Genome Landscapes and Bacteriophage Codon Usage

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Genome Landscapes and Bacteriophage Codon Usage

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Title: Genome Landscapes and Bacteriophage Codon Usage
Author: Lucks, Julius B.; Kudla, Grzegorz R.; Plotkin, Joshua B.; Regev, Aviv; Nelson, David R.

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Citation: Lucks, Julius B., David R. Nelson, Grzegorz R. Kudla, Joshua B. Plotkin, and Aviv Regev. 2008. Genome landscapes and bacteriophage codon usage. PLoS Computational Biology 4(2): e1000001.
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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.
Published Version: doi:10.1371/journal.pcbi.1000001
Other Sources: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2266997/pdf/
Terms of Use: This article is made available under the terms and conditions applicable to Other Posted Material, as set forth at http://nrs.harvard.edu/urn-3:HUL.InstRepos:dash.current.terms-of-use#LAA
Citable link to this page: http://nrs.harvard.edu/urn-3:HUL.InstRepos:4454673

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  • FAS Scholarly Articles [6463]
    Peer reviewed scholarly articles from the Faculty of Arts and Sciences of Harvard University
 
 

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