title: Escherichia coli and Staphylococcus phages: effect of translation initiation efficiency on differential codon adaptation mediated by virulent and temperate lifestyles.
abstract: Rapid biosynthesis is key to the success of bacteria and viruses. Highly expressed genes in bacteria exhibit a strong codon bias corresponding to the differential availability of tRNAs. However, a large clade of lambdoid coliphages exhibits relatively poor codon adaptation to the host translation machinery, in contrast to other coliphages that exhibit strong codon adaptation to the host. Three possible explanations were previously proposed but dismissed: (1) the phage-borne tRNA genes that reduce the dependence of phage translation on host tRNAs, (2) lack of time needed for evolving codon adaptation due to recent host switching, and (3) strong strand asymmetry with biased mutation disrupting codon adaptation. Here, we examined the possibility that phages with relatively poor codon adaptation have poor translation initiation which would weaken the selection on codon adaptation. We measured translation initiation by: (1) the strength and position of the Shine-Dalgarno (SD) sequence, and (2) the stability of the secondary structure of sequences flanking the SD and start codon known to affect accessibility of the SD sequence and start codon. Phage genes with strong codon adaptation had significantly stronger SD sequences than those with poor codon adaptation. The former also had significantly weaker secondary structure in sequences flanking the SD sequence and start codon than the latter. Thus, lambdoid phages do not exhibit strong codon adaptation because they have relatively inefficient translation initiation and would benefit little from increased elongation efficiency. We also provided evidence suggesting that phage lifestyle (virulent versus temperate) affected selection intensity on the efficiency of translation initiation and elongation.
authors.affiliation: Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, PO Box 450, Station A, Ottawa, Ontario K1N 6N5, Canada.
authors.forename: Ramanandan
authors.initials: R
authors.lastname: Prabhakaran
authors.affiliation: Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, PO Box 450, Station A, Ottawa, Ontario K1N 6N5, Canada.
authors.forename: Shivapriya
authors.initials: S
authors.lastname: Chithambaram
authors.affiliation: Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, 30 Marie Curie, PO Box 450, Station A, Ottawa, Ontario K1N 6N5, Canada.
authors.forename: Xuhua
authors.initials: X
authors.lastname: Xia
mesh_terms: D000220:Adaptation, Biological; D003062:Codon; D003090:Coliphages / Q000235:genetics* / Q000502:physiology*; D008242:Lysogeny; D014176:Protein Biosynthesis; D013204:Staphylococcus Phages / Q000235:genetics* / Q000502:physiology*; D014774:Virulence; D014779:Virus Replication
chemical_list: D003062:Codon