ArticleNucleic acids research2015
Trade-offs between tRNA abundance and mRNA secondary structure support smoothing of translation elongation rate.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 72 papers.
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Who cites it
72 citing papers in PubMed, 136 citations in OpenAlex.
- A multi-objective sequence engineering framework for rational genetic vaccine design.Journal of the Royal Society, Interface · 2026Article
- Essentiality and dynamic expression of the human tRNA pool during viral infection.Molecular systems biology · 2026Article
- Comprehensive analysis of chloroplast codon usage patterns in the important medicinal genusFrontiers in plant science · 2026Article
- Role of tRNA-Derived Fragments and Their Modifications in the Pathogenesis and Treatment of Alzheimer's Disease.Molecular neurobiology · 2025Review
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- Chemically modified tRNA enhances the translation capacity of mRNA rich in cognate codons.Nature communications · 2025Article
- Decrypting the Immune Symphony for RNA Vaccines.Vaccines · 2025Review
- Altered tRNA expression profile associated with codon-specific proteomic changes in the suicide brain.Molecular psychiatry · 2025Article
- Emerging mechanisms of human mitochondrial translation regulation.Trends in biochemical sciences · 2025Review
- Phylogenetic history and temperature adaptation contribute to structural and functional stability of proteins in marine mollusks.Communications biology · 2025Article
- Reversing the relative time courses of the peptide bond reaction with oligopeptides of different lengths and charged amino acid distributions in the ribosome exit tunnel.Computational and structural biotechnology journal · 2024Article
- Transfer learning for cross-context prediction of protein expression from 5'UTR sequence.Nucleic acids research · 2024Article
- Identification of an N-terminal tag (580N) that improves the biosynthesis of fluorescent proteins in Francisella tularensis and other Gram-negative bacteria.Molecular and cellular probes · 2024Article
- An interpretable RNA foundation model for exploring functional RNA motifs in plants.Nature machine intelligence · 2024Article
- Tailor made: the art of therapeutic mRNA design.Nature reviews. Drug discovery · 2024Review
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- Bioinformatic Analysis Reveals the Role of Translation Elongation Efficiency Optimisation in the Evolution ofBiology · 2023Article
- Comprehensive quantitative modeling of translation efficiency in a genome-reduced bacterium.Molecular systems biology · 2023Article
- Analysis of proteomic changes in cassava cv. Kasetsart 50 caused by Sri Lankan cassava mosaic virus infection.BMC plant biology · 2022Article
- Bioinformatic Assessment of Factors Affecting the Correlation between Protein Abundance and Elongation Efficiency in Prokaryotes.International journal of molecular sciences · 2022Article
12 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Translation of protein from mRNA is a complex multi-step process that occurs at a non-uniform rate. Variability in ribosome speed along an mRNA enables refinement of the proteome and plays a critical role in protein biogenesis. Detailed single protein studies have found both tRNA abundance and mRNA secondary structure as key modulators of translation elongation rate, but recent genome-wide ribosome profiling experiments have not observed significant influence of either on translation efficiency. Here we provide evidence that this results from an inherent trade-off between these factors. We find codons pairing to high-abundance tRNAs are preferentially used in regions of high secondary structure content, while codons read by significantly less abundant tRNAs are located in lowly structured regions. By considering long stretches of high and low mRNA secondary structure in Saccharomyces cerevisiae and Escherichia coli and comparing them to randomized-gene models and experimental expression data, we were able to distinguish clear selective pressures and increased protein expression for specific codon choices. The trade-off between secondary structure and tRNA-concentration based codon choice allows for compensation of their independent effects on translation, helping to smooth overall translational speed and reducing the chance of potentially detrimental points of excessively slow or fast ribosome movement.
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