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Identification of a radical SAM enzyme involved in the synthesis of archaeosine

Abstract

Archaeosine (G+), 7-formamidino-7-deazaguanosine, is an archaea-specific modified nucleoside found at the 15th position of tRNAs. In Euryarchaeota, 7-cyano-7-deazaguanine (preQ0)-containing tRNA (q0N-tRNA), synthesized by archaeal tRNA-guanine transglycosylase (ArcTGT), has been believed to be converted to G+-containing tRNA (G+-tRNA) by the paralog of ArcTGT, ArcS. However, we found that several euryarchaeal ArcSs have lysine transfer activity to q0N-tRNA to form q0kN-tRNA, which has a preQ0 lysine adduct as a base. Through comparative genomics and biochemical experiments, we found that ArcS forms a robust complex with a radical S-adenosylmethionine (SAM) enzyme named RaSEA. The ArcS–RaSEA complex anaerobically converted q0N-tRNA to G+-tRNA in the presence of SAM and lysine via q0kN-tRNA. We propose that ArcS and RaSEA should be considered an archaeosine synthase α-subunit (lysine transferase) and β-subunit (q0kN-tRNA lyase), respectively.

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Fig. 1: Lysine transfer activity of T. acidophilum and T. kodakarensis ArcSs.
Fig. 2: Chemical structure of preQ0-nucleoside lysine adduct.
Fig. 3: Physical interaction between TkRaSEA and TkArcS or TaArcS in E. coli.
Fig. 4: In vitro G+15-tRNA synthsis by ArcS–RaSEA complexes.
Fig. 5: G+15-tRNA synthesis in E. coli cells producing MaArcTGT and the MaArcS–MaRaSEA complex.
Fig. 6: Archaeosine biosynthesis pathway.

Data availability

The data supporting findings in this study are available from the corresponding author for reasonable requests.

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Acknowledgements

We are grateful to T. Inuzuka, O. Sakurada, S. Obata, Y. Onda, A. Izumoto, T. Okuda, M. Osawa and H. Miyawaki for technical assistance. This work was supported by JSPS KAKENHI grants JP16H04763 (to H.H.), JP17K05929 (to N.O.) and JP18K06088 (to A.H.), and the Koshiyama Science and Technology Foundation (to T.Y.). We thank J. Allen from Edanz Group (https://www.edanzediting.com/ac/) for editing a draft of this manuscript.

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Contributions

T.Y. prepared the preQ0Lys-nucleotide for NMR. Y.N. and A.Y. performed the series of experiments on ArcS. H.O. prepared and analyzed tRNAs and proteins. K.H. and S.N. performed the series of experiments on M. acetivorans and T. kodakarensis ArcS–RaSEA, respectively. N.O. measured NMR of the preQ0Lys-nucleotide and synthesized q0kN under the supervision of K.A. T.K. and A.H. constructed the series of T. kodakarensis strains under the supervision of H.H. S.O. performed MS analysis. All authors discussed the results and commented on the manuscript. T.Y. designed and supervised all the work.

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Correspondence to Takashi Yokogawa.

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Supplementary information

Supplementary Information

Supplementary Tables 1 and 2, and Figs. 1–21

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Supplementary Note

Synthetic procedures

Supplementary Dataset

Gene profiling of an enzyme involved in archaeosine synthesis

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Yokogawa, T., Nomura, Y., Yasuda, A. et al. Identification of a radical SAM enzyme involved in the synthesis of archaeosine. Nat Chem Biol 15, 1148–1155 (2019). https://doi.org/10.1038/s41589-019-0390-7

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