Local fitness landscape of the green fluorescent protein.


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.

Submission Details

ID: MPSZ3Nkk3

Submitter: Connie Wang

Submission Date: July 31, 2017, 11:46 a.m.

Version: 1

Publication Details
Sarkisyan KS;Bolotin DA;Meer MV;Usmanova DR;Mishin AS;Sharonov GV;Ivankov DN;Bozhanova NG;Baranov MS;Soylemez O;Bogatyreva NS;Vlasov PK;Egorov ES;Logacheva MD;Kondrashov AS;Chudakov DM;Putintseva EV;Mamedov IZ;Tawfik DS;Lukyanov KA;Kondrashov FA,Nature (2016) Local fitness landscape of the green fluorescent protein. PMID:27193686
Additional Information

Study Summary

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)


Relevant PDB Entries

Structure ID Release Date Resolution Structure Title
1B9C 1999-02-09T00:00:00+0000 2.4 Green Fluorescent Protein Mutant F99S, M153T and V163A
1BFP 1997-04-09T00:00:00+0000 2.1 BLUE VARIANT OF GREEN FLUORESCENT PROTEIN
1C4F 1999-08-21T00:00:00+0000 2.25 GREEN FLUORESCENT PROTEIN S65T AT PH 4.6
1CV7 1999-08-23T00:00:00+0000 2.5 Crystal structure of enhanced cyan-emission variant of GFP
1EMA 1996-08-01T00:00:00+0000 1.9 GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA
1EMB 1997-01-08T00:00:00+0000 2.13 GREEN FLUORESCENT PROTEIN (GFP) FROM AEQUOREA VICTORIA, GLN 80 REPLACED WITH ARG
1EMC 1997-03-31T00:00:00+0000 2.3 GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT
1EME 1997-03-31T00:00:00+0000 2.5 GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT
1EMF 1997-03-31T00:00:00+0000 2.4 GREEN FLUORESCENT PROTEIN FROM AEQUOREA VICTORIA, MUTANT
1EMG 1998-11-12T00:00:00+0000 2.0 GREEN FLUORESCENT PROTEIN (65-67 REPLACED BY CRO, S65T SUBSTITUTION, Q80R)

Relevant UniProtKB Entries

Percent Identity Matching Chains Protein Accession Entry Name
100.0 Green fluorescent protein P42212 GFP_AEQVI