Learning the pattern of epistasis linking genotype and phenotype in a protein

• Published in: Nature communications 2019-09, Vol.10 (1), p.4213-11, Article 4213
• Main Authors: Poelwijk, Frank J., Socolich, Michael, Ranganathan, Rama
• Format: Article
• Language: English
• Subjects: 49/31; 49/40; 49/47; 631/114; 631/181/735; 631/208/2490/1472; 631/553/2490/1472; 631/553/552; Combinatorial analysis; Computer applications; Epistasis; Epistasis, Genetic; Evolution, Molecular; Fluorescence; Genotype; Genotypes; Humanities and Social Sciences; Learning; multidisciplinary; Mutants; Mutation; Phenotype; Phenotypes; Proteins; Proteins - chemistry; Proteins - genetics; Science; Science (multidisciplinary); Solution space
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-019-12130-8

Understanding the pattern of epistasis—the non-independence of mutations—is critical for relating genotype and phenotype. However, the combinatorial complexity of potential epistatic interactions has severely limited the analysis of this problem. Using new mutational approaches, we report a comprehensive experimental study of all 2 13 mutants that link two phenotypically distinct variants of the Entacmaea quadricolor fluorescent protein—an opportunity to examine epistasis up to the 13 th order. The data show the existence of many high-order epistatic interactions between mutations, but also reveal extraordinary sparsity, enabling novel experimental and computational strategies for learning the relevant epistasis. We demonstrate that such information, in turn, can be used to accurately predict phenotypes in practical situations where the number of measurements is limited. Finally, we show how the observed epistasis shapes the solution space of single-mutation trajectories between the parental fluorescent proteins, informative about the protein’s evolutionary potential. This work provides conceptual and experimental strategies to profoundly characterize epistasis in a protein, relevant to both natural and laboratory evolution. Epistasis underlies the complexity of genotype-phenotype maps. Here, the authors analyze 8,192 mutants that link two phenotypically distinct variants of the Entacmaea quadricolor fluorescent protein, and show the existence, but also the sparsity, of high-order epistatic interactions.