Affinage

THUMPD3

tRNA (guanine(6)-N(2))-methyltransferase THUMP3 · UniProt Q9BV44

Round 2 corrected
Length
507 aa
Mass
57.0 kDa
Annotated
2026-04-28
43 papers in source corpus 4 papers cited in narrative 5 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

THUMPD3 is the catalytic subunit of the THUMPD3–TRMT112 heterodimeric tRNA methyltransferase that installs N2-methylguanosine (m2G) at position 6 of cytoplasmic tRNAs (and position 7 of tRNATrp), recognizing the 3′-CCA terminus of mature tRNAs; THUMPD3 alone is catalytically inactive and requires TRMT112 for methyltransferase activity (PMID:34669960). Loss of THUMPD3 impairs global protein synthesis and cell growth, and in pancreatic cancer the complex promotes TFEB translation via m2G modification of tRNALeu(CAG), thereby sustaining autophagic flux and proliferation (PMID:34669960, PMID:41530782). THUMPD3 depletion also selectively alters alternative splicing of extracellular matrix and cell-adhesion transcripts, including removal of the EDB-encoding exon of Fibronectin-1, linking its activity to cancer cell migration and proliferation (PMID:39656728).

Mechanistic history

Synthesis pass · year-by-year structured walk · 4 steps
  1. 2021 High

    Identification of THUMPD3 as a tRNA m2G6 methyltransferase resolved the long-unknown enzyme responsible for this modification in human cells, establishing that TRMT112 binding is an obligate activator and that substrate recognition depends on the 3′-CCA of mature tRNAs.

    Evidence In vitro reconstitution of THUMPD3–TRMT112 activity on 26 human tRNAs, RNA mass spectrometry, co-immunoprecipitation, and THUMPD3-KO cell lines

    PMID:34669960

    Open questions at the time
    • Structural basis for TRMT112-mediated activation of THUMPD3 is unknown
    • How THUMPD3 discriminates position 6 from other guanosines in tRNA has not been determined
    • Whether THUMPD3 modifies non-tRNA substrates was not addressed
  2. 2021 High

    Demonstrating that THUMPD3 knockout reduces global translation and cell proliferation established a physiological requirement for tRNA m2G modification in protein synthesis.

    Evidence THUMPD3-KO human cell lines assessed by global protein synthesis assay and growth assays

    PMID:34669960

    Open questions at the time
    • Which specific tRNAs or codons are rate-limiting upon m2G loss was not identified
    • Contribution of translational versus non-translational effects to the growth defect was not separated
  3. 2024 Medium

    Discovery that THUMPD3 depletion selectively perturbs alternative splicing of ECM transcripts—notably shifting Fibronectin-1 to an EDB-minus isoform—revealed a cancer-relevant function beyond global translation.

    Evidence siRNA knockdown in lung cancer cells with transcriptome-wide splicing analysis, RT-PCR validation, and proliferation/migration assays

    PMID:39656728

    Open questions at the time
    • Whether the splicing effect is a direct consequence of tRNA methylation or an indirect translational effect on splicing regulators is unknown
    • Findings from a single lab using siRNA; off-target effects not fully excluded
    • Relevance to non-lung cancer contexts has not been tested
  4. 2026 Medium

    Linking THUMPD3–TRMT112 to codon-biased translation of TFEB via tRNALeu(CAG) m2G modification and downstream autophagic flux provided the first codon-resolution mechanism connecting this modification to a specific oncogenic pathway.

    Evidence Knockdown in pancreatic cancer cells with in vivo xenograft, ribosome/translation analysis, and autophagic flux assays

    PMID:41530782

    Open questions at the time
    • Single-lab study; the tRNALeu(CAG)–TFEB codon-bias model awaits independent replication
    • Whether other Leu-codon-enriched transcripts are similarly affected was not systematically assessed
    • No structural or biochemical data on how m2G at position 6 of tRNALeu(CAG) influences decoding efficiency

Open questions

Synthesis pass · forward-looking unresolved questions
  • A high-resolution structure of the THUMPD3–TRMT112 complex, identification of the full scope of in vivo RNA substrates beyond tRNAs, and the direct molecular link between tRNA m2G loss and alternative splicing changes remain open questions.
  • No crystal or cryo-EM structure of the THUMPD3–TRMT112 complex
  • Transcriptome-wide m2G mapping has only been reported in preprint form and awaits peer-reviewed confirmation
  • Mechanism connecting tRNA methylation to alternative splicing regulation is unresolved

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016740 transferase activity 3
Localization
GO:0005829 cytosol 1
Pathway
R-HSA-392499 Metabolism of proteins 2 R-HSA-8953854 Metabolism of RNA 2 R-HSA-9612973 Autophagy 1
Partners
TRMT112
Complex memberships
THUMPD3-TRMT112

Evidence

Reading pass · 5 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2021 THUMPD3 forms a complex with TRMT112 (multifunctional methyltransferase subunit TRM112-like protein) to catalyze N2-methylguanosine (m2G) formation at position 6 of cytoplasmic tRNAs in human cells. THUMPD3 alone cannot modify tRNAs; TRMT112 interaction is required to activate its methyltransferase activity. In vitro, THUMPD3-TRMT112 methylates all 26 tested G6-containing human cytoplasmic tRNAs by recognizing the characteristic 3'-CCA of mature tRNAs. The complex also introduces m2G at position 7 of tRNATrp. Reverse genetics coupled with RNA-mass spectrometry; in vitro enzymatic assay; co-immunoprecipitation; THUMPD3-knockout cell lines Nucleic acids research High 34669960
2021 THUMPD3 knockout cells exhibit impaired global protein synthesis and reduced cell growth, demonstrating a functional consequence of loss of tRNA m2G6/7 modification in human cells. THUMPD3-knockout cell lines with global protein synthesis assay and growth assays Nucleic acids research High 34669960
2024 THUMPD3 depletion in lung cancer cells impairs proliferation and migration, and exogenous THUMPD3 expression in normal lung fibroblasts stimulates their proliferation. THUMPD3 maintains expression of a pro-tumour EDB-containing isoform of Fibronectin-1 (FN1) mRNA; depletion causes alternative splicing that removes the EDB-encoding exon. THUMPD3 depletion selectively and preferentially affects alternative splicing of ECM and cell adhesion molecule transcripts as well as neurodevelopmental protein-encoding transcripts. siRNA knockdown in lung cancer cells; transcriptome-wide analysis; exogenous overexpression in normal fibroblasts; proliferation and migration assays; RT-PCR validation of alternative splicing PloS one Medium 39656728
2024 Using an optimised PhOxi-seq method coupled to a novel bioinformatic pipeline, THUMPD3-dependent m2G sites were detected transcriptome-wide in a human cancer cell line, demonstrating that THUMPD3 modifies not only tRNAs but also low-abundance mRNAs, generating the first database of high-confidence THUMPD3-dependent m2G sites across multiple RNA classes. PhOxi-seq (chemical sequencing method for m2G detection) with optimised workflow and bioinformatic pipeline applied to human cancer cell line bioRxivpreprint Medium bio_10.1101_2024.08.15.608094
2026 The THUMPD3-TRMT112 m2G tRNA methyltransferase complex promotes pancreatic cancer cell growth and autophagy. Mechanistically, THUMPD3/TRMT112 deficiency suppresses TFEB translation by impairing m2G modification of tRNALeu(CAG), thereby inhibiting autophagic flux and cancer cell proliferation. Knockdown in pancreatic cancer cells (in vitro and in vivo xenograft); autophagic flux assays; ribosome/translation analysis linking tRNALeu(CAG) m2G modification to TFEB protein levels Molecular cancer Medium 41530782

Source papers

Stage 0 corpus · 43 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2002 Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America 1479 12477932
2015 The BioPlex Network: A Systematic Exploration of the Human Interactome. Cell 1118 26186194
2017 Architecture of the human interactome defines protein communities and disease networks. Nature 1085 28514442
2020 A reference map of the human binary protein interactome. Nature 849 32296183
2003 Complete sequencing and characterization of 21,243 full-length human cDNAs. Nature genetics 754 14702039
2021 Dual proteome-scale networks reveal cell-specific remodeling of the human interactome. Cell 705 33961781
2012 A census of human soluble protein complexes. Cell 689 22939629
2011 Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Briefings in bioinformatics 656 21873635
2018 High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies. Molecular cell 580 29395067
2004 The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome research 438 15489334
2005 Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome research 409 16344560
2015 Panorama of ancient metazoan macromolecular complexes. Nature 407 26344197
2021 A proximity-dependent biotinylation map of a human cell. Nature 339 34079125
2012 A high-throughput approach for measuring temporal changes in the interactome. Nature methods 273 22863883
2020 A High-Density Human Mitochondrial Proximity Interaction Network. Cell metabolism 148 32877691
2004 A protein interaction framework for human mRNA degradation. Genome research 123 15231747
2021 Systematically defining selective autophagy receptor-specific cargo using autophagosome content profiling. Molecular cell 105 33545068
2017 Mammalian APE1 controls miRNA processing and its interactome is linked to cancer RNA metabolism. Nature communications 99 28986522
2018 Proteomic profiling of VCP substrates links VCP to K6-linked ubiquitylation and c-Myc function. EMBO reports 92 29467282
2017 Cell cycle-dependent phosphorylation regulates RECQL4 pathway choice and ubiquitination in DNA double-strand break repair. Nature communications 89 29229926
2016 Substrate-Trapped Interactors of PHD3 and FIH Cluster in Distinct Signaling Pathways. Cell reports 77 26972000
2021 Histone deacetylase inhibitors inhibit cervical cancer growth through Parkin acetylation-mediated mitophagy. Acta pharmaceutica Sinica. B 66 35256949
2022 Scalable multiplex co-fractionation/mass spectrometry platform for accelerated protein interactome discovery. Nature communications 65 35831314
2015 Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. Science signaling 61 25921289
2021 THUMPD3-TRMT112 is a m2G methyltransferase working on a broad range of tRNA substrates. Nucleic acids research 49 34669960
2022 NUDT21 limits CD19 levels through alternative mRNA polyadenylation in B cell acute lymphoblastic leukemia. Nature immunology 46 36138187
2019 Gain of Additional BIRC3 Protein Functions through 3'-UTR-Mediated Protein Complex Formation. Molecular cell 42 30948266
2019 PLEKHA4/kramer Attenuates Dishevelled Ubiquitination to Modulate Wnt and Planar Cell Polarity Signaling. Cell reports 42 31091453
2021 The proximal proteome of 17 SARS-CoV-2 proteins links to disrupted antiviral signaling and host translation. PLoS pathogens 37 34597346
2018 KAP1 facilitates reinstatement of heterochromatin after DNA replication. Nucleic acids research 37 29955894
2021 LncRNA THUMPD3-AS1 enhances the proliferation and inflammatory response of chondrocytes in osteoarthritis. International immunopharmacology 35 34509934
2021 The involvement of Parkin-dependent mitophagy in the anti-cancer activity of Ginsenoside. Journal of ginseng research 31 35509820
2019 THUMPD3-AS1 Is Correlated With Non-Small Cell Lung Cancer And Regulates Self-Renewal Through miR-543 And ONECUT2. OncoTargets and therapy 31 31819483
2022 THUMPD3-AS1 facilitates cell growth and aggressiveness by the miR-218-5p/SKAP1 axis in colorectal cancer. Cell biochemistry and biophysics 11 35538197
2023 LncRNA THUMPD3-AS1 promotes invasion and EMT in gastric cancer by regulating the miR-1297/BCAT1 pathway. iScience 10 37705956
2022 THUMPD3-AS1 Is Correlated with Gastric Cancer and Regulates Cell Function through miR-1252-3p and CXCL17. Critical reviews in eukaryotic gene expression 9 36017917
2024 THUMPD3-AS1 inhibits ovarian cancer cell apoptosis through the miR-320d/ARF1 axis. FASEB journal : official publication of the Federation of American Societies for Experimental Biology 7 38963337
2025 LncRNA THUMPD3-AS1 promotes the proliferation and migration of esophageal cancer cells through the miR-29a-3p/ELK1/PRDX4 signaling pathway. Seminars in oncology 2 40639318
2024 THUMPD3 regulates alternative splicing of ECM transcripts in human lung cancer cells and promotes proliferation and migration. PloS one 2 39656728
2025 LncRNA THUMPD3-AS1/microRNA-4465/KPNA2 axis impacts human hepatocellular carcinoma cell phenotypes. Regenerative therapy 1 39925963
2025 LncRNA THUMPD3-AS1 Regulates Behavioral and Synaptic Structural Abnormalities in Schizophrenia via miR-485-5p and ARHGAP8. Advanced science (Weinheim, Baden-Wurttemberg, Germany) 1 41168987
2023 Erratum: LncRNA THUMPD3-AS1 promotes invasion and EMT in gastric cancer by regulating the miR-1297/BCAT1 pathway. iScience 1 37766972
2026 tRNA m2G methyltransferase complex THUMPD3-TRMT112 promotes pancreatic cancer progression and autophagy via modulating TFEB translation. Molecular cancer 0 41530782