Fitness landscape of a dynamic RNA structure

by Valerie W. C. Soo, Jacob B. Swadling, Andre J. Faure, Tobias Warnecke RNA structures are dynamic. As a consequence, mutational effects can be hard to rationalize with reference to a single static native structure. We reasoned that deep mutational scanning experiments, which couple molecular function to fitness, should capture mutational effects across multiple confo rmational states simultaneously. Here, we provide a proof-of-principle that this is indeed the case, using the self-splicing group I intron fromTetrahymena thermophila as a model system. We comprehensively mutagenized two 4-bp segments of the intron. These segments first come together to form the P1 extension (P1ex) helix at the 5 ’ splice site. Following cleavage at the 5’ splice site, the two halves of the helix dissociate to allow formation of an alternative helix (P10) at the 3’ splice site. Using anin vivo reporter system that couples splicing activity to fitness inE.coli, we demonstrate that fitness is driven jointly by constraints on P1ex and P10 formation. We further show that patterns of epistasis can be used to infer the presence of intramolecular pleiotropy. Using a machine learning approach that allows quantification of mutational effects in a genotype-specific manner, we demonstrate that the fitness landscape can be deconvoluted to implicate P1ex or P10 as the effective genetic background in which molecular fitness is compromised or enhanced. Our results highlight deep mutational scanning as...
Source: PLoS Genetics - Category: Genetics & Stem Cells Authors: Source Type: research