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

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

Most virus proteomes are rather simple and include o10 proteins. A minimal set of proteins comprises the virion structure by building the atomic units of the capsomers. Similarly, most viruses have a replication enzyme such as reverse transcriptase and RNA or DNA polymerase, according to their mode of replication, transcription, and regulation. In some instances (e.g., small DNA viruses and hepadnaviruses), the involvement of host polymerases is essential for the initial phase of viral replication. The rest of the proteome encodes diverse functions that are mostly uncharacterized and are often specialized to the life cycle of the particular virus. We tested the hypothesis that the evolutionary forces underlying codon usage adaptation of the virus may not be determined at the overall genomic level but may instead reflect some functional properties of its proteins.