An epistatic ratchet constrains the direction of glucocorticoid receptor evolution

Abstract

The extent to which evolution is reversible has long fascinated biologists1,2,3,4,5,6,7,8. Most previous work on the reversibility of morphological and life-history evolution9,10,11,12,13 has been indecisive, because of uncertainty and bias in the methods used to infer ancestral states for such characters14,15. Further, despite theoretical work on the factors that could contribute to irreversibility1,8,16, there is little empirical evidence on its causes, because sufficient understanding of the mechanistic basis for the evolution of new or ancestral phenotypes is seldom available3,8,17. By studying the reversibility of evolutionary changes in protein structure and function, these limitations can be overcome. Here we show, using the evolution of hormone specificity in the vertebrate glucocorticoid receptor as a case-study, that the evolutionary path by which this protein acquired its new function soon became inaccessible to reverse exploration. Using ancestral gene reconstruction, protein engineering and X-ray crystallography, we demonstrate that five subsequent ‘restrictive’ mutations, which optimized the new specificity of the glucocorticoid receptor, also destabilized elements of the protein structure that were required to support the ancestral conformation. Unless these ratchet-like epistatic substitutions are restored to their ancestral states, reversing the key function-switching mutations yields a non-functional protein. Reversing the restrictive substitutions first, however, does nothing to enhance the ancestral function. Our findings indicate that even if selection for the ancestral function were imposed, direct reversal would be extremely unlikely, suggesting an important role for historical contingency in protein evolution.

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Figure 1: Evolution and reversibility of glucocorticoid receptor function.
Figure 2: Identification of restrictive substitutions that impede reversibility.
Figure 3: Restrictive substitutions impede evolutionary reversibility.
Figure 4: Epistasis limits trajectories of reverse and forward evolution.

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Protein Data Bank

Data deposits

The atomic coordinates and structure factors for AncGR2 have been submitted to the Protein Data Bank (PDB) under accession number 3GN8.

References

  1. 1

    Muller, H. J. Reversibility in evolution considered from the standpoint of genetics. Biol. Rev. Camb. Philos. Soc. 14, 261–280 (1939)

  2. 2

    Simpson, G. G. The Major Features of Evolution 310–312 (Columbia Univ. Press, 1953)

  3. 3

    Crick, F. H. The origin of the genetic code. J. Mol. Biol. 38, 367–379 (1968)

  4. 4

    Gould, S. J. Dollo on Dollo’s law: irreversibility and the status of evolutionary laws. J. Hist. Biol. 3, 189–212 (1970)

  5. 5

    Dobzhansky, T. G. Genetics of the Evolutionary Process 428–430 (Columbia Univ. Press, 1971)

  6. 6

    Macbeth, N. Reflections on irreversibility. Syst. Zool. 29, 402–404 (1980)

  7. 7

    Bull, J. J. & Charnov, E. L. On irreversible evolution. Evolution 39, 1149–1155 (1985)

  8. 8

    Teotonio, H. & Rose, M. R. Perspective: reverse evolution. Evolution 55, 653–660 (2001)

  9. 9

    Collin, R. & Cipriani, R. Dollo’s law and the re-evolution of shell coiling. Proc. R. Soc. Lond. B. 270, 2551–2555 (2003)

  10. 10

    Domes, K., Norton, R. A., Maraun, M. & Scheu, S. Reevolution of sexuality breaks Dollo’s law. Proc. Natl Acad. Sci. USA 104, 7139–7144 (2007)

  11. 11

    Kohlsdorf, T. & Wagner, G. P. Evidence for the reversibility of digit loss: a phylogenetic study of limb evolution in Bachia (Gymnophthalmidae: Squamata). Evolution 60, 1896–1912 (2006)

  12. 12

    Whiting, M. F., Bradler, S. & Maxwell, T. Loss and recovery of wings in stick insects. Nature 421, 264–267 (2003)

  13. 13

    Chippindale, P. T., Bonett, R. M., Baldwin, A. S. & Wiens, J. J. Phylogenetic evidence for a major reversal of life-history evolution in plethodontid salamanders. Evolution 58, 2809–2822 (2004)

  14. 14

    Goldberg, E. E. & Igic, B. On phylogenetic tests of irreversible evolution. Evolution 62, 2727–2741 (2008)

  15. 15

    Collin, R. & Miglietta, M. P. Reversing opinions on Dollo’s Law. Trends Ecol. Evol. 23, 602–609 (2008)

  16. 16

    Wagner, G. P. The logical structure of irreversible systems transformations: a theorem concerning Dollo’s law and chaotic movement. J. Theor. Biol. 96, 337–346 (1982)

  17. 17

    Zufall, R. A. & Rausher, M. D. Genetic changes associated with floral adaptation restrict future evolutionary potential. Nature 428, 847–850 (2004)

  18. 18

    Lewontin, R. C. Is nature probable or capricious? Bioscience 16, 25–27 (1966)

  19. 19

    Pagel, M. Limpets break Dollo’s Law. Trends Ecol. Evol. 19, 278–280 (2004)

  20. 20

    Thornton, J. W. Resurrecting ancient genes: experimental analysis of extinct molecules. Nature Rev. Genet. 5, 366–375 (2004)

  21. 21

    Dean, A. M. & Thornton, J. W. Mechanistic approaches to the study of evolution: the functional synthesis. Nature Rev. Genet. 8, 675–688 (2007)

  22. 22

    Yokoyama, S., Tada, T., Zhang, H. & Britt, L. Elucidation of phenotypic adaptations: molecular analyses of dim-light vision proteins in vertebrates. Proc. Natl Acad. Sci. USA 105, 13480–13485 (2008)

  23. 23

    Bridgham, J. T., Carroll, S. M. & Thornton, J. W. Evolution of hormone-receptor complexity by molecular exploitation. Science 312, 97–101 (2006)

  24. 24

    Ortlund, E. A., Bridgham, J. T., Redinbo, M. R. & Thornton, J. W. Crystal structure of an ancient protein: evolution by conformational epistasis. Science 317, 1544–1548 (2007)

  25. 25

    Wurtz, J. M. et al. A canonical structure for the ligand-binding domain of nuclear receptors. Nature Struct. Biol. 3, 87–94 (1996)

  26. 26

    Smith, J. M. Natural selection and the concept of a protein space. Nature 225, 563–564 (1970)

  27. 27

    Majerus, M. E. N. Melanism: Evolution in Action 151–154 (Oxford Univ. Press, 1998)

  28. 28

    Dawkins, R. Blind Watchmaker (W.W. Norton, 1994)

  29. 29

    Weinreich, D. M., Delaney, N. F., Depristo, M. A. & Hartl, D. L. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 312, 111–114 (2006)

  30. 30

    Dennett, D. C. Darwin’s Dangerous Idea: Evolution and the Meanings of Life (Simon & Schuster, 1995)

  31. 31

    Yang, Z., Kumar, S. & Nei, M. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics 141, 1641–1650 (1995)

  32. 32

    Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997)

  33. 33

    McCoy, A. J. et al. Phaser crystallographic software. J. Appl. Crystallogr. 40, 658–674 (2007)

  34. 34

    Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. 60, 2126–2132 (2004)

  35. 35

    Brunger, A. T. et al. Crystallography & NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr. D 54, 905–921 (1998)

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Acknowledgements

Supported by National Science Foundation IOB-0546906, National Institutes of Health R01-GM081592 and F32-GM074398, and a Sloan Foundation Fellowship to J.W.T. We thank M. Harms and members of the Thornton, Cresko and Phillips laboratories for comments.

Author Contributions J.T.B. and J.W.T. conceived the experiments. J.T.B. performed the functional experiments, E.A.O. the structural analysis, and J.W.T. the phylogenetic analysis. J.T.B., E.A.O. and J.W.T. interpreted the results. J.T.B. and J.T. wrote the paper.

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Correspondence to Joseph W. Thornton.

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Bridgham, J., Ortlund, E. & Thornton, J. An epistatic ratchet constrains the direction of glucocorticoid receptor evolution. Nature 461, 515–519 (2009). https://doi.org/10.1038/nature08249

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