Transfer RNA Modification Profiles and Codon Decoding Strategies in Methanocaldococcus jannaschii

Abstract

Transfer RNAs (tRNAs) play a critical role in messenger RNA (mRNA) decoding, and post-transcriptional 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 codon decoding strategies, we have used liquid chromatography and tandem mass spectrometry to characterize and then map post-transcriptional modifications on 34 of the 35 unique tRNA sequences of Methanocaldococcus jannaschii. A new post-transcriptionally modified nucleoside, 5-cyanomethyl-2-thiouridine (cnm ⁵s ²U), 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 post-transcriptional 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.