Genome landscapes and bacteriophage codon usage

TL;DR

This study investigates codon usage patterns in 74 bacteriophages, revealing non-random genome-wide biases and supporting the role of translational selection in shaping viral gene codon preferences.

Contribution

Introduces the concept of genome landscapes and randomization tests to analyze long-range codon usage patterns in bacteriophages, highlighting translational selection effects.

Findings

33 phages show non-random GC3-content and codon usage patterns

Head and tail proteins preferentially use host-preferred codons

Evidence supports translational selection influencing viral gene codon usage

Abstract

Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonmous codons. Although alternative theories abound, translational selection has been accepted as an important mechanism that shapes the patterns of codon usage in prokaryotes and simple eukaryotes. Here we analyze patterns of codon usage across 74 diverse bacteriophages that infect E. coli, P. aeruginosa and L. lactis as their primary host. We introduce the concept of a `genome landscape,' which helps reveal non-trivial, long-range patterns in codon usage across a genome. We develop a series of randomization tests that allow us to interrogate the significance of one aspect of codon usage, such a GC content, while controlling for another aspect, such as adaptation to host-preferred codons. We find that 33 phage genomes exhibit highly non-random patterns in their GC3-content, use of host-preferred codons, or both. We show that the head and tail proteins of these phages exhibit significant bias towards host-preferred codons, relative to the non-structural phage proteins. Our results support the hypothesis of translational selection on viral genes for host-preferred codons, over a broad range of bacteriophages.