Local fitness landscape of the green fluorescent protein
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 t...
Ausführliche Beschreibung
Autor*in: |
Karen S Sarkisyan [verfasserIn] |
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Artikel |
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Englisch |
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2016 |
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Übergeordnetes Werk: |
Enthalten in: Nature - London : Macmillan Publishers Limited, part of Springer Nature, 1869, 533(2016), 7603, Seite 397 |
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Übergeordnetes Werk: |
volume:533 ; year:2016 ; number:7603 ; pages:397 |
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DOI / URN: |
10.1038/nature17995 |
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Katalog-ID: |
OLC1975207394 |
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520 | |a 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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10.1038/nature17995 doi PQ20160610 (DE-627)OLC1975207394 (DE-599)GBVOLC1975207394 (PRQ)g1106-b09c8c1cc03d6e233a610f605fc8ab38dbce1d8007b9a4ca228404134d29193c0 (KEY)0072945020160000533760300397localfitnesslandscapeofthegreenfluorescentprotein DE-627 ger DE-627 rakwb eng 070 500 DNB 500 AVZ BIODIV fid Karen S Sarkisyan verfasserin aut Local fitness landscape of the green fluorescent protein 2016 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier 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. Proteins Genotype & phenotype Amino acids Fluorescence Mutation Mutagenesis Dmitry A Bolotin oth Margarita V Meer oth Dinara R Usmanova oth Alexander S Mishin oth George V Sharonov oth Dmitry N Ivankov oth Nina G Bozhanova oth Mikhail S Baranov oth Onuralp Soylemez oth Natalya S Bogatyreva oth Peter K Vlasov oth Evgeny S Egorov oth Maria D Logacheva oth Alexey S Kondrashov oth Dmitry M Chudakov oth Ekaterina V Putintseva oth Ilgar Z Mamedov oth Dan S Tawfik oth Konstantin A Lukyanov oth Fyodor A Kondrashov oth Enthalten in Nature London : Macmillan Publishers Limited, part of Springer Nature, 1869 533(2016), 7603, Seite 397 (DE-627)129292834 (DE-600)120714-3 (DE-576)014473941 0028-0836 nnns volume:533 year:2016 number:7603 pages:397 http://dx.doi.org/10.1038/nature17995 Volltext http://www.ncbi.nlm.nih.gov/pubmed/27193686 http://search.proquest.com/docview/1790506337 GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-BIODIV SSG-OLC-PHY SSG-OLC-CHE SSG-OLC-MAT SSG-OLC-FOR SSG-OLC-SPO SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-FOR GBV_ILN_11 GBV_ILN_22 GBV_ILN_30 GBV_ILN_40 GBV_ILN_47 GBV_ILN_55 GBV_ILN_59 GBV_ILN_60 GBV_ILN_62 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_101 GBV_ILN_110 GBV_ILN_120 GBV_ILN_154 GBV_ILN_168 GBV_ILN_170 GBV_ILN_171 GBV_ILN_211 GBV_ILN_290 GBV_ILN_294 GBV_ILN_601 GBV_ILN_647 GBV_ILN_754 GBV_ILN_2001 GBV_ILN_2002 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2015 GBV_ILN_2016 GBV_ILN_2018 GBV_ILN_2020 GBV_ILN_2026 GBV_ILN_2095 GBV_ILN_2116 GBV_ILN_2120 GBV_ILN_2121 GBV_ILN_2219 GBV_ILN_2221 GBV_ILN_2279 GBV_ILN_2286 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4125 GBV_ILN_4219 GBV_ILN_4251 GBV_ILN_4277 GBV_ILN_4302 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4314 GBV_ILN_4317 GBV_ILN_4320 GBV_ILN_4324 GBV_ILN_4700 AR 533 2016 7603 397 |
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10.1038/nature17995 doi PQ20160610 (DE-627)OLC1975207394 (DE-599)GBVOLC1975207394 (PRQ)g1106-b09c8c1cc03d6e233a610f605fc8ab38dbce1d8007b9a4ca228404134d29193c0 (KEY)0072945020160000533760300397localfitnesslandscapeofthegreenfluorescentprotein DE-627 ger DE-627 rakwb eng 070 500 DNB 500 AVZ BIODIV fid Karen S Sarkisyan verfasserin aut Local fitness landscape of the green fluorescent protein 2016 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier 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. Proteins Genotype & phenotype Amino acids Fluorescence Mutation Mutagenesis Dmitry A Bolotin oth Margarita V Meer oth Dinara R Usmanova oth Alexander S Mishin oth George V Sharonov oth Dmitry N Ivankov oth Nina G Bozhanova oth Mikhail S Baranov oth Onuralp Soylemez oth Natalya S Bogatyreva oth Peter K Vlasov oth Evgeny S Egorov oth Maria D Logacheva oth Alexey S Kondrashov oth Dmitry M Chudakov oth Ekaterina V Putintseva oth Ilgar Z Mamedov oth Dan S Tawfik oth Konstantin A Lukyanov oth Fyodor A Kondrashov oth Enthalten in Nature London : Macmillan Publishers Limited, part of Springer Nature, 1869 533(2016), 7603, Seite 397 (DE-627)129292834 (DE-600)120714-3 (DE-576)014473941 0028-0836 nnns volume:533 year:2016 number:7603 pages:397 http://dx.doi.org/10.1038/nature17995 Volltext http://www.ncbi.nlm.nih.gov/pubmed/27193686 http://search.proquest.com/docview/1790506337 GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-BIODIV SSG-OLC-PHY SSG-OLC-CHE SSG-OLC-MAT SSG-OLC-FOR SSG-OLC-SPO SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-FOR GBV_ILN_11 GBV_ILN_22 GBV_ILN_30 GBV_ILN_40 GBV_ILN_47 GBV_ILN_55 GBV_ILN_59 GBV_ILN_60 GBV_ILN_62 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_101 GBV_ILN_110 GBV_ILN_120 GBV_ILN_154 GBV_ILN_168 GBV_ILN_170 GBV_ILN_171 GBV_ILN_211 GBV_ILN_290 GBV_ILN_294 GBV_ILN_601 GBV_ILN_647 GBV_ILN_754 GBV_ILN_2001 GBV_ILN_2002 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2015 GBV_ILN_2016 GBV_ILN_2018 GBV_ILN_2020 GBV_ILN_2026 GBV_ILN_2095 GBV_ILN_2116 GBV_ILN_2120 GBV_ILN_2121 GBV_ILN_2219 GBV_ILN_2221 GBV_ILN_2279 GBV_ILN_2286 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4125 GBV_ILN_4219 GBV_ILN_4251 GBV_ILN_4277 GBV_ILN_4302 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4314 GBV_ILN_4317 GBV_ILN_4320 GBV_ILN_4324 GBV_ILN_4700 AR 533 2016 7603 397 |
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10.1038/nature17995 doi PQ20160610 (DE-627)OLC1975207394 (DE-599)GBVOLC1975207394 (PRQ)g1106-b09c8c1cc03d6e233a610f605fc8ab38dbce1d8007b9a4ca228404134d29193c0 (KEY)0072945020160000533760300397localfitnesslandscapeofthegreenfluorescentprotein DE-627 ger DE-627 rakwb eng 070 500 DNB 500 AVZ BIODIV fid Karen S Sarkisyan verfasserin aut Local fitness landscape of the green fluorescent protein 2016 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier 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. Proteins Genotype & phenotype Amino acids Fluorescence Mutation Mutagenesis Dmitry A Bolotin oth Margarita V Meer oth Dinara R Usmanova oth Alexander S Mishin oth George V Sharonov oth Dmitry N Ivankov oth Nina G Bozhanova oth Mikhail S Baranov oth Onuralp Soylemez oth Natalya S Bogatyreva oth Peter K Vlasov oth Evgeny S Egorov oth Maria D Logacheva oth Alexey S Kondrashov oth Dmitry M Chudakov oth Ekaterina V Putintseva oth Ilgar Z Mamedov oth Dan S Tawfik oth Konstantin A Lukyanov oth Fyodor A Kondrashov oth Enthalten in Nature London : Macmillan Publishers Limited, part of Springer Nature, 1869 533(2016), 7603, Seite 397 (DE-627)129292834 (DE-600)120714-3 (DE-576)014473941 0028-0836 nnns volume:533 year:2016 number:7603 pages:397 http://dx.doi.org/10.1038/nature17995 Volltext http://www.ncbi.nlm.nih.gov/pubmed/27193686 http://search.proquest.com/docview/1790506337 GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-BIODIV SSG-OLC-PHY SSG-OLC-CHE SSG-OLC-MAT SSG-OLC-FOR SSG-OLC-SPO SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-FOR GBV_ILN_11 GBV_ILN_22 GBV_ILN_30 GBV_ILN_40 GBV_ILN_47 GBV_ILN_55 GBV_ILN_59 GBV_ILN_60 GBV_ILN_62 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_101 GBV_ILN_110 GBV_ILN_120 GBV_ILN_154 GBV_ILN_168 GBV_ILN_170 GBV_ILN_171 GBV_ILN_211 GBV_ILN_290 GBV_ILN_294 GBV_ILN_601 GBV_ILN_647 GBV_ILN_754 GBV_ILN_2001 GBV_ILN_2002 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2015 GBV_ILN_2016 GBV_ILN_2018 GBV_ILN_2020 GBV_ILN_2026 GBV_ILN_2095 GBV_ILN_2116 GBV_ILN_2120 GBV_ILN_2121 GBV_ILN_2219 GBV_ILN_2221 GBV_ILN_2279 GBV_ILN_2286 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4125 GBV_ILN_4219 GBV_ILN_4251 GBV_ILN_4277 GBV_ILN_4302 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4314 GBV_ILN_4317 GBV_ILN_4320 GBV_ILN_4324 GBV_ILN_4700 AR 533 2016 7603 397 |
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10.1038/nature17995 doi PQ20160610 (DE-627)OLC1975207394 (DE-599)GBVOLC1975207394 (PRQ)g1106-b09c8c1cc03d6e233a610f605fc8ab38dbce1d8007b9a4ca228404134d29193c0 (KEY)0072945020160000533760300397localfitnesslandscapeofthegreenfluorescentprotein DE-627 ger DE-627 rakwb eng 070 500 DNB 500 AVZ BIODIV fid Karen S Sarkisyan verfasserin aut Local fitness landscape of the green fluorescent protein 2016 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier 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. Proteins Genotype & phenotype Amino acids Fluorescence Mutation Mutagenesis Dmitry A Bolotin oth Margarita V Meer oth Dinara R Usmanova oth Alexander S Mishin oth George V Sharonov oth Dmitry N Ivankov oth Nina G Bozhanova oth Mikhail S Baranov oth Onuralp Soylemez oth Natalya S Bogatyreva oth Peter K Vlasov oth Evgeny S Egorov oth Maria D Logacheva oth Alexey S Kondrashov oth Dmitry M Chudakov oth Ekaterina V Putintseva oth Ilgar Z Mamedov oth Dan S Tawfik oth Konstantin A Lukyanov oth Fyodor A Kondrashov oth Enthalten in Nature London : Macmillan Publishers Limited, part of Springer Nature, 1869 533(2016), 7603, Seite 397 (DE-627)129292834 (DE-600)120714-3 (DE-576)014473941 0028-0836 nnns volume:533 year:2016 number:7603 pages:397 http://dx.doi.org/10.1038/nature17995 Volltext http://www.ncbi.nlm.nih.gov/pubmed/27193686 http://search.proquest.com/docview/1790506337 GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-BIODIV SSG-OLC-PHY SSG-OLC-CHE SSG-OLC-MAT SSG-OLC-FOR SSG-OLC-SPO SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-FOR GBV_ILN_11 GBV_ILN_22 GBV_ILN_30 GBV_ILN_40 GBV_ILN_47 GBV_ILN_55 GBV_ILN_59 GBV_ILN_60 GBV_ILN_62 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_101 GBV_ILN_110 GBV_ILN_120 GBV_ILN_154 GBV_ILN_168 GBV_ILN_170 GBV_ILN_171 GBV_ILN_211 GBV_ILN_290 GBV_ILN_294 GBV_ILN_601 GBV_ILN_647 GBV_ILN_754 GBV_ILN_2001 GBV_ILN_2002 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2015 GBV_ILN_2016 GBV_ILN_2018 GBV_ILN_2020 GBV_ILN_2026 GBV_ILN_2095 GBV_ILN_2116 GBV_ILN_2120 GBV_ILN_2121 GBV_ILN_2219 GBV_ILN_2221 GBV_ILN_2279 GBV_ILN_2286 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4125 GBV_ILN_4219 GBV_ILN_4251 GBV_ILN_4277 GBV_ILN_4302 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4314 GBV_ILN_4317 GBV_ILN_4320 GBV_ILN_4324 GBV_ILN_4700 AR 533 2016 7603 397 |
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10.1038/nature17995 doi PQ20160610 (DE-627)OLC1975207394 (DE-599)GBVOLC1975207394 (PRQ)g1106-b09c8c1cc03d6e233a610f605fc8ab38dbce1d8007b9a4ca228404134d29193c0 (KEY)0072945020160000533760300397localfitnesslandscapeofthegreenfluorescentprotein DE-627 ger DE-627 rakwb eng 070 500 DNB 500 AVZ BIODIV fid Karen S Sarkisyan verfasserin aut Local fitness landscape of the green fluorescent protein 2016 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier 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. Proteins Genotype & phenotype Amino acids Fluorescence Mutation Mutagenesis Dmitry A Bolotin oth Margarita V Meer oth Dinara R Usmanova oth Alexander S Mishin oth George V Sharonov oth Dmitry N Ivankov oth Nina G Bozhanova oth Mikhail S Baranov oth Onuralp Soylemez oth Natalya S Bogatyreva oth Peter K Vlasov oth Evgeny S Egorov oth Maria D Logacheva oth Alexey S Kondrashov oth Dmitry M Chudakov oth Ekaterina V Putintseva oth Ilgar Z Mamedov oth Dan S Tawfik oth Konstantin A Lukyanov oth Fyodor A Kondrashov oth Enthalten in Nature London : Macmillan Publishers Limited, part of Springer Nature, 1869 533(2016), 7603, Seite 397 (DE-627)129292834 (DE-600)120714-3 (DE-576)014473941 0028-0836 nnns volume:533 year:2016 number:7603 pages:397 http://dx.doi.org/10.1038/nature17995 Volltext http://www.ncbi.nlm.nih.gov/pubmed/27193686 http://search.proquest.com/docview/1790506337 GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-BIODIV SSG-OLC-PHY SSG-OLC-CHE SSG-OLC-MAT SSG-OLC-FOR SSG-OLC-SPO SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-FOR GBV_ILN_11 GBV_ILN_22 GBV_ILN_30 GBV_ILN_40 GBV_ILN_47 GBV_ILN_55 GBV_ILN_59 GBV_ILN_60 GBV_ILN_62 GBV_ILN_69 GBV_ILN_70 GBV_ILN_73 GBV_ILN_101 GBV_ILN_110 GBV_ILN_120 GBV_ILN_154 GBV_ILN_168 GBV_ILN_170 GBV_ILN_171 GBV_ILN_211 GBV_ILN_290 GBV_ILN_294 GBV_ILN_601 GBV_ILN_647 GBV_ILN_754 GBV_ILN_2001 GBV_ILN_2002 GBV_ILN_2003 GBV_ILN_2005 GBV_ILN_2007 GBV_ILN_2008 GBV_ILN_2015 GBV_ILN_2016 GBV_ILN_2018 GBV_ILN_2020 GBV_ILN_2026 GBV_ILN_2095 GBV_ILN_2116 GBV_ILN_2120 GBV_ILN_2121 GBV_ILN_2219 GBV_ILN_2221 GBV_ILN_2279 GBV_ILN_2286 GBV_ILN_4012 GBV_ILN_4035 GBV_ILN_4125 GBV_ILN_4219 GBV_ILN_4251 GBV_ILN_4277 GBV_ILN_4302 GBV_ILN_4305 GBV_ILN_4313 GBV_ILN_4314 GBV_ILN_4317 GBV_ILN_4320 GBV_ILN_4324 GBV_ILN_4700 AR 533 2016 7603 397 |
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Enthalten in Nature 533(2016), 7603, Seite 397 volume:533 year:2016 number:7603 pages:397 |
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Enthalten in Nature 533(2016), 7603, Seite 397 volume:533 year:2016 number:7603 pages:397 |
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Proteins Genotype & phenotype Amino acids Fluorescence Mutation Mutagenesis |
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Karen S Sarkisyan @@aut@@ Dmitry A Bolotin @@oth@@ Margarita V Meer @@oth@@ Dinara R Usmanova @@oth@@ Alexander S Mishin @@oth@@ George V Sharonov @@oth@@ Dmitry N Ivankov @@oth@@ Nina G Bozhanova @@oth@@ Mikhail S Baranov @@oth@@ Onuralp Soylemez @@oth@@ Natalya S Bogatyreva @@oth@@ Peter K Vlasov @@oth@@ Evgeny S Egorov @@oth@@ Maria D Logacheva @@oth@@ Alexey S Kondrashov @@oth@@ Dmitry M Chudakov @@oth@@ Ekaterina V Putintseva @@oth@@ Ilgar Z Mamedov @@oth@@ Dan S Tawfik @@oth@@ Konstantin A Lukyanov @@oth@@ Fyodor A Kondrashov @@oth@@ |
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2016-01-01T00:00:00Z |
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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. |
abstractGer |
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. |
abstract_unstemmed |
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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Local fitness landscape of the green fluorescent protein |
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|
score |
7.4010277 |