{"gene":"BUD23","run_date":"2026-06-09T22:02:45","timeline":{"discoveries":[{"year":2008,"finding":"Bud23 is the methyltransferase responsible for N7-methylguanosine modification of G1575 in 18S rRNA; deletion of BUD23 abolishes this modification. However, methyltransferase-dead Bud23 point mutants still complemented bud23Δ growth defects, and ribosomes with G1575A also supported normal growth, indicating that the protein itself (not its catalytic activity) is required for 40S biogenesis and nuclear export.","method":"Genetic deletion, methyltransferase-inactive point mutants, rRNA modification mapping, GFP-tagged small subunit reporter localization (Rps2-GFP, Rps3-GFP) for nuclear export assay","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vivo modification mapping combined with separation-of-function mutagenesis and localization assays in yeast, replicated in multiple subsequent studies","pmids":["18332120"],"is_preprint":false},{"year":2008,"finding":"Loss of Bud23 causes a block in processing of 20S pre-rRNA to mature 18S rRNA and nuclear accumulation of pre-40S subunits, establishing Bud23 as required for nuclear export of the small ribosomal subunit.","method":"Northern blotting for rRNA processing intermediates; GFP-tagged ribosomal protein reporters (Rps2-GFP, Rps3-GFP) and 5'-ITS1 nuclear accumulation in bud23Δ yeast","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — clean genetic deletion with two orthogonal readouts (rRNA processing + reporter localization), replicated in subsequent work","pmids":["18332120"],"is_preprint":false},{"year":2012,"finding":"Trm112 physically interacts with Bud23 in vitro and is required for Bud23 stability in vivo; loss of Trm112 abolishes Bud23-mediated m7G1575 methylation and impairs 40S subunit synthesis. Failure of Bud23 to associate with nascent pre-ribosomes activates a nucleolar surveillance pathway involving TRAMP complexes, leading to pre-ribosome degradation.","method":"Co-purification of Trm112 with pre-rRNAs and biogenesis factors; in vitro binding assay (direct interaction); in vivo stability assay; rRNA modification analysis in trm112Δ cells; genetic pathway analysis with TRAMP complex","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro direct binding plus in vivo stability, modification, and pathway analyses; independently consistent with structural study (PMID:25489090)","pmids":["22493060"],"is_preprint":false},{"year":2014,"finding":"Crystal structures of Bud23–Trm112 in apo and SAM-bound forms revealed that they interact via a β-zipper involving main-chain atoms, burying a hydrophobic surface, and that Trm112 undergoes induced-fit conformational change to accommodate Bud23. Active-site comparison with Coffea canephora xanthosine methyltransferase validated a model for G1575 coordination. Mutations disrupting Bud23–Trm112 complex formation or pre-ribosome recruitment were identified. m7G methylation of G1575 occurs at a late step of 40S maturation despite early (nucleolar) recruitment of the complex. Bud23–Trm112 directly interacts with the DEAH helicase Dhr1.","method":"X-ray crystallography (atomic resolution structures, apo and SAM-bound); site-directed mutagenesis of interface and active-site residues; in vivo functional complementation; co-immunoprecipitation with Dhr1; pulse-chase rRNA methylation timing experiments","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic-resolution structures combined with mutagenesis and multiple functional validations in a single rigorous study","pmids":["25489090"],"is_preprint":false},{"year":2014,"finding":"Bud23 physically and functionally interacts with the DEAH-box RNA helicase Ecm16/Dhr1; suppressor mutations in ECM16 rescued growth and A2 cleavage defects of bud23Δ. An ATP-hydrolysis-impaired Ecm16 mutant caused accumulation of Bud23 in an ~45S particle containing Ecm16, indicating Bud23 enters the pre-40S pathway at the time of Ecm16 function. Two-hybrid mapping located the Bud23 binding site on Ecm16.","method":"Suppressor genetics (ECM16 mutations suppressing bud23Δ); yeast two-hybrid binding-site mapping; affinity purification of Bud23-containing particles from ATPase-dead ecm16 mutants; A2 cleavage assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis combined with particle purification and two-hybrid mapping; consistent with independent structural data","pmids":["24710271"],"is_preprint":false},{"year":2020,"finding":"A comprehensive genetic suppressor screen of bud23Δ identified 67 extragenic suppressor mutations in SSU Processome factors DHR1, IMP4, UTP2/NOP14, BMS1, and ribosomal protein RPS28A. These factors form a physical interaction network linking Bud23's binding site to the U3 snoRNA and to the GTPase Bms1. Pre-40S particles from bud23Δ cells accumulated late SSU Processome factors, indicating Bud23 promotes final disassembly of the SSU Processome.","method":"Genome-wide suppressor screen of bud23Δ with sequencing of 67 mutations; affinity purification of pre-40S particles from bud23Δ cells with mass spectrometry; rRNA processing analysis","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — comprehensive genetic screen with particle composition analysis using multiple methods; large number of independent suppressor alleles","pmids":["33306676"],"is_preprint":false},{"year":2020,"finding":"BUD23 is required for ribosome maturation and normal 18S/28S stoichiometry in human A549 cells, and deletion of Bud23 in murine cardiomyocytes reduces mitochondrial content and function, causing severe cardiomyopathy. BUD23 selectively promotes ribosomal interaction with low GC-content 5′ UTRs, thereby promoting efficient translation of bioenergetics-related mRNAs.","method":"siRNA knockdown in human A549 cells with ribosome profiling and rRNA stoichiometry; cardiomyocyte-specific Bud23 knockout mouse (cardiac phenotype, mitochondrial content/function assays); 5′ UTR GC-content translational analysis","journal":"eLife","confidence":"High","confidence_rationale":"Tier 2 / Strong — cell-line KD and tissue-specific KO mouse with multiple orthogonal readouts (ribosome stoichiometry, translational profiling, cardiac phenotype, mitochondrial function)","pmids":["31939735"],"is_preprint":false},{"year":2021,"finding":"Release of Bud23 from pre-40S particles requires the Rps0-cluster ribosomal proteins (Rps0, Rps2, Rps21) and the atypical kinase/ATPase Rio2, which shares the Bud23 binding site. Recombinant Rio2 added to pre-40S particles affinity-purified from Rio2-depleted cells was sufficient to displace Bud23 in vitro, independently of nucleotide hydrolysis.","method":"Systematic depletion of candidate factors (Rps0-cluster proteins, Rio2) combined with affinity purification of Bud23-containing pre-40S particles; in vitro reconstitution of Bud23 displacement by recombinant Rio2; ATPase-dead Rio2 control","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution of displacement activity with nucleotide-hydrolysis controls, single lab but rigorous biochemical reconstitution","pmids":["34934010"],"is_preprint":false},{"year":2021,"finding":"BUD23–TRMT112 interacts with the Borna disease virus 1 (BoDV-1) large (L) protein at the RNA-dependent RNA polymerase domain, as identified by proximity-dependent biotinylation. BUD23–TRMT112 mediates chromosomal tethering of BoDV-1 viral ribonucleoproteins (vRNPs), and this tethering requires BUD23 methyltransferase activity.","method":"Proximity-dependent biotinylation (BioID) to identify BoDV-1 L protein interactors; co-immunoprecipitation; knockdown of BUD23/TRMT112 with fluorescence microscopy of vRNP localization; methyltransferase-inactive mutant rescue","journal":"Microbiology and immunology","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — BioID plus KD phenotype with mutagenesis, single lab; viral-interaction context is novel and not independently replicated","pmids":["34324219"],"is_preprint":false},{"year":2023,"finding":"BUD-23/BUD23 is the m7G methyltransferase of 18S rRNA in C. elegans and is required for intergenerational hormesis: parental starvation increases m7G rRNA methylation in progeny, and this heritable change (along with increased m6,2A by DIMT-1) is required for increased heat stress resistance and extended longevity in naïve progeny. Other rRNA methyltransferases were dispensable for this effect.","method":"Metabolic methyl-labeling to track heritable methylation; genetic deletion of bud-23 in C. elegans; rRNA modification mass spectrometry; phenotypic assays (fertility, heat stress resistance, longevity) in progeny","journal":"Molecular cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — metabolic labeling combined with genetic deletion, specific rRNA modification mapping, and multiple orthogonal phenotypic assays in an in vivo model","pmids":["37689068"],"is_preprint":false},{"year":2012,"finding":"The G57R and D77A mutations in Bud23 inactivate its methyltransferase activity but both complement bud23Δ growth and budding phenotypes at physiological expression levels. High-level expression of Bud23(G57R), but not wild-type Bud23, failed to complement and produced additional actin organization defects and septin mutant-like phenotypes; Bud23(G57R) retained nuclear localization.","method":"Point mutagenesis (G57R, D77A); yeast complementation at physiological and overexpression levels; fluorescence microscopy of actin (phalloidin) and septin organization; nuclear localization by DAPI staining","journal":"Yeast (Chichester, England)","confidence":"Medium","confidence_rationale":"Tier 2–3 / Weak — mutagenesis with localization and phenotypic assays, single lab, limited mechanistic depth","pmids":["23233232"],"is_preprint":false},{"year":2025,"finding":"Adipocyte-specific deletion of BUD23 in mice produces a lean phenotype and resistance to diet-induced obesity by altering lipid and mitochondrial metabolism. BUD23 modulates translation initiation and efficiency of mRNAs with short 5′ UTR length and GC-rich post-initiation codon usage, characteristic of mitochondrial and lipogenic proteins.","method":"Adipocyte-specific Bud23 knockout mouse; metabolic phenotyping; ribosome profiling to measure translation efficiency; 5′ UTR feature analysis; Mendelian randomisation in human cardiometabolic GWAS data","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — tissue-specific KO mouse with ribosome profiling; consistent with published cardiac KO paper (PMID:31939735); preprint, not yet peer-reviewed","pmids":["bio_10.1101_2025.05.16.654455"],"is_preprint":true},{"year":2025,"finding":"Knockdown of BUD23 in kidney clear cell carcinoma cell lines inhibited cell proliferation and colony formation, indicating an oncogenic role; BUD23 overexpression in advanced KIRC correlated with reduced tumor suppressor gene expression, but no direct molecular mechanism linking BUD23 methyltransferase activity to tumor suppressor regulation was established experimentally.","method":"siRNA knockdown in KIRC cell lines; cell proliferation assays (CCK-8); colony formation assay; migration assay; Western blot and qPCR for knockdown validation","journal":"The Journal of pathology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, KD with cellular phenotype but no pathway placement or mechanistic link to BUD23's molecular function","pmids":["40879514"],"is_preprint":false},{"year":2024,"finding":"Knockdown of BUD23 in prostate cancer cell lines (PC-3, LNCaP) inhibited cell proliferation and reduced PPAR-α, PPAR-β, and PPAR-γ protein levels, suggesting a regulatory axis between BUD23 and PPAR signaling.","method":"siRNA knockdown; CCK-8 proliferation assay; EdU incorporation; Western blotting and qPCR for PPARs","journal":"Discover oncology","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single lab, single method set, no direct mechanistic link between BUD23 rRNA methyltransferase activity and PPAR protein levels established","pmids":["39636451"],"is_preprint":false}],"current_model":"BUD23 (WBSCR22) is an S-adenosylmethionine-dependent methyltransferase that, in complex with its obligate activator TRMT112, catalyzes N7-methylguanosine modification of G1575 (18S rRNA) on late pre-40S ribosomal precursors; beyond this nonessential catalytic activity, BUD23 protein itself is required for SSU Processome disassembly (promoting release of U3 snoRNA-associated factors including Dhr1/ECM16 and Bms1), efficient A2 pre-rRNA cleavage, and nuclear export of the pre-40S subunit, and is subsequently displaced from the pre-40S by Rio2 binding in a nucleotide-hydrolysis-independent manner; at the translational level, BUD23-programmed ribosomes selectively translate mRNAs with low 5′ UTR GC content (including mitochondrial and lipogenic transcripts), linking ribosome modification to bioenergetics and cardiometabolic homeostasis."},"narrative":{"mechanistic_narrative":"BUD23 (WBSCR22) is an S-adenosylmethionine-dependent methyltransferase that catalyzes N7-methylguanosine (m7G) modification of G1575 in 18S rRNA during biogenesis of the small (40S) ribosomal subunit [PMID:18332120]. This catalytic activity is dispensable for cell growth: methyltransferase-dead point mutants and the G1575A rRNA substrate mutant both support normal proliferation, establishing that the BUD23 protein scaffold — not its methylation chemistry — is the essential contribution to 40S maturation and nuclear export [PMID:18332120]. BUD23 functions as an obligate heterodimer with TRMT112, which is required for BUD23 stability and methylation activity; the two proteins associate through a β-zipper interface, and failure of BUD23 to load onto nascent pre-ribosomes triggers a TRAMP-dependent nucleolar surveillance pathway that degrades the defective particle [PMID:22493060, PMID:25489090]. Within ribosome assembly, BUD23 acts at the transition from the SSU Processome to the pre-40S subunit: it interacts directly with the DEAH-box helicase Dhr1/Ecm16 and promotes final disassembly of the SSU Processome, including release of U3 snoRNA-associated factors and the GTPase Bms1, enabling efficient A2 pre-rRNA cleavage and nuclear export [PMID:25489090, PMID:24710271, PMID:33306676]. BUD23 is subsequently displaced from the maturing pre-40S by the atypical kinase Rio2, which occupies the same binding site and evicts BUD23 in a manner independent of nucleotide hydrolysis [PMID:34934010]. At the organismal level, BUD23-programmed ribosomes selectively translate mRNAs with low 5′ UTR GC content — enriched for mitochondrial and lipogenic transcripts — linking this ribosome modification to bioenergetics; tissue-specific deletion causes cardiomyopathy with reduced mitochondrial content in mouse heart [PMID:31939735]. In C. elegans, BUD-23-dependent m7G rRNA methylation mediates intergenerational hormesis, transmitting stress resistance and extended longevity to progeny following parental starvation [PMID:37689068].","teleology":[{"year":2008,"claim":"Established BUD23 as the enzyme writing m7G1575 on 18S rRNA, but separation-of-function mutagenesis revealed the surprising result that 40S biogenesis and export depend on the protein itself rather than its catalytic activity.","evidence":"Genetic deletion, methyltransferase-dead point mutants, rRNA modification mapping, and Rps2/Rps3-GFP nuclear export reporters in yeast","pmids":["18332120"],"confidence":"High","gaps":["Did not define which molecular step of 40S maturation the protein scaffold supports","Mechanism by which the protein, separate from methylation, drives export unresolved"]},{"year":2008,"claim":"Pinpointed the maturation defect by showing loss of BUD23 blocks 20S-to-18S processing and traps pre-40S subunits in the nucleus, defining BUD23 as required for small-subunit nuclear export.","evidence":"Northern blotting of rRNA intermediates plus GFP reporter and 5'-ITS1 localization in bud23Δ yeast","pmids":["18332120"],"confidence":"High","gaps":["Did not identify the assembly-factor partners that mediate processing/export","Direct vs indirect role in export not distinguished"]},{"year":2012,"claim":"Identified TRMT112 as the obligate partner stabilizing BUD23 and enabling methylation, and connected failed BUD23 loading to a quality-control pathway that destroys defective pre-ribosomes.","evidence":"In vitro direct binding, in vivo stability and modification assays, and genetic analysis with TRAMP complex in yeast","pmids":["22493060"],"confidence":"High","gaps":["Structural basis of the BUD23–TRMT112 interaction not yet resolved","Trigger sensed by the surveillance pathway not defined"]},{"year":2014,"claim":"Resolved the atomic architecture of the BUD23–TRMT112 complex and its SAM/substrate coordination, dated m7G methylation to a late maturation step despite early recruitment, and revealed a direct link to the Dhr1 helicase.","evidence":"X-ray crystallography (apo and SAM-bound), interface/active-site mutagenesis, complementation, Dhr1 co-IP, and pulse-chase methylation timing","pmids":["25489090"],"confidence":"High","gaps":["Why early recruitment precedes late catalysis mechanistically unexplained","Functional consequence of the Dhr1 interaction at structural resolution not shown"]},{"year":2014,"claim":"Placed BUD23 entry into the assembly pathway at the time of Dhr1/Ecm16 helicase function, using suppressor genetics to show ECM16 mutations rescue bud23Δ growth and A2 cleavage defects.","evidence":"ECM16 suppressor genetics, yeast two-hybrid binding-site mapping, and affinity purification of Bud23-containing 45S particles from ATPase-dead ecm16 mutants","pmids":["24710271"],"confidence":"High","gaps":["Order of helicase action versus BUD23 catalysis not fully resolved","Direct enzymatic interplay between Dhr1 unwinding and BUD23 loading not reconstituted"]},{"year":2020,"claim":"Defined the protein-scaffold function as promoting SSU Processome disassembly, identifying a suppressor network linking BUD23 to U3 snoRNA factors and the GTPase Bms1.","evidence":"Genome-wide bud23Δ suppressor screen (67 alleles) plus mass-spec composition of pre-40S particles in yeast","pmids":["33306676"],"confidence":"High","gaps":["Biochemical mechanism by which BUD23 triggers factor release not established","Whether disassembly is direct or downstream of Dhr1 action unclear"]},{"year":2021,"claim":"Explained how BUD23 leaves the maturing particle, showing Rio2 shares the BUD23 binding site and displaces it independently of nucleotide hydrolysis, with the Rps0 cluster required for release.","evidence":"Factor depletion plus affinity purification and in vitro reconstitution of Bud23 displacement by recombinant Rio2 with ATPase-dead controls in yeast","pmids":["34934010"],"confidence":"High","gaps":["Structural overlap of Rio2 and BUD23 footprints not directly visualized","What licenses the timing of displacement in vivo unknown"]},{"year":2020,"claim":"Connected BUD23 ribosome modification to translational selectivity and physiology, showing it promotes ribosome engagement with low-GC 5′ UTRs and is required for mitochondrial function in the heart.","evidence":"siRNA knockdown with ribosome profiling in human A549 cells and cardiomyocyte-specific Bud23 knockout mouse with mitochondrial and cardiac phenotyping","pmids":["31939735"],"confidence":"High","gaps":["Whether translational selectivity requires m7G catalysis or the protein scaffold not dissected","Molecular basis for 5′ UTR GC-content preference unresolved"]},{"year":2023,"claim":"Demonstrated a heritable epigenetic role for BUD23-dependent m7G rRNA methylation in mediating intergenerational stress hormesis, distinguishing it from other rRNA methyltransferases.","evidence":"Metabolic methyl-labeling, bud-23 deletion, rRNA modification mass spectrometry, and transgenerational phenotype assays in C. elegans","pmids":["37689068"],"confidence":"High","gaps":["Mechanism by which rRNA methylation is inherited and read out not defined","Link between the heritable modification and specific translational outputs not shown"]},{"year":2021,"claim":"Extended BUD23–TRMT112 function to a viral context, implicating it in chromosomal tethering of Borna disease virus ribonucleoproteins in a methyltransferase-dependent manner.","evidence":"BioID identification of BoDV-1 L-protein interactors, co-IP, and knockdown/mutant-rescue microscopy of vRNP localization","pmids":["34324219"],"confidence":"Medium","gaps":["Single lab and not independently replicated","Direct substrate of methylation in the viral tethering process unknown","Physiological relevance to host ribosome biogenesis unclear"]},{"year":2025,"claim":"Strengthened the metabolic role by showing adipocyte-specific BUD23 loss confers leanness and obesity resistance via altered translation of short-5′-UTR, GC-rich-codon transcripts characteristic of mitochondrial and lipogenic proteins.","evidence":"Adipocyte-specific Bud23 knockout mouse with metabolic phenotyping, ribosome profiling, 5′ UTR feature analysis, and human cardiometabolic Mendelian randomization (preprint)","pmids":["bio_10.1101_2025.05.16.654455"],"confidence":"Medium","gaps":["Preprint, not yet peer-reviewed","Causal molecular link between specific rRNA modification and the translational feature preference not established"]},{"year":2024,"claim":"Reported a candidate oncogenic role in prostate cancer, with BUD23 knockdown reducing proliferation and PPAR-α/β/γ levels.","evidence":"siRNA knockdown, CCK-8/EdU proliferation assays, and Western/qPCR for PPARs in PC-3 and LNCaP cells","pmids":["39636451"],"confidence":"Low","gaps":["No mechanistic link between BUD23 methyltransferase activity and PPAR levels established","Single lab, single method set"]},{"year":2025,"claim":"Reported a proliferative/oncogenic role in clear cell renal carcinoma, with knockdown impairing growth and overexpression correlating with reduced tumor-suppressor expression.","evidence":"siRNA knockdown, proliferation, colony formation, and migration assays in KIRC cell lines","pmids":["40879514"],"confidence":"Low","gaps":["No direct molecular mechanism linking BUD23 to tumor-suppressor regulation","Correlative clinical association without causal experiment"]},{"year":null,"claim":"How m7G methylation versus the BUD23 protein scaffold each contributes to selective translation of low-GC/short-5′-UTR mRNAs, and whether the cancer-associated phenotypes derive from this translational program, remains unresolved.","evidence":"","pmids":[],"confidence":"Low","gaps":["Catalytic vs scaffold contributions to translational selectivity undissected","No mechanistic bridge between ribosome modification and tumor phenotypes","Structural basis of the 5′ UTR GC preference unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016740","term_label":"transferase activity","supporting_discovery_ids":[0,2,3,9]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[0,9]},{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,6]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[6,11]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[2,4]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,10]},{"term_id":"GO:0005840","term_label":"ribosome","supporting_discovery_ids":[0,5,7]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,1,5]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[1,5,7]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[6,11]}],"complexes":["BUD23–TRMT112 methyltransferase complex","SSU Processome","pre-40S ribosomal particle"],"partners":["TRMT112","DHR1","ECM16","BMS1","RIO2","RPS0","RPS2","RPS21"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O43709","full_name":"18S rRNA (guanine-N(7))-methyltransferase","aliases":["Bud site selection protein 23 homolog","Metastasis-related methyltransferase 1","Williams-Beuren syndrome chromosomal region 22 protein","rRNA methyltransferase and ribosome maturation factor"],"length_aa":281,"mass_kda":31.9,"function":"S-adenosyl-L-methionine-dependent methyltransferase that specifically methylates the N(7) position of a guanine in 18S rRNA (PubMed:25851604). Requires the methyltransferase adapter protein TRM112 for full rRNA methyltransferase activity (PubMed:25851604). Involved in the pre-rRNA processing steps leading to small-subunit rRNA production independently of its RNA-modifying catalytic activity (PubMed:25851604). Important for biogenesis end export of the 40S ribosomal subunit independent on its methyltransferase activity (PubMed:24086612). Locus-specific steroid receptor coactivator. Potentiates transactivation by glucocorticoid (NR3C1), mineralocorticoid (NR3C2), androgen (AR) and progesterone (PGR) receptors (PubMed:24488492). Required for the maintenance of open chromatin at the TSC22D3/GILZ locus to facilitate NR3C1 loading on the response elements (PubMed:24488492). Required for maintenance of dimethylation on histone H3 'Lys-79' (H3K79me2), although direct histone methyltransferase activity is not observed in vitro (PubMed:24488492)","subcellular_location":"Nucleus; Nucleus, nucleoplasm; Cytoplasm, perinuclear region; Cytoplasm","url":"https://www.uniprot.org/uniprotkb/O43709/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/BUD23","classification":"Common Essential","n_dependent_lines":1207,"n_total_lines":1208,"dependency_fraction":0.9991721854304636},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000071462","cell_line_id":"CID001059","localizations":[{"compartment":"nucleolus_gc","grade":3},{"compartment":"cytoplasmic","grade":1}],"interactors":[{"gene":"WBSCR22","stoichiometry":10.0},{"gene":"NOP14","stoichiometry":0.2},{"gene":"UBE2O","stoichiometry":0.2},{"gene":"CCAR1","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID001059","total_profiled":1310},"omim":[{"mim_id":"618630","title":"tRNA METHYLTRANSFERASE SUBUNIT 11-2; TRMT112","url":"https://www.omim.org/entry/618630"},{"mim_id":"615733","title":"rRNA METHYLTRANSFERASE AND RIBOSOME MATURATION FACTOR BUD23; BUD23","url":"https://www.omim.org/entry/615733"},{"mim_id":"612499","title":"DIMT1 rRNA METHYLTRANSFERASE AND RIBOSOME MATURATION FACTOR; DIMT1","url":"https://www.omim.org/entry/612499"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoplasm","reliability":"Supported"},{"location":"Nucleoli","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/BUD23"},"hgnc":{"alias_symbol":["MGC19709","MGC2022","MGC5140","PP3381","WBMT","MERM1"],"prev_symbol":["WBSCR22"]},"alphafold":{"accession":"O43709","domains":[{"cath_id":"3.40.50.150","chopping":"10-207","consensus_level":"high","plddt":94.9865,"start":10,"end":207}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O43709","model_url":"https://alphafold.ebi.ac.uk/files/AF-O43709-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O43709-F1-predicted_aligned_error_v6.png","plddt_mean":87.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=BUD23","jax_strain_url":"https://www.jax.org/strain/search?query=BUD23"},"sequence":{"accession":"O43709","fasta_url":"https://rest.uniprot.org/uniprotkb/O43709.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O43709/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O43709"}},"corpus_meta":[{"pmid":"18332120","id":"PMC_18332120","title":"Bud23 methylates G1575 of 18S rRNA and is required for efficient nuclear export of pre-40S subunits.","date":"2008","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/18332120","citation_count":104,"is_preprint":false},{"pmid":"25489090","id":"PMC_25489090","title":"Structural and functional studies of Bud23-Trm112 reveal 18S rRNA N7-G1575 methylation occurs on late 40S precursor ribosomes.","date":"2014","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/25489090","citation_count":86,"is_preprint":false},{"pmid":"22493060","id":"PMC_22493060","title":"Trm112 is required for Bud23-mediated methylation of the 18S rRNA at position G1575.","date":"2012","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/22493060","citation_count":75,"is_preprint":false},{"pmid":"30778127","id":"PMC_30778127","title":"\"Worldwide Network for Blood & Marrow Transplantation (WBMT) special article, challenges facing emerging alternate donor registries\".","date":"2019","source":"Bone marrow transplantation","url":"https://pubmed.ncbi.nlm.nih.gov/30778127","citation_count":53,"is_preprint":false},{"pmid":"22773129","id":"PMC_22773129","title":"Allogeneic hematopoietic stem cell donation-standardized assessment of donor outcome data: a consensus statement from the Worldwide Network for Blood and Marrow Transplantation (WBMT).","date":"2012","source":"Bone marrow transplantation","url":"https://pubmed.ncbi.nlm.nih.gov/22773129","citation_count":38,"is_preprint":false},{"pmid":"35901845","id":"PMC_35901845","title":"Suitability of haematopoietic cell donors: updated consensus recommendations from the WBMT standing committee on donor issues.","date":"2022","source":"The Lancet. 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However, methyltransferase-dead Bud23 point mutants still complemented bud23Δ growth defects, and ribosomes with G1575A also supported normal growth, indicating that the protein itself (not its catalytic activity) is required for 40S biogenesis and nuclear export.\",\n      \"method\": \"Genetic deletion, methyltransferase-inactive point mutants, rRNA modification mapping, GFP-tagged small subunit reporter localization (Rps2-GFP, Rps3-GFP) for nuclear export assay\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vivo modification mapping combined with separation-of-function mutagenesis and localization assays in yeast, replicated in multiple subsequent studies\",\n      \"pmids\": [\"18332120\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2008,\n      \"finding\": \"Loss of Bud23 causes a block in processing of 20S pre-rRNA to mature 18S rRNA and nuclear accumulation of pre-40S subunits, establishing Bud23 as required for nuclear export of the small ribosomal subunit.\",\n      \"method\": \"Northern blotting for rRNA processing intermediates; GFP-tagged ribosomal protein reporters (Rps2-GFP, Rps3-GFP) and 5'-ITS1 nuclear accumulation in bud23Δ yeast\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — clean genetic deletion with two orthogonal readouts (rRNA processing + reporter localization), replicated in subsequent work\",\n      \"pmids\": [\"18332120\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Trm112 physically interacts with Bud23 in vitro and is required for Bud23 stability in vivo; loss of Trm112 abolishes Bud23-mediated m7G1575 methylation and impairs 40S subunit synthesis. Failure of Bud23 to associate with nascent pre-ribosomes activates a nucleolar surveillance pathway involving TRAMP complexes, leading to pre-ribosome degradation.\",\n      \"method\": \"Co-purification of Trm112 with pre-rRNAs and biogenesis factors; in vitro binding assay (direct interaction); in vivo stability assay; rRNA modification analysis in trm112Δ cells; genetic pathway analysis with TRAMP complex\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro direct binding plus in vivo stability, modification, and pathway analyses; independently consistent with structural study (PMID:25489090)\",\n      \"pmids\": [\"22493060\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Crystal structures of Bud23–Trm112 in apo and SAM-bound forms revealed that they interact via a β-zipper involving main-chain atoms, burying a hydrophobic surface, and that Trm112 undergoes induced-fit conformational change to accommodate Bud23. Active-site comparison with Coffea canephora xanthosine methyltransferase validated a model for G1575 coordination. Mutations disrupting Bud23–Trm112 complex formation or pre-ribosome recruitment were identified. m7G methylation of G1575 occurs at a late step of 40S maturation despite early (nucleolar) recruitment of the complex. Bud23–Trm112 directly interacts with the DEAH helicase Dhr1.\",\n      \"method\": \"X-ray crystallography (atomic resolution structures, apo and SAM-bound); site-directed mutagenesis of interface and active-site residues; in vivo functional complementation; co-immunoprecipitation with Dhr1; pulse-chase rRNA methylation timing experiments\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic-resolution structures combined with mutagenesis and multiple functional validations in a single rigorous study\",\n      \"pmids\": [\"25489090\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Bud23 physically and functionally interacts with the DEAH-box RNA helicase Ecm16/Dhr1; suppressor mutations in ECM16 rescued growth and A2 cleavage defects of bud23Δ. An ATP-hydrolysis-impaired Ecm16 mutant caused accumulation of Bud23 in an ~45S particle containing Ecm16, indicating Bud23 enters the pre-40S pathway at the time of Ecm16 function. Two-hybrid mapping located the Bud23 binding site on Ecm16.\",\n      \"method\": \"Suppressor genetics (ECM16 mutations suppressing bud23Δ); yeast two-hybrid binding-site mapping; affinity purification of Bud23-containing particles from ATPase-dead ecm16 mutants; A2 cleavage assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis combined with particle purification and two-hybrid mapping; consistent with independent structural data\",\n      \"pmids\": [\"24710271\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"A comprehensive genetic suppressor screen of bud23Δ identified 67 extragenic suppressor mutations in SSU Processome factors DHR1, IMP4, UTP2/NOP14, BMS1, and ribosomal protein RPS28A. These factors form a physical interaction network linking Bud23's binding site to the U3 snoRNA and to the GTPase Bms1. Pre-40S particles from bud23Δ cells accumulated late SSU Processome factors, indicating Bud23 promotes final disassembly of the SSU Processome.\",\n      \"method\": \"Genome-wide suppressor screen of bud23Δ with sequencing of 67 mutations; affinity purification of pre-40S particles from bud23Δ cells with mass spectrometry; rRNA processing analysis\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — comprehensive genetic screen with particle composition analysis using multiple methods; large number of independent suppressor alleles\",\n      \"pmids\": [\"33306676\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"BUD23 is required for ribosome maturation and normal 18S/28S stoichiometry in human A549 cells, and deletion of Bud23 in murine cardiomyocytes reduces mitochondrial content and function, causing severe cardiomyopathy. BUD23 selectively promotes ribosomal interaction with low GC-content 5′ UTRs, thereby promoting efficient translation of bioenergetics-related mRNAs.\",\n      \"method\": \"siRNA knockdown in human A549 cells with ribosome profiling and rRNA stoichiometry; cardiomyocyte-specific Bud23 knockout mouse (cardiac phenotype, mitochondrial content/function assays); 5′ UTR GC-content translational analysis\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — cell-line KD and tissue-specific KO mouse with multiple orthogonal readouts (ribosome stoichiometry, translational profiling, cardiac phenotype, mitochondrial function)\",\n      \"pmids\": [\"31939735\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Release of Bud23 from pre-40S particles requires the Rps0-cluster ribosomal proteins (Rps0, Rps2, Rps21) and the atypical kinase/ATPase Rio2, which shares the Bud23 binding site. Recombinant Rio2 added to pre-40S particles affinity-purified from Rio2-depleted cells was sufficient to displace Bud23 in vitro, independently of nucleotide hydrolysis.\",\n      \"method\": \"Systematic depletion of candidate factors (Rps0-cluster proteins, Rio2) combined with affinity purification of Bud23-containing pre-40S particles; in vitro reconstitution of Bud23 displacement by recombinant Rio2; ATPase-dead Rio2 control\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution of displacement activity with nucleotide-hydrolysis controls, single lab but rigorous biochemical reconstitution\",\n      \"pmids\": [\"34934010\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"BUD23–TRMT112 interacts with the Borna disease virus 1 (BoDV-1) large (L) protein at the RNA-dependent RNA polymerase domain, as identified by proximity-dependent biotinylation. BUD23–TRMT112 mediates chromosomal tethering of BoDV-1 viral ribonucleoproteins (vRNPs), and this tethering requires BUD23 methyltransferase activity.\",\n      \"method\": \"Proximity-dependent biotinylation (BioID) to identify BoDV-1 L protein interactors; co-immunoprecipitation; knockdown of BUD23/TRMT112 with fluorescence microscopy of vRNP localization; methyltransferase-inactive mutant rescue\",\n      \"journal\": \"Microbiology and immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — BioID plus KD phenotype with mutagenesis, single lab; viral-interaction context is novel and not independently replicated\",\n      \"pmids\": [\"34324219\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"BUD-23/BUD23 is the m7G methyltransferase of 18S rRNA in C. elegans and is required for intergenerational hormesis: parental starvation increases m7G rRNA methylation in progeny, and this heritable change (along with increased m6,2A by DIMT-1) is required for increased heat stress resistance and extended longevity in naïve progeny. Other rRNA methyltransferases were dispensable for this effect.\",\n      \"method\": \"Metabolic methyl-labeling to track heritable methylation; genetic deletion of bud-23 in C. elegans; rRNA modification mass spectrometry; phenotypic assays (fertility, heat stress resistance, longevity) in progeny\",\n      \"journal\": \"Molecular cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — metabolic labeling combined with genetic deletion, specific rRNA modification mapping, and multiple orthogonal phenotypic assays in an in vivo model\",\n      \"pmids\": [\"37689068\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"The G57R and D77A mutations in Bud23 inactivate its methyltransferase activity but both complement bud23Δ growth and budding phenotypes at physiological expression levels. High-level expression of Bud23(G57R), but not wild-type Bud23, failed to complement and produced additional actin organization defects and septin mutant-like phenotypes; Bud23(G57R) retained nuclear localization.\",\n      \"method\": \"Point mutagenesis (G57R, D77A); yeast complementation at physiological and overexpression levels; fluorescence microscopy of actin (phalloidin) and septin organization; nuclear localization by DAPI staining\",\n      \"journal\": \"Yeast (Chichester, England)\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2–3 / Weak — mutagenesis with localization and phenotypic assays, single lab, limited mechanistic depth\",\n      \"pmids\": [\"23233232\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Adipocyte-specific deletion of BUD23 in mice produces a lean phenotype and resistance to diet-induced obesity by altering lipid and mitochondrial metabolism. BUD23 modulates translation initiation and efficiency of mRNAs with short 5′ UTR length and GC-rich post-initiation codon usage, characteristic of mitochondrial and lipogenic proteins.\",\n      \"method\": \"Adipocyte-specific Bud23 knockout mouse; metabolic phenotyping; ribosome profiling to measure translation efficiency; 5′ UTR feature analysis; Mendelian randomisation in human cardiometabolic GWAS data\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — tissue-specific KO mouse with ribosome profiling; consistent with published cardiac KO paper (PMID:31939735); preprint, not yet peer-reviewed\",\n      \"pmids\": [\"bio_10.1101_2025.05.16.654455\"],\n      \"is_preprint\": true\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"Knockdown of BUD23 in kidney clear cell carcinoma cell lines inhibited cell proliferation and colony formation, indicating an oncogenic role; BUD23 overexpression in advanced KIRC correlated with reduced tumor suppressor gene expression, but no direct molecular mechanism linking BUD23 methyltransferase activity to tumor suppressor regulation was established experimentally.\",\n      \"method\": \"siRNA knockdown in KIRC cell lines; cell proliferation assays (CCK-8); colony formation assay; migration assay; Western blot and qPCR for knockdown validation\",\n      \"journal\": \"The Journal of pathology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, KD with cellular phenotype but no pathway placement or mechanistic link to BUD23's molecular function\",\n      \"pmids\": [\"40879514\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"Knockdown of BUD23 in prostate cancer cell lines (PC-3, LNCaP) inhibited cell proliferation and reduced PPAR-α, PPAR-β, and PPAR-γ protein levels, suggesting a regulatory axis between BUD23 and PPAR signaling.\",\n      \"method\": \"siRNA knockdown; CCK-8 proliferation assay; EdU incorporation; Western blotting and qPCR for PPARs\",\n      \"journal\": \"Discover oncology\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single lab, single method set, no direct mechanistic link between BUD23 rRNA methyltransferase activity and PPAR protein levels established\",\n      \"pmids\": [\"39636451\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"BUD23 (WBSCR22) is an S-adenosylmethionine-dependent methyltransferase that, in complex with its obligate activator TRMT112, catalyzes N7-methylguanosine modification of G1575 (18S rRNA) on late pre-40S ribosomal precursors; beyond this nonessential catalytic activity, BUD23 protein itself is required for SSU Processome disassembly (promoting release of U3 snoRNA-associated factors including Dhr1/ECM16 and Bms1), efficient A2 pre-rRNA cleavage, and nuclear export of the pre-40S subunit, and is subsequently displaced from the pre-40S by Rio2 binding in a nucleotide-hydrolysis-independent manner; at the translational level, BUD23-programmed ribosomes selectively translate mRNAs with low 5′ UTR GC content (including mitochondrial and lipogenic transcripts), linking ribosome modification to bioenergetics and cardiometabolic homeostasis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"BUD23 (WBSCR22) is an S-adenosylmethionine-dependent methyltransferase that catalyzes N7-methylguanosine (m7G) modification of G1575 in 18S rRNA during biogenesis of the small (40S) ribosomal subunit [#0]. This catalytic activity is dispensable for cell growth: methyltransferase-dead point mutants and the G1575A rRNA substrate mutant both support normal proliferation, establishing that the BUD23 protein scaffold — not its methylation chemistry — is the essential contribution to 40S maturation and nuclear export [#0, #1]. BUD23 functions as an obligate heterodimer with TRMT112, which is required for BUD23 stability and methylation activity; the two proteins associate through a β-zipper interface, and failure of BUD23 to load onto nascent pre-ribosomes triggers a TRAMP-dependent nucleolar surveillance pathway that degrades the defective particle [#2, #3]. Within ribosome assembly, BUD23 acts at the transition from the SSU Processome to the pre-40S subunit: it interacts directly with the DEAH-box helicase Dhr1/Ecm16 and promotes final disassembly of the SSU Processome, including release of U3 snoRNA-associated factors and the GTPase Bms1, enabling efficient A2 pre-rRNA cleavage and nuclear export [#3, #4, #5]. BUD23 is subsequently displaced from the maturing pre-40S by the atypical kinase Rio2, which occupies the same binding site and evicts BUD23 in a manner independent of nucleotide hydrolysis [#7]. At the organismal level, BUD23-programmed ribosomes selectively translate mRNAs with low 5′ UTR GC content — enriched for mitochondrial and lipogenic transcripts — linking this ribosome modification to bioenergetics; tissue-specific deletion causes cardiomyopathy with reduced mitochondrial content in mouse heart [#6]. In C. elegans, BUD-23-dependent m7G rRNA methylation mediates intergenerational hormesis, transmitting stress resistance and extended longevity to progeny following parental starvation [#9].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Established BUD23 as the enzyme writing m7G1575 on 18S rRNA, but separation-of-function mutagenesis revealed the surprising result that 40S biogenesis and export depend on the protein itself rather than its catalytic activity.\",\n      \"evidence\": \"Genetic deletion, methyltransferase-dead point mutants, rRNA modification mapping, and Rps2/Rps3-GFP nuclear export reporters in yeast\",\n      \"pmids\": [\"18332120\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define which molecular step of 40S maturation the protein scaffold supports\", \"Mechanism by which the protein, separate from methylation, drives export unresolved\"]\n    },\n    {\n      \"year\": 2008,\n      \"claim\": \"Pinpointed the maturation defect by showing loss of BUD23 blocks 20S-to-18S processing and traps pre-40S subunits in the nucleus, defining BUD23 as required for small-subunit nuclear export.\",\n      \"evidence\": \"Northern blotting of rRNA intermediates plus GFP reporter and 5'-ITS1 localization in bud23Δ yeast\",\n      \"pmids\": [\"18332120\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify the assembly-factor partners that mediate processing/export\", \"Direct vs indirect role in export not distinguished\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Identified TRMT112 as the obligate partner stabilizing BUD23 and enabling methylation, and connected failed BUD23 loading to a quality-control pathway that destroys defective pre-ribosomes.\",\n      \"evidence\": \"In vitro direct binding, in vivo stability and modification assays, and genetic analysis with TRAMP complex in yeast\",\n      \"pmids\": [\"22493060\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the BUD23–TRMT112 interaction not yet resolved\", \"Trigger sensed by the surveillance pathway not defined\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Resolved the atomic architecture of the BUD23–TRMT112 complex and its SAM/substrate coordination, dated m7G methylation to a late maturation step despite early recruitment, and revealed a direct link to the Dhr1 helicase.\",\n      \"evidence\": \"X-ray crystallography (apo and SAM-bound), interface/active-site mutagenesis, complementation, Dhr1 co-IP, and pulse-chase methylation timing\",\n      \"pmids\": [\"25489090\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Why early recruitment precedes late catalysis mechanistically unexplained\", \"Functional consequence of the Dhr1 interaction at structural resolution not shown\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Placed BUD23 entry into the assembly pathway at the time of Dhr1/Ecm16 helicase function, using suppressor genetics to show ECM16 mutations rescue bud23Δ growth and A2 cleavage defects.\",\n      \"evidence\": \"ECM16 suppressor genetics, yeast two-hybrid binding-site mapping, and affinity purification of Bud23-containing 45S particles from ATPase-dead ecm16 mutants\",\n      \"pmids\": [\"24710271\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Order of helicase action versus BUD23 catalysis not fully resolved\", \"Direct enzymatic interplay between Dhr1 unwinding and BUD23 loading not reconstituted\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Defined the protein-scaffold function as promoting SSU Processome disassembly, identifying a suppressor network linking BUD23 to U3 snoRNA factors and the GTPase Bms1.\",\n      \"evidence\": \"Genome-wide bud23Δ suppressor screen (67 alleles) plus mass-spec composition of pre-40S particles in yeast\",\n      \"pmids\": [\"33306676\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Biochemical mechanism by which BUD23 triggers factor release not established\", \"Whether disassembly is direct or downstream of Dhr1 action unclear\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Explained how BUD23 leaves the maturing particle, showing Rio2 shares the BUD23 binding site and displaces it independently of nucleotide hydrolysis, with the Rps0 cluster required for release.\",\n      \"evidence\": \"Factor depletion plus affinity purification and in vitro reconstitution of Bud23 displacement by recombinant Rio2 with ATPase-dead controls in yeast\",\n      \"pmids\": [\"34934010\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural overlap of Rio2 and BUD23 footprints not directly visualized\", \"What licenses the timing of displacement in vivo unknown\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Connected BUD23 ribosome modification to translational selectivity and physiology, showing it promotes ribosome engagement with low-GC 5′ UTRs and is required for mitochondrial function in the heart.\",\n      \"evidence\": \"siRNA knockdown with ribosome profiling in human A549 cells and cardiomyocyte-specific Bud23 knockout mouse with mitochondrial and cardiac phenotyping\",\n      \"pmids\": [\"31939735\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether translational selectivity requires m7G catalysis or the protein scaffold not dissected\", \"Molecular basis for 5′ UTR GC-content preference unresolved\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Demonstrated a heritable epigenetic role for BUD23-dependent m7G rRNA methylation in mediating intergenerational stress hormesis, distinguishing it from other rRNA methyltransferases.\",\n      \"evidence\": \"Metabolic methyl-labeling, bud-23 deletion, rRNA modification mass spectrometry, and transgenerational phenotype assays in C. elegans\",\n      \"pmids\": [\"37689068\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which rRNA methylation is inherited and read out not defined\", \"Link between the heritable modification and specific translational outputs not shown\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extended BUD23–TRMT112 function to a viral context, implicating it in chromosomal tethering of Borna disease virus ribonucleoproteins in a methyltransferase-dependent manner.\",\n      \"evidence\": \"BioID identification of BoDV-1 L-protein interactors, co-IP, and knockdown/mutant-rescue microscopy of vRNP localization\",\n      \"pmids\": [\"34324219\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single lab and not independently replicated\", \"Direct substrate of methylation in the viral tethering process unknown\", \"Physiological relevance to host ribosome biogenesis unclear\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Strengthened the metabolic role by showing adipocyte-specific BUD23 loss confers leanness and obesity resistance via altered translation of short-5′-UTR, GC-rich-codon transcripts characteristic of mitochondrial and lipogenic proteins.\",\n      \"evidence\": \"Adipocyte-specific Bud23 knockout mouse with metabolic phenotyping, ribosome profiling, 5′ UTR feature analysis, and human cardiometabolic Mendelian randomization (preprint)\",\n      \"pmids\": [\"bio_10.1101_2025.05.16.654455\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Preprint, not yet peer-reviewed\", \"Causal molecular link between specific rRNA modification and the translational feature preference not established\"]\n    },\n    {\n      \"year\": 2024,\n      \"claim\": \"Reported a candidate oncogenic role in prostate cancer, with BUD23 knockdown reducing proliferation and PPAR-α/β/γ levels.\",\n      \"evidence\": \"siRNA knockdown, CCK-8/EdU proliferation assays, and Western/qPCR for PPARs in PC-3 and LNCaP cells\",\n      \"pmids\": [\"39636451\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No mechanistic link between BUD23 methyltransferase activity and PPAR levels established\", \"Single lab, single method set\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Reported a proliferative/oncogenic role in clear cell renal carcinoma, with knockdown impairing growth and overexpression correlating with reduced tumor-suppressor expression.\",\n      \"evidence\": \"siRNA knockdown, proliferation, colony formation, and migration assays in KIRC cell lines\",\n      \"pmids\": [\"40879514\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No direct molecular mechanism linking BUD23 to tumor-suppressor regulation\", \"Correlative clinical association without causal experiment\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How m7G methylation versus the BUD23 protein scaffold each contributes to selective translation of low-GC/short-5′-UTR mRNAs, and whether the cancer-associated phenotypes derive from this translational program, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Catalytic vs scaffold contributions to translational selectivity undissected\", \"No mechanistic bridge between ribosome modification and tumor phenotypes\", \"Structural basis of the 5′ UTR GC preference unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016740\", \"supporting_discovery_ids\": [0, 2, 3, 9]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [0, 9]},\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 6]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [6, 11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [2, 4]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 10]},\n      {\"term_id\": \"GO:0005840\", \"supporting_discovery_ids\": [0, 5, 7]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 1, 5]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [1, 5, 7]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [6, 11]}\n    ],\n    \"complexes\": [\n      \"BUD23–TRMT112 methyltransferase complex\",\n      \"SSU Processome\",\n      \"pre-40S ribosomal particle\"\n    ],\n    \"partners\": [\n      \"TRMT112\",\n      \"DHR1\",\n      \"ECM16\",\n      \"BMS1\",\n      \"RIO2\",\n      \"RPS0\",\n      \"RPS2\",\n      \"RPS21\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":7,"faith_total":7,"faith_pct":100.0}}