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Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity

Author

Listed:
  • Xinyi Wan

    (University of Edinburgh
    University of Edinburgh)

  • Filipe Pinto

    (University of Edinburgh
    University of Edinburgh)

  • Luyang Yu

    (Zhejiang University
    Zhejiang University-University of Edinburgh Institute, Zhejiang University)

  • Baojun Wang

    (University of Edinburgh
    University of Edinburgh
    Zhejiang University
    Zhejiang University-University of Edinburgh Institute, Zhejiang University)

Abstract

Versatile tools for gene expression regulation are vital for engineering gene networks of increasing scales and complexity with bespoke responses. Here, we investigate and repurpose a ubiquitous, indirect gene regulation mechanism from nature, which uses decoy protein-binding DNA sites, named DNA sponge, to modulate target gene expression in Escherichia coli. We show that synthetic DNA sponges can be designed to reshape the response profiles of gene circuits, lending multifaceted tuning capacities including reducing basal leakage by >20-fold, increasing system output amplitude by >130-fold and dynamic range by >70-fold, and mitigating host growth inhibition by >20%. Further, multi-layer DNA sponges for decoying multiple regulatory proteins provide an additive tuning effect on the responses of layered circuits compared to single-layer sponges. Our work shows synthetic DNA sponges offer a simple yet generalizable route to systematically engineer the performance of synthetic gene circuits, expanding the current toolkit for gene regulation with broad potential applications.

Suggested Citation

  • Xinyi Wan & Filipe Pinto & Luyang Yu & Baojun Wang, 2020. "Synthetic protein-binding DNA sponge as a tool to tune gene expression and mitigate protein toxicity," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:11:y:2020:i:1:d:10.1038_s41467-020-19552-9
    DOI: 10.1038/s41467-020-19552-9
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    Cited by:

    1. Shivang Hina-Nilesh Joshi & Chentao Yong & Andras Gyorgy, 2022. "Inducible plasmid copy number control for synthetic biology in commonly used E. coli strains," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Miles V. Rouches & Yasu Xu & Louis Brian Georges Cortes & Guillaume Lambert, 2022. "A plasmid system with tunable copy number," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    3. Yuanli Gao & Lei Wang & Baojun Wang, 2023. "Customizing cellular signal processing by synthetic multi-level regulatory circuits," Nature Communications, Nature, vol. 14(1), pages 1-14, December.

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