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

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

The degeneracy of the genetic code implies that multiple triplets code for the same amino acid. The frequencies with which different codons are used vary significantly between organisms and between proteins within the same organism (Akashi, 2001) . Many studies have focused on the bias in codon usage among species. In single cell organisms (prokaryotes, archaea, and some fungi), the codon usage is strongly tuned for highly expressed genes and was thus concluded to be optimized for translational efficiency (Sharp et al, 1988) . However, the main trends in multicellular organism codon usage were attributed to the isochore-dependent genome composition (GC) content, gene architecture, and chromosomal locations (see discussion in Costantini et al, 2009) . Still, evidence for codon usage bias toward highly expressed genes and its correlation to tRNA abundance argues that translational efficiency does have a role for some plant, fly, and worm proteomes (Duret, 2000 and references within) . Evolutionary forces and multiple molecular processes (e.g., unbiased gene conversion, mutation rates, and genetic drift) have also participated in shaping codon usage in higher eukaryotes (Bernardi, 1986; Duret, 2002) . The molecular determinants that have globally influenced the translational efficiency in Escherichia coli (Kudla et al, 2009) and the evolution of polymerase genes in the influenza A virus (Brower-Sinning et al, 2009) indicate that, in addition to GC content, RNA folding processes also affect the adaptability and translational capacity of viral sequences.