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

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

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

179 Scopus citations

Abstract

Viruses differ markedly in their specificity toward host organisms. Here, we test the level of general sequence adaptation that viruses display toward their hosts. We compiled a representative data set of viruses that infect hosts ranging from bacteria to humans. We consider their respective amino acid and codon usages and compare them among the viruses and their hosts. We show that bacteria-infecting viruses are strongly adapted to their specific hosts, but that they differ from other unrelated bacterial hosts. Viruses that infect humans, but not those that infect other mammals or aves, show a strong resemblance to most mammalian and avian hosts, in terms of both amino acid and codon preferences. In groups of viruses that infect humans or other mammals, the highest observed level of adaptation of viral proteins to host codon usages is for those proteins that appear abundantly in the virion. In contrast, proteins that are known to participate in host-specific recognition do not necessarily adapt to their respective hosts. The implication for the potential of viral infectivity is discussed.

Original languageAmerican English
Article number311
JournalMolecular Systems Biology
Volume5
DOIs
StatePublished - 20 Jan 2009

Keywords

  • Capsid
  • Codon usage
  • Host tropism
  • Protein classification
  • UniProt database
  • Viral proteome

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