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Metals induce transient folding and activation of the twister ribozyme

Nature Chemical Biology volume 13, pages 1109–1114 (2017)Cite this article

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Abstract

Twister is a small ribozyme present in almost all kingdoms of life that rapidly self-cleaves in variety of divalent metal ions. We used activity assays, bulk FRET and single-molecule FRET (smFRET) to understand how different metal ions promote folding and self-cleavage of the Oryza sativa twister ribozyme. Although most ribozymes require additional Mg2+ for catalysis, twister inverts this expectation, requiring 20–30 times less Mg2+ to self-cleave than to fold. Transition metals such as Co2+, Ni2+ and Zn2+ activate twister more efficiently than Mg2+ ions. Although twister is fully active in ≤ 0.5 mM MgCl2, smFRET experiments showed that the ribozyme visits the folded state infrequently under these conditions. Comparison of folding and self-cleavage rates indicates that most folding events lead to catalysis, which correlates with metal bond strength. Thus, the robust activity of twister reports on transient metal ion binding under physiological conditions.

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Figure 1: Self-cleavage of a minimal Oryza sativa twister ribozyme at low Mg2+.
Figure 2: Folding of twister ribozyme in MgCl2.
Figure 3: Pseudoknot mutations impair folding.
Figure 4: Kinetics of RNA folding.
Figure 5: Twister is efficiently activated by transition metal ions.

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Acknowledgements

The authors thank K. Sarkar and S. Abeysirigunawardena for their assistance and M. Greenberg, K. Karlin and J. Morrow for helpful discussion. This work was supported by a grant from the National Science Foundation (MCB-1616081 to S.W.) and the US National Institutes of Health (GM 065367 to T.H.).

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Authors and Affiliations

  1. T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland, USA

    Subrata Panja, Diego Zegarra, Taekjip Ha & Sarah A Woodson

  2. Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, Maryland, USA

    Boyang Hua & Taekjip Ha

  3. Howard Hughes Medical Institute, Baltimore, Maryland, USA

    Taekjip Ha

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  1. Subrata Panja
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Contributions

S.P., T.H. and S.A.W. designed the experiments; S.P. and B.H. performed the single-molecule experiments and analyzed the data; S.P. and D.Z. performed activity assays; S.P. performed other experiments; S.P., T.H. and S.A.W. wrote the manuscript; and all of the authors interpreted the data and reviewed the text and figures.

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Correspondence to Subrata Panja.

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Panja, S., Hua, B., Zegarra, D. et al. Metals induce transient folding and activation of the twister ribozyme. Nat Chem Biol 13, 1109–1114 (2017). https://doi.org/10.1038/nchembio.2459

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