Search for characteristic structural features of mammalian mitochondrial tRNAs

TLDR

Mitochondrial tRNAs frequently deviate from the classic cloverleaf and L‑shaped structures, leading to their general classification as “bizarre” tRNAs. The study aimed to define the structural characteristics of mammalian mitochondrial tRNAs by comparing the 22 tRNA genes across 31 fully sequenced genomes, and to aid assessment of disease‑associated point mutations. Vertical and horizontal sequence alignments were used to evaluate conservation and variability, identify potential tertiary interactions, and classify tRNAs by genomic strand to reveal strand‑specific mismatches, G‑T pairs, and low G/C content, yielding 22 representative sequences for phylogenetic analysis. The analysis revealed large size variations in D‑ and T‑loops, loss of conserved nucleotides G18G19 and T54T55C56, suggesting absent classical tertiary interactions, and produced 22 typical mitochondrial sequences that form a phylogenetic basis for future structural and functional studies.

Abstract

A number of mitochondrial (mt) tRNAs have strong structural deviations from the classical tRNA cloverleaf secondary structure and from the conventional L-shaped tertiary structure. As a consequence, there is a general trend to consider all mitochondrial tRNAs as “bizarre” tRNAs. Here, a large sequence comparison of the 22 tRNA genes within 31 fully sequenced mammalian mt genomes has been performed to define the structural characteristics of this specific group of tRNAs. Vertical alignments define the degree of conservation/variability of primary sequences and secondary structures and search for potential tertiary interactions within each of the 22 families. Further horizontal alignments ascertain that, with the exception of serine-specific tRNAs, mammalian mt tRNAs do fold into cloverleaf structures with mostly classical features. However, deviations exist and concern large variations in size of the D- and T-loops. The predominant absence of the conserved nucleotides G18G19 and T54T55C56, respectively in these loops, suggests that classical tertiary interactions between both domains do not take place. Classification of the tRNA sequences according to their genomic origin (G-rich or G-poor DNA strand) highlight specific features such as richness/poorness in mismatches or G-T pairs in stems and extremely low G-content or C-content in the D- and T-loops. The resulting 22 “typical” mammalian mitochondrial sequences built up a phylogenetic basis for experimental structural and functional investigations. Moreover, they are expected to help in the evaluation of the possible impacts of those point mutations detected in human mitochondrial tRNA genes and correlated with pathologies.