Archaeology and evolution of transfer RNA genes in the Escherichia coli genome

Abstract

Transfer RNA genes tend to be presented in multiple copies in the genomes of most organisms, from bacteria to eukaryotes. The evolution and genomic structure of tRNA genes has been a somewhat neglected area of molecular evolution. Escherichia coli, the first phylogenetic species for which more than two different strains have been sequenced, provides an invaluable framework to study the evolution of tRNA genes. In this work, a detailed analysis of the tRNA structure of the genomes of Escherichia coli strains K12, CFT073, and O157:H7, Shigella flexneri 2a 301, and Salmonella typhimurium LT2 was carried out. A phylogenetic analysis of these organisms was completed, and an archaeological map depicting the main events in the evolution of tRNA genes was drawn. It is shown that duplications, deletions, and horizontal gene transfers are the main factors driving tRNA evolution in these genomes. On average, 0.64 tRNA insertions/duplications occur every million years (Myr) per genome per lineage, while deletions occur at the slower rate of 0.30 per million years per genome per lineage. This work provides a first genomic glance at the problem of tRNA evolution as a repetitive process, and the relationship of this mechanism to genome evolution and codon usage is discussed.

Evolution of optimal codon choices in the family Enterobacteriaceae

“…This is striking, given the differences in lifestyles, effective population sizes, generation times, ecological niches, metabolic routes, genomic GC, etc., that characterize the different micro-organisms. Withers et al (2006) found that for most of the tested genomes, CU frequencies matched more closely to the putative ancestral set of tRNA genes than to extant ones. Our results support this statement, which has important implications for understanding CU and tRNA coevolution.…”

Insights from Comparative Genomics of the Genus Salmonella

“…The number of tRNA genes present in the Salmonella reference genome is 85, representing 47 diferent tRNA molecules that together cover the 40 required anticodons [20]. These numbers can vary between genomes and serovars.…”

Evolution of Genome Organization by Duplication and Loss: An Alignment Approach

“…They are usually grouped in the genome within clusters (or operons in the case of microbial genomes), representing highly repetitive regions, causing genomic instability through illegitimate homologous recombination. In consequence, stable RNA families are rapidly evolving by duplication and loss [35,3,28].…”

“…In parallel, gene losses through pseudogenization and segmental deletions, appear generally to maintain a minimum number of functional gene copies [5,9,10,12,16,22,25]. Transfer RNAs (tRNAs) are typical examples of gene families that are continually duplicated and lost [3,28,31,35]. Indeed, tRNA clusters (or operons in microbial genomes) are highly dynamic and unstable genomic regions.…”

“…Indeed, tRNA clusters (or operons in microbial genomes) are highly dynamic and unstable genomic regions. In Escherichia coli for example, the rate of tRNA gene duplication/loss events has been estimated to be about one event every 1.5 million years [3,35].…”