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Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases

Nature Chemical Biology volume 4, pages 617–623 (2008)Cite this article

Abstract

Throughout molecular evolution, organisms create assorted chemicals in response to varying ecological niches. Catalytic landscapes underlie metabolic evolution, wherein mutational steps alter the biosynthetic properties of enzymes. Here we report the first systematic quantitative characterization of the catalytic landscape underlying the evolution of sesquiterpene chemical diversity. On the basis of our previous discovery of a set of nine naturally occurring amino acid substitutions that functionally interconverted orthologous sesquiterpene synthases from Nicotiana tabacum and Hyoscyamus muticus, we created a library of all possible residue combinations (29 = 512) in the N. tabacum enzyme. The product spectra of 418 active enzymes revealed a rugged landscape where several minimal combinations of the nine mutations encode convergent solutions to the interconversions of parental activities. Quantitative comparisons indicated context dependence for mutational effects—epistasis—in product specificity and promiscuity. These results provide a measure of the mutational accessibility of phenotypic variability in a diverging lineage of terpene synthases.

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Figure 1: Terminal cyclization steps of TEAS and HPS terpene synthases.
Figure 2: Overall structure of TEAS and location and identity of M9 residues.
Figure 3: Phylogenetic distribution of solanaceous TEAS- and HPS-like terpene synthases.
Figure 4: Activities of the M9 lineage.
Figure 5: Biosynthetic tree of the M9 library.
Figure 6: AID in chemical and sequence space.

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Acknowledgements

We thank M. Austin and J. Melnick for critical review of the manuscript, Y. Zhai for computational support and J. Gullberg and A. Nordstom for insightful discussions. This work was supported by National Institutes of Health grant GM54029 to J.C. and J.P.N. J.P.N. is supported by the Howard Hughes Medical Institute.

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Authors and Affiliations

  1. Howard Hughes Medical Institute, The Salk Institute for Biological Studies, Jack H. Skirball Center for Chemical Biology & Proteomics, 10010 North Torrey Pines Road, La Jolla, 92037, California, USA

    Paul E O'Maille, Arthur Malone, Nikki Dellas, Iseult Sheehan & Joseph P Noel

  2. Department of Chemistry, University of California San Diego, 9500 Gilman Drive, La Jolla, 92093, California, USA

    Nikki Dellas

  3. Department of Chemistry, Vanderbilt University, 7330 Stevenson Center, Station B 351822, Nashville, 37235, Tennessee, USA

    B Andes Hess Jr & Lidia Smentek

  4. Institute of Physics, Nicolaus Copernicus University, Grudziadzka 5/7, 87-100 Toruń, Poland.,

    Lidia Smentek

  5. Department of Plant & Soil Sciences, Plant Biology Program, University of Kentucky, 105 Plant Science Building, 1405 Veterans Drive, Lexington, 40546, Kentucky, USA

    Bryan T Greenhagen & Joe Chappell

  6. The Salk Institute for Biological Studies, Razavi Newman Center for Bioinformatics, 10010 North Torrey Pines Road, La Jolla, 92037, California, USA

    Gerard Manning

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Contributions

P.E.O. designed the study, conducted experiments, analyzed data and wrote the manuscript; A.M. conducted experiments and developed small-scale protein purification; N.D. conducted experiments, analyzed data and contributed revisions to the manuscript; B.A.H. conducted quantum mechanics calculations and contributed revisions to the manuscript; L.S. conducted quantum mechanics calculations; I.S. conducted experiments; B.T.G. and J.C. designed the study and contributed revisions to the manuscript; G.M. analyzed data, developed the biosynthetic tree and chemical distance analysis, and contributed revisions to the manuscript; J.P.N. designed the study, analyzed the data and wrote the manuscript.

Corresponding author

Correspondence to Joseph P Noel.

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Competing interests

J.P.N. and J.C. declare an interest in Allylix, Inc. as scientific co-founders and stockholders. Allylix, Inc. is engaged in the commercial production of high-value sesquiterpene products.

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O'Maille, P., Malone, A., Dellas, N. et al. Quantitative exploration of the catalytic landscape separating divergent plant sesquiterpene synthases. Nat Chem Biol 4, 617–623 (2008). https://doi.org/10.1038/nchembio.113

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