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.

Comparative patterns of modified nucleotides in individual tRNA species from a mesophilic and two thermophilic archaea

“…All these observations complete and reinforce similar conclusions made by others about the importance of certain post-transcriptional modifications for correct tRNA folding and on final cellular stability of the already G/C-rich tRNAs in thermophiles (Edmonds et al 1991;Kowalak et al 1994;McCloskey et al 2001;Noon et al 2003;reviewed in Lorenz et al 2017;Hori et al 2018;Machnicka et al 2014). As a rule, methylations promote precise H-bonded pairs (e.g.…”

“…Similarly, the 26-44 pair displays a frequent G26 modification (m 2 G, m 2 2G but also m 2 2Gm), forming either G26oU44 or G26-A44 pairs ( Figure S11D), rarely G26-C44 (with a slight bias toward m 2 2G at position 26 when pairing with U44, especially for the long-arm tRNAs Leu and Ser). Surprisingly, in tRNA-Ser(GGA) of P. furiosus, MS/MS data and T1 cleavage analysis (Table S1) 2001; Grosjean et al 2008b;Hori et al 2018).…”

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

“…As noted before, the vast majority (41 of 61) arise from Haloferax volcanii (15,16). The remainder are distributed among six other archaea: Halobacterium salinarum (formerly Halobacterium cutirubrum), 12 sequences (38,39); Thermoplasma acidophilum, three sequences (14,(40)(41)(42); Methanobacterium thermoautotrophicum, two sequences (43); and Halococcus morrhuae (40), Methanosarcina barkeri (44), and Sulfolobus acidocaldarius (14,40), one sequence each.…”

“…While C/D box small RNAs (sRNAs) are often responsible for ribose methylations (54,55), even in tRNAs, M. jannaschii tRNA introns do not contain guide RNAs. As M. jannaschii does not have a homolog of TrmH, unlike several other archaea (14), the enzyme and mechanism responsible for ribose methylation at this site are unknown.…”

“…Our understanding of tRNA modification profiles (i.e., the specific modifications and locations in each tRNA) in archaea is limited (14). To date, the only archaeal tRNA sequences whose modification profiles are almost completely characterized are from Haloferax volcanii (15,16).…”