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.

FIGURE 1.

UPGMA tree for the five genomes analyzed in this study. Divergence times are given in million years (Myr). The black circle indicates the point of the ancestral tRNA reconstruction.

FIGURE 2.

Distribution of number of tRNA species vs. gene copy number for each genome analyzed.

FIGURE 3.

Orthologous tRNA gene sets for the five organisms analyzed. Blue and yellow boxes show polycistronic tRNA clusters in EcK12, and gray boxes show mixed rRNA–tRNA operons (Inokuchi and Yamao 1995). Purple boxes show inverted regions when compared with the ancestral reconstruction. Orange boxes show regions with a high number of insertions. The numbers on the left indicate the genomic coordinates of tRNA genes in EcK12. The numbers at the bottom indicate the total number of functional tRNA genes in each genome.

FIGURE 4.

Kernel density estimate of COVE scores for all tRNA genes identified by tRNAscan-SE in the Escherichia–Shigella clade.