Witnessing the structural evolution of an RNA enzyme

  1. Xavier Portillo
  2. Yu-Ting Huang
  3. Ronald R Breaker
  4. David P Horning  Is a corresponding author
  5. Gerald F Joyce  Is a corresponding author
  1. Yale University, United States
  2. The Salk Institute, United States

Abstract

An RNA polymerase ribozyme that has been the subject of extensive directed evolution efforts has attained the ability to synthesize complex functional RNAs, including a full-length copy of its own evolutionary ancestor. During the course of evolution, the catalytic core of the ribozyme has undergone a major structural rearrangement, resulting in a novel tertiary structural element that lies in close proximity to the active site. Through a combination of site-directed mutagenesis, structural probing, and deep sequencing analysis, the trajectory of evolution was seen to involve the progressive stabilization of the new structure, which provides the basis for improved catalytic activity of the ribozyme. Multiple paths to the new structure were explored by the evolving population, converging upon a common solution. Tertiary structural remodeling of RNA is known to occur in nature, as evidenced by the phylogenetic analysis of extant organisms, but this type of structural innovation had not previously been observed in an experimental setting. Despite prior speculation that the catalytic core of the ribozyme had become trapped in a narrow local fitness optimum, the evolving population has broken through to a new fitness locale, raising the possibility that further improvement of polymerase activity may be achievable.

Data availability

Source data, including raw gel electrophoresis images (*.tiff files) and tables listing all datapoints and model fitting parameters, for all applicable graphs and plots, are provided for Figures 1, 2-supplement-2, 3 (and supplements 1 and 2), 4 (and supplement 1), and 5 (and supplement 5). High-throughput sequencing data and analysis used to generate Figure 1-supplement 1, Figure 5, and Supplemental file 2 are available and archived at the Dryad Digital Repository.

The following data sets were generated

Article and author information

Author details

  1. Xavier Portillo

    Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1225-1133
  2. Yu-Ting Huang

    The Salk Institute, La Jolla, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Ronald R Breaker

    Yale University, New Haven, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2165-536X
  4. David P Horning

    The Salk Institute, La Jolla, United States
    For correspondence
    dhorning@salk.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3357-6092
  5. Gerald F Joyce

    The Salk Institute, La Jolla, United States
    For correspondence
    gjoyce@salk.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0603-2874

Funding

National Aeronautics and Space Administration (NSSC19K0481)

  • Gerald F Joyce

Simons Foundation (287624)

  • Gerald F Joyce

National Institutes of Health (P01GM022778)

  • Ronald R Breaker

Howard Hughes Medical Institute

  • Ronald R Breaker

National Science Foundation (DGE1752134)

  • Xavier Portillo

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Timothy W Nilsen, Case Western Reserve University, United States

Publication history

  1. Preprint posted: June 22, 2021 (view preprint)
  2. Received: June 23, 2021
  3. Accepted: September 8, 2021
  4. Accepted Manuscript published: September 9, 2021 (version 1)
  5. Version of Record published: September 23, 2021 (version 2)

Copyright

© 2021, Portillo et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Xavier Portillo
  2. Yu-Ting Huang
  3. Ronald R Breaker
  4. David P Horning
  5. Gerald F Joyce
(2021)
Witnessing the structural evolution of an RNA enzyme
eLife 10:e71557.
https://doi.org/10.7554/eLife.71557

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