Genome Landscapes and Bacteriophage Codon Usage Export

@article{citeulike:3124072, 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 \^{a}€{\oe}genome landscape,\^{a}€� 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.}, address = {FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA.}, author = {Lucks, Julius B. and Nelson, David R. and Kudla, Grzegorz R. and Plotkin, Joshua B.}, citeulike-article-id = {3124072}, citeulike-linkout-0 = {http://dx.doi.org/10.1371/journal.pcbi.1000001}, citeulike-linkout-1 = {http://view.ncbi.nlm.nih.gov/pubmed/18463708}, citeulike-linkout-2 = {http://www.hubmed.org/display.cgi?uids=18463708}, day = {29}, doi = {10.1371/journal.pcbi.1000001}, issn = {1553-7358}, journal = {PLoS Comput Biol}, month = {February}, number = {2}, pages = {e1000001+}, posted-at = {2009-11-14 10:57:56}, priority = {2}, publisher = {Public Library of Science}, title = {Genome Landscapes and Bacteriophage Codon Usage}, url = {http://dx.doi.org/10.1371/journal.pcbi.1000001}, volume = {4}, year = {2008} }

TY - JOUR ID - citeulike:3124072 L3 - citeulike-article-id:3124072 N2 - 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. IS - 2 JF - PLoS Comput Biol SN - 1553-7358 AD - FAS Center for Systems Biology, Harvard University, Cambridge, Massachusetts, USA. TI - Genome Landscapes and Bacteriophage Codon Usage PB - Public Library of Science VL - 4 SP - e1000001 AU - Lucks, Julius AU - Nelson, David AU - Kudla, Grzegorz AU - Plotkin, Joshua PY - 2008/02/29/ UR - http://dx.doi.org/10.1371/journal.pcbi.1000001 ER -