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.
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All data are available in the manuscript or the supplementary materials. SMRT sequencing data are available at the National Center for Biotechnology Information with a BioProject ID PRJNA833567 (https://www.ncbi.nlm.nih.gov/bioproject/PRJNA833567).
Custom code used in this study is available in a public GitHub repository (https://github.com/dasmeh/Discrete_Time_Markov_Chain_Evolution).
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This project has received funding from the European Research Council under grant agreement number 739874. We would also like to acknowledge support by Swiss National Science Foundation grant 31003A_172887, by the University Priority Research Program in Evolutionary Biology and by the flow cytometry facility and the functional genomics centre at the University of Zurich. S.K. thanks B.R. Iyengar and M. Olombrada for discussions and support.
The authors declare no competing interests.
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Karve, S., Dasmeh, P., Zheng, J. et al. Low protein expression enhances phenotypic evolvability by intensifying selection on folding stability. Nat Ecol Evol 6, 1155–1164 (2022). https://doi.org/10.1038/s41559-022-01797-w