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An aminoacylation ribozyme evolved from a natural tRNA-sensing T-box riboswitch

Nature Chemical Biology volume 16, pages 702–709 (2020)Cite this article

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Abstract

When the primitive translation system first emerged in the hypothetical RNA world, ribozymes could have been responsible for aminoacylation. Given that naturally occurring T-box riboswitches selectively sense the aminoacylation status of cognate tRNAs, we introduced a domain of random sequence into a T-box–tRNA conjugate and isolated ribozymes that were self-aminoacylating on the 3′-terminal hydroxyl group. One of them, named Tx2.1, recognizes the anticodon and D-loop of tRNA via interaction with its stem I domain, similarly to the parental T-box, and selectively charges N-biotinyl-l-phenylalanine (Bio-lPhe) onto the 3′ end of the cognate tRNA in trans. We also demonstrated the ribosomal synthesis of a Bio-lPhe-initiated peptide in a Tx2.1-coupled in vitro translation system, in which Tx2.1 catalyzed specific tRNA aminoacylation in situ. This suggests that such ribozymes could have coevolved with a primitive translation system in the RNA world.

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Fig. 1: Strategy to obtain aminoacylating ribozymes from a T-box riboswitch.
Fig. 2: Result after seven rounds of selection and sequence alignment of recovered clones observed more than once in total reads.
Fig. 3: Aminoacylation activity of five ribozymes obtained from in vitro selection.
Fig. 4: Characteristics of Tx2.1.
Fig. 5: Coupling of Tx2.1 with in vitro translation.

Data availability

All raw data are available from the corresponding author upon reasonable request.

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Acknowledgements

This work was supported by Japan Society for the Promotion of Science (JSPS) Grants-in-Aid for Research S (26220204), the Human Frontier Science Program (RGP0015/2017), the Japan Science and Technology (JST) agency and CREST-Molecular Technology (JPMJCR12L2) to H.S. N.T. is supported by Grants-in-Aid for JSPS Fellows (12J08188) and Grants-in-Aid for Early-Career Scientists (19K16200). S.I. was supported by Grants-in-Aid for JSPS Fellows (JP16J04031). T.K. is supported by a JSPS Grant-in-Aid for Challenging Exploratory Research (26560429).

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  1. These authors contributed equally: Satoshi Ishida, Naohiro Terasaka.

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  1. Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan

    Satoshi Ishida, Naohiro Terasaka, Takayuki Katoh & Hiroaki Suga

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  1. Satoshi Ishida
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S.I. and N.T. conducted biochemical and chemical studies, and T.K. and H.S. supervised the research. All authors contributed to writing the manuscript.

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Correspondence to Hiroaki Suga.

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Ishida, S., Terasaka, N., Katoh, T. et al. An aminoacylation ribozyme evolved from a natural tRNA-sensing T-box riboswitch. Nat Chem Biol 16, 702–709 (2020). https://doi.org/10.1038/s41589-020-0500-6

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