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New catalytic structures from an existing ribozyme

Abstract

Although protein enzymes with new catalytic activities can arise from existing scaffolds, less is known about the origin of ribozymes with new activities. Furthermore, mechanisms by which new macromolecular folds arise are not well characterized for either protein or RNA. Here we investigate how readily ribozymes with new catalytic activities and folds can arise from an existing ribozyme scaffold. Using in vitro selection, we isolated 23 distinct kinase ribozymes from a pool of sequence variants of an aminoacylase parent ribozyme. Analysis of these new kinases showed that ribozymes with new folds and biochemical activities can be found within a short mutational distance of a given ribozyme. However, the probability of finding such ribozymes increases considerably as the mutational distance from the parental ribozyme increases, indicating a need to escape the fold of the parent.

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Figure 1: Aminoacylase and kinase ribozymes.
Figure 2: Distribution of kinase ribozymes with respect to the parent ribozyme.
Figure 3: Secondary structure of the aminoacylase parent ribozyme.
Figure 4: Secondary structure of a kinase ribozyme derived from the aminoacylase parent ribozyme.
Figure 5: Secondary structure of a second kinase ribozyme derived from the aminoacylase parent ribozyme.
Figure 6: Comparison of the secondary structures of the parent ribozyme and two kinase ribozymes isolated in this selection.

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Acknowledgements

We thank M. Lawrence for comments on this manuscript, and members of the lab for helpful discussions. This work was supported by a grant from the National Institutes of Health.

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Correspondence to David P Bartel.

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Supplementary information

Supplementary Fig. 1

Testing the secondary structure model of the parent ribozyme by site-directed mutagenesis (PDF 221 kb)

Supplementary Fig. 2

Testing the secondary structure model of kinase ribozyme 5-16 by site-directed mutagenesis (PDF 225 kb)

Supplementary Fig. 3

Testing the secondary structure model of kinase ribozyme 7-16 by site-directed mutagenesis (PDF 231 kb)

Supplementary Methods (PDF 42 kb)

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Curtis, E., Bartel, D. New catalytic structures from an existing ribozyme. Nat Struct Mol Biol 12, 994–1000 (2005). https://doi.org/10.1038/nsmb1003

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