Letter | Published:

Historical contingency and its biophysical basis in glucocorticoid receptor evolution

Nature volume 512, pages 203207 (14 August 2014) | Download Citation

Abstract

Understanding how chance historical events shape evolutionary processes is a central goal of evolutionary biology1,2,3,4,5,6,7. Direct insights into the extent and causes of evolutionary contingency have been limited to experimental systems7,8,9, because it is difficult to know what happened in the deep past and to characterize other paths that evolution could have followed. Here we combine ancestral protein reconstruction, directed evolution and biophysical analysis to explore alternative ‘might-have-been’ trajectories during the ancient evolution of a novel protein function. We previously found that the evolution of cortisol specificity in the ancestral glucocorticoid receptor (GR) was contingent on permissive substitutions, which had no apparent effect on receptor function but were necessary for GR to tolerate the large-effect mutations that caused the shift in specificity6. Here we show that alternative mutations that could have permitted the historical function-switching substitutions are extremely rare in the ensemble of genotypes accessible to the ancestral GR. In a library of thousands of variants of the ancestral protein, we recovered historical permissive substitutions but no alternative permissive genotypes. Using biophysical analysis, we found that permissive mutations must satisfy at least three physical requirements—they must stabilize specific local elements of the protein structure, maintain the correct energetic balance between functional conformations, and be compatible with the ancestral and derived structures—thus revealing why permissive mutations are rare. These findings demonstrate that GR evolution depended strongly on improbable, non-deterministic events, and this contingency arose from intrinsic biophysical properties of the protein.

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Acknowledgements

We thank J. Bridgham, members of the Thornton laboratory, and B. Buckley McAllister for technical assistance and fruitful discussions. We thank M. Stallcup for sharing plasmids and the University of Oregon ACISS cluster for computing resources (National Science Foundation (NSF) OCI-0960354). This work was supported by National Institutes of Health (NIH) F32-GM090650 (M.J.H.), NIH R01-GM081592 (J.W.T.) and R01-GM104397 (J.W.T.), NSF IOB-0546906 (J.W.T.) and a Howard Hughes Medical Institute Early Career Scientist award (J.W.T.).

Author information

Affiliations

  1. Institute of Molecular Biology and Department of Chemistry & Biochemistry, University of Oregon, Eugene, Oregon 97403, USA

    • Michael J. Harms
  2. Departments of Human Genetics and Ecology & Evolution, University of Chicago, Chicago, Illinois 60637, USA

    • Michael J. Harms
    •  & Joseph W. Thornton
  3. Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon 97403, USA

    • Joseph W. Thornton

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Contributions

M.J.H. and J.W.T. conceived the project, designed the experiments and wrote the paper. M.J.H. performed the experiments and analysed the data.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Joseph W. Thornton.

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https://doi.org/10.1038/nature13410

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