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A widespread self-cleaving ribozyme class is revealed by bioinformatics

Nature Chemical Biology volume 10, pages 56–60 (2014)Cite this article

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Abstract

Ribozymes are noncoding RNAs that promote chemical transformations with rate enhancements approaching those of protein enzymes. Although ribozymes are likely to have been abundant during the RNA world era, only ten classes are known to exist among contemporary organisms. We report the discovery and analysis of an additional self-cleaving ribozyme class, called twister, which is present in many species of bacteria and eukarya. Nearly 2,700 twister ribozymes were identified that conform to a secondary structure consensus that is small yet complex, with three stems conjoined by internal and terminal loops. Two pseudoknots provide tertiary structure contacts that are critical for catalytic activity. The twister ribozyme motif provides another example of a natural RNA catalyst and calls attention to the potentially varied biological roles of this and other classes of widely distributed self-cleaving RNAs.

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Figure 1: Consensus sequence and secondary-structure model for twister self-cleaving ribozymes.
Figure 2: Common associations between various genetic elements and twister or hammerhead RNAs.
Figure 3: Sequence, structure and activity of a twister ribozyme from N. vitripennis.
Figure 4: Kinetic characteristics of a twister ribozyme derived from an environmental DNA sequence.

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Acknowledgements

We thank M. Murdock for performing the twister ribozyme ligation assay, P. McCown and other members of the Breaker laboratory for helpful discussions, R. Knight for alerting us to useful metagenome data sets, S.L. Tausta and T. Nelson (Yale University) for providing us with rice seeds, and N. Carriero and R. Bjornson for assistance with the Yale Life Sciences High Performance Computing Center (US National Institutes of Health (NIH) grant RR19895-02). This work was supported by the NIH (GM022778) and by the Howard Hughes Medical Institute. P.B.K. was supported by the Gruber Science Fellowship.

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Author notes

  1. Adam Roth & Zasha Weinberg

    Present address: Present address: Phosplatin Therapeutics, New York, New York, USA.,

  2. Tyler D Ames: These authors contributed equally to this work.

Authors and Affiliations

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

    Adam Roth, Zasha Weinberg, Andy G Y Chen, Peter B Kim, Tyler D Ames & Ronald R Breaker

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

    Adam Roth, Zasha Weinberg, Tyler D Ames & Ronald R Breaker

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

    Ronald R Breaker

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Contributions

Z.W. and T.D.A. conducted the bioinformatics analyses; A.R., A.G.Y.C. and P.B.K. conducted the biochemical and genetic analyses; R.R.B. prepared the manuscript; and all of the authors interpreted data, designed experiments and critically reviewed the text and figures.

Corresponding author

Correspondence to Ronald R Breaker.

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Supplementary information

Supplementary Text and Figures

Supplementary Results, Supplementary Table 1 and Supplementary Figures 1–13. This file also contains the legend for Supplementary Data Set 1. (PDF 3774 kb)

Supplementary Data Set 1

This separate file displays the taxa, sequence accession numbers, coordinates, gene neighborhoods and multiple sequence alignments corresponding to the identified twister ribozyme representatives. In additional separate files, alignments of type P1, type P3 and type P5 twister ribozyme sequences are provided individually in Stockholm formats. (PDF 4863 kb)

Supplementary Data Set 2

Type P1 sequence alignment file in Stockholm format. (TXT 457 kb)

Supplementary Data Set 3

Type P3 sequence alignment file in Stockholm format. (TXT 1 kb)

Supplementary Data Set 4

Type P5 sequence alignment file in Stockholm format. (TXT 47 kb)

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Roth, A., Weinberg, Z., Chen, A. et al. A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nat Chem Biol 10, 56–60 (2014). https://doi.org/10.1038/nchembio.1386

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