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In vitro evolution suggests multiple origins for the hammerhead ribozyme

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Abstract

The hammerhead ribozyme was originally discovered in a group of RNAs associated with plant viruses, and has subsequently been identified in the genome of the newt (Notophthalamus viridescens)1,2, in schistosomes3 and in cave crickets (Dolichopoda species)4. The sporadic occurrence of this self-cleaving RNA motif in highly divergent organisms could be a consequence of the very early evolution of the hammerhead ribozyme4,5, with all extant examples being descended from a single ancestral progenitor. Alternatively, the hammerhead ribozyme may have evolved independently many times. To better understand the observed distribution of hammerhead ribozymes, we used in vitro selection to search an unbiased sample of random sequences for comparably active self-cleaving motifs. Here we show that, under near-physiological conditions, the hammerhead ribozyme motif is the most common (and thus the simplest) RNA structure capable of self-cleavage at biologically observed rates. Our results suggest that the evolutionary process may have been channelled, in nature as in the laboratory, towards repeated selection of the simplest solution to a biochemical problem.

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Figure 1: Pool design.
Figure 2: Self-cleavage of pool RNAs.
Figure 3: Alignments of unique hammerhead-type clones from rounds 12 and 16.

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Acknowledgements

We thank P. Svec for assistance in cloning and sequencing, and members of the laboratory for their comments on the manuscript. This work was supported in part by a grant from the National Institutes of Health. J.W.S. is an investigator of the Howard Hughes Medical Institute.

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Authors and Affiliations

  1. Howard Hughes Medical Institute, and Department of Molecular Biology, Massachusetts General Hospital, Boston, 02114, Massachusetts, USA

    Kourosh Salehi-Ashtiani & Jack W. Szostak

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  1. Kourosh Salehi-Ashtiani
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  2. Jack W. Szostak
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Correspondence to Jack W. Szostak.

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Salehi-Ashtiani, K., Szostak, J. In vitro evolution suggests multiple origins for the hammerhead ribozyme. Nature 414, 82–84 (2001). https://doi.org/10.1038/35102081

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