tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

Abstract

tRNAs play a critical role in mRNA decoding, and posttranscriptional modifications within tRNAs drive decoding efficiency and accuracy. The types and positions of tRNA modifications in model bacteria have been extensively studied, and tRNA modifications in a few eukaryotic organisms have also been characterized and localized to particular tRNA sequences. However, far less is known regarding tRNA modifications in archaea. While the identities of modifications have been determined for multiple archaeal organisms, Haloferax volcanii is the only organism for which modifications have been extensively localized to specific tRNA sequences. To improve our understanding of archaeal tRNA modification patterns and codondecoding strategies, we have used liquid chromatography and tandem mass spectrometry to characterize and then map posttranscriptional modifications on 34 of the 35 unique tRNA sequences of Methanocaldococcus jannaschii. A new posttranscriptionally modified nucleoside, 5-cyanomethyl-2-thiouridine (cnm 5 s 2 U), was discovered and localized to position 34. Moreover, data consistent with wyosine pathway modifications were obtained beyond the canonical tRNA Phe as is typical for eukaryotes. The high-quality mapping of tRNA anticodon loops enriches our understanding of archaeal tRNA modification profiles and decoding strategies. IMPORTANCE While many posttranscriptional modifications in M. jannaschii tRNAs are also found in bacteria and eukaryotes, several that are unique to archaea were identified. By RNA modification mapping, the modification profiles of M. jannaschii tRNA anticodon loops were characterized, allowing a comparative analysis with H. volcanii modification profiles as well as a general comparison with bacterial and eukaryotic decoding strategies. This general comparison reveals that M. jannaschii, like H. volcanii, follows codon-decoding strategies similar to those used by bacteria, although position 37 appears to be modified to a greater extent than seen in H. volcanii.

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

“…acidocaldarius, wyosine derivatives are present in tRNA-Asp(GUC), tRNA-Ser(UGA), tRNA-Phe(GAA), tRNA-Trp(CCA) and tRNA-Tyr(GUA). This surprising result was noted in the case of M. jannaschii (Yu et al 2019) where besides tRNA-Phe, the tRNA-Arg(UCG),…”

“…Eukaryotes and Bacteria (Machnicka et al 2014). However, in most Archaea (mainly Euryarchaeota), a 1-methylpseudouridine (m 1 Ψ) is generally found instead (Pang et al 1982;Gupta 1984;McCloskey et al 2001;Chatterjee et al 2012;Yu et al 2019). Such a modification adds a methyl group to the pseudouridine (Ψ) at the free N1 atom, a position structurally equivalent to the C5 atom of T54.…”

“…In Archaea, although studied for a long time, the landscape of tRNA modifications remained disperse, and known only for a few particular tRNA isoacceptors or bulk cellular tRNAs (see for examples: Kuchino et al 1982;Edmonds et al 1991;Tomikawa et al 2013). Only in the cases of Haloferax volcanii (Gupta 1984(Gupta , 1986Grosjean et al 2008a) and very recently in the case of Methanocaldococcus jannaschii (Yu et al 2019), the modification landscape of a complete set of cellular tRNAs has been elucidated. These data reveal that a few modifications are unique to certain archaea, while others are present in most, if not all archaeal species studied so far.…”

RNA stabilization in hyperthermophilic archaea

“…The tRNA populations of hyperthermophilic archaea were found to be heavily chemically modified, and highly diverse populations of nucleoside modifications were identified via mass spectrometry . Modifications have been mapped for 34 tRNAs of M. jannaschii , revealing several modifications that are unique to archaea and proposed to stabilize the structure of tRNAs or its anticodon–codon interactions . Many nucleosides were shown to contain a 2ʹ‐ O ‐methyl group, which provides protection against phosphodiester bond cleavage and confers thermodynamic stabilization of the C3ʹ‐endo conformer .…”

“…[23][24][25] Modifications have been mapped for 34 tRNAs of M. jannaschii, revealing several modifications that are unique to archaea and proposed to stabilize the structure of tRNAs or its anticodon-codon interactions. 26 Many nucleosides were shown to contain a 2ʹ-O-methyl group, which provides protection against phosphodiester bond cleavage and confers thermodynamic stabilization of the C3ʹ-endo conformer. 27 Increased levels of 2ʹ-O-ribose methylation are also found for other structured RNAs of hyperthermophilic organisms.…”