Losing the stem-loop structure from metazoan mitochondrial tRNAs and co-evolution of interacting factors

Abstract

Conventional tRNAs have highly conserved sequences, four-armed cloverleaf secondary structures, and L-shaped tertiary structures. However, metazoan mitochondrial tRNAs contain several exceptional structures. Almost all tRNAs(Ser) for AGY/N codons lack the D-arm. Furthermore, in some nematodes, no four-armed cloverleaf-type tRNAs are present: two tRNAs(Ser) without the D-arm and 20 tRNAs without the T-arm are found. Previously, we showed that in nematode mitochondria, an extra elongation factor Tu (EF-Tu) has evolved to support interaction with tRNAs lacking the T-arm, which interact with C-terminal domain 3 in conventional EF-Tu. Recent mitochondrial genome analyses have suggested that in metazoan lineages other than nematodes, tRNAs without the T-arm are present. Furthermore, even more simplified tRNAs are predicted in some lineages. In this review, we discuss mitochondrial tRNAs with divergent structures, as well as protein factors, including EF-Tu, that support the function of truncated metazoan mitochondrial tRNAs.

Keywords: D-arm; T-arm; aminoacyl-tRNA synthetase; elongation factor Tu; mitochondrial tRNA; ribosome; tRNA nucleotidyltransferase.

FIGURE 1

Secondary and tertiary structures of tRNAs. (A) Cloverleaf tRNA. (B) L-shape tertiary structure of cloverleaf tRNA (Saccharomyces cerevisiae tRNA^Phe, PDB code 6TNA). (C) D-arm-lacking tRNA (bovine mt tRNA^Ser(GCU), accession number: X15132. Modification data from tRNAdb (Jühling et al., 2009), tRNAdb ID: tdbR0000402). (D) T-arm-lacking tRNA (Ascaris suum mt tRNA^Met, accession number: D28746; Watanabe et al., 1994; Sakurai et al., 2005b). (E) L-shape model of T-arm-lacking tRNA (Ohtsuki et al., 1998) built with reference to the crystal structure of yeast tRNA^Phe. This model was built from computational analysis including molecular dynamics calculations to arrange the base locations according to tertiary interactions deduced from NMR observations (Ohtsuki et al., 1998), sequence alignment (Wolstenholme et al., 1994), and structural probing experiments (Watanabe et al., 1994).

FIGURE 2

(A) Docking model of mammalian mt SerRS and yeast tRNA^Phe (Chimnaronk et al., 2005). Two subunits of the enzyme are shown in green (monomer 1), and gray (monomer 2), respectively. Distal helix of monomer 1 and C-tail of monomer 2 which are mitochondrial-specific extensions and possibly interact with the tRNA, are shown in yellow and pink, respectively. In the tRNA, D-arm, variable loop, and T-arm are shown in purple, sky blue, and red, respectively. (B) Putative interactions between the N-terminal coiled–coil region and the C-tail distal helix with the T-arm of the tRNA. The interactions are inferred by mutational analysis of the enzyme (Chimnaronk et al., 2005). Residues in N-terminal coiled–coil region and distal helix involved in the interaction with tRNA are shown in stick model (Chimnaronk et al., 2005).

FIGURE 3

(A) Ternary complex of conventional tRNA/EF-Tu/GTP (Nissen et al., 1995). (B) Summary of ethylnitrosourea (ENU) modification interference studies of T-arm-lacking mt tRNA with C. elegans mt EF-Tu1 (Sakurai et al., 2006). The phosphate groups important for EF-Tu1 binding are shown with arrows. (C) A model of the ternary complex of T-arm-lacking tRNA/mt EF-Tu1/GTP (Sakurai et al., 2006). The model was based on the structure shown in (A) and in Figure 1E. A possible interaction between the C-terminal extension of EF-Tu1 and the region around position 9 in T-arm-lacking tRNA is suggested by modification interference as summarized in (B), cross-linking studies, and the tRNA binding activity of the C-terminal deletion mutants of EF-Tu1 (Ohtsuki et al., 2001; Sakurai et al., 2006). (D) Summary of ENU modification interference study of D-arm-lacking mt tRNA with C. elegans mt EF-Tu2 (Suematsu et al., 2005). The tRNA structure was inferred from the model proposed by Steinberg and his co-workers (Steinberg et al., 1994). The phosphate groups important for EF-Tu2 binding are shown by arrows. (E) A model of the ternary complex of D-arm-lacking mt tRNA^Ser/C. elegans mt EF-Tu2/GTP (Suematsu et al., 2005). A possible interaction between the C-terminal extension of EF-Tu2 and acceptor-T helix in D-arm-lacking tRNA is suggested by modification interference study as summarized in (D), binding assays of mutant tRNAs, and the binding activity of EF-Tu mutants with C-terminal deletions (Suematsu et al., 2005).