An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape

• Published in: PLoS genetics Vol. 15; no. 4; p. e1008079
• Main Authors: Pokusaeva, Victoria O, Usmanova, Dinara R, Putintseva, Ekaterina V, Espinar, Lorena, Sarkisyan, Karen S, Mishin, Alexander S, Bogatyreva, Natalya S, Ivankov, Dmitry N, Akopyan, Arseniy V, Avvakumov, Sergey Ya, Povolotskaya, Inna S, Filion, Guillaume J, Carey, Lucas B, Kondrashov, Fyodor A
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 10-04-2019; Public Library of Science (PLoS)
• Subjects: Amino Acid Sequence; Amino Acid Substitution; Amino acids; Amino Acids - genetics; Amino Acids - metabolism; Bioassay; Bioinformatics; Biology; Enzymes; Epistasis; Epistasis, Genetic; Evolution; Evolution, Molecular; Evolutionary genetics; Fitness (Genetics); Fitness epistasis; Funding; Fungal Proteins - chemistry; Fungal Proteins - genetics; Fungal Proteins - metabolism; Genes; Genes, Fungal; Genetic aspects; Genetic Fitness; Genetic research; Genetics; Genomes; Genomics; Genotype; Genotype & phenotype; Genotypes; Histidine; Hydro-Lyases - chemistry; Hydro-Lyases - genetics; Hydro-Lyases - metabolism; Laboratories; Methods; Models, Genetic; Models, Molecular; Mutation; Phylogeny; Physiological aspects; Protein sequencing; Proteins; Reproductive fitness; Saccharomyces cerevisiae; Saccharomyces cerevisiae - genetics; Saccharomyces cerevisiae - metabolism; Saccharomyces cerevisiae Proteins - chemistry; Saccharomyces cerevisiae Proteins - genetics; Saccharomyces cerevisiae Proteins - metabolism; Sign epistasis; Software; Supervision; Variant genotypes; Yeasts - genetics; Yeasts - metabolism; Austria; Spain; Russia
• ISSN: 1553-7404; 1553-7390; 1553-7404
• DOI: 10.1371/journal.pgen.1008079

Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible.