Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme
The relationship between genotype and phenotype is often described as an adaptive fitness landscape. In this study, we used a combination of recombination, in vitro selection, and comparative sequence analysis to characterize the fitness landscape of a previously isolated kinase ribozyme. Point muta...
| 主要な著者: | , |
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| その他の著者: | |
| フォーマット: | 論文 |
| 言語: | en_US |
| 出版事項: |
Cold Spring Harbor Laboratory Press
2015
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| オンライン･アクセス: | http://hdl.handle.net/1721.1/96216 https://orcid.org/0000-0002-3872-2856 |
| _version_ | 1826199685989138432 |
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| author | Bartel, David Curtis, Edward A. |
| author2 | Massachusetts Institute of Technology. Department of Biology |
| author_facet | Massachusetts Institute of Technology. Department of Biology Bartel, David Curtis, Edward A. |
| author_sort | Bartel, David |
| collection | MIT |
| description | The relationship between genotype and phenotype is often described as an adaptive fitness landscape. In this study, we used a combination of recombination, in vitro selection, and comparative sequence analysis to characterize the fitness landscape of a previously isolated kinase ribozyme. Point mutations present in improved variants of this ribozyme were recombined in vitro in more than 10[superscript 14] different arrangements using synthetic shuffling, and active variants were isolated by in vitro selection. Mutual information analysis of 65 recombinant ribozymes isolated in the selection revealed a rugged fitness landscape in which approximately one-third of the 91 pairs of positions analyzed showed evidence of correlation. Pairs of correlated positions overlapped to form densely connected networks, and groups of maximally connected nucleotides occurred significantly more often in these networks than they did in randomized control networks with the same number of links. The activity of the most efficient recombinant ribozyme isolated from the synthetically shuffled pool was 30-fold greater than that of any of the ribozymes used to build it, which indicates that synthetic shuffling can be a rich source of ribozyme variants with improved properties. |
| first_indexed | 2024-09-23T11:24:24Z |
| format | Article |
| id | mit-1721.1/96216 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T11:24:24Z |
| publishDate | 2015 |
| publisher | Cold Spring Harbor Laboratory Press |
| record_format | dspace |
| spelling | mit-1721.1/962162022-10-01T03:22:01Z Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme Bartel, David Curtis, Edward A. Massachusetts Institute of Technology. Department of Biology Bartel, David The relationship between genotype and phenotype is often described as an adaptive fitness landscape. In this study, we used a combination of recombination, in vitro selection, and comparative sequence analysis to characterize the fitness landscape of a previously isolated kinase ribozyme. Point mutations present in improved variants of this ribozyme were recombined in vitro in more than 10[superscript 14] different arrangements using synthetic shuffling, and active variants were isolated by in vitro selection. Mutual information analysis of 65 recombinant ribozymes isolated in the selection revealed a rugged fitness landscape in which approximately one-third of the 91 pairs of positions analyzed showed evidence of correlation. Pairs of correlated positions overlapped to form densely connected networks, and groups of maximally connected nucleotides occurred significantly more often in these networks than they did in randomized control networks with the same number of links. The activity of the most efficient recombinant ribozyme isolated from the synthetically shuffled pool was 30-fold greater than that of any of the ribozymes used to build it, which indicates that synthetic shuffling can be a rich source of ribozyme variants with improved properties. National Institutes of Health (U.S.) (Grant GM061835) 2015-03-27T16:14:25Z 2015-03-27T16:14:25Z 2013-06 2012-12 Article http://purl.org/eprint/type/JournalArticle 1355-8382 1469-9001 http://hdl.handle.net/1721.1/96216 Curtis, E. A., and D. P. Bartel. “Synthetic Shuffling and in Vitro Selection Reveal the Rugged Adaptive Fitness Landscape of a Kinase Ribozyme.” RNA 19, no. 8 (June 24, 2013): 1116–1128. https://orcid.org/0000-0002-3872-2856 en_US http://dx.doi.org/10.1261/rna.037572.112 RNA Creative Commons Attribution-NonCommercial 3.0 Unported Licence http://creativecommons.org/licenses/by-nc/3.0/ application/pdf Cold Spring Harbor Laboratory Press Cold Spring Harbor Laboratory Press |
| spellingShingle | Bartel, David Curtis, Edward A. Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme |
| title | Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme |
| title_full | Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme |
| title_fullStr | Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme |
| title_full_unstemmed | Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme |
| title_short | Synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme |
| title_sort | synthetic shuffling and in vitro selection reveal the rugged adaptive fitness landscape of a kinase ribozyme |
| url | http://hdl.handle.net/1721.1/96216 https://orcid.org/0000-0002-3872-2856 |
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