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

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

In the case of bacterial viruses (Lucks et al, 2008) , we were unable to consistently and reliably partition the proteins that are involved in recognition from those that are abundant, because of the enormous variability in shape and recognition mode among bacteriophages. Our results agree with a role of translational selection and extend it toward mammalian viruses, where it may have a role in their evolutionary fitness. However, this adaptation may be of lesser importance, as a critical obstacle for viruses that infect mammals is the need to invade their host cells, while bypassing an active immune system (whereas no such extensive system exists in bacterial hosts). For example, the HIV virus has adopted recognition strategies that overcome the immune barrier (Holmes et al, 1992) .