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Light-switchable transcription factors obtained by direct screening in mammalian cells

Author

Listed:
  • Liyuan Zhu

    (Princeton University)

  • Harold M. McNamara

    (Princeton University
    Princeton University)

  • Jared E. Toettcher

    (Princeton University)

Abstract

Optogenetic tools can provide fine spatial and temporal control over many biological processes. Yet the development of new light-switchable protein variants remains challenging, and the field still lacks general approaches to engineering or discovering protein variants with light-switchable biological functions. Here, we adapt strategies for protein domain insertion and mammalian-cell expression to generate and screen a library of candidate optogenetic tools directly in mammalian cells. The approach is based on insertion of the AsLOV2 photoswitchable domain at all possible positions in a candidate protein of interest, introduction of the library into mammalian cells, and light/dark selection for variants with photoswitchable activity. We demonstrate the approach’s utility using the Gal4-VP64 transcription factor as a model system. Our resulting LightsOut transcription factor exhibits a > 150-fold change in transcriptional activity between dark and blue light conditions. We show that light-switchable function generalizes to analogous insertion sites in two additional Cys6Zn2 and C2H2 zinc finger domains, providing a starting point for optogenetic regulation of a broad class of transcription factors. Our approach can streamline the identification of single-protein optogenetic switches, particularly in cases where structural or biochemical knowledge is limited.

Suggested Citation

  • Liyuan Zhu & Harold M. McNamara & Jared E. Toettcher, 2023. "Light-switchable transcription factors obtained by direct screening in mammalian cells," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-38993-6
    DOI: 10.1038/s41467-023-38993-6
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    References listed on IDEAS

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    1. Dana C. Nadler & Stacy-Anne Morgan & Avi Flamholz & Kaitlyn E. Kortright & David F. Savage, 2016. "Rapid construction of metabolite biosensors using domain-insertion profiling," Nature Communications, Nature, vol. 7(1), pages 1-11, November.
    2. Amir Taslimi & Justin D. Vrana & Daniel Chen & Sofya Borinskaya & Bruce J. Mayer & Matthew J. Kennedy & Chandra L. Tucker, 2014. "An optimized optogenetic clustering tool for probing protein interaction and function," Nature Communications, Nature, vol. 5(1), pages 1-9, December.
    3. César Carrasco-López & Evan M. Zhao & Agnieszka A. Gil & Nathan Alam & Jared E. Toettcher & José L. Avalos, 2020. "Development of light-responsive protein binding in the monobody non-immunoglobulin scaffold," Nature Communications, Nature, vol. 11(1), pages 1-13, December.
    4. Yi I. Wu & Daniel Frey & Oana I. Lungu & Angelika Jaehrig & Ilme Schlichting & Brian Kuhlman & Klaus M. Hahn, 2009. "A genetically encoded photoactivatable Rac controls the motility of living cells," Nature, Nature, vol. 461(7260), pages 104-108, September.
    5. Agnieszka A. Gil & César Carrasco-López & Liyuan Zhu & Evan M. Zhao & Pavithran T. Ravindran & Maxwell Z. Wilson & Alexander G. Goglia & José L. Avalos & Jared E. Toettcher, 2020. "Optogenetic control of protein binding using light-switchable nanobodies," Nature Communications, Nature, vol. 11(1), pages 1-12, December.
    6. Armin Baumschlager & Marc Rullan & Mustafa Khammash, 2020. "Exploiting natural chemical photosensitivity of anhydrotetracycline and tetracycline for dynamic and setpoint chemo-optogenetic control," Nature Communications, Nature, vol. 11(1), pages 1-10, December.
    7. Liting Duan & Jen Hope & Qunxiang Ong & Hsin-Ya Lou & Namdoo Kim & Comfrey McCarthy & Victor Acero & Michael Z. Lin & Bianxiao Cui, 2017. "Understanding CRY2 interactions for optical control of intracellular signaling," Nature Communications, Nature, vol. 8(1), pages 1-10, December.
    8. Dominik Niopek & Pierre Wehler & Julia Roensch & Roland Eils & Barbara Di Ventura, 2016. "Optogenetic control of nuclear protein export," Nature Communications, Nature, vol. 7(1), pages 1-9, April.
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    1. Deqiang Kong & Yang Zhou & Yu Wei & Xinyi Wang & Qin Huang & Xianyun Gao & Hang Wan & Mengyao Liu & Liping Kang & Guiling Yu & Jianli Yin & Ningzi Guan & Haifeng Ye, 2024. "Exploring plant-derived phytochrome chaperone proteins for light-switchable transcriptional regulation in mammals," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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