ArticleNature ecology & evolution2020
Dissimilation of synonymous codon usage bias in virus-host coevolution due to translational selection.
Article in Nature ecology & evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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Who cites it
74 citing papers in PubMed.
- Transgene sequence codon optimization and composition determines replication competence of self-amplifying RNA.Molecular therapy : the journal of the American Society of Gene Therapy · 2026Article
- DNA viruses are constrained to ecological niches and share similar environmental adaptations with hosts.Nature communications · 2026Article
- Host mature tRNAome as a decoding switch regulates antiviral and proviral responses.Nature communications · 2026Article
- Temporal and gene-specific dynamics of codon usage evolution in SARS-CoV-2 genomes.BMC genomics · 2026Article
- A slight mismatch between a gene's codon usage and the cellular tRNA supply is beneficial.Nature communications · 2026Article
- Genetic diversity, codon usage, and evolutionary dynamics of bovine parainfluenza virus type-3.The Journal of veterinary medical science · 2026Article
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- RNA editing signatures and codon adaptation reveal potential translational compatibility between Hendra virus and its natural host Pteropus Alecto.Archives of microbiology · 2025Article
- Mapping evolutionary paradigm of bovine viral diarrhea virusVirulence · 2025Article
- Codon usage of human DNA viruses and its similarity to certain host genes.Scientific reports · 2025Article
- Functional synonymous mutations and their evolutionary consequences.Nature reviews. Genetics · 2025Review
- Codon Usage Bias in Human RNA Viruses and Its Impact on Viral Translation, Fitness, and Evolution.Viruses · 2025Review
- tRNA Modifications: A Tale of Two Viruses-SARS-CoV-2 and ZIKV.International journal of molecular sciences · 2025Article
- Comparative Genomics and Phylogenetics of Chloroplasts Reveal Lower Rates of Genetic Variation in Mango (Ecology and evolution · 2025Article
- Ciprofloxacin-driven purifying selection on viral genomes accelerates soil NProceedings of the National Academy of Sciences of the United States of America · 2025Article
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- Predicting viral host codon fitness and path shifting through tree-based learning on codon usage biases and genomic characteristics.Scientific reports · 2025Article
- An Expanding Universe of Mutational Signatures and Its Rapid Evolution in Single-Stranded RNA Viruses.Molecular biology and evolution · 2025Article
14 more citing papers are in PubMed but not listed here.
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9 authors.
Funding
Abstract
Eighteen of the 20 amino acids are each encoded by more than one synonymous codon. Due to differential transfer RNA supply within the cell, synonymous codons are not used with equal frequency, a phenomenon termed codon usage bias (CUB). Previous studies have demonstrated that CUB of endogenous genes trans-regulates the translational efficiency of other genes. We hypothesized similar effects for CUB of exogenous genes on host translation, and tested it in the case of viral infection, a common form of naturally occurring exogenous gene translation. We analysed public Ribo-Seq datasets from virus-infected yeast and human cells and showed that virus CUB trans-regulated tRNA availability, and therefore the relative decoding time of codons. Manipulative experiments in yeast using 37 synonymous fluorescent proteins confirmed that an exogenous gene with CUB more similar to that of the host would apply decreased translational load on the host per unit of expression, whereas expression of the exogenous gene was elevated. The combination of these two effects was that exogenous genes with CUB overly similar to that of the host severely impeded host translation. Finally, using a manually curated list of viruses and natural and symptomatic hosts, we found that virus CUB tended to be more similar to that of symptomatic hosts than that of natural hosts, supporting a general deleterious effect of excessive CUB similarity between virus and host. Our work revealed repulsion between virus and host CUBs when they are overly similar, a previously unrecognized complexity in the coevolution of virus and host.
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