title: Evolution of optimal codon choices in the family Enterobacteriaceae.
abstract: The Enterobacteriaceae are a large family of Proteobacteria that include many well-known prokaryotic genera, such as Escherichia, Yersinia and Salmonella. The main ideas of synonymous codon usage (CU) evolution and translational selection have been deeply influenced by studies with these bacterial groups. In this work we report the analysis of the CU pattern of completely sequenced bacterial genomes that belong to the Enterobacteriaceae. The effect of selection in translation acting at the levels of speed and accuracy, and phylogenetic trends within this group are described. Preferred (optimal) codons were identified. The evolutionary dynamics of these codons were studied and following a Bayesian approach these preferences were traced back to the common ancestor of the family. We found that there is some level of variation in selection among the analysed micro-organisms that is probably associated with lineage-specific trends. The codon bias was largely conserved across the evolutionary time of the family in highly expressed genes and protein conserved regions, suggesting a major role of negative selection. In this sense, the results support the idea that the extant CU bias is finely tuned over the ancestral well-conserved pool of tRNAs.
authors.affiliation: Área Genética, Depto. de Genética y Mejora Animal, Facultad de Veterinaria (UDELAR), Av. A. Lasplaces 1550, CP 11600, Montevideo, Uruguay.|Laboratorio de Evolución, Facultad de Ciencias (UDELAR), Iguá 4225, 11400 Montevideo, Uruguay.|Laboratorio de Organización y Evolución del Genoma, Facultad de Ciencias (UDELAR), Iguá 4225, 11400 Montevideo, Uruguay.
authors.forename: Andrés
authors.initials: A
authors.lastname: Iriarte
authors.affiliation: Laboratorio de Organización y Evolución del Genoma, Facultad de Ciencias (UDELAR), Iguá 4225, 11400 Montevideo, Uruguay.
authors.forename: Juan Diego
authors.initials: JD
authors.lastname: Baraibar
authors.affiliation: Laboratorio de Organización y Evolución del Genoma, Facultad de Ciencias (UDELAR), Iguá 4225, 11400 Montevideo, Uruguay.
authors.forename: Héctor
authors.initials: H
authors.lastname: Romero
authors.affiliation: Sección Bioquímica y Biología Molecular, Facultad de Ciencias (UDELAR), Iguá 4225, 11400 Montevideo, Uruguay.
authors.forename: Susana
authors.initials: S
authors.lastname: Castro-Sowinski
authors.affiliation: Laboratorio de Organización y Evolución del Genoma, Facultad de Ciencias (UDELAR), Iguá 4225, 11400 Montevideo, Uruguay.
authors.forename: Héctor
authors.initials: H
authors.lastname: Musto
mesh_terms: D003062:Codon; D004755:Enterobacteriaceae / Q000235:genetics*; D019143:Evolution, Molecular; D014176:Protein Biosynthesis; D012641:Selection, Genetic
chemical_list: D003062:Codon