ArticleMolecular biology and evolution2014
Differential codon adaptation between dsDNA and ssDNA phages in Escherichia coli.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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26 citing papers in PubMed, 51 citations in OpenAlex.
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- Genomic AT Bias Coupled with Amino Acid Metabolism Modulates Codon Usage.Journal of molecular evolution · 2025Article
- Assessing the transcriptional landscape of Pseudomonas phage 201ϕ2-1: Uncovering the small regulatory details of a giant phage.Microbial biotechnology · 2024Article
- Differential Selection for Translation Efficiency Shapes Translation Machineries in Bacterial Species.Microorganisms · 2024Article
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- Variation in Release Factor Abundance Is Not Needed to Explain Trends in Bacterial Stop Codon Usage.Molecular biology and evolution · 2022Article
- Rapid discovery of novel prophages using biological feature engineering and machine learning.NAR genomics and bioinformatics · 2021Article
- ΦX174 Attenuation by Whole-Genome Codon Deoptimization.Genome biology and evolution · 2021Article
- Nucleotide Composition and Codon Usage Across Viruses and Their Respective Hosts.Frontiers in microbiology · 2021Article
- Improving Phylogenetic Signals of Mitochondrial Genes Using a New Method of Codon Degeneration.Life (Basel, Switzerland) · 2020Article
- Dissimilation of synonymous codon usage bias in virus-host coevolution due to translational selection.Nature ecology & evolution · 2020Article
- An improved estimation of tRNA expression to better elucidate the coevolution between tRNA abundance and codon usage in bacteria.Scientific reports · 2019Article
- GlobalViruses · 2019Article
- Genomic characterization of three novel Basilisk-like phages infecting Bacillus anthracis.BMC genomics · 2018Article
- The Evolution of Molecular Compatibility between Bacteriophage ΦX174 and its Host.Scientific reports · 2018Article
- Bacteriophage evolution differs by host, lifestyle and genome.Nature microbiology · 2017Article
- Isolation and Characterization of a Shewanella Phage-Host System from the Gut of the Tunicate, Ciona intestinalis.Viruses · 2017Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Because phages use their host translation machinery, their codon usage should evolve toward that of highly expressed host genes. We used two indices to measure codon adaptation of phages to their host, rRSCU (the correlation in relative synonymous codon usage [RSCU] between phages and their host) and Codon Adaptation Index (CAI) computed with highly expressed host genes as the reference set (because phage translation depends on host translation machinery). These indices used for this purpose are appropriate only when hosts exhibit little mutation bias, so only phages parasitizing Escherichia coli were included in the analysis. For double-stranded DNA (dsDNA) phages, both r(RSCU) and CAI decrease with increasing number of transfer RNA genes encoded by the phage genome. r(RSCU) is greater for dsDNA phages than for single-stranded DNA (ssDNA) phages, and the low r(RSCU) values are mainly due to poor concordance in RSCU values for Y-ending codons between ssDNA phages and the E. coli host, consistent with the predicted effect of C→T mutation bias in the ssDNA phages. Strong C→T mutation bias would improve codon adaptation in codon families (e.g., Gly) where U-ending codons are favored over C-ending codons ("U-friendly" codon families) by highly expressed host genes but decrease codon adaptation in other codon families where highly expressed host genes favor C-ending codons against U-ending codons ("U-hostile" codon families). It is remarkable that ssDNA phages with increasing C→T mutation bias also increased the usage of codons in the "U-friendly" codon families, thereby achieving CAI values almost as large as those of dsDNA phages. This represents a new type of codon adaptation.
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