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Low protein expression enhances phenotypic evolvability by intensifying selection on folding stability

Shraddha Karve,P. Dasmeh,Jia Zheng,A. Wagner

Published 2022 in Nature Ecology & Evolution

ABSTRACT

Protein abundance affects the evolution of protein genotypes, but we do not know how it affects the evolution of protein phenotypes. Here we investigate the role of protein abundance in the evolvability of green fluorescent protein (GFP) towards the novel phenotype of cyan fluorescence. We evolve GFP in E. coli through multiple cycles of mutation and selection and show that low GFP expression facilitates the evolution of cyan fluorescence. A computational model whose predictions we test experimentally helps explain why: lowly expressed proteins are under stronger selection for proper folding, which facilitates their evolvability on short evolutionary time scales. The reason is that high fluorescence can be achieved by either few proteins that fold well or by many proteins that fold less well. In other words, we observe a synergy between a protein’s scarcity and its stability. Because many proteins meet the essential requirements for this scarcity–stability synergy, it may be a widespread mechanism by which low expression helps proteins evolve new phenotypes and functions. Directed evolution shows that low expression of the green fluorescent protein facilitates the evolution of cyan fluorescence in E. coli, which can be explained by synergy between the protein’s scarcity and its stability.

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