Transfer RNA Modification Enzymes from Thermophiles and Their Modified Nucleosides in tRNA

Abstract

To date, numerous modified nucleosides in tRNA as well as tRNA modification enzymes have been identified not only in thermophiles but also in mesophiles. Because most modified nucleosides in tRNA from thermophiles are common to those in tRNA from mesophiles, they are considered to work essentially in steps of protein synthesis at high temperatures. At high temperatures, the structure of unmodified tRNA will be disrupted. Therefore, thermophiles must possess strategies to stabilize tRNA structures. To this end, several thermophile-specific modified nucleosides in tRNA have been identified. Other factors such as RNA-binding proteins and polyamines contribute to the stability of tRNA at high temperatures. Thermus thermophilus, which is an extreme-thermophilic eubacterium, can adapt its protein synthesis system in response to temperature changes via the network of modified nucleosides in tRNA and tRNA modification enzymes. Notably, tRNA modification enzymes from thermophiles are very stable. Therefore, they have been utilized for biochemical and structural studies. In the future, thermostable tRNA modification enzymes may be useful as biotechnology tools and may be utilized for medical science.

Keywords: RNA modification; archaea; methylation; pseudouridine; tRNA methyltransferase; tRNA modification.

Figure 1

The structure of tRNA. (A) Representation of secondary structure of tRNA in a cloverleaf structure. This figure shows tRNA with a short variable region. Conserved nucleosides are shown with position numbers. Abbreviations: R, purine. Y, pyrimidine. (B) The L-shaped structure of Saccharomyces cerevisiae tRNA^Phe. The colors of nucleosides correspond to those in (A).

Figure 2

Sequences of tRNA from thermophiles. The modified nucleosides are indicated in red with their positions. Parentheses indicate that a portion of the modified nucleoside is further modified to its derivative. Abbreviations of modified nucleosides are given in Supplementary Table S1. (A) Geobacillus stearothermophilus tRNA^Leu. (B) G. stearothermophilus tRNA^Phe. (C) G. stearothermophilus tRNA^Tyr. (D) G. stearothermophilus tRNA^Val. (E) Aquifex aeolicus tRNA^Cys. (F) Thermus thermophilus tRNA^Asp. (G) T. thermophilus tRNA^Ile. (H) T. thermophilus tRNA^Met_f1. (I) T. thermophilus tRNA^Phe. (J) Thermoplasma acidophilum initiator tRNA^Met. (K) T. acidophilum elongator tRNA^Met. (L) T. acidophilum tRNA^Leu. (M) Sulfolobus acidocaldarius initiator tRNA^Met In A. aeolicus tRNA^Cys (E) the nucleotides shown in gray could not be determined and cyanoethylated tRNA^Cys was not analyzed. Therefore, this tRNA may possess additional modifications (e.g., Ψ₃₉, Ψ₅₅ and m¹A58). Thermus thermophilus possesses two tRNA^Met_f species. The difference of tRNA^Met_f2 is single G-C base pair, which is indicated in purple in (H). In S. acidocaldarius initiator tRNA^Met (M), the nucleosides at positions 9 and 26 may be m¹A₉ and m²₂Gm₂₆, respectively.

Figure 2

Sequences of tRNA from thermophiles. The modified nucleosides are indicated in red with their positions. Parentheses indicate that a portion of the modified nucleoside is further modified to its derivative. Abbreviations of modified nucleosides are given in Supplementary Table S1. (A) Geobacillus stearothermophilus tRNA^Leu. (B) G. stearothermophilus tRNA^Phe. (C) G. stearothermophilus tRNA^Tyr. (D) G. stearothermophilus tRNA^Val. (E) Aquifex aeolicus tRNA^Cys. (F) Thermus thermophilus tRNA^Asp. (G) T. thermophilus tRNA^Ile. (H) T. thermophilus tRNA^Met_f1. (I) T. thermophilus tRNA^Phe. (J) Thermoplasma acidophilum initiator tRNA^Met. (K) T. acidophilum elongator tRNA^Met. (L) T. acidophilum tRNA^Leu. (M) Sulfolobus acidocaldarius initiator tRNA^Met In A. aeolicus tRNA^Cys (E) the nucleotides shown in gray could not be determined and cyanoethylated tRNA^Cys was not analyzed. Therefore, this tRNA may possess additional modifications (e.g., Ψ₃₉, Ψ₅₅ and m¹A58). Thermus thermophilus possesses two tRNA^Met_f species. The difference of tRNA^Met_f2 is single G-C base pair, which is indicated in purple in (H). In S. acidocaldarius initiator tRNA^Met (M), the nucleosides at positions 9 and 26 may be m¹A₉ and m²₂Gm₂₆, respectively.

Figure 3

Thermophile-specific modified nucleosides in tRNA. Abbreviations of modified nucleosides are given in Supplementary Table S1. (A) m⁵s²U. (B) m⁵Cm. (C) m¹Im. (D) m²₂Gm. (E) m^{2, 7}Gm. The modifications are indicated in red.