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Designed divergent evolution of enzyme function

Nature volume 440, pages 1078–1082 (2006)Cite this article

Abstract

It is generally believed that proteins with promiscuous functions divergently evolved to acquire higher specificity and activity1,2,3,4,5, and that this process was highly dependent on the ability of proteins to alter their functions with a small number of amino acid substitutions (plasticity)6. The application of this theory of divergent molecular evolution to promiscuous enzymes may allow us to design enzymes with more specificity and higher activity. Many structural and biochemical analyses have identified the active or binding site residues important for functional plasticity (plasticity residues)6,7,8,9,10. To understand how these residues contribute to molecular evolution, and thereby formulate a design methodology, plasticity residues were probed in the active site of the promiscuous sesquiterpene synthase γ-humulene synthase11,12. Identified plasticity residues were systematically recombined based on a mathematical model in order to construct novel terpene synthases, each catalysing the synthesis of one or a few very different sesquiterpenes. Here we present the construction of seven specific and active synthases that use different reaction pathways to produce the specific and very different products. Creation of these enzymes demonstrates the feasibility of exploiting the underlying evolvability of this scaffold, and provides evidence that rational approaches based on these ideas are useful for enzyme design.

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Figure 1: γ-Humulene synthase cyclization reaction mechanisms.
Figure 2: The homology structural model for the γ-humulene synthase active site.
Figure 3: Systematic remodelling of plasticity residues to design β-bisabolene synthase.
Figure 4: Divergent evolution of novel sesquiterpene synthases from γ-humulene synthase.

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Acknowledgements

We would like to thank P. C. Babbitt, J. D. Newman, M. C. Chang and S. C.-H. Pegg for discussions and critical reading of the manuscript. We are also grateful for D. Herschlag for critical comments. This research was funded by the Bill & Melinda Gates Foundation, the US Department of Agriculture, and the National Science Foundation.Author Contributions Y.Y. and J.D.K. conceived the project; Y.Y., J.D.K. and T.E.F. designed the experiments; and Y.Y. and J.D.K. wrote the paper.

Author information

Authors and Affiliations

  1. UCSF/UCB Joint Graduate Group in Bioengineering,

    Yasuo Yoshikuni, Thomas E. Ferrin & Jay D. Keasling

  2. Department of Chemical Engineering,

    Jay D. Keasling

  3. California Institute for Quantitative Biomedical Research (QB3), University of California at Berkeley, California, 94720, Berkeley, USA

    Jay D. Keasling

  4. Synthetic Biology Department, Physical Bioscience Division, Lawrence Berkeley National Laboratory, California, 94710, Berkeley, USA

    Yasuo Yoshikuni & Jay D. Keasling

  5. Department of Pharmaceutical Chemistry and Biopharmaceutical Sciences, University of California at San Francisco, California, 94143, San Francisco, USA

    Thomas E. Ferrin

Authors
  1. Yasuo Yoshikuni
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  3. Jay D. Keasling
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Corresponding author

Correspondence to Jay D. Keasling.

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Competing interests

J.D.K. owns stock in, and is a founder of, Amyris Biotechnologies. Amyris may use this technology to produce terpenes. However, Amyris currently has no plans to use the technology.

Supplementary information

Supplementary Tables

This file contains Supplementary Tables 1–9. (PDF 175 kb)

Supplementary Figures

This file contains Supplementary Figures 1–11. *In Figure 1 and Supplementary Figure 1, the structure of longifolene (4) has been corrected (it was missing a methyl group). In Supplementary Figure 1, the longipinene structure was also wrongly labelled 'longifolene' and vice versa. This correction was made on 27 February 2006. (DOC 1686 kb)

Supplementary Data 1

Three-dimensional coordinates for the homology structure of γ-humulene synthase (PDF 158 kb)

Supplementary Data 2

DNA sequence of designed γ-humulene synthase (PDF 59 kb)

Supplementary Methods 1

Additional methods used in this study. (PDF 110 kb)

Supplementary Methods 2

Detailed protocols for systematic remodeling of plasticity residues (PDF 103 kb)

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Yoshikuni, Y., Ferrin, T. & Keasling, J. Designed divergent evolution of enzyme function. Nature 440, 1078–1082 (2006). https://doi.org/10.1038/nature04607

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