Fitness landscape of a dynamic RNA structure


Autoři: Valerie W. C. Soo aff001;  Jacob B. Swadling aff001;  Andre J. Faure aff003;  Tobias Warnecke aff001
Působiště autorů: Medical Research Council London Institute of Medical Sciences, London, United Kingdom aff001;  Institute of Clinical Sciences, Faculty of Medicine, Imperial College London, London, United Kingdom aff002;  Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain aff003
Vyšlo v časopise: Fitness landscape of a dynamic RNA structure. PLoS Genet 17(2): e1009353. doi:10.1371/journal.pgen.1009353
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1009353

Souhrn

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 conformational states simultaneously. Here, we provide a proof-of-principle that this is indeed the case, using the self-splicing group I intron from Tetrahymena 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 an in vivo reporter system that couples splicing activity to fitness in E. 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 a tool to study alternative conformational states, with the capacity to provide critical insights into the structure, evolution and evolvability of RNAs as dynamic ensembles. Our findings also suggest that, in the future, deep mutational scanning approaches might help reverse-engineer multiple alternative or successive conformations from a single fitness landscape.

Klíčová slova:

Fitness epistasis – Introns – Mutation detection – Natural selection – Nucleotides – RNA structure – Tetrahymena – Tetrahymena thermophila


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