{"gene":"TRMT112","run_date":"2026-06-10T10:51:56","timeline":{"discoveries":[{"year":2012,"finding":"Trm112 is required for Bud23 stability in vivo; deletion of Trm112 phenocopies bud23Δ and results in defective 40S small ribosomal subunit biogenesis. Genetic analysis further reveals a 60S biogenesis defect in trm112Δ dependent on Nop2 and Rcm1 (additional Trm112 interactors), extending Trm112 function to both ribosomal subunits.","method":"Sucrose gradient sedimentation, co-immunoprecipitation, genetic epistasis (double mutant analysis), yeast deletion strains","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal Co-IP and genetic epistasis with multiple orthogonal methods, replicated across two independent yeast studies (PMID:22956767 and PMID:22493060)","pmids":["22956767"],"is_preprint":false},{"year":2012,"finding":"Trm112 interacts directly with Bud23 in vitro, is required for Bud23 stability in vivo, and is necessary for Bud23-mediated N7-methylguanosine (m7G) modification at position G1575 of 18S rRNA. Loss of Trm112 leads to Bud23 failing to bind nascent preribosomes, activating a nucleolar surveillance pathway via TRAMP complexes and causing pre-ribosome degradation.","method":"In vitro binding assay, yeast genetics (deletion strains), rRNA methylation assay, co-purification with pre-rRNAs","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — direct in vitro interaction, in vivo stability assay, rRNA methylation measurement, replicated in multiple studies","pmids":["22493060"],"is_preprint":false},{"year":2011,"finding":"Trm112 activates the Mtq2 catalytic subunit (eRF1 glutamine methyltransferase) through a common structural mechanism. Crystal structure of Mtq2-Trm112 complex with active site mapping showed that the same Trm112 surface activates Trm9 and Trm11 tRNA methyltransferases, indicating Trm112 uses a conserved strategy to activate multiple methyltransferases modifying components of the translation machinery.","method":"X-ray crystallography, site-directed mutagenesis, in vivo functional experiments","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure combined with mutagenesis and in vivo functional validation in a single rigorous study","pmids":["21478168"],"is_preprint":false},{"year":2014,"finding":"Crystal structures of Bud23-Trm112 (apo and SAM-bound forms) revealed that Bud23 and Trm112 interact through a β-zipper involving main-chain atoms, burying a hydrophobic surface. Trm112 undergoes induced-fit structural rearrangement upon binding Bud23. The structures further show Bud23-Trm112 binds pre-ribosomes at an early nucleolar stage but m7G methylation of G1575 occurs at a late step of 40S biogenesis, implying delayed catalytic activation. Bud23-Trm112 also directly interacts with the DEAH RNA helicase Dhr1.","method":"X-ray crystallography (apo and SAM-bound), mutagenesis, co-immunoprecipitation with pre-ribosomes and Dhr1","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic resolution structures with mutagenesis validation and functional co-IP, single rigorous study","pmids":["25489090"],"is_preprint":false},{"year":2015,"finding":"Human WBSCR22-TRMT112 is the functional homologue of yeast Bud23-Trm112, required for distinct pre-rRNA processing reactions leading to 18S rRNA synthesis. Ribosome biogenesis requires the presence of the modification enzyme rather than its RNA-modifying catalytic activity, indicating a conserved quality control mechanism where methyltransferase binding to nascent pre-rRNA is a prerequisite to processing.","method":"RNAi knockdown, pre-rRNA processing analysis, catalytic mutant complementation assays in human cells","journal":"Molecular biology of the cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — loss-of-function with specific rRNA processing phenotype, catalytic mutant analysis, conserved from yeast to human","pmids":["25851604"],"is_preprint":false},{"year":2015,"finding":"TRMT112 is identified as an interaction partner of WBSCR22 by SILAC-coupled co-immunoprecipitation. Knockdown of TRMT112 decreases WBSCR22 protein levels, indicating TRMT112 stabilizes WBSCR22. The WBSCR22-TRMT112 complex localizes to the cell nucleus, and TRMT112 subcellular localization is determined by WBSCR22. WBSCR22 is ubiquitinated and degraded via the proteasome pathway when transiently expressed without its stabilizing partner.","method":"SILAC co-immunoprecipitation, siRNA knockdown, immunofluorescence localization, ubiquitination assay, proteasome inhibition","journal":"PloS one","confidence":"High","confidence_rationale":"Tier 2 / Moderate — reciprocal SILAC-Co-IP, multiple orthogonal methods (knockdown, localization, ubiquitination), single lab","pmids":["26214185"],"is_preprint":false},{"year":2015,"finding":"Crystal structure of the Trm9-Trm112 complex reveals the structural basis for Trm112's role as an obligate activating platform for tRNA mcm5U modification. Trm112 interacts with Trm9 through a similar mode as other Trm112-MTase complexes despite <20% sequence identity among partners, demonstrating structural plasticity in the Trm112 interaction surface.","method":"X-ray crystallography, structure-function analysis, sequence and structural comparison","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — atomic resolution crystal structure with structural comparison, single lab","pmids":["26438534"],"is_preprint":false},{"year":2017,"finding":"Trm112 activates Trm11 enzymatic activity by influencing S-adenosyl-L-methionine (SAM) binding and contributing to tRNA binding. Hydrogen-deuterium exchange mass spectrometry showed the Trm11-Trm112 interaction relies on the same molecular bases as other Trm112-methyltransferase complexes, and all Trm112-dependent methyltransferases compete to interact with this partner.","method":"Enzymatic activity assays, hydrogen-deuterium exchange mass spectrometry (HDX-MS), binding assays","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro enzymatic assay plus HDX-MS structural method, multiple orthogonal methods in single study","pmids":["27986851"],"is_preprint":false},{"year":2019,"finding":"METTL5 forms a heterodimeric complex with TRMT112 to gain metabolic stability in cells; METTL5 is identified as the enzyme responsible for the N6-methyladenosine (m6A) modification of 18S rRNA. The first atomic resolution crystal structure of METTL5-TRMT112 was determined, revealing an RNA-binding mode distinct from other m6A RNA methyltransferases, with structural similarities to a DNA methyltransferase suggesting base extrusion as the modification mechanism.","method":"X-ray crystallography, in vitro methylation assay, co-immunoprecipitation, metabolic stability assays in cells","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — atomic resolution crystal structure combined with in vitro activity assays and cellular stability experiments, replicated in independent study (PMID:35033535)","pmids":["31328227"],"is_preprint":false},{"year":2019,"finding":"Crystal structure of human N6AMT1 (HEMK2)-TRMT112 in complex with SAM shows that TRMT112 binds a hydrophobic surface of N6AMT1 to stabilize its structure but does not directly contribute to substrate binding or catalysis. Biochemical data confirm the complex cannot bind DNA and has no methyltransferase activity for DNA, but exhibits methyltransferase activity for Gln185 of eRF1, establishing N6AMT1 as a protein glutamine methyltransferase rather than a DNA methyltransferase.","method":"X-ray crystallography, DNA binding assay, in vitro methyltransferase activity assay","journal":"Cell discovery","confidence":"High","confidence_rationale":"Tier 1 / Moderate — crystal structure with biochemical activity assays, negative DNA MTase result explicitly confirmed, single lab multiple methods","pmids":["31636962"],"is_preprint":false},{"year":2018,"finding":"In archaea (Haloferax volcanii), Trm112 interacts with and activates multiple methyltransferases targeting translation machinery components, including enzymes functionally orthologous to eukaryotic Trm112 partners and some with bacterial methyltransferase similarities, demonstrating that Trm112 functions as a general methyltransferase activator conserved across all three domains of life.","method":"Functional and structural characterization, co-immunoprecipitation, mass spectrometry interactome","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional and structural characterization in archaea, single lab, consistent with eukaryotic findings","pmids":["30010922"],"is_preprint":false},{"year":2021,"finding":"THUMPD3 interacts with TRMT112 to form the m2G6 tRNA methyltransferase complex responsible for N2-methylguanosine at position 6 of human cytoplasmic tRNAs. In vitro, THUMPD3 alone cannot modify tRNAs, but THUMPD3-TRMT112 methylates all 26 tested G6-containing human cytoplasmic tRNAs, recognizing the 3'-CCA terminus of mature tRNAs. Knockout of THUMPD3-TRMT112 impairs global protein synthesis and reduces cell growth.","method":"Reverse genetics, RNA mass spectrometry, in vitro methylation assay, THUMPD3 knockout cell line","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — in vitro reconstitution with defined substrates, RNA-MS verification, KO phenotype, multiple orthogonal methods in single study","pmids":["34669960"],"is_preprint":false},{"year":2021,"finding":"Seven methyltransferases (N6AMT1, WBSCR22, METTL5, ALKBH8, THUMPD2, THUMPD3, TRMT11) are identified as TRMT112 interaction partners by SILAC screen. TRMT112 stabilizes all seven MTases in cells, and TRMT112 with its MTase partners exhibit a strong mutual feedback loop upon co-expression. Single amino acid mutations on TRMT112 surface reveal partner-specific interaction differences.","method":"SILAC co-immunoprecipitation screen, co-expression stability assays, site-directed mutagenesis","journal":"International journal of molecular sciences","confidence":"High","confidence_rationale":"Tier 2 / Moderate — SILAC-Co-IP screen validated with mutagenesis and co-expression assays, single lab multiple methods","pmids":["34948388"],"is_preprint":false},{"year":2020,"finding":"Two crystal structures of HEMK2 (N6AMT1)-TRMT112 (SAM-bound and SAH/methylglutamine-bound post-catalytic complex) reveal a specific pocket in HEMK2 for glutamine substrate accommodation and catalysis of eRF1 Gln185 methylation. Mass spectrometry confirmed in vitro methylation of eRF1 glutamine.","method":"X-ray crystallography (two structures), mass spectrometry-based methylation assay","journal":"The Biochemical journal","confidence":"High","confidence_rationale":"Tier 1 / Moderate — two crystal structures including post-catalytic complex, with MS biochemical validation, single lab","pmids":["32969463"],"is_preprint":false},{"year":2022,"finding":"The METTL5-TRMT112 complex installs m6A at position 1832 of human 18S rRNA, and TRMT112 is required for METTL5 stability. Human METTL5 mutations associated with microcephaly and intellectual disability disrupt the METTL5-TRMT112 interaction. Loss of METTL5 regulates gene expression at the translational level in human cancer cell lines and mice.","method":"Knockdown/knockout in human cells and mice, rRNA methylation mapping, co-immunoprecipitation, polysome profiling, in vivo mouse model","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (KO, rRNA methylation, Co-IP, polysome profiling), replicated findings confirming PMID:31328227","pmids":["35033535"],"is_preprint":false},{"year":2019,"finding":"TRMT112 regulates the expression of N6AMT1 isoforms by selectively stabilizing isoform 1; the alternatively spliced N6AMT1 isoform (lacking substrate-binding motif) cannot interact with TRMT112 and is rapidly degraded. Knockdown of TRMT112 does not affect N6AMT1 protein levels, indicating that WBSCR22 and N6AMT1 are differently regulated by their common cofactor.","method":"Co-immunoprecipitation, siRNA knockdown, protein stability assay, isoform expression analysis","journal":"Biomolecules","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP and knockdown with stability assay, single lab, two orthogonal methods","pmids":["31466382"],"is_preprint":false},{"year":2021,"finding":"BUD23-TRMT112 binds the RNA-dependent RNA polymerase domain of Borna disease virus L protein and mediates chromosomal tethering of viral ribonucleoproteins (vRNPs). The methyltransferase activity of BUD23-TRMT112 is necessary for the chromosomal tethering process.","method":"Proximity-dependent biotinylation (BioID), co-immunoprecipitation, loss-of-function assays with MTase-dead mutants","journal":"Microbiology and immunology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — BioID proximity labeling and Co-IP with catalytic mutant, single lab, two orthogonal methods","pmids":["34324219"],"is_preprint":false},{"year":2020,"finding":"Archaeal AfTrm11 from Archaeoglobus fulgidus directly interacts with AfTrm112, and while AfTrm11 is active as a single protein, its enzymatic activity is strongly enhanced by AfTrm112. Crystal structures of the AfTrm11-Trm112 complex and AfTrm11 alone reveal conservation of the interaction mechanism with eukaryotic enzymes.","method":"X-ray crystallography (AfTrm11-Trm112 complex, AfTrm11 alone, sinefungin-bound), in vitro methyltransferase activity assay, binding assay","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — crystal structures with in vitro enzymatic assay, archaeal ortholog, single lab","pmids":["33035335"],"is_preprint":false},{"year":2026,"finding":"Chemical probes (bicyclopyrrolidine acrylamide stereoprobes) react covalently with C100 of TRMT112 exclusively within the METTL5-TRMT112 complex but not with uncomplexed TRMT112 or other TRMT112:MT complexes. A co-crystal structure reveals stereoprobe binding to a composite pocket at the TRMT112-METTL5 interface templated by METTL5. Stereoprobe binding induces structural rearrangements that allosterically agonize METTL5 activity, demonstrating that covalent ligands can confer partner-specific functional effects on a pleiotropic adaptor.","method":"Chemical proteomics, co-crystal structure, allosteric activity assay, recombinant protein binding assay","journal":"Nature chemical biology","confidence":"High","confidence_rationale":"Tier 1 / Moderate — co-crystal structure with chemical proteomics and functional agonism assay, multiple orthogonal methods, single rigorous study","pmids":["41507545"],"is_preprint":false},{"year":2022,"finding":"WBSCR22 and TRMT112 function synergistically in pancreatic cancer; concurrent overexpression of both WBSCR22 and TRMT112 further suppresses tumor proliferation, migration, invasion, and tumorigenesis compared to either alone, and WBSCR22-OE negatively regulates ISG15 transcription as a downstream effector.","method":"Overexpression in cancer cell lines, in vivo tumor model, RNA-sequencing, functional rescue assays","journal":"International journal of oncology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — multiple functional assays with specific mechanistic pathway (ISG15 regulation), in vivo confirmation, single lab","pmids":["35088887"],"is_preprint":false},{"year":2027,"finding":"The THUMPD3-TRMT112 m2G tRNA methyltransferase complex promotes pancreatic cancer cell growth and autophagy by supporting TFEB translation via m2G modification of tRNALeu(CAG). Knockdown of THUMPD3 or TRMT112 suppressed autophagic flux and reduced TFEB translation, revealing a tRNA modification-dependent translational control mechanism.","method":"siRNA knockdown, in vitro and in vivo tumor growth assays, polysome/translation analysis, tRNA modification mapping","journal":"Molecular cancer","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — KD with specific translational phenotype and mechanistic pathway (tRNALeu(CAG) m2G → TFEB translation), in vivo confirmation, single lab","pmids":["41530782"],"is_preprint":false},{"year":2024,"finding":"In Drosophila, Mettl5 forms a complex with Trmt112 to influence 18S rRNA methylation and translational regulation; a Trmt112 mutation recapitulates the sleep disturbances seen in Mettl5 mutants, implicating the Mettl5/Trmt112 complex in translational control of PERIOD protein levels via effects on proteasome component expression.","method":"Genetic rescue experiments, RNA-seq, Ribo-seq, Drosophila mutant analysis","journal":"bioRxiv","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis in Drosophila with Ribo-seq, preprint, single lab","pmids":["40475643"],"is_preprint":true}],"current_model":"TRMT112 is a small, evolutionarily conserved 'hub' adaptor protein that functions as an obligate co-factor and stabilizer for at least seven distinct methyltransferases (WBSCR22/BUD23, METTL5, N6AMT1/HEMK2, TRMT11, TRM9/ALKBH8, THUMPD3, and THUMPD2) targeting all major components of the translation machinery—18S rRNA (m7G and m6A), tRNAs (m2G, mcm5U), and the translation termination factor eRF1 (glutamine methylation)—by binding each partner through a conserved β-zipper/hydrophobic interface that induces induced-fit stabilization, prevents proteasomal degradation of the catalytic subunit, and in some cases directly contributes to SAM and substrate binding to activate enzymatic activity."},"narrative":{"mechanistic_narrative":"TRMT112 is a small, evolutionarily conserved adaptor protein that functions as an obligate co-factor and stabilizing platform for a family of methyltransferases that modify components of the translation machinery [PMID:21478168, PMID:34948388]. It binds each catalytic partner through a conserved β-zipper and hydrophobic interface, undergoing induced-fit rearrangement that buries an interaction surface used promiscuously despite low sequence identity among partners [PMID:25489090, PMID:26438534]. A SILAC interactome defined at least seven human methyltransferase partners (WBSCR22, METTL5, N6AMT1/HEMK2, ALKBH8, THUMPD2, THUMPD3, TRMT11), all of which are stabilized by TRMT112 and compete for the same binding surface [PMID:27986851, PMID:34948388]. Through these partnerships TRMT112 enables 18S rRNA modification—m7G1575 via WBSCR22/Bud23 and m6A1832 via METTL5 [PMID:22493060, PMID:35033535]—N2-methylguanosine at position 6 of cytoplasmic tRNAs via THUMPD3 [PMID:34669960], and glutamine methylation of the translation termination factor eRF1 via N6AMT1/HEMK2 [PMID:31636962, PMID:32969463]. Mechanistically, TRMT112 acts in distinct modes: for some partners it is required principally for metabolic stability, preventing proteasomal degradation of the catalytic subunit [PMID:26214185, PMID:31328227], while for others it directly contributes to SAM and substrate binding to activate catalysis [PMID:27986851]. The WBSCR22-TRMT112 complex couples 18S rRNA methyltransferase loading to pre-rRNA processing as a quality-control checkpoint, where enzyme binding rather than catalytic activity gates ribosome maturation [PMID:25851604]. This translational-control axis has physiological consequences: the THUMPD3-TRMT112 complex supports global protein synthesis and cell growth [PMID:34669960], and human METTL5 mutations that disrupt the METTL5-TRMT112 interface cause microcephaly and intellectual disability [PMID:35033535].","teleology":[{"year":2011,"claim":"Established that Trm112 is not a single-enzyme cofactor but uses one conserved surface to activate multiple translation-machinery methyltransferases, defining its hub role.","evidence":"Crystal structure of the Mtq2-Trm112 complex with active-site mapping and in vivo functional validation in yeast","pmids":["21478168"],"confidence":"High","gaps":["Did not enumerate the full partner set","Activation mechanism for each partner not biochemically dissected"]},{"year":2012,"claim":"Demonstrated that Trm112 stabilizes its methyltransferase partner Bud23 and is required for m7G1575 18S rRNA modification, linking the adaptor to ribosome biogenesis quality control.","evidence":"In vitro binding, yeast deletion strains, rRNA methylation assays, sucrose gradient sedimentation and genetic epistasis with Nop2/Rcm1","pmids":["22956767","22493060"],"confidence":"High","gaps":["Structural basis of the interaction not yet resolved","Whether stabilization is the sole role versus catalytic contribution unclear"]},{"year":2014,"claim":"Resolved the structural basis of partner recognition—a main-chain β-zipper with induced-fit rearrangement—and showed enzyme loading precedes catalysis in 40S maturation.","evidence":"Apo and SAM-bound crystal structures of Bud23-Trm112 with mutagenesis and pre-ribosome/Dhr1 co-IP","pmids":["25489090"],"confidence":"High","gaps":["Trigger for delayed catalytic activation during 40S biogenesis unknown","Role of Dhr1 interaction in timing unresolved"]},{"year":2015,"claim":"Showed the human WBSCR22-TRMT112 complex is the functional homologue of the yeast pair and that enzyme presence, not catalytic activity, is the prerequisite for pre-rRNA processing, defining a conserved checkpoint.","evidence":"RNAi knockdown, catalytic-mutant complementation and pre-rRNA processing analysis in human cells; SILAC Co-IP, ubiquitination and proteasome-inhibition assays","pmids":["25851604","26214185"],"confidence":"High","gaps":["How nascent pre-rRNA processing senses enzyme occupancy not defined","Determinants of WBSCR22 ubiquitination not identified"]},{"year":2015,"claim":"Confirmed structural plasticity of the Trm112 interface by showing it engages Trm9 (mcm5U tRNA methyltransferase) via a similar mode despite <20% partner sequence identity.","evidence":"X-ray crystallography of Trm9-Trm112 with structural and sequence comparison","pmids":["26438534"],"confidence":"High","gaps":["Quantitative affinity differences across partners not measured","How a single surface achieves selectivity unresolved"]},{"year":2017,"claim":"Distinguished an activating (rather than merely stabilizing) role for Trm112 by showing it promotes SAM and tRNA binding for Trm11, and demonstrated partners compete for one binding surface.","evidence":"Enzymatic activity assays, HDX-MS and binding assays on the Trm11-Trm112 complex","pmids":["27986851"],"confidence":"High","gaps":["Whether competition is regulated in cells unknown","Stoichiometry of competing complexes not determined"]},{"year":2019,"claim":"Identified METTL5 as the 18S rRNA m6A methyltransferase that depends on TRMT112 for metabolic stability, and resolved its distinct RNA-binding mode by structure.","evidence":"Crystal structure, in vitro methylation assay, Co-IP and cellular metabolic stability assays","pmids":["31328227"],"confidence":"High","gaps":["Base-extrusion modification mechanism inferred, not directly captured","rRNA substrate engagement not visualized at the time"]},{"year":2019,"claim":"Reassigned N6AMT1/HEMK2-TRMT112 from a DNA methyltransferase to an eRF1 glutamine methyltransferase, with TRMT112 acting as a stabilizer that does not contribute to catalysis.","evidence":"SAM-bound crystal structure, DNA-binding assay (negative) and in vitro methyltransferase assays on eRF1 Gln185","pmids":["31636962"],"confidence":"High","gaps":["Cellular consequences of eRF1 methylation on termination fidelity not addressed","Why this partner does not require Trm112 for catalysis mechanistically unexplained"]},{"year":2019,"claim":"Revealed partner-selective regulation: TRMT112 selectively stabilizes N6AMT1 isoform 1 while N6AMT1 levels overall are insensitive to TRMT112 knockdown, showing differential dependence among partners.","evidence":"Co-IP, siRNA knockdown, isoform expression and protein stability assays","pmids":["31466382"],"confidence":"Medium","gaps":["Single-lab observation without independent confirmation","Why partners differ in TRMT112 dependence not mechanistically resolved"]},{"year":2020,"claim":"Captured the post-catalytic state of HEMK2-TRMT112 to define the glutamine substrate pocket and catalytic mechanism for eRF1 Gln185 methylation.","evidence":"Two crystal structures (SAM-bound and SAH/methylglutamine-bound) with MS-based methylation assay","pmids":["32969463"],"confidence":"High","gaps":["eRF1 full-length recognition determinants beyond Gln185 not defined","In vivo regulation of complex activity not addressed"]},{"year":2021,"claim":"Defined THUMPD3-TRMT112 as the m2G6 tRNA methyltransferase whose activity requires the adaptor and whose loss impairs global protein synthesis, linking TRMT112 to bulk translation capacity.","evidence":"In vitro reconstitution with 26 defined tRNA substrates, RNA-MS, and THUMPD3 knockout cell line","pmids":["34669960"],"confidence":"High","gaps":["Mechanism by which m2G6 loss reduces translation not pinpointed","THUMPD2 role within the family not characterized here"]},{"year":2021,"claim":"Systematically defined the seven-member TRMT112 methyltransferase interactome, confirmed stabilization of all partners, and mapped surface residues governing partner-specific binding.","evidence":"SILAC Co-IP screen with co-expression stability assays and site-directed mutagenesis","pmids":["34948388"],"confidence":"High","gaps":["Relative cellular abundance and dynamic partitioning of complexes not quantified","Whether all seven are simultaneously active not determined"]},{"year":2021,"claim":"Extended TRMT112 biology to host-pathogen interaction, showing BUD23-TRMT112 tethers Borna disease virus ribonucleoproteins to chromosomes in a methyltransferase-activity-dependent manner.","evidence":"BioID proximity labeling, Co-IP and loss-of-function with MTase-dead mutants","pmids":["34324219"],"confidence":"Medium","gaps":["Single-lab study without reciprocal validation","Direct substrate of the tethering methylation event unknown"]},{"year":2022,"claim":"Tied the METTL5-TRMT112 complex to disease, mapping m6A1832 of 18S rRNA, confirming TRMT112-dependent METTL5 stability, and showing microcephaly/intellectual-disability mutations disrupt the interface.","evidence":"Knockdown/knockout in cells and mice, rRNA methylation mapping, Co-IP and polysome profiling","pmids":["35033535"],"confidence":"High","gaps":["Translational targets downstream of m6A1832 loss not fully defined","Tissue-specific requirements for the modification unresolved"]},{"year":2022,"claim":"Implicated WBSCR22-TRMT112 in cancer phenotypes, showing concurrent overexpression suppresses tumor behavior with ISG15 as a downstream transcriptional effector.","evidence":"Overexpression in cancer cell lines, in vivo tumor model, RNA-seq and rescue assays","pmids":["35088887"],"confidence":"Medium","gaps":["Single-lab study","Mechanistic link from rRNA methylation to ISG15 regulation not established"]},{"year":2026,"claim":"Demonstrated that covalent chemical probes can confer partner-specific functional effects on the pleiotropic adaptor by binding a composite pocket templated only within the METTL5-TRMT112 complex.","evidence":"Chemical proteomics, co-crystal structure and allosteric activity assay on recombinant complexes","pmids":["41507545"],"confidence":"High","gaps":["Cellular efficacy and selectivity of probes not established","Whether analogous selective pockets exist for other partner complexes unknown"]},{"year":null,"claim":"How TRMT112 partner choice is regulated in cells—the dynamic partitioning, stoichiometry, and signals that direct the limiting adaptor among seven competing methyltransferases—remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No cellular measurement of competing complex abundance","No regulatory input identified that biases partner selection","Physiological consequences of partner competition not tested"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[2,7,12]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[2,5,12]},{"term_id":"GO:0140096","term_label":"catalytic activity, acting on a protein","supporting_discovery_ids":[9,13]},{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[1,8,11]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[5]},{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[1,4]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[1,8,11,14]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[9,11,13]},{"term_id":"R-HSA-1852241","term_label":"Organelle biogenesis and maintenance","supporting_discovery_ids":[0,4]}],"complexes":["WBSCR22(BUD23)-TRMT112","METTL5-TRMT112","N6AMT1(HEMK2)-TRMT112","THUMPD3-TRMT112"],"partners":["WBSCR22","METTL5","N6AMT1","THUMPD3","TRMT11","ALKBH8","THUMPD2","MTQ2"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9UI30","full_name":"Multifunctional methyltransferase subunit TRM112-like protein","aliases":["tRNA methyltransferase 112 homolog"],"length_aa":125,"mass_kda":14.2,"function":"Acts as an activator of both rRNA/tRNA and protein methyltransferases (PubMed:18539146, PubMed:20308323, PubMed:25851604, PubMed:31061526, PubMed:31328227, PubMed:31636962, PubMed:37283053). Together with methyltransferase BUD23, methylates the N(7) position of a guanine in 18S rRNA (PubMed:25851604). The heterodimer with N6AMT1/HEMK2 catalyzes N5-methylation of ETF1 on 'Gln-185', using S-adenosyl L-methionine as methyl donor (PubMed:18539146, PubMed:31061526, PubMed:31636962). The heterodimer with N6AMT1/HEMK2 also monomethylates 'Lys-12' of histone H4 (H4K12me1) (PubMed:31061526). The heterodimer with ALKBH8 catalyzes the methylation of 5-carboxymethyl uridine to 5-methylcarboxymethyl uridine at the wobble position of the anticodon loop in target tRNA species (PubMed:20308323). Together with methyltransferase THUMPD3, catalyzes the formation of N(2)-methylguanosine at position 6 in a broad range of tRNA substrates and at position 7 of tRNA(Trp) (PubMed:34669960, PubMed:37283053). Involved in the pre-rRNA processing steps leading to small-subunit rRNA production (PubMed:25851604). Together with methyltransferase METTL5, specifically methylates the 6th position of adenine in position 1832 of 18S rRNA (PubMed:31328227, PubMed:33428944, PubMed:35033535, PubMed:37283053)","subcellular_location":"Nucleus, nucleoplasm; Cytoplasm, perinuclear region","url":"https://www.uniprot.org/uniprotkb/Q9UI30/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/TRMT112","classification":"Common Essential","n_dependent_lines":1207,"n_total_lines":1208,"dependency_fraction":0.9991721854304636},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"FAM207A","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/TRMT112","total_profiled":1310},"omim":[{"mim_id":"621532","title":"THUMP DOMAIN PROTEIN 3, tRNA GUANOSINE METHYLTRANSFERASE; THUMPD3","url":"https://www.omim.org/entry/621532"},{"mim_id":"621531","title":"tRNA METHYLTRANSFERASE 11; TRMT11","url":"https://www.omim.org/entry/621531"},{"mim_id":"618630","title":"tRNA METHYLTRANSFERASE SUBUNIT 11-2; TRMT112","url":"https://www.omim.org/entry/618630"},{"mim_id":"618628","title":"METHYLTRANSFERASE 5, N6-ADENOSINE; METTL5","url":"https://www.omim.org/entry/618628"},{"mim_id":"615733","title":"rRNA METHYLTRANSFERASE AND RIBOSOME MATURATION FACTOR BUD23; BUD23","url":"https://www.omim.org/entry/615733"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Microtubules","reliability":"Approved"},{"location":"Nucleoplasm","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TRMT112"},"hgnc":{"alias_symbol":["HSPC152","HSPC170","TRM112","TRMT11-2","hTrm112"],"prev_symbol":[]},"alphafold":{"accession":"Q9UI30","domains":[{"cath_id":"2.20.25.10","chopping":"2-117","consensus_level":"high","plddt":94.2036,"start":2,"end":117}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UI30","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UI30-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9UI30-F1-predicted_aligned_error_v6.png","plddt_mean":92.12},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TRMT112","jax_strain_url":"https://www.jax.org/strain/search?query=TRMT112"},"sequence":{"accession":"Q9UI30","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9UI30.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9UI30/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9UI30"}},"corpus_meta":[{"pmid":"31328227","id":"PMC_31328227","title":"The human 18S rRNA m6A methyltransferase METTL5 is stabilized by TRMT112.","date":"2019","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/31328227","citation_count":430,"is_preprint":false},{"pmid":"25851604","id":"PMC_25851604","title":"The human 18S rRNA base methyltransferases DIMT1L and WBSCR22-TRMT112 but not rRNA modification are required for ribosome biogenesis.","date":"2015","source":"Molecular biology of the cell","url":"https://pubmed.ncbi.nlm.nih.gov/25851604","citation_count":143,"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 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<i>Drosophila</i>","date":"2024-10-25","source":"bioRxiv","url":"https://doi.org/10.1101/2024.10.24.620129","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":16329,"output_tokens":5802,"usd":0.068008,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":14284,"output_tokens":4985,"usd":0.098022,"stage2_stop_reason":"end_turn"},"total_usd":0.16603,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2012,\n      \"finding\": \"Trm112 is required for Bud23 stability in vivo; deletion of Trm112 phenocopies bud23Δ and results in defective 40S small ribosomal subunit biogenesis. Genetic analysis further reveals a 60S biogenesis defect in trm112Δ dependent on Nop2 and Rcm1 (additional Trm112 interactors), extending Trm112 function to both ribosomal subunits.\",\n      \"method\": \"Sucrose gradient sedimentation, co-immunoprecipitation, genetic epistasis (double mutant analysis), yeast deletion strains\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal Co-IP and genetic epistasis with multiple orthogonal methods, replicated across two independent yeast studies (PMID:22956767 and PMID:22493060)\",\n      \"pmids\": [\"22956767\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"Trm112 interacts directly with Bud23 in vitro, is required for Bud23 stability in vivo, and is necessary for Bud23-mediated N7-methylguanosine (m7G) modification at position G1575 of 18S rRNA. Loss of Trm112 leads to Bud23 failing to bind nascent preribosomes, activating a nucleolar surveillance pathway via TRAMP complexes and causing pre-ribosome degradation.\",\n      \"method\": \"In vitro binding assay, yeast genetics (deletion strains), rRNA methylation assay, co-purification with pre-rRNAs\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — direct in vitro interaction, in vivo stability assay, rRNA methylation measurement, replicated in multiple studies\",\n      \"pmids\": [\"22493060\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2011,\n      \"finding\": \"Trm112 activates the Mtq2 catalytic subunit (eRF1 glutamine methyltransferase) through a common structural mechanism. Crystal structure of Mtq2-Trm112 complex with active site mapping showed that the same Trm112 surface activates Trm9 and Trm11 tRNA methyltransferases, indicating Trm112 uses a conserved strategy to activate multiple methyltransferases modifying components of the translation machinery.\",\n      \"method\": \"X-ray crystallography, site-directed mutagenesis, in vivo functional experiments\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure combined with mutagenesis and in vivo functional validation in a single rigorous study\",\n      \"pmids\": [\"21478168\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"Crystal structures of Bud23-Trm112 (apo and SAM-bound forms) revealed that Bud23 and Trm112 interact through a β-zipper involving main-chain atoms, burying a hydrophobic surface. Trm112 undergoes induced-fit structural rearrangement upon binding Bud23. The structures further show Bud23-Trm112 binds pre-ribosomes at an early nucleolar stage but m7G methylation of G1575 occurs at a late step of 40S biogenesis, implying delayed catalytic activation. Bud23-Trm112 also directly interacts with the DEAH RNA helicase Dhr1.\",\n      \"method\": \"X-ray crystallography (apo and SAM-bound), mutagenesis, co-immunoprecipitation with pre-ribosomes and Dhr1\",\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 with mutagenesis validation and functional co-IP, single rigorous study\",\n      \"pmids\": [\"25489090\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Human WBSCR22-TRMT112 is the functional homologue of yeast Bud23-Trm112, required for distinct pre-rRNA processing reactions leading to 18S rRNA synthesis. Ribosome biogenesis requires the presence of the modification enzyme rather than its RNA-modifying catalytic activity, indicating a conserved quality control mechanism where methyltransferase binding to nascent pre-rRNA is a prerequisite to processing.\",\n      \"method\": \"RNAi knockdown, pre-rRNA processing analysis, catalytic mutant complementation assays in human cells\",\n      \"journal\": \"Molecular biology of the cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — loss-of-function with specific rRNA processing phenotype, catalytic mutant analysis, conserved from yeast to human\",\n      \"pmids\": [\"25851604\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"TRMT112 is identified as an interaction partner of WBSCR22 by SILAC-coupled co-immunoprecipitation. Knockdown of TRMT112 decreases WBSCR22 protein levels, indicating TRMT112 stabilizes WBSCR22. The WBSCR22-TRMT112 complex localizes to the cell nucleus, and TRMT112 subcellular localization is determined by WBSCR22. WBSCR22 is ubiquitinated and degraded via the proteasome pathway when transiently expressed without its stabilizing partner.\",\n      \"method\": \"SILAC co-immunoprecipitation, siRNA knockdown, immunofluorescence localization, ubiquitination assay, proteasome inhibition\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal SILAC-Co-IP, multiple orthogonal methods (knockdown, localization, ubiquitination), single lab\",\n      \"pmids\": [\"26214185\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Crystal structure of the Trm9-Trm112 complex reveals the structural basis for Trm112's role as an obligate activating platform for tRNA mcm5U modification. Trm112 interacts with Trm9 through a similar mode as other Trm112-MTase complexes despite <20% sequence identity among partners, demonstrating structural plasticity in the Trm112 interaction surface.\",\n      \"method\": \"X-ray crystallography, structure-function analysis, sequence and structural comparison\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — atomic resolution crystal structure with structural comparison, single lab\",\n      \"pmids\": [\"26438534\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Trm112 activates Trm11 enzymatic activity by influencing S-adenosyl-L-methionine (SAM) binding and contributing to tRNA binding. Hydrogen-deuterium exchange mass spectrometry showed the Trm11-Trm112 interaction relies on the same molecular bases as other Trm112-methyltransferase complexes, and all Trm112-dependent methyltransferases compete to interact with this partner.\",\n      \"method\": \"Enzymatic activity assays, hydrogen-deuterium exchange mass spectrometry (HDX-MS), binding assays\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro enzymatic assay plus HDX-MS structural method, multiple orthogonal methods in single study\",\n      \"pmids\": [\"27986851\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"METTL5 forms a heterodimeric complex with TRMT112 to gain metabolic stability in cells; METTL5 is identified as the enzyme responsible for the N6-methyladenosine (m6A) modification of 18S rRNA. The first atomic resolution crystal structure of METTL5-TRMT112 was determined, revealing an RNA-binding mode distinct from other m6A RNA methyltransferases, with structural similarities to a DNA methyltransferase suggesting base extrusion as the modification mechanism.\",\n      \"method\": \"X-ray crystallography, in vitro methylation assay, co-immunoprecipitation, metabolic stability assays in cells\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — atomic resolution crystal structure combined with in vitro activity assays and cellular stability experiments, replicated in independent study (PMID:35033535)\",\n      \"pmids\": [\"31328227\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Crystal structure of human N6AMT1 (HEMK2)-TRMT112 in complex with SAM shows that TRMT112 binds a hydrophobic surface of N6AMT1 to stabilize its structure but does not directly contribute to substrate binding or catalysis. Biochemical data confirm the complex cannot bind DNA and has no methyltransferase activity for DNA, but exhibits methyltransferase activity for Gln185 of eRF1, establishing N6AMT1 as a protein glutamine methyltransferase rather than a DNA methyltransferase.\",\n      \"method\": \"X-ray crystallography, DNA binding assay, in vitro methyltransferase activity assay\",\n      \"journal\": \"Cell discovery\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structure with biochemical activity assays, negative DNA MTase result explicitly confirmed, single lab multiple methods\",\n      \"pmids\": [\"31636962\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"In archaea (Haloferax volcanii), Trm112 interacts with and activates multiple methyltransferases targeting translation machinery components, including enzymes functionally orthologous to eukaryotic Trm112 partners and some with bacterial methyltransferase similarities, demonstrating that Trm112 functions as a general methyltransferase activator conserved across all three domains of life.\",\n      \"method\": \"Functional and structural characterization, co-immunoprecipitation, mass spectrometry interactome\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional and structural characterization in archaea, single lab, consistent with eukaryotic findings\",\n      \"pmids\": [\"30010922\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"THUMPD3 interacts with TRMT112 to form the m2G6 tRNA methyltransferase complex responsible for N2-methylguanosine at position 6 of human cytoplasmic tRNAs. In vitro, THUMPD3 alone cannot modify tRNAs, but THUMPD3-TRMT112 methylates all 26 tested G6-containing human cytoplasmic tRNAs, recognizing the 3'-CCA terminus of mature tRNAs. Knockout of THUMPD3-TRMT112 impairs global protein synthesis and reduces cell growth.\",\n      \"method\": \"Reverse genetics, RNA mass spectrometry, in vitro methylation assay, THUMPD3 knockout cell line\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — in vitro reconstitution with defined substrates, RNA-MS verification, KO phenotype, multiple orthogonal methods in single study\",\n      \"pmids\": [\"34669960\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"Seven methyltransferases (N6AMT1, WBSCR22, METTL5, ALKBH8, THUMPD2, THUMPD3, TRMT11) are identified as TRMT112 interaction partners by SILAC screen. TRMT112 stabilizes all seven MTases in cells, and TRMT112 with its MTase partners exhibit a strong mutual feedback loop upon co-expression. Single amino acid mutations on TRMT112 surface reveal partner-specific interaction differences.\",\n      \"method\": \"SILAC co-immunoprecipitation screen, co-expression stability assays, site-directed mutagenesis\",\n      \"journal\": \"International journal of molecular sciences\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — SILAC-Co-IP screen validated with mutagenesis and co-expression assays, single lab multiple methods\",\n      \"pmids\": [\"34948388\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Two crystal structures of HEMK2 (N6AMT1)-TRMT112 (SAM-bound and SAH/methylglutamine-bound post-catalytic complex) reveal a specific pocket in HEMK2 for glutamine substrate accommodation and catalysis of eRF1 Gln185 methylation. Mass spectrometry confirmed in vitro methylation of eRF1 glutamine.\",\n      \"method\": \"X-ray crystallography (two structures), mass spectrometry-based methylation assay\",\n      \"journal\": \"The Biochemical journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — two crystal structures including post-catalytic complex, with MS biochemical validation, single lab\",\n      \"pmids\": [\"32969463\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"The METTL5-TRMT112 complex installs m6A at position 1832 of human 18S rRNA, and TRMT112 is required for METTL5 stability. Human METTL5 mutations associated with microcephaly and intellectual disability disrupt the METTL5-TRMT112 interaction. Loss of METTL5 regulates gene expression at the translational level in human cancer cell lines and mice.\",\n      \"method\": \"Knockdown/knockout in human cells and mice, rRNA methylation mapping, co-immunoprecipitation, polysome profiling, in vivo mouse model\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (KO, rRNA methylation, Co-IP, polysome profiling), replicated findings confirming PMID:31328227\",\n      \"pmids\": [\"35033535\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"TRMT112 regulates the expression of N6AMT1 isoforms by selectively stabilizing isoform 1; the alternatively spliced N6AMT1 isoform (lacking substrate-binding motif) cannot interact with TRMT112 and is rapidly degraded. Knockdown of TRMT112 does not affect N6AMT1 protein levels, indicating that WBSCR22 and N6AMT1 are differently regulated by their common cofactor.\",\n      \"method\": \"Co-immunoprecipitation, siRNA knockdown, protein stability assay, isoform expression analysis\",\n      \"journal\": \"Biomolecules\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP and knockdown with stability assay, single lab, two orthogonal methods\",\n      \"pmids\": [\"31466382\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2021,\n      \"finding\": \"BUD23-TRMT112 binds the RNA-dependent RNA polymerase domain of Borna disease virus L protein and mediates chromosomal tethering of viral ribonucleoproteins (vRNPs). The methyltransferase activity of BUD23-TRMT112 is necessary for the chromosomal tethering process.\",\n      \"method\": \"Proximity-dependent biotinylation (BioID), co-immunoprecipitation, loss-of-function assays with MTase-dead mutants\",\n      \"journal\": \"Microbiology and immunology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — BioID proximity labeling and Co-IP with catalytic mutant, single lab, two orthogonal methods\",\n      \"pmids\": [\"34324219\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"Archaeal AfTrm11 from Archaeoglobus fulgidus directly interacts with AfTrm112, and while AfTrm11 is active as a single protein, its enzymatic activity is strongly enhanced by AfTrm112. Crystal structures of the AfTrm11-Trm112 complex and AfTrm11 alone reveal conservation of the interaction mechanism with eukaryotic enzymes.\",\n      \"method\": \"X-ray crystallography (AfTrm11-Trm112 complex, AfTrm11 alone, sinefungin-bound), in vitro methyltransferase activity assay, binding assay\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — crystal structures with in vitro enzymatic assay, archaeal ortholog, single lab\",\n      \"pmids\": [\"33035335\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"Chemical probes (bicyclopyrrolidine acrylamide stereoprobes) react covalently with C100 of TRMT112 exclusively within the METTL5-TRMT112 complex but not with uncomplexed TRMT112 or other TRMT112:MT complexes. A co-crystal structure reveals stereoprobe binding to a composite pocket at the TRMT112-METTL5 interface templated by METTL5. Stereoprobe binding induces structural rearrangements that allosterically agonize METTL5 activity, demonstrating that covalent ligands can confer partner-specific functional effects on a pleiotropic adaptor.\",\n      \"method\": \"Chemical proteomics, co-crystal structure, allosteric activity assay, recombinant protein binding assay\",\n      \"journal\": \"Nature chemical biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — co-crystal structure with chemical proteomics and functional agonism assay, multiple orthogonal methods, single rigorous study\",\n      \"pmids\": [\"41507545\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"WBSCR22 and TRMT112 function synergistically in pancreatic cancer; concurrent overexpression of both WBSCR22 and TRMT112 further suppresses tumor proliferation, migration, invasion, and tumorigenesis compared to either alone, and WBSCR22-OE negatively regulates ISG15 transcription as a downstream effector.\",\n      \"method\": \"Overexpression in cancer cell lines, in vivo tumor model, RNA-sequencing, functional rescue assays\",\n      \"journal\": \"International journal of oncology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — multiple functional assays with specific mechanistic pathway (ISG15 regulation), in vivo confirmation, single lab\",\n      \"pmids\": [\"35088887\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2027,\n      \"finding\": \"The THUMPD3-TRMT112 m2G tRNA methyltransferase complex promotes pancreatic cancer cell growth and autophagy by supporting TFEB translation via m2G modification of tRNALeu(CAG). Knockdown of THUMPD3 or TRMT112 suppressed autophagic flux and reduced TFEB translation, revealing a tRNA modification-dependent translational control mechanism.\",\n      \"method\": \"siRNA knockdown, in vitro and in vivo tumor growth assays, polysome/translation analysis, tRNA modification mapping\",\n      \"journal\": \"Molecular cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — KD with specific translational phenotype and mechanistic pathway (tRNALeu(CAG) m2G → TFEB translation), in vivo confirmation, single lab\",\n      \"pmids\": [\"41530782\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2024,\n      \"finding\": \"In Drosophila, Mettl5 forms a complex with Trmt112 to influence 18S rRNA methylation and translational regulation; a Trmt112 mutation recapitulates the sleep disturbances seen in Mettl5 mutants, implicating the Mettl5/Trmt112 complex in translational control of PERIOD protein levels via effects on proteasome component expression.\",\n      \"method\": \"Genetic rescue experiments, RNA-seq, Ribo-seq, Drosophila mutant analysis\",\n      \"journal\": \"bioRxiv\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis in Drosophila with Ribo-seq, preprint, single lab\",\n      \"pmids\": [\"40475643\"],\n      \"is_preprint\": true\n    }\n  ],\n  \"current_model\": \"TRMT112 is a small, evolutionarily conserved 'hub' adaptor protein that functions as an obligate co-factor and stabilizer for at least seven distinct methyltransferases (WBSCR22/BUD23, METTL5, N6AMT1/HEMK2, TRMT11, TRM9/ALKBH8, THUMPD3, and THUMPD2) targeting all major components of the translation machinery—18S rRNA (m7G and m6A), tRNAs (m2G, mcm5U), and the translation termination factor eRF1 (glutamine methylation)—by binding each partner through a conserved β-zipper/hydrophobic interface that induces induced-fit stabilization, prevents proteasomal degradation of the catalytic subunit, and in some cases directly contributes to SAM and substrate binding to activate enzymatic activity.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TRMT112 is a small, evolutionarily conserved adaptor protein that functions as an obligate co-factor and stabilizing platform for a family of methyltransferases that modify components of the translation machinery [#2, #12]. It binds each catalytic partner through a conserved β-zipper and hydrophobic interface, undergoing induced-fit rearrangement that buries an interaction surface used promiscuously despite low sequence identity among partners [#3, #6]. A SILAC interactome defined at least seven human methyltransferase partners (WBSCR22, METTL5, N6AMT1/HEMK2, ALKBH8, THUMPD2, THUMPD3, TRMT11), all of which are stabilized by TRMT112 and compete for the same binding surface [#7, #12]. Through these partnerships TRMT112 enables 18S rRNA modification—m7G1575 via WBSCR22/Bud23 and m6A1832 via METTL5 [#1, #14]—N2-methylguanosine at position 6 of cytoplasmic tRNAs via THUMPD3 [#11], and glutamine methylation of the translation termination factor eRF1 via N6AMT1/HEMK2 [#9, #13]. Mechanistically, TRMT112 acts in distinct modes: for some partners it is required principally for metabolic stability, preventing proteasomal degradation of the catalytic subunit [#5, #8], while for others it directly contributes to SAM and substrate binding to activate catalysis [#7]. The WBSCR22-TRMT112 complex couples 18S rRNA methyltransferase loading to pre-rRNA processing as a quality-control checkpoint, where enzyme binding rather than catalytic activity gates ribosome maturation [#4]. This translational-control axis has physiological consequences: the THUMPD3-TRMT112 complex supports global protein synthesis and cell growth [#11], and human METTL5 mutations that disrupt the METTL5-TRMT112 interface cause microcephaly and intellectual disability [#14].\",\n  \"teleology\": [\n    {\n      \"year\": 2011,\n      \"claim\": \"Established that Trm112 is not a single-enzyme cofactor but uses one conserved surface to activate multiple translation-machinery methyltransferases, defining its hub role.\",\n      \"evidence\": \"Crystal structure of the Mtq2-Trm112 complex with active-site mapping and in vivo functional validation in yeast\",\n      \"pmids\": [\"21478168\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not enumerate the full partner set\", \"Activation mechanism for each partner not biochemically dissected\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Demonstrated that Trm112 stabilizes its methyltransferase partner Bud23 and is required for m7G1575 18S rRNA modification, linking the adaptor to ribosome biogenesis quality control.\",\n      \"evidence\": \"In vitro binding, yeast deletion strains, rRNA methylation assays, sucrose gradient sedimentation and genetic epistasis with Nop2/Rcm1\",\n      \"pmids\": [\"22956767\", \"22493060\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the interaction not yet resolved\", \"Whether stabilization is the sole role versus catalytic contribution unclear\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Resolved the structural basis of partner recognition—a main-chain β-zipper with induced-fit rearrangement—and showed enzyme loading precedes catalysis in 40S maturation.\",\n      \"evidence\": \"Apo and SAM-bound crystal structures of Bud23-Trm112 with mutagenesis and pre-ribosome/Dhr1 co-IP\",\n      \"pmids\": [\"25489090\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Trigger for delayed catalytic activation during 40S biogenesis unknown\", \"Role of Dhr1 interaction in timing unresolved\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Showed the human WBSCR22-TRMT112 complex is the functional homologue of the yeast pair and that enzyme presence, not catalytic activity, is the prerequisite for pre-rRNA processing, defining a conserved checkpoint.\",\n      \"evidence\": \"RNAi knockdown, catalytic-mutant complementation and pre-rRNA processing analysis in human cells; SILAC Co-IP, ubiquitination and proteasome-inhibition assays\",\n      \"pmids\": [\"25851604\", \"26214185\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How nascent pre-rRNA processing senses enzyme occupancy not defined\", \"Determinants of WBSCR22 ubiquitination not identified\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Confirmed structural plasticity of the Trm112 interface by showing it engages Trm9 (mcm5U tRNA methyltransferase) via a similar mode despite <20% partner sequence identity.\",\n      \"evidence\": \"X-ray crystallography of Trm9-Trm112 with structural and sequence comparison\",\n      \"pmids\": [\"26438534\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Quantitative affinity differences across partners not measured\", \"How a single surface achieves selectivity unresolved\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Distinguished an activating (rather than merely stabilizing) role for Trm112 by showing it promotes SAM and tRNA binding for Trm11, and demonstrated partners compete for one binding surface.\",\n      \"evidence\": \"Enzymatic activity assays, HDX-MS and binding assays on the Trm11-Trm112 complex\",\n      \"pmids\": [\"27986851\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether competition is regulated in cells unknown\", \"Stoichiometry of competing complexes not determined\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Identified METTL5 as the 18S rRNA m6A methyltransferase that depends on TRMT112 for metabolic stability, and resolved its distinct RNA-binding mode by structure.\",\n      \"evidence\": \"Crystal structure, in vitro methylation assay, Co-IP and cellular metabolic stability assays\",\n      \"pmids\": [\"31328227\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Base-extrusion modification mechanism inferred, not directly captured\", \"rRNA substrate engagement not visualized at the time\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Reassigned N6AMT1/HEMK2-TRMT112 from a DNA methyltransferase to an eRF1 glutamine methyltransferase, with TRMT112 acting as a stabilizer that does not contribute to catalysis.\",\n      \"evidence\": \"SAM-bound crystal structure, DNA-binding assay (negative) and in vitro methyltransferase assays on eRF1 Gln185\",\n      \"pmids\": [\"31636962\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cellular consequences of eRF1 methylation on termination fidelity not addressed\", \"Why this partner does not require Trm112 for catalysis mechanistically unexplained\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Revealed partner-selective regulation: TRMT112 selectively stabilizes N6AMT1 isoform 1 while N6AMT1 levels overall are insensitive to TRMT112 knockdown, showing differential dependence among partners.\",\n      \"evidence\": \"Co-IP, siRNA knockdown, isoform expression and protein stability assays\",\n      \"pmids\": [\"31466382\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab observation without independent confirmation\", \"Why partners differ in TRMT112 dependence not mechanistically resolved\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Captured the post-catalytic state of HEMK2-TRMT112 to define the glutamine substrate pocket and catalytic mechanism for eRF1 Gln185 methylation.\",\n      \"evidence\": \"Two crystal structures (SAM-bound and SAH/methylglutamine-bound) with MS-based methylation assay\",\n      \"pmids\": [\"32969463\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"eRF1 full-length recognition determinants beyond Gln185 not defined\", \"In vivo regulation of complex activity not addressed\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Defined THUMPD3-TRMT112 as the m2G6 tRNA methyltransferase whose activity requires the adaptor and whose loss impairs global protein synthesis, linking TRMT112 to bulk translation capacity.\",\n      \"evidence\": \"In vitro reconstitution with 26 defined tRNA substrates, RNA-MS, and THUMPD3 knockout cell line\",\n      \"pmids\": [\"34669960\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism by which m2G6 loss reduces translation not pinpointed\", \"THUMPD2 role within the family not characterized here\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Systematically defined the seven-member TRMT112 methyltransferase interactome, confirmed stabilization of all partners, and mapped surface residues governing partner-specific binding.\",\n      \"evidence\": \"SILAC Co-IP screen with co-expression stability assays and site-directed mutagenesis\",\n      \"pmids\": [\"34948388\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Relative cellular abundance and dynamic partitioning of complexes not quantified\", \"Whether all seven are simultaneously active not determined\"]\n    },\n    {\n      \"year\": 2021,\n      \"claim\": \"Extended TRMT112 biology to host-pathogen interaction, showing BUD23-TRMT112 tethers Borna disease virus ribonucleoproteins to chromosomes in a methyltransferase-activity-dependent manner.\",\n      \"evidence\": \"BioID proximity labeling, Co-IP and loss-of-function with MTase-dead mutants\",\n      \"pmids\": [\"34324219\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab study without reciprocal validation\", \"Direct substrate of the tethering methylation event unknown\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Tied the METTL5-TRMT112 complex to disease, mapping m6A1832 of 18S rRNA, confirming TRMT112-dependent METTL5 stability, and showing microcephaly/intellectual-disability mutations disrupt the interface.\",\n      \"evidence\": \"Knockdown/knockout in cells and mice, rRNA methylation mapping, Co-IP and polysome profiling\",\n      \"pmids\": [\"35033535\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Translational targets downstream of m6A1832 loss not fully defined\", \"Tissue-specific requirements for the modification unresolved\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Implicated WBSCR22-TRMT112 in cancer phenotypes, showing concurrent overexpression suppresses tumor behavior with ISG15 as a downstream transcriptional effector.\",\n      \"evidence\": \"Overexpression in cancer cell lines, in vivo tumor model, RNA-seq and rescue assays\",\n      \"pmids\": [\"35088887\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab study\", \"Mechanistic link from rRNA methylation to ISG15 regulation not established\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Demonstrated that covalent chemical probes can confer partner-specific functional effects on the pleiotropic adaptor by binding a composite pocket templated only within the METTL5-TRMT112 complex.\",\n      \"evidence\": \"Chemical proteomics, co-crystal structure and allosteric activity assay on recombinant complexes\",\n      \"pmids\": [\"41507545\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Cellular efficacy and selectivity of probes not established\", \"Whether analogous selective pockets exist for other partner complexes unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TRMT112 partner choice is regulated in cells—the dynamic partitioning, stoichiometry, and signals that direct the limiting adaptor among seven competing methyltransferases—remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No cellular measurement of competing complex abundance\", \"No regulatory input identified that biases partner selection\", \"Physiological consequences of partner competition not tested\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [2, 7, 12]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [2, 5, 12]},\n      {\"term_id\": \"GO:0140096\", \"supporting_discovery_ids\": [9, 13]},\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [1, 8, 11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [5]},\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [1, 4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [1, 8, 11, 14]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [9, 11, 13]},\n      {\"term_id\": \"R-HSA-1852241\", \"supporting_discovery_ids\": [0, 4]}\n    ],\n    \"complexes\": [\n      \"WBSCR22(BUD23)-TRMT112\",\n      \"METTL5-TRMT112\",\n      \"N6AMT1(HEMK2)-TRMT112\",\n      \"THUMPD3-TRMT112\"\n    ],\n    \"partners\": [\n      \"WBSCR22\",\n      \"METTL5\",\n      \"N6AMT1\",\n      \"THUMPD3\",\n      \"TRMT11\",\n      \"ALKBH8\",\n      \"THUMPD2\",\n      \"MTQ2\"\n    ],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":7,"faith_pct":85.71428571428571}}