Abstract

Whole-cell biocatalysts have proven a tractable path toward sustainable production of bulk and fine chemicals. Yet the screening of libraries of cellular designs to identify best-performing biocatalysts is most often a low-throughput endeavor. For this reason, the development of biosensors enabling real-time monitoring of production has attracted attention. Here we applied systematic engineering of multiple parameters to search for a general biosensor design in the budding yeast Saccharomyces cerevisiae based on small-molecule binding transcriptional activators from the prokaryote superfamily of LysR-type transcriptional regulators (LTTRs). We identified a design supporting LTTR-dependent activation of reporter gene expression in the presence of cognate small-molecule inducers. As proof of principle, we applied the biosensors for in vivo screening of cells producing naringenin or cis,cis-muconic acid at different levels, and found that reporter gene output correlated with production. The transplantation of prokaryotic transcriptional activators into the eukaryotic chassis illustrates the potential of a hitherto untapped biosensor resource useful for biotechnological applications.

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Acknowledgements

This work was supported by the Novo Nordisk Foundation and by the European Union Seventh Framework Programme (FP7-KBBE-2013-7-single-stage) under grant agreement no. 613745, Promys (M.E. & S.S.). We acknowledge A. Koza and E. Özdemir for technical assistance.

Author information

Author notes

    • Mette L Skjoedt
    •  & Tim Snoek

    These authors contributed equally to this work.

Affiliations

  1. The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark.

    • Mette L Skjoedt
    • , Tim Snoek
    • , Kanchana R Kildegaard
    • , Dushica Arsovska
    • , Tobias J Goedecke
    • , Arun S Rajkumar
    • , Jie Zhang
    • , Mette Kristensen
    • , Solvej Siedler
    • , Irina Borodina
    • , Michael K Jensen
    •  & Jay D Keasling
  2. Evolva SA, Reinach, Switzerland.

    • Michael Eichenberger
  3. Department of Biology, Technical University Darmstadt, Darmstadt, Germany.

    • Michael Eichenberger
  4. Evolva Biotech A/S, Copenhagen, Denmark.

    • Beata J Lehka
  5. Department of Science and Environment, Roskilde University, Roskilde, Denmark.

    • Beata J Lehka
  6. Joint BioEnergy Institute, Emeryville, California, USA.

    • Jay D Keasling
  7. Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

    • Jay D Keasling
  8. Department of Chemical and Biomolecular Engineering, University of California, Berkeley, Berkeley, California, USA.

    • Jay D Keasling
  9. Department of Bioengineering, University of California, Berkeley, Berkeley, California, USA.

    • Jay D Keasling

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Contributions

M.L.S., T.S., J.D.K. and M.K.J. conceived this project. M.L.S., T.S. and M.K.J. designed all of the experiments. M.L.S., T.S. and D.A. performed all flow cytometry analyses. M.L.S., T.S., D.A., B.J.L., J.Z., K.R.K., S.S., T.J.G. and M.E. constructed all strains and plasmids. M.K. and K.R.K. performed all analytical measurements, and M.K.J. performed the RNA-seq experiment. M.L.S., T.S., M.K.J., I.B., A.S.R. and K.R.K. analyzed the data. M.K.J. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Michael K Jensen.

Supplementary information

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    Supplementary Text and Figures

    Supplementary Results, Supplementary Figures 1–7 and Supplementary Tables 1–5.

Excel files

  1. 1.

    Supplementary Dataset 1

    RNA-seq gene list.

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DOI

https://doi.org/10.1038/nchembio.2177

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