ArticlePLoS genetics2015
Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation.
Article in PLoS genetics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers, 1 of them a synthesis that pooled it.
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Who cites it
73 citing papers in PubMed, 1 synthesis or guideline pooled it, 118 citations in OpenAlex.
- Synonymous but Not Silent: The Codon Usage Code for Gene Expression and Protein Folding.Annual review of biochemistry · 2021Pooled it
- MiaA-mediated tRNA modifications couple tryptophan attenuation and changes in tRNA abundance to complex phenotypes in Pseudomonas aeruginosa.Nucleic acids research · 2026Article
- Elp3 uses a conserved molecular tunnel to transport acetate between distant active sites and catalyze tRNA wobble base modification.Nature communications · 2026Article
- Coronaviruses reprogram the tRNA epitranscriptome to favor viral protein expression.Nature communications · 2026Article
- Synonymous codon usage defines functional gene families.BMC biology · 2026Article
- Emerging roles of tRNA modification-mediated codon-specific translational reprogramming in cancer biology.Cell death & disease · 2026Review
- ALKBH8-mediated codon-specific translation promotes colorectal tumorigenesis.Nature communications · 2025Article
- Post-Transcriptional Regulation of the MiaA Prenyl Transferase by CsrA and the Small RNA CsrB inInternational journal of molecular sciences · 2025Article
- Comprehensive Analysis of Small RNA Modifications inMetabolites · 2025Article
- Genes and Pathways Comprising the Human and Mouse ORFeomes Display Distinct Codon Bias Signatures that Can Regulate Protein Levels.bioRxiv : the preprint server for biology · 2025Article
- Decoding Codon Bias: The Role of tRNA Modifications in Tissue-Specific Translation.International journal of molecular sciences · 2025Article
- tRNA modification enzyme-dependent redox homeostasis regulates synapse formation and memory.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Lifespan Extension by Retrotransposons under Conditions of Mild Stress Requires Genes Involved in tRNA Modifications and Nucleotide Metabolism.International journal of molecular sciences · 2024Article
- RNA modifying enzymes shape tRNA biogenesis and function.The Journal of biological chemistry · 2024Review
- mNature communications · 2024Article
- tRNA modification reprogramming contributes to artemisinin resistance in Plasmodium falciparum.Nature microbiology · 2024Article
- tRNA epitranscriptome determines pathogenicity of the opportunistic pathogenProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Translational response to mitochondrial stresses is orchestrated by tRNA modifications.bioRxiv : the preprint server for biology · 2024Article
- Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing.Nature biotechnology · 2024Article
- Molecular Coping Mechanisms: Reprogramming tRNAs To Regulate Codon-Biased Translation of Stress Response Proteins.Accounts of chemical research · 2023Article
13 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
Abstract
Post-transcriptional modifications of transfer RNAs (tRNAs) have long been recognized to play crucial roles in regulating the rate and fidelity of translation. However, the extent to which they determine global protein production remains poorly understood. Here we use quantitative proteomics to show a direct link between wobble uridine 5-methoxycarbonylmethyl (mcm5) and 5-methoxy-carbonyl-methyl-2-thio (mcm5s2) modifications catalyzed by tRNA methyltransferase 9 (Trm9) in tRNAArg(UCU) and tRNAGlu(UUC) and selective translation of proteins from genes enriched with their cognate codons. Controlling for bias in protein expression and alternations in mRNA expression, we find that loss of Trm9 selectively impairs expression of proteins from genes enriched with AGA and GAA codons under both normal and stress conditions. Moreover, we show that AGA and GAA codons occur with high frequency in clusters along the transcripts, which may play a role in modulating translation. Consistent with these results, proteins subject to enhanced ribosome pausing in yeast lacking mcm5U and mcm5s2U are more likely to be down-regulated and contain a larger number of AGA/GAA clusters. Together, these results suggest that Trm9-catalyzed tRNA modifications play a significant role in regulating protein expression within the cell.
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Registered trials
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