Abstract
The codon usage pattern is a specific characteristic of each species; however, the codon usage of all of the genes in a genome is not uniform. Intriguingly, most viruses have codon usage patterns that are vastly different from the optimal codon usage of their hosts. How viral genes with different codon usage patterns are efficiently expressed during a viral infection is unclear. An analysis of the similarity between viral codon usage and the codon usage of the individual genes of a host genome has never been performed. In this study, we demonstrated that the codon usage of human RNA viruses is similar to that of some human genes, especially those involved in the cell cycle. This finding was substantiated by its concordance with previous reports of an upregulation at the protein level of some of these biological processes. It therefore suggests that some suboptimal viral codon usage patterns may actually be compatible with cellular translational machineries in infected conditions.
Highlights
IntroductionThere are correlations between the codon usage bias and other factors related to translation efficiency (such as available tRNAs, mRNA secondary structure, translation elongation rate, and the intragenic and intergenic codon bias) that cannot be explained by mutation pressure
The RSCU was calculated from the protein coding sequences of the human and RNA viruses
The RSCU of each gene consists of 59 values corresponding to 59 synonymous codons; the PCA was performed to simplify the data to a smaller number of principal factors as a summary feature of the codon usage pattern of each gene
Summary
There are correlations between the codon usage bias and other factors related to translation efficiency (such as available tRNAs, mRNA secondary structure, translation elongation rate, and the intragenic and intergenic codon bias) that cannot be explained by mutation pressure. The cellular tRNA level was found to be unchanged following vaccinia and influenza A virus (IAV) infection, whereas an alteration in the polysome-associated tRNA population was observed, the population of polysome tRNA isoacceptors correlated with viral codon usage [35] These findings suggest that the codon usage pattern and the regulation of translational machineries may influence gene expression in some viruses. A comparison of the codon usage at the genome level is too generalized; a more precise comparison at the single-gene level may provide a better insight into the viral codon usage bias
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