title: The effect of mutation and selection on codon adaptation in Escherichia coli bacteriophage.
abstract: Studying phage codon adaptation is important not only for understanding the process of translation elongation, but also for reengineering phages for medical and industrial purposes. To evaluate the effect of mutation and selection on phage codon usage, we developed an index to measure selection imposed by host translation machinery, based on the difference in codon usage between all host genes and highly expressed host genes. We developed linear and nonlinear models to estimate the C→T mutation bias in different phage lineages and to evaluate the relative effect of mutation and host selection on phage codon usage. C→T-biased mutations occur more frequently in single-stranded DNA (ssDNA) phages than in double-stranded DNA (dsDNA) phages and affect not only synonymous codon usage, but also nonsynonymous substitutions at second codon positions, especially in ssDNA phages. The host translation machinery affects codon adaptation in both dsDNA and ssDNA phages, with a stronger effect on dsDNA phages than on ssDNA phages. Strand asymmetry with the associated local variation in mutation bias can significantly interfere with codon adaptation in both dsDNA and ssDNA phages.
authors.affiliation: Department of Biology and Center for Advanced Research in Environmental Genomics, University of Ottawa, Ottawa, Ontario, K1N 6N5, Canada.
authors.forename: Shivapriya
authors.initials: S
authors.lastname: Chithambaram
authors.forename: Ramanandan
authors.initials: R
authors.lastname: Prabhakaran
authors.forename: Xuhua
authors.initials: X
authors.lastname: Xia
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics*; D001435:Bacteriophages / Q000235:genetics* / Q000502:physiology; D003062:Codon / Q000235:genetics*; D004277:DNA, Single-Stranded / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics / Q000821:virology*; D019143:Evolution, Molecular; D008957:Models, Genetic; D009154:Mutation; D014176:Protein Biosynthesis; D012641:Selection, Genetic
chemical_list: D003062:Codon; D004277:DNA, Single-Stranded
keywords: Escherichia coli; bacteriophage; codon adaptation; mutation bias; strand asymmetry; tRNA-mediated selection