Negative Epistasis in Experimental RNA Fitness Landscapes
Mutations and their effects on fitness are a fundamental component of evolution. The effects of some mutations change in the presence of other mutations, and this is referred to as epistasis. Epistasis can occur between mutations in different genes or within the same gene. A systematic study of epistasis requires the analysis of numerous mutations and their combinations, which has recently become feasible with advancements in DNA synthesis and sequencing. Here we review the mutational effects and epistatic interactions within RNA molecules revealed by several recent high-throughput mutational studies involving two ribozymes studied in vitro, as well as a tRNA and a snoRNA studied in yeast. The data allow an analysis of the distribution of fitness effects of individual mutations as well as combinations of two or more mutations. Two different approaches to measuring epistasis in the data both reveal a predominance of negative epistasis, such that higher combinations of two or more mutations are typically lower in fitness than expected from the effect of each individual mutation. These data are in contrast to past studies of epistasis that used computationally predicted secondary structures of RNA that revealed a predominance of positive epistasis. The RNA data reviewed here are more similar to that found from mutational experiments on individual protein enzymes, suggesting that a common thermodynamic framework may explain negative epistasis between mutations within macromolecules.
KeywordsEpistasis Evolution Mutations ncRNA Fitness landscapes
We would like to thank J. Zhang, G. Kudla, and Y. Yokobayashi and the members of their labs for kindly granting access to the high-throughput sequencing data used in this project. This study was supported by Boise State University (Biomolecular Sciences Graduate Programs), University of California, Los Angeles (Department of Ecology and Evolutionary Biology), National Science Foundation Directorate for Biological Sciences (Grant No. MCB-1413664), National Science Foundation Office of Integrative Activities (Grant No. OIA-1738865), National Aeronautics and Space Administration (Grant No. 80NSSC17K0738), Idaho State University (Fall 2016 MRCF Seed Grant).
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