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

Nature Ecology & Evolution volume 6, pages 1155–1164 (2022)Cite this article

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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.

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Fig. 1: Low GFP expression promotes evolution of a novel cyan fluorescence phenotype.
Fig. 2: L populations harbour fewer non-synonymous and neo-functionalizing variants.
Fig. 3: Modelled H populations retain more destabilizing mutations.
Fig. 4: Evolvability of GFP becomes indistinguishable in H and L populations when the starting population is robust to destabilizing variants.

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Data availability

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).

Code availability

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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Acknowledgements

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.

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Authors and Affiliations

  1. Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland

    Shraddha Karve, Pouria Dasmeh, Jia Zheng & Andreas Wagner

  2. Ashoka University, Sonipat, India

    Shraddha Karve

  3. Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, Lausanne, Switzerland

    Pouria Dasmeh, Jia Zheng & Andreas Wagner

  4. The Santa Fe Institute, Santa Fe, NM, USA

    Andreas Wagner

  5. Stellenbosch Institute for Advanced Study (STIAS), Wallenberg Research Centre at Stellenbosch University, Stellenbosch, South Africa

    Andreas Wagner

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Contributions

S.K., P.D. and A.W. were involved in the conceptualization of the study. S.K. and P.D. performed the experiments. P.D. performed computational modelling and formulated theoretical predictions. J.Z. provided the resources and training for working with fluorescent proteins. S.K., P.D., J.Z. and A.W. contributed to data analysis and edited the manuscript.

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Correspondence to Andreas Wagner.

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Nature Ecology & Evolution thanks Jian-Rong (Philip) Yang, Rohan Maddamsetti and Claus Wilke for their contribution to the peer review of this work. Peer reviewer reports are available.

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Supplementary Figs. 1–14, Tables 1–5 and information for the theoretical analysis and simulations of GFP evolution.

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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

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