000004067 001__ 4067
000004067 041__ $$aen_US
000004067 100__ $$aLucks, Julius B.
000004067 245__ $$aGenome Landscapes and Bacteriophage Codon Usage
000004067 260__ $$bPublic Library of Science$$c2010-09-30T17:13:16Z
000004067 500__ $$aAcross 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.
000004067 520__ $$aPhysics
000004067 65017 $$acomputational biology
000004067 6557_ $$aJournal Article
000004067 700__ $$aKudla, Grzegorz R.
000004067 700__ $$aPlotkin, Joshua B.
000004067 700__ $$aRegev, Aviv
000004067 700__ $$aNelson, David K
000004067 7860_ $$ndoi:10.1371/journal.pcbi.1000001
000004067 8564_ $$uhttp://dash.harvard.edu/handle/1/4454673$$zDASH:1/4454673
000004067 909C0 $$Y2008
000004067 909C4 $$dhttp://dash.harvard.edu/handle/1/4454673$$pDASH:1/4454673
000004067 980__ $$aDASH