Cited by 591Evolution and Genetic DynamicsRNA and protein synthesis mechanismsProtein Structure and Dynamics

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Local fitness landscape of the green fluorescent protein

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Sarkisyan, Karen S., Bolotin, Dmitry A., Meer, Margarita V., Usmanova, Dinara R., Mishin, Alexander S., Sharonov, George V., Ivankov, Dmitry N., Bozhanova, Nina G., Baranov, Mikhail S., Soylemez, Onuralp, Bogatyreva, Natalya S., Vlasov, Peter K., Egorov, Evgeny S., Logacheva, Maria D., Kondrashov, Alexey S., Chudakov, Dmitry M., Putintseva, Ekaterina V., Mamedov, Ilgar Z., Tawfik, Dan S., Lukyanov, Konstantin A., Kondrashov, Fyodor A.·2016·Nature

DOI 10.1038/nature17995PMC PMC4968632

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Abstract

Fitness landscapes depict how genotypes manifest at the phenotypic level and form the basis of our understanding of many areas of biology, yet their properties remain elusive. Previous studies have analysed specific genes, often using their function as a proxy for fitness, experimentally assessing the effect on function of single mutations and their combinations in a specific sequence or in different sequences. However, systematic high-throughput studies of the local fitness landscape of an entire protein have not yet been reported. Here we visualize an extensive region of the local fitness landscape of the green fluorescent protein from Aequorea victoria (avGFP) by measuring the native function (fluorescence) of tens of thousands of derivative genotypes of avGFP. We show that the fitness landscape of avGFP is narrow, with 3/4 of the derivatives with a single mutation showing reduced fluorescence and half of the derivatives with four mutations being completely non-fluorescent. The narrowness is enhanced by epistasis, which was detected in up to 30% of genotypes with multiple mutations and mostly occurred through the cumulative effect of slightly deleterious mutations causing a threshold-like decrease in protein stability and a concomitant loss of fluorescence. A model of orthologous sequence divergence spanning hundreds of millions of years predicted the extent of epistasis in our data, indicating congruence between the fitness landscape properties at the local and global scales. The characterization of the local fitness landscape of avGFP has important implications for several fields including molecular evolution, population genetics and protein design.

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Authors: Sarkisyan, K. S., Bolotin, D. A., Meer, M. V., Usmanova, D. R., Mishin, A. S., Sharonov, G. V., Ivankov, D. N., Bozhanova, N. G., Baranov, M. S., Soylemez, O., Bogatyreva, N. S., Vlasov, P. K., Egorov, E. S., Logacheva, M. D., Kondrashov, A. S., Chudakov, D. M., Putintseva, E. V., Mamedov, I. Z., Tawfik, D. S., Lukyanov, K. A., & Kondrashov, F. A.
Affiliations: Universitat Pompeu Fabra (ES)
Moscow Institute of Physics and Technology (RU)
Institute of Bioorganic Chemistry (RU)
Lomonosov Moscow State University (RU)
Russian Academy of Sciences (RU)
Pirogov Russian National Research Medical University (RU)
Masaryk University (CZ)
Weizmann Institute of Science (IL)
Institució Catalana de Recerca i Estudis Avançats (ES)
Corresponding author: Kondrashov, Fyodor A.
ORCID: Sarkisyan, Karen S.
Meer, Margarita V.
Usmanova, Dinara R.
Mishin, Alexander S.
Sharonov, George V.
Ivankov, Dmitry N.
Bozhanova, Nina G.
Baranov, Mikhail S.
Bogatyreva, Natalya S.
Vlasov, Peter K.
Egorov, Evgeny S.
Logacheva, Maria D.
Kondrashov, Alexey S.
Putintseva, Ekaterina V.
Mamedov, Ilgar Z.
Tawfik, Dan S.
Lukyanov, Konstantin A.
Kondrashov, Fyodor A.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2016-05
Volume: 533
Issue: 7603
Pages: 397-401
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature17995
PMC: PMC4968632
OpenAlex: W2379594833
Cited by: 591
References: 29
Citations by year: 2026: 52 · 2025: 71 · 2024: 85 · 2023: 93 · 2022: 55 · 2021: 65 · 2020: 52 · 2019: 41 · 2018: 40 · 2017: 26 · 2016: 10
FWCI: 31.41
Type: journal article
Language: en
Open access: green
www.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Funders: Howard Hughes Medical Institute (55007424)
Russian Science Foundation
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
Keywords: green fluorescent protein, fitness landscape, epistasis, genotype-phenotype mapping, Aequorea victoria, fluorescence loss, deleterious mutations, protein stability, DNA barcoding, molecular evolution, protein design
MeSH terms: Animals, Epistasis, Genetic, Fluorescence, Genotype, Mutation, Phenotype, Evolution, Molecular, Hydrozoa, Green Fluorescent Proteins, Mutant Proteins, Genetic Fitness, Genetic Association Studies

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