tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

Ningxi Yu; Manasses Jora; Beulah Solivio; Priti Thakur; Carlos G Acevedo-Rocha; Lennart Randau; Valérie de Crécy-Lagard; Balasubrahmanyam Addepalli; Patrick A Limbach

doi:10.1128/JB.00690-18

tRNA Modification Profiles and Codon-Decoding Strategies in Methanocaldococcus jannaschii

J Bacteriol. 2019 Apr 9;201(9):e00690-18. doi: 10.1128/JB.00690-18. Print 2019 May 1.

Authors

Ningxi Yu¹, Manasses Jora¹, Beulah Solivio¹, Priti Thakur¹, Carlos G Acevedo-Rocha², Lennart Randau², Valérie de Crécy-Lagard³, Balasubrahmanyam Addepalli¹, Patrick A Limbach⁴

Affiliations

¹ Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA.
² Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.
³ Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, Florida, USA.
⁴ Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, Cincinnati, Ohio, USA Pat.Limbach@uc.edu.

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 codon-decoding 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 (cnm⁵s²U), 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.

Keywords: 5-cyanomethyl-2-thiouridine; LC-MS/MS; anticodon loop; archaea; modified nucleosides; posttranscriptional modification; tRNA.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Anticodon*
Methanocaldococcus / genetics*
Methanocaldococcus / metabolism*
Protein Biosynthesis*
RNA Processing, Post-Transcriptional*
RNA, Transfer / genetics*
RNA, Transfer / metabolism*

Substances

Anticodon
RNA, Transfer

Grants and funding

R01 GM070641/GM/NIGMS NIH HHS/United States