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

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

We found that for mammalian viruses, the proteins that appear in virion in high numbers (Figure 7 , marked 'H') are the ones with codon usage most similar to that of their hosts. In the case of human viruses, we can see that highly expressed genes in different viruses that infect the same host preferentially use codons similar to that of humans and of each other ( Figure 7C ). On the other hand, the surface proteins that participate in recognition are often expressed in lower quantities displaying a rather low adaptation level toward their hosts (marked 'R'). A complementary explanation may rely on the positive selection paradigm that was proposed in virus-host recognition (Sawyer et al, 2005) . The enzymes (marked 'EC'), which are generally expressed in minute amounts, show only an intermediate codon usage similarity. Thus, overall, these results further strengthen the case for translational selection. Note that earlier studies did not find evidence for translational selection operating on mammalian genes (see discussion in (dos Reis and Wernisch, 2009; Semon et al, 2006 #544 ) and references within). It may be possible that such selection does exist, but these phenomena are weak because of the low effective mammalian population sizes. On the other hand, viruses affecting mammals have larger effective population sizes and a shorter generation time (dos Reis and Wernisch, 2009) . Thus, similar analysis to that performed here may be able to identify translational selection in genomes in which it was impossible to do so earlier.