Viral adaptation to host: a proteome-based analysis of codon usage and amino acid preferences

Bahir, Iris; Fromer, Menachem; Prat, Yosef; Linial, Michal

It is known that the GC content is a strong determinant in shaping codon usage, specifically in the higher multicellular eukaryotes. As a control experiment, a comparison of the GC content between viruses and their cognate hosts shows that viruses have an overall weak, but significant (R 2 ¼0.575, Po10 À5 ), correlation with their host GC content ( Figure 6A ). In fact, for bacteria, the partition by host GC content provides a very strong linear association ( Figure 6A , blue points, R 2 ¼0.927, Po10 À5 ). However, no significant associations are found between the GC contents of viruses and their hosts for other taxonomic groups. For example, for the 11 mammals analyzed in this study, the correlation was extremely poor (R 2 ¼0.065). This can be explained by the fact that although the GC content in mammal-infecting viruses ranges between 35 and 56%, the GC content of the proteomes of the mammal hosts studied (Supplementary Table S3 ) is rather narrow (50-53%). Thus, we conclude that the correlation between the GC contents of the viruses and their hosts ( Figure 6A ) is dominated by the bacteriophages matching their unique bacteria.