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Predictive genetic circuit design for phenotype reprogramming in plants

Author

Listed:
  • Ci Kong

    (Tsinghua University
    Beijing Life Science Academy)

  • Yin Yang

    (Tsinghua University)

  • Tiancong Qi

    (Tsinghua University)

  • Shuyi Zhang

    (Tsinghua University
    Tsinghua University
    Tsinghua University
    Tsinghua University)

Abstract

Plants, with intricate molecular networks for environmental adaptation, offer groundbreaking potential for reprogramming with predictive genetic circuits. However, realizing this goal is challenging due to the long cultivation cycle of plants, as well as the lack of reproducible, quantitative methods and well-characterized genetic parts. Here, we establish a rapid (~10 days), quantitative, and predictive framework in plants. A group of orthogonal sensors, modular synthetic promoters, and NOT gates are constructed and quantitatively characterized. A predictive model is developed to predict the designed circuits’ behavior accurately. Our versatile and robust framework, validated by constructing 21 two-input circuits with high prediction accuracy (R2 = 0.81), enables multi-state phenotype control in both Arabidopsis thaliana and Nicotiana benthamiana in response to chemical inducers. Our study achieves predictable design and application of synthetic circuits in plants, offering valuable tools for the rapid engineering of plant traits in biotechnology and agriculture.

Suggested Citation

  • Ci Kong & Yin Yang & Tiancong Qi & Shuyi Zhang, 2025. "Predictive genetic circuit design for phenotype reprogramming in plants," Nature Communications, Nature, vol. 16(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-56042-2
    DOI: 10.1038/s41467-025-56042-2
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    References listed on IDEAS

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    1. Bruno Pok Man Ngou & Hee-Kyung Ahn & Pingtao Ding & Jonathan D. G. Jones, 2021. "Mutual potentiation of plant immunity by cell-surface and intracellular receptors," Nature, Nature, vol. 592(7852), pages 110-115, April.
    2. Timothy Frei & Federica Cella & Fabiana Tedeschi & Joaquín Gutiérrez & Guy-Bart Stan & Mustafa Khammash & Velia Siciliano, 2020. "Characterization and mitigation of gene expression burden in mammalian cells," Nature Communications, Nature, vol. 11(1), pages 1-14, December.
    3. Christoph Weiste & Wolfgang Dröge-Laser, 2014. "The Arabidopsis transcription factor bZIP11 activates auxin-mediated transcription by recruiting the histone acetylation machinery," Nature Communications, Nature, vol. 5(1), pages 1-12, September.
    4. Alireza Yazdani & Lu Lu & Maziar Raissi & George Em Karniadakis, 2020. "Systems biology informed deep learning for inferring parameters and hidden dynamics," PLOS Computational Biology, Public Library of Science, vol. 16(11), pages 1-19, November.
    5. Julia Bailey-Serres & Jane E. Parker & Elizabeth A. Ainsworth & Giles E. D. Oldroyd & Julian I. Schroeder, 2019. "Genetic strategies for improving crop yields," Nature, Nature, vol. 575(7781), pages 109-118, November.
    6. Chenrui Qin & Yanhui Xiang & Jie Liu & Ruilin Zhang & Ziming Liu & Tingting Li & Zhi Sun & Xiaoyi Ouyang & Yeqing Zong & Haoqian M. Zhang & Qi Ouyang & Long Qian & Chunbo Lou, 2023. "Precise programming of multigene expression stoichiometry in mammalian cells by a modular and programmable transcriptional system," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    7. Michael B. Elowitz & Stanislas Leibler, 2000. "A synthetic oscillatory network of transcriptional regulators," Nature, Nature, vol. 403(6767), pages 335-338, January.
    8. Timothy S. Gardner & Charles R. Cantor & James J. Collins, 2000. "Construction of a genetic toggle switch in Escherichia coli," Nature, Nature, vol. 403(6767), pages 339-342, January.
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