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. 2022 Apr 27;605(7909):372–379. doi: 10.1038/s41586-022-04677-2

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© The Author(s) 2022

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 3 — a, Venn diagram showing unique and shared genes among the Bacteria (E. coli), Eukarya (Homo sapiens, S. cerevisiae and Arabidopsis thaliana) and Archaea (Methanosarcina acetivorans, Thermoplasma acidophilum, S. tokodaii, Sulfolobus acidocaldarius, Saccharolobus solfataricus, Aeropyrum pernix, Pyrobaculum oguniense, T. kodakarensis and Nitrososphaera viennensis) domains possessing (+) or lacking (–) U^p47. The pale red area includes genes unique to archaea having U^p47. b, Comparative genomic analysis performed to narrow down the candidate genes responsible for U^p47 modification. c, LC–MS nucleotide analysis of tRNA fractions from wild-type (WT, KU216) (left) and Δtk2051 (right) strains of T. kodakarensis. The upper panel shows the UV trace at 254 nm. The peaks for pA, pU, pC and pG are marked. The lower panel shows the XIC for the proton adduct of the dimer pU^pm⁵C (m/z 724.1, z = 1). d, Growth measurement (OD₆₀₀) of wild-type (KU216) (open circles), ΔqueE (squares), ΔarkI (closed circles) and ΔarkIΔqueE (triangles) strains of T. kodakarensis at 83 °C (left), 87 °C (middle) and 91 °C (right). Data represent the average values of technical triplicates ± s.d. e, In vitro reconstitution of U^p47 with recombinant TkArkI in the presence (right panels) or absence (left panels) of ATP. XICs show the sum of monovalent and divalent negative ions from RNase T₁-digested fragments containing U^p47 (upper panels) or U47 (lower panels). f, Kinetic measurements of in vitro U^p47 formation by TkArkI. The initial velocity (V_i) of the phosphorylation reaction was measured at the indicated concentrations of tRNA (left) and ATP (right). Data represent the average values of technical triplicates ± s.d. The K_m and V_max values are shown below each graph.

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