Rapid cell-free forward engineering of novel genetic ring oscillators

Henrike Niederholtmeyer, Zachary Z. Sun, Yutaka Hori, Enoch Yeung, Amanda Verpoorte, Richard M. Murray, Sebastian J. Maerkl

Research output: Contribution to journalArticle

97 Citations (Scopus)

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 hr. 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.

Original languageEnglish
Article numbere09771
JournaleLife
Volume4
Issue numberOCTOBER2015
DOIs
Publication statusPublished - 2015 Oct 2

ASJC Scopus subject areas

  • Neuroscience(all)
  • Immunology and Microbiology(all)
  • Biochemistry, Genetics and Molecular Biology(all)

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    Niederholtmeyer, H., Sun, Z. Z., Hori, Y., Yeung, E., Verpoorte, A., Murray, R. M., & Maerkl, S. J. (2015). Rapid cell-free forward engineering of novel genetic ring oscillators. eLife, 4(OCTOBER2015), [e09771]. https://doi.org/10.7554/eLife.09771