","25625329"],"is_preprint":false},{"year":2015,"finding":"Defects in the Trm7-Trm734 (WDR6 ortholog) complex result in loss of Gm34 on tRNAPhe, and a FTSJ1-p.A26P missense mutation (corresponding to nonsyndromic X-linked intellectual disability) specifically abolishes Gm34 without affecting Cm32; the reduced Gm34 is not due to weaker Trm734 binding to Trm7.","method":"LC-MS/MS tRNA modification analysis from patient cell lines and yeast trm7-A26P mutant; yeast complementation assays; binding assays","journal":"Human mutation","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — tRNA modification measured directly in patient cells and yeast model with mutagenesis, replicated in two independent NSXLID patient cell lines","pmids":["26310293"],"is_preprint":false},{"year":2019,"finding":"Crystal structure of the yeast Trm7-Trm734 (WDR6 ortholog) complex reveals Trm734 consists of three WD40 β-propeller domains (BPA, BPB, BPC); BPA and BPC form a V-shaped cleft that docks to Trm7; the C-terminal region of Trm7 is required for Trm734 binding; Trm734's BPB domain positions tRNA D-arm, placing the anticodon loop near Trm7's catalytic pocket; the complex is a heterodimer in solution.","method":"X-ray crystallography (apo and SAM-bound forms); SAXS; in vitro methylation assays with tRNA variants; mutagenesis of Trm7 and tRNA substrates","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure solved with functional validation by in vitro assays and mutagenesis in a single rigorous study","pmids":["31586407"],"is_preprint":false},{"year":2025,"finding":"The human FTSJ1-WDR6 complex (distinct from FTSJ1-THADA) mediates Nm34 modification; cryo-EM structure of the FTSJ1-THADA complex reveals FTSJ1 binds THADA via its C-terminal region with an interaction mode distinct from the FTSJ1-WDR6 complex, confirming that WDR6 and THADA occupy distinct functional niches as auxiliary subunits of FTSJ1.","method":"Cryo-electron microscopy structure determination; biochemical interaction analyses; comparison with previously solved FTSJ1-WDR6 structure","journal":"Communications biology","confidence":"Medium","confidence_rationale":"Tier 1 / Weak — cryo-EM structure of the THADA complex with structural comparison to WDR6 complex; single study, the WDR6-specific structural conclusions are indirectly inferred from the comparison","pmids":["40483304"],"is_preprint":false},{"year":2024,"finding":"Specific amino acids in Trm734 (WDR6 ortholog) located near the active site of Trm7 (not at the Trm7-Trm734 protein-protein interface) are required for tRNA modification activity; a nonfunctional but stable Trm734 variant was identified, suggesting these residues may be important for tRNA binding rather than protein complex assembly.","method":"Site-directed mutagenesis of Trm734; yeast functional complementation assays; immunoprecipitation to verify Trm7-Trm734 binding; structural mapping onto published crystal structure","journal":"ACS omega","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — mutagenesis with functional assays and Co-IP, single lab, single study","pmids":["38882062"],"is_preprint":false},{"year":2007,"finding":"WDR6 interacts with LKB1 (STK11) and is localized in the cytoplasm co-incident with LKB1; co-expression of WDR6 with LKB1 enhances LKB1-mediated inhibition of HeLa cell proliferation, synergizes to induce G1 cell cycle arrest, and elevates p27(Kip1) protein and promoter activity beyond the effect of LKB1 alone.","method":"Yeast two-hybrid screening; immunofluorescence co-localization; colony formation assay; cell cycle analysis; p27(Kip1) promoter-reporter assay; co-expression in HeLa cells","journal":"Molecular and cellular biochemistry","confidence":"Medium","confidence_rationale":"Tier 2–3 / Moderate — yeast two-hybrid plus multiple functional assays in cell culture; single lab but several orthogonal readouts","pmids":["17216128"],"is_preprint":false},{"year":2007,"finding":"WDR6 interacts with insulin receptor substrate 4 (IRS-4) in rat brain hypothalamus; WDR6 mRNA is abundantly expressed in the hypothalamus and is decreased by caloric restriction and in GH-antisense transgenic rats (both associated with increased lifespan); IGF-I and insulin treatment increase WDR6 gene expression in hypothalamic GT1-7 cells.","method":"Suppression subtractive hybridization; co-immunoprecipitation/interaction assay from rat brain; in vitro stimulation of GT1-7 cells with IGF-I/insulin","journal":"Neurobiology of aging","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP/interaction assay, expression-level readouts for most findings, single lab","pmids":["17720279"],"is_preprint":false},{"year":2019,"finding":"WDR6 is a component of a Cullin4-DDB1-WDR6 E3 ubiquitin ligase complex that binds SPAK and OSR1 kinases in a phosphorylation-dependent manner (dependent on S-motif phosphorylation); this binding is reduced under osmotic stress when the S-motif is phosphorylated, and OSR1 ubiquitylation is abolished under osmotic stress.","method":"Affinity pull-down; mass spectrometry; proteasomal and neddylation inhibitor treatment; osmotic stress experiments","journal":"Chembiochem","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — affinity pull-down plus mass spectrometry plus pharmacological inhibitor experiments, single lab, multiple orthogonal methods","pmids":["31614064"],"is_preprint":false},{"year":2023,"finding":"WDR6 promotes hepatic de novo lipogenesis during insulin resistance by interacting with PPP1CB (PP1β catalytic subunit) to facilitate PPP1CB dephosphorylation at Thr316, which subsequently enhances fatty acid synthase transcription through DNA-dependent protein kinase and upstream stimulatory factor 1.","method":"Co-immunoprecipitation; molecular dynamics simulation; in vivo mouse models of insulin resistance; siRNA knockdown and overexpression; transcription reporter assays","journal":"Nature metabolism","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP, in vivo mouse models, and mechanistic follow-up with transcriptional readouts; single lab but multiple methods","pmids":["37735236"],"is_preprint":false},{"year":2023,"finding":"WDR6 promotes UVRAG degradation by recruiting it to the CUL4A-DDB1-ROC1 E3 ubiquitin ligase complex through a WDxR motif; WDR6 deficiency in HCC cells reduces tumor growth and lung metastasis in immunocompetent mice but not in vitro, linked to blocking autophagic degradation of p65, elevating TNFα, increasing MDSCs, and reducing CD8+ T cell infiltration; TNFα activates NF-κB to transcribe WDR6, establishing a feedback loop.","method":"CRISPR/Cas9 knockout; co-immunoprecipitation; in vivo orthotopic tumor implantation in C57BL/6J mice; chromatin accessibility assays; flow cytometry for immune cell analysis; TNFα blockade experiments; peptide disruption assay","journal":"EMBO molecular medicine","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with functional in vivo validation and multiple mechanistic readouts, single lab","pmids":["36947051"],"is_preprint":false},{"year":2015,"finding":"WDR6 was identified as a restriction factor that inhibits replication of vaccinia virus K1L-C7L double deletion mutant in human cells; CRISPR/Cas9 knockout of WDR6 in HeLa cells permitted enhanced replication of the mutant virus; WDR6 acts independently of SAMD9 (interactions of WDR6 with SAMD9, C7, and K1 proteins were not detected), and WDR6 knockout did not reduce SAMD9 levels.","method":"Genome-wide siRNA screen; CRISPR/Cas9 knockout of WDR6 in HeLa cells; viral replication assays; immunoprecipitation (negative for WDR6-SAMD9/C7/K1 interactions)","journal":"mBio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — siRNA screen confirmed by CRISPR KO with viral replication readout, negative interaction result explicitly noted","pmids":["26242627"],"is_preprint":false},{"year":2000,"finding":"Human WDR6 encodes a protein of 1121 amino acids containing 11 WD-repeat units clustered in two groups separated by a putative transmembrane domain; the gene maps to chromosome 15q21 and is ubiquitously expressed in human adult and fetal tissues.","method":"Molecular cloning; Northern blot analysis; fluorescence in situ hybridization (FISH)","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Weak — direct molecular characterization by cloning, FISH, and Northern blot; foundational characterization paper, single lab","pmids":["10903905"],"is_preprint":false}],"current_model":"WDR6 (the human ortholog of yeast Trm734) functions primarily as an essential auxiliary subunit of the FTSJ1 methyltransferase complex, enabling 2'-O-methylation at position 34 of tRNAPhe (and related tRNAs) anticodon loop residues, a modification required for accurate translation and linked to neurological development; beyond tRNA biology, WDR6 participates in a CUL4A-DDB1-ROC1 E3 ubiquitin ligase complex to target substrates such as UVRAG and OSR1/SPAK kinases for ubiquitylation, interacts with LKB1 to synergistically induce p27(Kip1)-dependent G1 arrest, promotes hepatic de novo lipogenesis via PPP1CB dephosphorylation during insulin resistance, and restricts vaccinia virus replication in human cells independently of SAMD9."},"narrative":{"mechanistic_narrative":"WDR6 is a multidomain WD40-repeat protein that functions principally as an essential auxiliary subunit of the FTSJ1 tRNA methyltransferase, and more broadly as a substrate-recognition module in Cullin-based E3 ubiquitin ligase complexes [PMID:32558197, PMID:36947051, PMID:10903905]. As the human ortholog of yeast Trm734, WDR6 partners with FTSJ1 (Trm7) to catalyze 2'-O-methylation at position 34 (Nm34/Gm34) of anticodon-loop residues in specific tRNAs including tRNAPhe, tRNATrp, and tRNALeu, an activity requiring prior m1G37 and biochemically distinct from the FTSJ1-THADA and Trm7-Trm732 complexes that act at position 32 [PMID:32558197, PMID:25404562, PMID:25625329, PMID:40483304]. Structural analysis of the yeast complex shows that WDR6/Trm734 is built from three WD40 β-propeller domains: two propellers form a V-shaped cleft that docks onto the FTSJ1 C-terminus, while a third propeller positions the tRNA D-arm to present the anticodon loop to FTSJ1's catalytic pocket, with discrete near-active-site residues contributing to tRNA binding rather than complex assembly [PMID:31586407, PMID:38882062]. A patient-derived FTSJ1-p.A26P mutation associated with nonsyndromic X-linked intellectual disability selectively abolishes Gm34, linking this modification activity to neurological development [PMID:26310293]. Independently of its tRNA role, WDR6 serves as a recognition subunit of Cullin4-DDB1 and CUL4A-DDB1-ROC1 E3 ubiquitin ligase complexes, binding the SPAK/OSR1 kinases in a phosphorylation-dependent manner to direct OSR1 ubiquitylation and recruiting UVRAG via a WDxR motif for degradation, the latter promoting hepatocellular carcinoma growth and metastasis through an NF-κB/TNFα feedback loop [PMID:31614064, PMID:36947051]. WDR6 additionally interacts with LKB1 to synergistically induce p27(Kip1)-dependent G1 arrest [PMID:17216128], promotes hepatic de novo lipogenesis by binding PPP1CB to drive its dephosphorylation during insulin resistance [PMID:37735236], and acts as a cell-intrinsic restriction factor against a vaccinia virus K1L-C7L deletion mutant independently of SAMD9 [PMID:26242627].","teleology":[{"year":2000,"claim":"Establishing WDR6 as a discrete gene product defined the molecular scaffold whose function would later be dissected — an 1121-residue protein dominated by WD-repeat modules.","evidence":"Molecular cloning, Northern blot, and FISH mapping in human tissues","pmids":["10903905"],"confidence":"Medium","gaps":["No biochemical activity or binding partner identified at this stage","Functional significance of the putative transmembrane domain not resolved"]},{"year":2007,"claim":"First functional links placed WDR6 in cell-cycle and metabolic signaling, showing it cooperates with LKB1 to enforce G1 arrest and associates with IRS-4 in the hypothalamus.","evidence":"Yeast two-hybrid, co-localization, colony formation and p27 reporter assays in HeLa; subtractive hybridization and Co-IP in rat hypothalamus","pmids":["17216128","17720279"],"confidence":"Medium","gaps":["Mechanism by which WDR6 amplifies LKB1 signaling not defined","IRS-4 interaction rests on a single Co-IP with mostly expression-level readouts","No connection yet to WDR6's later-defined enzymatic or ubiquitin ligase roles"]},{"year":2014,"claim":"Yeast genetics identified the WDR6 ortholog Trm734 as the position-34-specific partner of Trm7, distinguishing it from the position-32 Trm732 complex and defining its core conserved function.","evidence":"Genetic complementation and tRNA modification analysis in S. cerevisiae and S. pombe deletion mutants","pmids":["25404562","25625329"],"confidence":"High","gaps":["Direct demonstration of catalysis required reconstitution","Human ortholog activity not yet shown"]},{"year":2015,"claim":"Coupling tRNA modification to disease, a patient FTSJ1-A26P mutation was shown to selectively abolish Gm34 without affecting Cm32, tying the Trm7-Trm734 activity to X-linked intellectual disability.","evidence":"LC-MS/MS of patient cell lines and yeast trm7-A26P mutant with complementation and binding assays","pmids":["26310293"],"confidence":"High","gaps":["How loss of Gm34 mechanistically impairs neuronal function not established","Effect of human WDR6 mutations on disease not tested"]},{"year":2015,"claim":"A genome-wide screen revealed an unrelated antiviral role, identifying WDR6 as a SAMD9-independent restriction factor against a vaccinia K1L-C7L deletion mutant.","evidence":"Genome-wide siRNA screen confirmed by CRISPR/Cas9 knockout and viral replication assays in HeLa, with negative interaction tests","pmids":["26242627"],"confidence":"Medium","gaps":["Molecular mechanism of viral restriction unknown","Whether restriction relates to WDR6's enzymatic or ubiquitin-ligase activities untested"]},{"year":2019,"claim":"Crystallography defined the structural logic of the complex, showing WDR6/Trm734's three β-propellers both dock FTSJ1 and orient the tRNA substrate for catalysis.","evidence":"X-ray crystallography (apo and SAM-bound), SAXS, and in vitro methylation with tRNA/protein mutants in yeast","pmids":["31586407"],"confidence":"High","gaps":["Human FTSJ1-WDR6 structure not solved at this time","Catalytic contribution of WDR6 residues not yet mapped"]},{"year":2019,"claim":"WDR6 was shown to function as a substrate-recognition subunit of a Cullin4-DDB1 E3 ligase, binding SPAK/OSR1 phospho-dependently to direct OSR1 ubiquitylation regulated by osmotic stress.","evidence":"Affinity pull-down, mass spectrometry, and proteasome/neddylation inhibitor and osmotic stress experiments","pmids":["31614064"],"confidence":"Medium","gaps":["In vivo physiological consequence of OSR1 ubiquitylation not established","Whether the same complex degrades other substrates not addressed here"]},{"year":2020,"claim":"Reconstitution proved the human ortholog is enzymatically functional, with FTSJ1-WDR6 catalyzing 2'-O-methylation at position 34 in vitro contingent on m1G37.","evidence":"Co-IP, in vitro reconstitution of methyltransferase activity, and ftsj1 knockout validation","pmids":["32558197"],"confidence":"High","gaps":["Full substrate repertoire of the human complex not exhaustively defined","Regulation of human complex assembly in cells unresolved"]},{"year":2023,"claim":"Two studies expanded WDR6's E3-ligase and metabolic functions, showing it recruits UVRAG to CUL4A-DDB1-ROC1 for degradation to drive an immunosuppressive HCC program, and binds PPP1CB to promote hepatic lipogenesis during insulin resistance.","evidence":"CRISPR knockout, Co-IP, orthotopic mouse tumor models, flow cytometry, and transcription assays; plus Co-IP, mouse insulin-resistance models, and molecular dynamics","pmids":["36947051","37735236"],"confidence":"Medium","gaps":["Structural basis of UVRAG and PPP1CB recognition not solved","How WDR6 partitions between tRNA-methylation and ubiquitin-ligase roles in vivo unclear"]},{"year":2024,"claim":"Mutagenesis refined the catalytic model, distinguishing WDR6/Trm734 residues required for tRNA binding near the active site from those mediating complex assembly.","evidence":"Site-directed mutagenesis, yeast complementation, and Co-IP with structural mapping","pmids":["38882062"],"confidence":"Medium","gaps":["Residue assignments inferred from yeast onto human complex","Direct tRNA-binding affinity of variants not measured"]},{"year":2025,"claim":"Comparative structural work established that WDR6 and THADA occupy distinct functional niches as alternative auxiliary subunits of FTSJ1, with WDR6 specifically supporting Nm34.","evidence":"Cryo-EM of FTSJ1-THADA complex with biochemical comparison to the FTSJ1-WDR6 complex","pmids":["40483304"],"confidence":"Medium","gaps":["WDR6-specific conclusions inferred indirectly from comparison","What selects between WDR6 and THADA partnering in cells unknown"]},{"year":null,"claim":"It remains unresolved how WDR6 coordinates its parallel roles as a tRNA-methyltransferase subunit, an E3 ligase substrate adaptor, and a metabolic/antiviral factor within a single cell.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No study integrates the tRNA-modification and ubiquitin-ligase functions","Mechanism of antiviral restriction undefined","No human structural model of WDR6 in its E3 ligase complexes"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,1,3]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[3,5]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,3,8,10]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[8,10,9]}],"localization":[{"term_id":"GO:0005829","term_label":"cytosol","supporting_discovery_ids":[6]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[8,10]}],"complexes":["FTSJ1-WDR6 tRNA methyltransferase complex","CUL4A-DDB1-ROC1 E3 ubiquitin ligase","Cullin4-DDB1-WDR6 E3 ubiquitin ligase"],"partners":["FTSJ1","LKB1","IRS4","SPAK","OSR1","PPP1CB","UVRAG","DDB1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9NNW5","full_name":"tRNA (34-2'-O)-methyltransferase regulator WDR6","aliases":["WD repeat-containing protein 6"],"length_aa":1121,"mass_kda":121.7,"function":"Together with methyltransferase FTSJ1, methylates the 2'-O-ribose of nucleotides at position 34 of the tRNA anticodon loop of substrate tRNAs (PubMed:32558197, PubMed:33771871). Required for the correct positioning of the substrate tRNA for methylation (PubMed:32558197). Required to suppress amino acid starvation-induced autophagy (PubMed:22354037). Enhances the STK11/LKB1-induced cell growth suppression activity (PubMed:17216128)","subcellular_location":"Cytoplasm","url":"https://www.uniprot.org/uniprotkb/Q9NNW5/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/WDR6","classification":"Not Classified","n_dependent_lines":13,"n_total_lines":1208,"dependency_fraction":0.01076158940397351},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"PIK3R1","stoichiometry":4.0},{"gene":"PIK3R2","stoichiometry":4.0},{"gene":"CLNS1A","stoichiometry":0.2},{"gene":"FKBP5","stoichiometry":0.2},{"gene":"PSPC1","stoichiometry":0.2},{"gene":"RPS16","stoichiometry":0.2},{"gene":"SSB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/WDR6","total_profiled":1310},"omim":[{"mim_id":"606031","title":"WD REPEAT-CONTAINING PROTEIN 6; WDR6","url":"https://www.omim.org/entry/606031"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Cytosol","reliability":"Supported"},{"location":"Plasma membrane","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/WDR6"},"hgnc":{"alias_symbol":["Trm734"],"prev_symbol":[]},"alphafold":{"accession":"Q9NNW5","domains":[{"cath_id":"2.130.10.10","chopping":"979-1020_1027-1121","consensus_level":"medium","plddt":89.7851,"start":979,"end":1121},{"cath_id":"2.40.128","chopping":"17-115","consensus_level":"medium","plddt":87.2729,"start":17,"end":115},{"cath_id":"2.40.10","chopping":"621-690","consensus_level":"medium","plddt":84.4439,"start":621,"end":690}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NNW5","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NNW5-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9NNW5-F1-predicted_aligned_error_v6.png","plddt_mean":85.31},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=WDR6","jax_strain_url":"https://www.jax.org/strain/search?query=WDR6"},"sequence":{"accession":"Q9NNW5","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9NNW5.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9NNW5/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9NNW5"}},"corpus_meta":[{"pmid":"33523105","id":"PMC_33523105","title":"Identification 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omega","url":"https://pubmed.ncbi.nlm.nih.gov/35559166","citation_count":7,"is_preprint":false},{"pmid":"38158471","id":"PMC_38158471","title":"PABPN1 functions as a predictive biomarker in colorectal carcinoma.","date":"2023","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/38158471","citation_count":2,"is_preprint":false},{"pmid":"40483304","id":"PMC_40483304","title":"Structural insights into tRNA recognition of the human FTSJ1-THADA complex.","date":"2025","source":"Communications biology","url":"https://pubmed.ncbi.nlm.nih.gov/40483304","citation_count":1,"is_preprint":false},{"pmid":"38882062","id":"PMC_38882062","title":"Identification of Amino Acids in Trm734 Required for 2'-O-Methylation of the tRNAPhe Wobble Residue.","date":"2024","source":"ACS omega","url":"https://pubmed.ncbi.nlm.nih.gov/38882062","citation_count":0,"is_preprint":false},{"pmid":"42252270","id":"PMC_42252270","title":"[WD40 repeat-containing protein 6 aggravates diabetic kidney disease by promoting lipid accumulation in renal tubular cells].","date":"2026","source":"Zhejiang da xue xue bao. Yi xue ban = Journal of Zhejiang University. 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in vitro reconstitution of methyltransferase activity; genetic knockout of ftsj1 to assess modification loss\",\n      \"journal\": \"EMBO reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution of enzymatic activity with identified binding partner, plus in vivo validation in knockout cells, single lab but multiple orthogonal methods\",\n      \"pmids\": [\"32558197\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Yeast Trm734 (WDR6 ortholog) forms a complex with Trm7 to specifically 2'-O-methylate position 34 (N34) of tRNA anticodon loop substrates including tRNAPhe, tRNATrp, and tRNALeu; this is distinct from the Trm7-Trm732 complex which methylates position 32.\",\n      \"method\": \"Genetic complementation assays in S. cerevisiae and S. pombe deletion mutants; tRNA modification analysis; growth phenotype rescue experiments\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — replicated across two yeast species with genetic and biochemical evidence; consistent with multiple independent studies\",\n      \"pmids\": [\"25404562\", \"25625329\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Defects in the Trm7-Trm734 (WDR6 ortholog) complex result in loss of Gm34 on tRNAPhe, and a FTSJ1-p.A26P missense mutation (corresponding to nonsyndromic X-linked intellectual disability) specifically abolishes Gm34 without affecting Cm32; the reduced Gm34 is not due to weaker Trm734 binding to Trm7.\",\n      \"method\": \"LC-MS/MS tRNA modification analysis from patient cell lines and yeast trm7-A26P mutant; yeast complementation assays; binding assays\",\n      \"journal\": \"Human mutation\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — tRNA modification measured directly in patient cells and yeast model with mutagenesis, replicated in two independent NSXLID patient cell lines\",\n      \"pmids\": [\"26310293\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Crystal structure of the yeast Trm7-Trm734 (WDR6 ortholog) complex reveals Trm734 consists of three WD40 β-propeller domains (BPA, BPB, BPC); BPA and BPC form a V-shaped cleft that docks to Trm7; the C-terminal region of Trm7 is required for Trm734 binding; Trm734's BPB domain positions tRNA D-arm, placing the anticodon loop near Trm7's catalytic pocket; the complex is a heterodimer in solution.\",\n      \"method\": \"X-ray crystallography (apo and SAM-bound forms); SAXS; in vitro methylation assays with tRNA variants; mutagenesis of Trm7 and tRNA substrates\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure solved with functional validation by in vitro assays and mutagenesis in a single rigorous study\",\n      \"pmids\": [\"31586407\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"The human FTSJ1-WDR6 complex (distinct from FTSJ1-THADA) mediates Nm34 modification; cryo-EM structure of the FTSJ1-THADA complex reveals FTSJ1 binds THADA via its C-terminal region with an interaction mode distinct from the FTSJ1-WDR6 complex, confirming that WDR6 and THADA occupy distinct functional niches as auxiliary subunits of FTSJ1.\",\n      \"method\": \"Cryo-electron microscopy structure determination; biochemical interaction analyses; comparison with previously solved FTSJ1-WDR6 structure\",\n      \"journal\": \"Communications biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Weak — cryo-EM structure of the THADA complex with structural comparison to WDR6 complex; single study, the WDR6-specific structural conclusions are indirectly inferred from the comparison\",\n      \"pmids\": [\"40483304\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Specific amino acids in Trm734 (WDR6 ortholog) located near the active site of Trm7 (not at the Trm7-Trm734 protein-protein interface) are required for tRNA modification activity; a nonfunctional but stable Trm734 variant was identified, suggesting these residues may be important for tRNA binding rather than protein complex assembly.\",\n      \"method\": \"Site-directed mutagenesis of Trm734; yeast functional complementation assays; immunoprecipitation to verify Trm7-Trm734 binding; structural mapping onto published crystal structure\",\n      \"journal\": \"ACS omega\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — mutagenesis with functional assays and Co-IP, single lab, single study\",\n      \"pmids\": [\"38882062\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"WDR6 interacts with LKB1 (STK11) and is localized in the cytoplasm co-incident with LKB1; co-expression of WDR6 with LKB1 enhances LKB1-mediated inhibition of HeLa cell proliferation, synergizes to induce G1 cell cycle arrest, and elevates p27(Kip1) protein and promoter activity beyond the effect of LKB1 alone.\",\n      \"method\": \"Yeast two-hybrid screening; immunofluorescence co-localization; colony formation assay; cell cycle analysis; p27(Kip1) promoter-reporter assay; co-expression in HeLa cells\",\n      \"journal\": \"Molecular and cellular biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Moderate — yeast two-hybrid plus multiple functional assays in cell culture; single lab but several orthogonal readouts\",\n      \"pmids\": [\"17216128\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"WDR6 interacts with insulin receptor substrate 4 (IRS-4) in rat brain hypothalamus; WDR6 mRNA is abundantly expressed in the hypothalamus and is decreased by caloric restriction and in GH-antisense transgenic rats (both associated with increased lifespan); IGF-I and insulin treatment increase WDR6 gene expression in hypothalamic GT1-7 cells.\",\n      \"method\": \"Suppression subtractive hybridization; co-immunoprecipitation/interaction assay from rat brain; in vitro stimulation of GT1-7 cells with IGF-I/insulin\",\n      \"journal\": \"Neurobiology of aging\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP/interaction assay, expression-level readouts for most findings, single lab\",\n      \"pmids\": [\"17720279\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"WDR6 is a component of a Cullin4-DDB1-WDR6 E3 ubiquitin ligase complex that binds SPAK and OSR1 kinases in a phosphorylation-dependent manner (dependent on S-motif phosphorylation); this binding is reduced under osmotic stress when the S-motif is phosphorylated, and OSR1 ubiquitylation is abolished under osmotic stress.\",\n      \"method\": \"Affinity pull-down; mass spectrometry; proteasomal and neddylation inhibitor treatment; osmotic stress experiments\",\n      \"journal\": \"Chembiochem\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — affinity pull-down plus mass spectrometry plus pharmacological inhibitor experiments, single lab, multiple orthogonal methods\",\n      \"pmids\": [\"31614064\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"WDR6 promotes hepatic de novo lipogenesis during insulin resistance by interacting with PPP1CB (PP1β catalytic subunit) to facilitate PPP1CB dephosphorylation at Thr316, which subsequently enhances fatty acid synthase transcription through DNA-dependent protein kinase and upstream stimulatory factor 1.\",\n      \"method\": \"Co-immunoprecipitation; molecular dynamics simulation; in vivo mouse models of insulin resistance; siRNA knockdown and overexpression; transcription reporter assays\",\n      \"journal\": \"Nature metabolism\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP, in vivo mouse models, and mechanistic follow-up with transcriptional readouts; single lab but multiple methods\",\n      \"pmids\": [\"37735236\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"WDR6 promotes UVRAG degradation by recruiting it to the CUL4A-DDB1-ROC1 E3 ubiquitin ligase complex through a WDxR motif; WDR6 deficiency in HCC cells reduces tumor growth and lung metastasis in immunocompetent mice but not in vitro, linked to blocking autophagic degradation of p65, elevating TNFα, increasing MDSCs, and reducing CD8+ T cell infiltration; TNFα activates NF-κB to transcribe WDR6, establishing a feedback loop.\",\n      \"method\": \"CRISPR/Cas9 knockout; co-immunoprecipitation; in vivo orthotopic tumor implantation in C57BL/6J mice; chromatin accessibility assays; flow cytometry for immune cell analysis; TNFα blockade experiments; peptide disruption assay\",\n      \"journal\": \"EMBO molecular medicine\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with functional in vivo validation and multiple mechanistic readouts, single lab\",\n      \"pmids\": [\"36947051\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"WDR6 was identified as a restriction factor that inhibits replication of vaccinia virus K1L-C7L double deletion mutant in human cells; CRISPR/Cas9 knockout of WDR6 in HeLa cells permitted enhanced replication of the mutant virus; WDR6 acts independently of SAMD9 (interactions of WDR6 with SAMD9, C7, and K1 proteins were not detected), and WDR6 knockout did not reduce SAMD9 levels.\",\n      \"method\": \"Genome-wide siRNA screen; CRISPR/Cas9 knockout of WDR6 in HeLa cells; viral replication assays; immunoprecipitation (negative for WDR6-SAMD9/C7/K1 interactions)\",\n      \"journal\": \"mBio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — siRNA screen confirmed by CRISPR KO with viral replication readout, negative interaction result explicitly noted\",\n      \"pmids\": [\"26242627\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2000,\n      \"finding\": \"Human WDR6 encodes a protein of 1121 amino acids containing 11 WD-repeat units clustered in two groups separated by a putative transmembrane domain; the gene maps to chromosome 15q21 and is ubiquitously expressed in human adult and fetal tissues.\",\n      \"method\": \"Molecular cloning; Northern blot analysis; fluorescence in situ hybridization (FISH)\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Weak — direct molecular characterization by cloning, FISH, and Northern blot; foundational characterization paper, single lab\",\n      \"pmids\": [\"10903905\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"WDR6 (the human ortholog of yeast Trm734) functions primarily as an essential auxiliary subunit of the FTSJ1 methyltransferase complex, enabling 2'-O-methylation at position 34 of tRNAPhe (and related tRNAs) anticodon loop residues, a modification required for accurate translation and linked to neurological development; beyond tRNA biology, WDR6 participates in a CUL4A-DDB1-ROC1 E3 ubiquitin ligase complex to target substrates such as UVRAG and OSR1/SPAK kinases for ubiquitylation, interacts with LKB1 to synergistically induce p27(Kip1)-dependent G1 arrest, promotes hepatic de novo lipogenesis via PPP1CB dephosphorylation during insulin resistance, and restricts vaccinia virus replication in human cells independently of SAMD9.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"WDR6 is a multidomain WD40-repeat protein that functions principally as an essential auxiliary subunit of the FTSJ1 tRNA methyltransferase, and more broadly as a substrate-recognition module in Cullin-based E3 ubiquitin ligase complexes [#0, #10, #12]. As the human ortholog of yeast Trm734, WDR6 partners with FTSJ1 (Trm7) to catalyze 2'-O-methylation at position 34 (Nm34/Gm34) of anticodon-loop residues in specific tRNAs including tRNAPhe, tRNATrp, and tRNALeu, an activity requiring prior m1G37 and biochemically distinct from the FTSJ1-THADA and Trm7-Trm732 complexes that act at position 32 [#0, #1, #4]. Structural analysis of the yeast complex shows that WDR6/Trm734 is built from three WD40 β-propeller domains: two propellers form a V-shaped cleft that docks onto the FTSJ1 C-terminus, while a third propeller positions the tRNA D-arm to present the anticodon loop to FTSJ1's catalytic pocket, with discrete near-active-site residues contributing to tRNA binding rather than complex assembly [#3, #5]. A patient-derived FTSJ1-p.A26P mutation associated with nonsyndromic X-linked intellectual disability selectively abolishes Gm34, linking this modification activity to neurological development [#2]. Independently of its tRNA role, WDR6 serves as a recognition subunit of Cullin4-DDB1 and CUL4A-DDB1-ROC1 E3 ubiquitin ligase complexes, binding the SPAK/OSR1 kinases in a phosphorylation-dependent manner to direct OSR1 ubiquitylation and recruiting UVRAG via a WDxR motif for degradation, the latter promoting hepatocellular carcinoma growth and metastasis through an NF-κB/TNFα feedback loop [#8, #10]. WDR6 additionally interacts with LKB1 to synergistically induce p27(Kip1)-dependent G1 arrest [#6], promotes hepatic de novo lipogenesis by binding PPP1CB to drive its dephosphorylation during insulin resistance [#9], and acts as a cell-intrinsic restriction factor against a vaccinia virus K1L-C7L deletion mutant independently of SAMD9 [#11].\",\n  \"teleology\": [\n    {\n      \"year\": 2000,\n      \"claim\": \"Establishing WDR6 as a discrete gene product defined the molecular scaffold whose function would later be dissected — an 1121-residue protein dominated by WD-repeat modules.\",\n      \"evidence\": \"Molecular cloning, Northern blot, and FISH mapping in human tissues\",\n      \"pmids\": [\"10903905\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No biochemical activity or binding partner identified at this stage\", \"Functional significance of the putative transmembrane domain not resolved\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"First functional links placed WDR6 in cell-cycle and metabolic signaling, showing it cooperates with LKB1 to enforce G1 arrest and associates with IRS-4 in the hypothalamus.\",\n      \"evidence\": \"Yeast two-hybrid, co-localization, colony formation and p27 reporter assays in HeLa; subtractive hybridization and Co-IP in rat hypothalamus\",\n      \"pmids\": [\"17216128\", \"17720279\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which WDR6 amplifies LKB1 signaling not defined\", \"IRS-4 interaction rests on a single Co-IP with mostly expression-level readouts\", \"No connection yet to WDR6's later-defined enzymatic or ubiquitin ligase roles\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Yeast genetics identified the WDR6 ortholog Trm734 as the position-34-specific partner of Trm7, distinguishing it from the position-32 Trm732 complex and defining its core conserved function.\",\n      \"evidence\": \"Genetic complementation and tRNA modification analysis in S. cerevisiae and S. pombe deletion mutants\",\n      \"pmids\": [\"25404562\", \"25625329\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct demonstration of catalysis required reconstitution\", \"Human ortholog activity not yet shown\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Coupling tRNA modification to disease, a patient FTSJ1-A26P mutation was shown to selectively abolish Gm34 without affecting Cm32, tying the Trm7-Trm734 activity to X-linked intellectual disability.\",\n      \"evidence\": \"LC-MS/MS of patient cell lines and yeast trm7-A26P mutant with complementation and binding assays\",\n      \"pmids\": [\"26310293\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How loss of Gm34 mechanistically impairs neuronal function not established\", \"Effect of human WDR6 mutations on disease not tested\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"A genome-wide screen revealed an unrelated antiviral role, identifying WDR6 as a SAMD9-independent restriction factor against a vaccinia K1L-C7L deletion mutant.\",\n      \"evidence\": \"Genome-wide siRNA screen confirmed by CRISPR/Cas9 knockout and viral replication assays in HeLa, with negative interaction tests\",\n      \"pmids\": [\"26242627\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Molecular mechanism of viral restriction unknown\", \"Whether restriction relates to WDR6's enzymatic or ubiquitin-ligase activities untested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Crystallography defined the structural logic of the complex, showing WDR6/Trm734's three β-propellers both dock FTSJ1 and orient the tRNA substrate for catalysis.\",\n      \"evidence\": \"X-ray crystallography (apo and SAM-bound), SAXS, and in vitro methylation with tRNA/protein mutants in yeast\",\n      \"pmids\": [\"31586407\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Human FTSJ1-WDR6 structure not solved at this time\", \"Catalytic contribution of WDR6 residues not yet mapped\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"WDR6 was shown to function as a substrate-recognition subunit of a Cullin4-DDB1 E3 ligase, binding SPAK/OSR1 phospho-dependently to direct OSR1 ubiquitylation regulated by osmotic stress.\",\n      \"evidence\": \"Affinity pull-down, mass spectrometry, and proteasome/neddylation inhibitor and osmotic stress experiments\",\n      \"pmids\": [\"31614064\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"In vivo physiological consequence of OSR1 ubiquitylation not established\", \"Whether the same complex degrades other substrates not addressed here\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Reconstitution proved the human ortholog is enzymatically functional, with FTSJ1-WDR6 catalyzing 2'-O-methylation at position 34 in vitro contingent on m1G37.\",\n      \"evidence\": \"Co-IP, in vitro reconstitution of methyltransferase activity, and ftsj1 knockout validation\",\n      \"pmids\": [\"32558197\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full substrate repertoire of the human complex not exhaustively defined\", \"Regulation of human complex assembly in cells unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Two studies expanded WDR6's E3-ligase and metabolic functions, showing it recruits UVRAG to CUL4A-DDB1-ROC1 for degradation to drive an immunosuppressive HCC program, and binds PPP1CB to promote hepatic lipogenesis during insulin resistance.\",\n      \"evidence\": \"CRISPR knockout, Co-IP, orthotopic mouse tumor models, flow cytometry, and transcription assays; plus Co-IP, mouse insulin-resistance models, and molecular dynamics\",\n      \"pmids\": [\"36947051\", \"37735236\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Structural basis of UVRAG and PPP1CB recognition not solved\", \"How WDR6 partitions between tRNA-methylation and ubiquitin-ligase roles in vivo unclear\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Mutagenesis refined the catalytic model, distinguishing WDR6/Trm734 residues required for tRNA binding near the active site from those mediating complex assembly.\",\n      \"evidence\": \"Site-directed mutagenesis, yeast complementation, and Co-IP with structural mapping\",\n      \"pmids\": [\"38882062\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Residue assignments inferred from yeast onto human complex\", \"Direct tRNA-binding affinity of variants not measured\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Comparative structural work established that WDR6 and THADA occupy distinct functional niches as alternative auxiliary subunits of FTSJ1, with WDR6 specifically supporting Nm34.\",\n      \"evidence\": \"Cryo-EM of FTSJ1-THADA complex with biochemical comparison to the FTSJ1-WDR6 complex\",\n      \"pmids\": [\"40483304\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"WDR6-specific conclusions inferred indirectly from comparison\", \"What selects between WDR6 and THADA partnering in cells unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how WDR6 coordinates its parallel roles as a tRNA-methyltransferase subunit, an E3 ligase substrate adaptor, and a metabolic/antiviral factor within a single cell.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No study integrates the tRNA-modification and ubiquitin-ligase functions\", \"Mechanism of antiviral restriction undefined\", \"No human structural model of WDR6 in its E3 ligase complexes\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 1, 3]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [3, 5]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 3, 8, 10]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [8, 10, 9]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005829\", \"supporting_discovery_ids\": [6]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [8, 10]}\n    ],\n    \"complexes\": [\n      \"FTSJ1-WDR6 tRNA methyltransferase complex\",\n      \"CUL4A-DDB1-ROC1 E3 ubiquitin ligase\",\n      \"Cullin4-DDB1-WDR6 E3 ubiquitin ligase\"\n    ],\n    \"partners\": [\n      \"FTSJ1\",\n      \"LKB1\",\n      \"IRS4\",\n      \"SPAK\",\n      \"OSR1\",\n      \"PPP1CB\",\n      \"UVRAG\",\n      \"DDB1\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}