ArticleScientific reports2019
An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- Translation accuracy in E. coli.Nucleic acids research · 2026Article
- Structural and biochemical characterization of yeast Tcd enzymes installing the post-transcriptional modification ct6A in tRNA.Nucleic acids research · 2026Article
- Evolution of Translational Machinery in Fast- and Slow-Growing Bacteria.Microorganisms · 2026Article
- Biology of host-dependent restriction-modification in prokaryotes.EcoSal Plus · 2025Review
- Bacterial gene 5' ends have unusual mutation rates that can mislead tests of selection.PLoS biology · 2025Article
- Cell Compartment is a Predictor of Protein Rate of Evolution, but not in the Manner Expected: Evidence Against the Extended Complexity Hypothesis.Genome biology and evolution · 2025Article
- Unravelling Prokaryotic Codon Usage: Insights from Phylogeny, Influencing Factors and Pathogenicity.Current genomics · 2025Review
- Adaptive loss of tRNA gene expression leads to phage resistance in a marine Synechococcus cyanobacterium.Nature microbiology · 2025Article
- Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species.Microorganisms · 2024Article
- Codon-optimization in gene therapy: promises, prospects and challenges.Frontiers in bioengineering and biotechnology · 2024Review
- The distinct translational landscapes of gram-negative Salmonella and gram-positive Listeria.Nature communications · 2023Article
- Bioinformatic Analysis Reveals the Role of Translation Elongation Efficiency Optimisation in the Evolution ofBiology · 2023Article
- The organellar genomes of Pellidae (Marchantiophyta): the evidence of cryptic speciation, conflicting phylogenies and extraordinary reduction of mitogenomes in simple thalloid liverwort lineage.Scientific reports · 2023Article
- Ribonucleosides from tRNA in hyperglycemic mammalian cells and diabetic murine cardiac models.Life sciences · 2023Article
- Translation Comes First: Ancient and Convergent Selection of Codon Usage Bias Across Prokaryotic Genomes.Journal of molecular evolution · 2022Article
- tRNA methylation resolves codon usage bias at the limit of cell viability.Cell reports · 2022Article
- Bioinformatic Assessment of Factors Affecting the Correlation between Protein Abundance and Elongation Efficiency in Prokaryotes.International journal of molecular sciences · 2022Article
- Setting Up a Better Infection: Overexpression of the Early Bacteriophage T4 GenePHAGE (New Rochelle, N.Y.) · 2022Article
- Preferred synonymous codons are translated more accurately: Proteomic evidence, among-species variation, and mechanistic basis.Science advances · 2022Article
- Genome-wide analysis of theProceedings of the National Academy of Sciences of the United States of America · 2022Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The degree to which codon usage can be explained by tRNA abundance in bacterial species is often inadequate, partly because differential tRNA abundance is often approximated by tRNA copy numbers. To better understand the coevolution between tRNA abundance and codon usage, we provide a better estimate of tRNA abundance by profiling tRNA mapped reads (tRNA tpm) using publicly available RNA Sequencing data. To emphasize the feasibility of our approach, we demonstrate that tRNA tpm is consistent with tRNA abundances derived from RNA fingerprinting experiments in Escherichia coli, Bacillus subtilis, and Salmonella enterica. Furthermore, we do not observe an appreciable reduction in tRNA sequencing efficiency due to post-transcriptional methylations in the seven bacteria studied. To determine optimal codons, we calculate codon usage in highly and lowly expressed genes determined by protein per transcript. We found that tRNA tpm is sensitive to identify more translationally optimal codons than gene copy number and early tRNA fingerprinting abundances. Additionally, tRNA tpm improves the predictive power of tRNA adaptation index over codon preference. Our results suggest that dependence of codon usage on tRNA availability is not always associated with species growth-rate. Conversely, tRNA availability is better optimized to codon usage in fast-growing than slow-growing species.
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