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

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

In this paper, we observed that all mammalian genomes have similar codon usage. Furthermore, we found that human viruses share this common codon usage with their human Theoretically, this could derive from a situation where, for some reason, only human viruses are required to adapt their codon usage to successfully infect their host, whereas this adaptation does not seem critical for the viruses of other mammals. More likely explanations may be related to the recent expansion of humans and the co-evolution of their viruses, or to the hypothesis that large portions of the human genome are actually of viral origin (Kazazian, 2004) . A high similarity was reported earlier between the codon usage of bacteriophages and their hosts (Lucks et al, 2008) . In that study, the authors analyzed a large set of bacteriophages and isolated the effect of the GC (i.e., GC content) and the adaptation of specific viral codons toward the primary bacterial host. Interestingly, for about 40% of the viruses, host-preferred codons were selected, which suggests that adaptation toward the host has a strong role in viral evolution. In addition, they found that structural proteins show maximal similarity toward the host-preferred codon, in accordance with our finding regarding the high degree of adaptation for highly abundant proteins ( Figure 7C ).