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Bioprospecting and evolving alternative xylose and arabinose pathway enzymes for use in Saccharomyces cerevisiae

  • Bioenergy and biofuels
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Abstract

Bioprospecting is an effective way to find novel enzymes from strains with desirable phenotypes. Such bioprospecting has enabled organisms such as Saccharomyces cerevisiae to utilize nonnative pentose sugars. Yet, the efficiency of this pentose catabolism (especially for the case of arabinose) remains suboptimal. Thus, further pathway optimization or identification of novel, optimal pathways is needed. Previously, we identified a novel set of xylan catabolic pathway enzymes from a superior pentose-utilizing strain of Ustilago bevomyces. These enzymes were used to successfully engineer a xylan-utilizing S. cerevisiae through a blended approach of bioprospecting and evolutionary engineering. Here, we expanded this approach to xylose and arabinose catabolic pathway engineering and demonstrated that bioprospected xylose and arabinose catabolic pathways from U. bevomyces offer alternative choices for enabling efficient pentose catabolism in S. cerevisiae. By introducing a novel set of xylose catabolic genes from U. bevomyces, growth rates were improved up to 85 % over a set of traditional Scheffersomyces stipitis pathway genes. In addition, we suggested an alternative arabinose catabolic pathway which, after directed evolution and pathway engineering, enabled S. cerevisiae to grow on arabinose as a sole carbon source in minimal medium with growth rates upwards of 0.05 h−1. This pathway represents the most efficient growth of yeast on pure arabinose minimal medium. These pathways provide great starting points for further strain development and demonstrate the utility of bioprospecting from U. bevomyces.

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Acknowledgments

We acknowledge financial support for this project from the University of Texas at Austin Research Grant Program, DuPont Young Investigator Award, and National Science Foundation under Grant CBET-1067506. We thank Scott Hunicke-Smith and the UT GSAF for assistance in whole genome sequencing and analysis.

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  1. Taylor Jellison

    Present address: Polymers Technology, ExxonMobil Chemical Company, 5200 Bayway Drive, Baytown, TX, 77520, USA

Authors and Affiliations

  1. Clean Energy Research Center, Korea Institute of Science and Technology, Hwarang-ro 14-gil 5, Seongbuk-gu, Seoul, 136-791, South Korea

    Sun-Mi Lee

  2. McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St., C0400, Austin, TX, 78712, USA

    Taylor Jellison & Hal S. Alper

  3. Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, C0400, Austin, TX, 78712, USA

    Hal S. Alper

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  1. Sun-Mi Lee
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Correspondence to Hal S. Alper.

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This study was funded by National Science Foundation (CBET-1067506).

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Lee, SM., Jellison, T. & Alper, H.S. Bioprospecting and evolving alternative xylose and arabinose pathway enzymes for use in Saccharomyces cerevisiae . Appl Microbiol Biotechnol 100, 2487–2498 (2016). https://doi.org/10.1007/s00253-015-7211-z

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