Abstract
The mitochondrion is the power plant of the eukaryotic cell, and tRNAs are the fundamental components of its translational machinery. In the present paper, the evolution of mitochondrial tRNAs was investigated in the Cetacea, a clade of Cetartiodactyla that retuned to water and thus had to adapt its metabolism to a different medium than that of its mainland ancestors. Our analysis focussed on identifying the factors that influenced the evolution of Cetacea tRNA double-helix elements, which play a pivotal role in the formation of the secondary and tertiary structures of each tRNA and consequently manipulate the whole translation machinery of the mitochondrion. Our analyses showed that the substitution pathways in the stems of different tRNAs were influenced by various factors, determining a molecular evolution that was unique to each of the 22 tRNAs. Our data suggested that the composition, AT-skew, and GC-skew of the tRNA stems were the main factors influencing the substitution process. In particular, the range of variation and the fluctuation of these parameters affected the fate of single tRNAs. Strong heterogeneity was observed among the different species of Cetacea. Finally, it appears that the evolution of mitochondrial tRNAs was also shaped by the environments in which the Cetacean taxa differentiated. This latter effect was particularly evident in toothed whales that either live in freshwater or are deep divers.
Highlights
Mitochondrial transfer RNA (tRNA) are fundamental components of the translational machinery of the mitochondrion, which is the powerhouse of the eukaryotic cell
The Z. cavirostris genome contained the 37 genes almost universally found in animal mtDNAs i.e., 13 PCGs, two ribosomal ribosomal RNA (rRNA) and 22 tRNAs
Our analysis focussed on the changes that occurred in the stems of 22 tRNAs because they have a major impact on the structural integrity of these molecules
Summary
Mitochondrial tRNAs are fundamental components of the translational machinery of the mitochondrion, which is the powerhouse of the eukaryotic cell. In most Metazoa, the mitochondrial genome (mtDNA) contains 22 tRNAs genes (hereafter named trnX, where X is the single letter IUPAC code for the corresponding amino acid). A single tRNA represents the whole codon family. Leucine and Serine are the only known exceptions and possess two tRNAs belonging to two distinct families (i.e., trnL1 and tnL2, and trnS1 and trnS2, respectively). Multiple copies of the same tRNA are present in animal mtDNAs. Occasionally, multiple copies of the same tRNA are present in animal mtDNAs In this latter case, they are the product of duplication/multiplication processes and do not represent distinct codon families [1]
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