ArticleNucleic acids research2012
Dynamic changes in translational efficiency are deduced from codon usage of the transcriptome.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 41 papers.
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Who cites it
41 citing papers in PubMed.
- Evidence for Non-optimal Codon Choice in Highly Transcribed Sex-Biased Genes of Drosophila melanogaster.Genome biology and evolution · 2026Article
- tRNA-modifying enzymes in bacterial stress adaptation.Open biology · 2025Review
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- Unconventional codon usage bias mediates mRNA translational dynamics in macrophages.PLoS biology · 2025Article
- Coupling tRNAGly gene redundancy with staphylococcal cell wall integrity, antibiotic susceptibility, and virulence potential.Nucleic acids research · 2025Article
- A primer on tRNAs, tRNA-mFrontiers in cell and developmental biology · 2025Review
- Effect of Translation-Enhancing Nascent SKIK Peptide on the Arrest Peptides Containing Consecutive Proline.ACS synthetic biology · 2024Article
- tRNA expression and modification landscapes, and their dynamics during zebrafish embryo development.Nucleic acids research · 2024Article
- tRNA epitranscriptome determines pathogenicity of the opportunistic pathogenProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Codon usage bias in yeasts and its correlation with gene expression, growth temperature, and protein structure.Frontiers in microbiology · 2024Article
- Race with virus evolution: The development and application of mRNA vaccines against SARS-CoV-2.Biomedical journal · 2023Review
- The Ramp Atlas: facilitating tissue and cell-specific ramp sequence analyses through an intuitive web interface.NAR genomics and bioinformatics · 2022Article
- Upregulation of tRNA-Ser-AGA-2-1 Promotes Malignant Behavior in Normal Bronchial Cells.Frontiers in molecular biosciences · 2022Article
- Cold Regulation of Genes Encoding Ion Transport Systems in the Oligotrophic Bacterium Caulobacter crescentus.Microbiology spectrum · 2021Article
- The genomic loci of specific human tRNA genes exhibit ageing-related DNA hypermethylation.Nature communications · 2021Article
- Adaptation of codon and amino acid use for translational functions in highly expressed cricket genes.BMC genomics · 2021Article
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- Translational adaptation of human viruses to the tissues they infect.Cell reports · 2021Article
- The effects of codon bias and optimality on mRNA and protein regulation.Cellular and molecular life sciences : CMLS · 2021Review
- Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Translation of a gene is assumed to be efficient if the supply of the tRNAs that translate it is high. Yet high-abundance tRNAs are often also at high demand since they correspond to preferred codons in genomes. Thus to fully model translational efficiency one must gauge the supply-to-demand ratio of the tRNAs that are required by the transcriptome at a given time. The tRNAs' supply is often approximated by their gene copy number in the genome. Yet neither the demand for each tRNA nor the extent to which its concentration changes across environmental conditions has been extensively examined. Here we compute changes in the codon usage of the transcriptome across different conditions in several organisms by inspecting conventional mRNA expression data. We find recurring dynamics of codon usage in the transcriptome in multiple stressful conditions. In particular, codons that are translated by rare tRNAs become over-represented in the transcriptome in response to stresses. These results raise the possibility that the tRNA pool might dynamically change upon stress to support efficient translation of stress-transcribed genes. Alternatively, stress genes may be typically translated with low efficiency, presumably due to lack of sufficient evolutionary optimization pressure on their codon usage.
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