Design of a palette of SNAP-tag mimics of fluorescent proteins and their use as cell reporters

Dasheng Zhang; Zhengda Chen; Zengmin Du; Bingkun Bao; Ni Su; Xianjun Chen; Yihui Ge; Qiuning Lin; Lipeng Yang; Yujie Hua; Shuo Wang; Xin Hua; Fangting Zuo; Ningfeng Li; Renmei Liu; Li Jiang; Chunyan Bao; Yuzheng Zhao; Joseph Loscalzo; Yi Yang; Linyong Zhu

doi:10.1038/s41421-023-00546-y

Design of a palette of SNAP-tag mimics of fluorescent proteins and their use as cell reporters

Cell Discov. 2023 Jun 13;9(1):56. doi: 10.1038/s41421-023-00546-y.

Authors

Dasheng Zhang^#^{1

2}, Zhengda Chen^#^{1

2}, Zengmin Du^#^{1

2}, Bingkun Bao^#^{1

3}, Ni Su^#^{1

2}, Xianjun Chen^{4

5}, Yihui Ge^{1

2}, Qiuning Lin^{1

3}, Lipeng Yang^{1

3}, Yujie Hua^{1

3}, Shuo Wang^{1

2}, Xin Hua^{1

3}, Fangting Zuo^{1

2}, Ningfeng Li^{1

3}, Renmei Liu^{1

2}, Li Jiang^{1

3}, Chunyan Bao¹, Yuzheng Zhao^{1

2}, Joseph Loscalzo⁶, Yi Yang^{7

8}, Linyong Zhu^{9

10

11}

Affiliations

¹ Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China.
² Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China.
³ School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China.
⁴ Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China. xianjunchen@ecust.edu.cn.
⁵ Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China. xianjunchen@ecust.edu.cn.
⁶ Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
⁷ Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China. yiyang@ecust.edu.cn.
⁸ Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China. yiyang@ecust.edu.cn.
⁹ Optogenetics & Synthetic Biology Interdisciplinary Research Center, State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China. linyongzhu@ecust.edu.cn.
¹⁰ Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, School of Pharmacy, East China University of Science and Technology, Shanghai, China. linyongzhu@ecust.edu.cn.
¹¹ School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai, China. linyongzhu@ecust.edu.cn.

^# Contributed equally.

Abstract

Naturally occurring fluorescent proteins (FPs) are the most widely used tools for tracking cellular proteins and sensing cellular events. Here, we chemically evolved the self-labeling SNAP-tag into a palette of SNAP-tag mimics of fluorescent proteins (SmFPs) that possess bright, rapidly inducible fluorescence ranging from cyan to infrared. SmFPs are integral chemical-genetic entities based on the same fluorogenic principle as FPs, i.e., induction of fluorescence of non-emitting molecular rotors by conformational locking. We demonstrate the usefulness of these SmFPs in real-time tracking of protein expression, degradation, binding interactions, trafficking, and assembly, and show that these optimally designed SmFPs outperform FPs like GFP in many important ways. We further show that the fluorescence of circularly permuted SmFPs is sensitive to the conformational changes of their fusion partners, and that these fusion partners can be used for the development of single SmFP-based genetically encoded calcium sensors for live cell imaging.