1. Biochemistry and Chemical Biology
  2. Computational and Systems Biology
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Rapid cell-free forward engineering of novel genetic ring oscillators

  1. Henrike Niederholtmeyer
  2. Zachary Z Sun
  3. Yutaka Hori
  4. Enoch Yeung
  5. Amanda Verpoorte
  6. Richard M Murray
  7. Sebastian J Maerkl  Is a corresponding author
  1. École Polytechnique Fédérale de Lausanne, Switzerland
  2. California Institute of Technology, United States
Research Article
  • Cited 99
  • Views 6,219
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Cite this article as: eLife 2015;4:e09771 doi: 10.7554/eLife.09771

Abstract

While complex dynamic biological networks control gene expression in all living organisms, the forward engineering of comparable synthetic networks remains challenging. The current paradigm of characterizing synthetic networks in cells results in lengthy design-build-test cycles, minimal data collection, and poor quantitative characterization. Cell-free systems are appealing alternative environments, but it remains questionable whether biological networks behave similarly in cell-free systems and in cells. We characterized in a cell-free system the 'repressilator,' a three-node synthetic oscillator. We then engineered novel three, four, and five-gene ring architectures, from characterization of circuit components to rapid analysis of complete networks. When implemented in cells, our novel 3-node networks produced population-wide oscillations and 95% of 5-node oscillator cells oscillated for up to 72 hours. Oscillation periods in cells matched the cell-free system results for all networks tested. An alternate forward engineering paradigm using cell-free systems can thus accurately capture cellular behavior.

Article and author information

Author details

  1. Henrike Niederholtmeyer

    Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
    Competing interests
    No competing interests declared.
  2. Zachary Z Sun

    Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
    Competing interests
    Zachary Z Sun, ZZS has ownership in a company that commercializes the cell-free technology utilized in this paper..
  3. Yutaka Hori

    Division of Engineering and Applied Science, California Institute of Technology, Pasadena, United States
    Competing interests
    No competing interests declared.
  4. Enoch Yeung

    Division of Engineering and Applied Science, California Institute of Technology, Pasadena, United States
    Competing interests
    No competing interests declared.
  5. Amanda Verpoorte

    Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
    Competing interests
    No competing interests declared.
  6. Richard M Murray

    Division of Biology and Bioengineering, California Institute of Technology, Pasadena, United States
    Competing interests
    Richard M Murray, RMM has ownership in a company that commercializes the cell-free technology utilized in this paper..
  7. Sebastian J Maerkl

    Institute of Bioengineering, School of Engineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
    For correspondence
    sebastian.maerkl@epfl.ch
    Competing interests
    No competing interests declared.

Reviewing Editor

  1. Friedrich Simmel, Technische Universität München, Germany

Publication history

  1. Received: June 29, 2015
  2. Accepted: October 1, 2015
  3. Accepted Manuscript published: October 2, 2015 (version 1)
  4. Accepted Manuscript updated: October 5, 2015 (version 2)
  5. Version of Record published: December 9, 2015 (version 3)

Copyright

© 2015, Niederholtmeyer et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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