scnRCA: A Novel Method to Detect Consistent Patterns of Translational Selection in Mutationally-Biased Genomes

O'Neill, Patrick K.; Or, Mindy; Erill, Ivan

scnRCA: A Novel Method to Detect Consistent Patterns of Translational Selection in Mutationally-Biased Genomes

dc.contributor.author	O'Neill, Patrick K.
dc.contributor.author	Or, Mindy
dc.contributor.author	Erill, Ivan
dc.date.accessioned	2021-03-08T19:43:36Z
dc.date.available	2021-03-08T19:43:36Z
dc.date.issued	2013-10-07
dc.description.abstract	Codon usage bias (CUB) results from the complex interplay between translational selection and mutational biases. Current methods for CUB analysis apply heuristics to integrate both components, limiting the depth and scope of CUB analysis as a technique to probe into the evolution and optimization of protein-coding genes. Here we introduce a self-consistent CUB index (scnRCA) that incorporates implicit correction for mutational biases, facilitating exploration of the translational selection component of CUB. We validate this technique using gene expression data and we apply it to a detailed analysis of CUB in the Pseudomonadales. Our results illustrate how the selective enrichment of specific codons among highly expressed genes is preserved in the context of genome-wide shifts in codon frequencies, and how the balance between mutational and translational biases leads to varying definitions of codon optimality. We extend this analysis to other moderate and fast growing bacteria and we provide unified support for the hypothesis that C- and A-ending codons of two-box amino acids, and the U-ending codons of four-box amino acids, are systematically enriched among highly expressed genes across bacteria. The use of an unbiased estimator of CUB allows us to report for the first time that the signature of translational selection is strongly conserved in the Pseudomonadales in spite of drastic changes in genome composition, and extends well beyond the core set of highly optimized genes in each genome. We generalize these results to other moderate and fast growing bacteria, hinting at selection for a universal pattern of gene expression that is conserved and detectable in conserved patterns of codon usage bias.	en_US
dc.description.sponsorship	The authors would like to thank Philip Farabaugh for insightful discussions and helpful suggestions in the interpretation of results, and Sefa Kılıç for providing critical insight on the code.	en_US
dc.description.uri	https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0076177	en_US
dc.format.extent	11 pages	en_US
dc.genre	journal articles	en_US
dc.identifier	doi:10.13016/m21y8w-zfvz
dc.identifier.citation	O'Neill PK, Or M, Erill I (2013) scnRCA: A Novel Method to Detect Consistent Patterns of Translational Selection in Mutationally-Biased Genomes. PLoS ONE 8(10): e76177. https://doi.org/10.1371/journal.pone.0076177	en_US
dc.identifier.uri	https://doi.org/10.1371/journal.pone.0076177
dc.identifier.uri	http://hdl.handle.net/11603/21101
dc.language.iso	en_US	en_US
dc.publisher	PLOS	en_US
dc.relation.isAvailableAt	The University of Maryland, Baltimore County (UMBC)
dc.relation.ispartof	UMBC Biological Sciences Department Collection
dc.relation.ispartof	UMBC Faculty Collection
dc.relation.ispartof	UMBC Student Collection
dc.rights	This item is likely protected under Title 17 of the U.S. Copyright Law. Unless on a Creative Commons license, for uses protected by Copyright Law, contact the copyright holder or the author.
dc.rights	Attribution 4.0 International	*
dc.rights.uri	https://creativecommons.org/licenses/by/4.0/	*
dc.title	scnRCA: A Novel Method to Detect Consistent Patterns of Translational Selection in Mutationally-Biased Genomes	en_US
dc.type	Text	en_US