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Genome landscapes and bacteriophage codon usage.

Lucks JB, Nelson DR, Kudla GR, Plotkin JB - PLoS Comput. Biol. (2008)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA.

ABSTRACT
Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonymous 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 use 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 as 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.

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Combined Fisher p-values for the green and orange randomization tests across 50 phage genomes.Phage names are listed on the x-axis, and are sorted by their orange p-value. A total of 29 genomes exhibit non-random GC3 content controlling for CAI (green test); and a total of 22 genome exhibit non-random CAI content controlling for GC3 (orange test). 17 genomes pass both of these tests. The dashed horizontal line indicates the threshold for significance after Bonfernni correction (i.e. 5%/50). Upwards arrows indicate p-values that lie beyond the limits of the y-axis. See Table 2 for phage properties, including the p-values for these tests. Twenty four phage genomes that failed the aqua GC3 or CAI control tests are not included in this figure.
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pcbi-1000001-g008: Combined Fisher p-values for the green and orange randomization tests across 50 phage genomes.Phage names are listed on the x-axis, and are sorted by their orange p-value. A total of 29 genomes exhibit non-random GC3 content controlling for CAI (green test); and a total of 22 genome exhibit non-random CAI content controlling for GC3 (orange test). 17 genomes pass both of these tests. The dashed horizontal line indicates the threshold for significance after Bonfernni correction (i.e. 5%/50). Upwards arrows indicate p-values that lie beyond the limits of the y-axis. See Table 2 for phage properties, including the p-values for these tests. Twenty four phage genomes that failed the aqua GC3 or CAI control tests are not included in this figure.

Mentions: Properties are listed for all phages included in Figure 8, in the same order based on the orange p-value. Lifestyle annotations are T (temperate), NT (non-temperate), U (unknown). The coding length refers to the length of all coding sequences concatenated together (see Methods).


Genome landscapes and bacteriophage codon usage.

Lucks JB, Nelson DR, Kudla GR, Plotkin JB - PLoS Comput. Biol. (2008)

Combined Fisher p-values for the green and orange randomization tests across 50 phage genomes.Phage names are listed on the x-axis, and are sorted by their orange p-value. A total of 29 genomes exhibit non-random GC3 content controlling for CAI (green test); and a total of 22 genome exhibit non-random CAI content controlling for GC3 (orange test). 17 genomes pass both of these tests. The dashed horizontal line indicates the threshold for significance after Bonfernni correction (i.e. 5%/50). Upwards arrows indicate p-values that lie beyond the limits of the y-axis. See Table 2 for phage properties, including the p-values for these tests. Twenty four phage genomes that failed the aqua GC3 or CAI control tests are not included in this figure.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2266997&req=5

pcbi-1000001-g008: Combined Fisher p-values for the green and orange randomization tests across 50 phage genomes.Phage names are listed on the x-axis, and are sorted by their orange p-value. A total of 29 genomes exhibit non-random GC3 content controlling for CAI (green test); and a total of 22 genome exhibit non-random CAI content controlling for GC3 (orange test). 17 genomes pass both of these tests. The dashed horizontal line indicates the threshold for significance after Bonfernni correction (i.e. 5%/50). Upwards arrows indicate p-values that lie beyond the limits of the y-axis. See Table 2 for phage properties, including the p-values for these tests. Twenty four phage genomes that failed the aqua GC3 or CAI control tests are not included in this figure.
Mentions: Properties are listed for all phages included in Figure 8, in the same order based on the orange p-value. Lifestyle annotations are T (temperate), NT (non-temperate), U (unknown). The coding length refers to the length of all coding sequences concatenated together (see Methods).

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA.

ABSTRACT
Across all kingdoms of biological life, protein-coding genes exhibit unequal usage of synonymous 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 use 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 as 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.

Show MeSH