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

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

The variability in viral structure, size, complexity, and shape is enormous. Despite such diversity, we assigned all viral proteins to four mutually exclusive functional sets (Figure 7 ; see Materials and methods). Figure 7C shows that structural proteins ('H') that do not function as host recognition elements are characterized by the highest levels of codon usage similarity with their respective host (i.e., lower L 2 distance measure). This diverse group includes proteins that participate in packing and covering the DNA, as well as the structural proteins that build the core of the virions. On the other hand, proteins that are expressed on the surface ('R'), which are molecules that participate in recognition of the host receptors, show the largest deviation from the host relative to the other defined groups. The polymerases and additional nucleic acid-related enzymes ('EC') show an intermediate level of resemblance to host codon usage.