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Popović M, Ellingson AQ, Chu TP, Wei C, Pohorille A, Ditzler MA. In vitro selections with RNAs of variable length converge on a robust catalytic core. Nucleic Acids Res 2021; 49:674-683. [PMID: 33367725 PMCID: PMC7826250 DOI: 10.1093/nar/gkaa1238] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/05/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022] Open
Abstract
In vitro selection is a powerful tool that can be used to understand basic principles of molecular evolution. We used in vitro selection to understand how changes in length and the accumulation of point mutations enable the evolution of functional RNAs. Using RNA populations of various lengths, we performed a series of in vitro experiments to select for ribozymes with RNA ligase activity. We identified a core ribozyme structure that was robust to changes in RNA length, high levels of mutagenesis, and increased selection pressure. Elaboration on this core structure resulted in improved activity which we show is consistent with a larger trend among functional RNAs in which increasing motif size can lead to an exponential improvement in fitness. We conclude that elaboration on conserved core structures is a preferred mechanism in RNA evolution. This conclusion, drawn from selections of RNAs from random sequences, is consistent with proposed evolutionary histories of specific biological RNAs. More generally, our results indicate that modern RNA structures can be used to infer ancestral structures. Our observations also suggest a mechanism by which structural outcomes of early RNA evolution would be largely reproducible even though RNA fitness landscapes consist of disconnected clusters of functional sequences.
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Affiliation(s)
- Milena Popović
- Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Blue Marble Space Institute of Science, Seattle, WA 98145, USA
| | | | - Theresa P Chu
- Blue Marble Space Institute of Science, Seattle, WA 98145, USA
| | - Chenyu Wei
- Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Andrew Pohorille
- Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, CA 94158, USA
| | - Mark A Ditzler
- Center for the Emergence of Life, NASA Ames Research Center, Moffett Field, CA 94035, USA
- Exobiology Branch, Space Science and Astrobiology Division, NASA Ames Research Center, Moffett Field, CA 94035, USA
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Liberles DA. 2019 Zuckerkandl Prize. J Mol Evol 2019; 88:121. [PMID: 31853573 DOI: 10.1007/s00239-019-09924-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- David A Liberles
- Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, PA, 19122, USA.
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