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Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells

Nature Methods volume 20, pages 908–917 (2023)Cite this article

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Abstract

The incorporation of light-responsive domains into engineered proteins has enabled control of protein localization, interactions and function with light. We integrated optogenetic control into proximity labeling, a cornerstone technique for high-resolution proteomic mapping of organelles and interactomes in living cells. Through structure-guided screening and directed evolution, we installed the light-sensitive LOV domain into the proximity labeling enzyme TurboID to rapidly and reversibly control its labeling activity with low-power blue light. ‘LOV-Turbo’ works in multiple contexts and dramatically reduces background in biotin-rich environments such as neurons. We used LOV-Turbo for pulse-chase labeling to discover proteins that traffic between endoplasmic reticulum, nuclear and mitochondrial compartments under cellular stress. We also showed that instead of external light, LOV-Turbo can be activated by bioluminescence resonance energy transfer from luciferase, enabling interaction-dependent proximity labeling. Overall, LOV-Turbo increases the spatial and temporal precision of proximity labeling, expanding the scope of experimental questions that can be addressed with proximity labeling.

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Fig. 1: Design and directed evolution of LOV-Turbo.
Fig. 2: Characterization of LOV-Turbo.
Fig. 3: LOV-Turbo is reversible and works in multiple cell types and in the rodent brain.
Fig. 4: Applications of LOV-Turbo.
Fig. 5: Mapping proteome dynamics with LOV-Turbo by mass spectrometry.

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Data availability

The data associated with this study are available in the article and the Supplementary Information. The original mass spectra, spectral library and the protein sequence database used for searches have been deposited in the public proteomics repository MassIVE (http://massive.ucsd.edu) and are accessible at ftp://massive.ucsd.edu/MSV000090683/. Additional data beyond that provided in the figures and Supplementary Information are available from the corresponding author on request.

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Acknowledgements

Rat cortical neurons were a kind gift from M. Lin (Stanford University). We thank J. Reinstein (Max Planck Institute) for helpful feedback. This work was supported by the NIH (grant nos. R01-DK121409 and RC2DK129964 to A.Y.T., R01-OD026223 to A.Y.T. and S.A.C. and T32GM007276 to J.S.C.), the Stanford Wu Tsai Neurosciences Institute (A.Y.T.), the National Science Foundation (NeuroNex grant no. 2014862 to A.Y.T. and GRFP DGE-1656518 to J.S.C.), the National Research Foundation of Korea grant no. NRF-2019R1A6A3A03033677 (S.-Y.L.), the Stanford Gerald J. Lieberman Fellowship (J.S.C.) and the Burroughs Wellcome Fund grant no. CASI 1019469 (C.K.K.). A.Y.T. is a Chan Zuckerberg Biohub – San Francisco Investigator.

Author information

Author notes

  1. Christina K. Kim

    Present address: Center for Neuroscience and Department of Neurology, University of California, Davis, CA, USA

  2. Kelvin F. Cho

    Present address: Amgen Research, South San Francisco, CA, USA

  3. These authors contributed equally: Song-Yi Lee, Joleen S. Cheah.

Authors and Affiliations

  1. Department of Genetics, Stanford University, Stanford, CA, USA

    Song-Yi Lee, Boxuan Zhao, Christina K. Kim, Kelvin F. Cho & Alice Y. Ting

  2. Department of Biology, Stanford University, Stanford, CA, USA

    Joleen S. Cheah & Alice Y. Ting

  3. Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Charles Xu, Namrata D. Udeshi & Steven A. Carr

  4. Department of Chemistry, Stanford University, Stanford, CA, USA

    Heegwang Roh & Alice Y. Ting

  5. Chan Zuckerberg Biohub–San Francisco, San Francisco, CA, USA

    Alice Y. Ting

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Contributions

S.-Y.L. and A.Y.T. conceived this project. S.-Y.L., J.S.C. and A.Y.T. designed experiments and analyzed all the data except those noted. S.-Y.L. and J.S.C. performed all experiments, unless otherwise noted. N.D.U., C.X. and S.A.C. performed post-streptavidin-enrichment sample processing, mass spectrometry, and initial data analysis. B.Z. and S.-Y.L. performed the mouse brain experiments. C.K.K., K.F.C. and S.-Y.L. performed cultured rat cortical neuron experiments. H.R. and S.-Y.L. performed BRET experiments. S.-Y.L., J.S.C. and A.Y.T. wrote the paper with input from all authors.

Corresponding author

Correspondence to Alice Y. Ting.

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Competing interests

S.-Y.L., J.S.C. and A.Y.T. have filed a patent application covering some aspects of this work (US Provisional Patent Application No. 63/488,940; CZ SF ref. CZB-273S-P1; Stanford ref. S22-487; KT ref. 110221-1361830-009500PR). The remaining authors declare no competing interests.

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Nature Methods thanks Angelos Constantinou, Tatsuya Sawasaki and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: Rita Strack, in collaboration with the Nature Methods team.

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Supplementary information

Supplementary Information

Supplementary Figs. 1–8, Table 1, Legends of Tables 2–4, Note 1, Methods, Antibodies list, Genetic constructs list and References.

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Supplementary Table 2–4

Table 2: Proteomic data for ERM to nucleus pulse-chase experiment. Table 3: Proteomic data for ERM to mitochondria pulse-chase experiment. Table 4: Proteomic data at peptide level for ERM to nucleus pulse-chase experiment.

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Lee, SY., Cheah, J.S., Zhao, B. et al. Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells. Nat Methods 20, 908–917 (2023). https://doi.org/10.1038/s41592-023-01880-5

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