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New classes of self-cleaving ribozymes revealed by comparative genomics analysis

Nature Chemical Biology volume 11, pages 606–610 (2015)Cite this article

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Abstract

Enzymes made of RNA catalyze reactions that are essential for protein synthesis and RNA processing. However, such natural ribozymes are exceedingly rare, as evidenced by the fact that the discovery rate for new classes has dropped to one per decade from about one per year during the 1980s. Indeed, only 11 distinct ribozyme classes have been experimentally validated to date. Recently, we recognized that self-cleaving ribozymes frequently associate with certain types of genes from bacteria. Herein we exploited this association to identify divergent architectures for two previously known ribozyme classes and to discover additional noncoding RNA motifs that are self-cleaving RNA candidates. We identified three new self-cleaving classes, which we named twister sister, pistol and hatchet, from this collection, suggesting that even more ribozymes remain hidden in modern cells.

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Figure 1: Self-cleaving ribozyme candidates.
Figure 2: Activity of a bimolecular twister sister ribozyme.
Figure 3: Structure and activity of pistol self-cleaving ribozymes.
Figure 4: Structure and activity of hatchet self-cleaving ribozymes.

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Acknowledgements

We thank A. Roth and other members of the Breaker laboratory for helpful discussions, and N. Carriero and R. Bjornson for assistance with the Yale Life Sciences High Performance Computing Center funded by the US National Institutes of Health (NIH; RR19895-02). P.B.K. was supported by an NIH Genetics Training Grant (5T32GM007499). C.E.L. was supported by the Deutsche Forschungsgemeinschaft (LU1889/1-1). This work was also supported by an NIH grant (GM022778) to R.R.B. and by the Howard Hughes Medical Institute.

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Author notes

  1. Zasha Weinberg and Peter B Kim: These authors contributed equally to this work.

Authors and Affiliations

  1. Howard Hughes Medical Institute, Yale University, New Haven, Connecticut, USA

    Zasha Weinberg, Sanshu Li, Kimberly A Harris & Ronald R Breaker

  2. Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut, USA

    Zasha Weinberg, Peter B Kim, Sanshu Li, Kimberly A Harris, Christina E Lünse & Ronald R Breaker

  3. Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA

    Tony H Chen & Ronald R Breaker

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Contributions

Z.W. conducted all bioinformatics searches and created the RNA consensus models. Validation studies were conducted for twister sister by P.B.K. and T.H.C., for pistol by K.A.H., for hatchet by S.L., for hammerhead by P.B.K. and for HDV by P.B.K. and S.L. P.B.K., T.H.C. and C.E.L. screened additional noncleaving RNAs. R.R.B. worked with all authors to plan experiments, interpret data and write the manuscript.

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Correspondence to Ronald R Breaker.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Tables 1–5 and Supplementary Figures 1–13 (PDF 2888 kb)

Supplementary Data Set 1

Printable alignments, genomic contexts and taxonomy of self-cleaving ribozyme candidates (PDF 6312 kb)

Supplementary Data Set 2

Machine-readable alignments of self-cleaving ribozyme candidates (ZIP 125 kb)

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Weinberg, Z., Kim, P., Chen, T. et al. New classes of self-cleaving ribozymes revealed by comparative genomics analysis. Nat Chem Biol 11, 606–610 (2015). https://doi.org/10.1038/nchembio.1846

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