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Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling

Author

Listed:
  • Yansheng Zhai

    (Shenzhen Bay Laboratory)

  • Xiaoyan Huang

    (Shenzhen Bay Laboratory)

  • Keren Zhang

    (Shenzhen Bay Laboratory)

  • Yuchen Huang

    (Shenzhen Bay Laboratory)

  • Yanlong Jiang

    (UF Scripps Biomedical Research)

  • Jingwei Cui

    (Shenzhen Bay Laboratory)

  • Zhe Zhang

    (Shenzhen Bay Laboratory
    University of Science and Technology of China)

  • Cookson K. C. Chiu

    (Shenzhen Bay Laboratory)

  • Weiye Zhong

    (Shenzhen Bay Laboratory)

  • Gang Li

    (Shenzhen Bay Laboratory)

Abstract

Enzymatic-based proximity labeling approaches based on activated esters or phenoxy radicals have been widely used for mapping subcellular proteome and protein interactors in living cells. However, activated esters are poorly reactive which leads to a wide labeling radius and phenoxy radicals generated by peroxide treatment may disturb redox-sensitive pathways. Herein, we report a photoactivation-dependent proximity labeling (PDPL) method designed by genetically attaching photosensitizer protein miniSOG to a protein of interest. Triggered by blue light and tunned by irradiation time, singlet oxygen is generated, thereafter enabling spatiotemporally-resolved aniline probe labeling of histidine residues. We demonstrate its high-fidelity through mapping of organelle-specific proteomes. Side-by-side comparison of PDPL with TurboID reveals more specific and deeper proteomic coverage by PDPL. We further apply PDPL to the disease-related transcriptional coactivator BRD4 and E3 ligase Parkin, and discover previously unknown interactors. Through over-expression screening, two unreported substrates Ssu72 and SNW1 are identified for Parkin, whose degradation processes are mediated by the ubiquitination-proteosome pathway.

Suggested Citation

  • Yansheng Zhai & Xiaoyan Huang & Keren Zhang & Yuchen Huang & Yanlong Jiang & Jingwei Cui & Zhe Zhang & Cookson K. C. Chiu & Weiye Zhong & Gang Li, 2022. "Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling," Nature Communications, Nature, vol. 13(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-32689-z
    DOI: 10.1038/s41467-022-32689-z
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    References listed on IDEAS

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    1. Maik Müller & Fabienne Gräbnitz & Niculò Barandun & Yang Shen & Fabian Wendt & Sebastian N. Steiner & Yannik Severin & Stefan U. Vetterli & Milon Mondal & James R. Prudent & Raphael Hofmann & Marc Oos, 2021. "Light-mediated discovery of surfaceome nanoscale organization and intercellular receptor interaction networks," Nature Communications, Nature, vol. 12(1), pages 1-17, December.
    2. Shan Tang & Adam T. Beattie & Lucie Kafkova & Gianluca Petris & Nicolas Huguenin-Dezot & Marc Fiedler & Matthew Freeman & Jason W. Chin, 2022. "Mechanism-based traps enable protease and hydrolase substrate discovery," Nature, Nature, vol. 602(7898), pages 701-707, February.
    3. Johannes Zuber & Junwei Shi & Eric Wang & Amy R. Rappaport & Harald Herrmann & Edward A. Sison & Daniel Magoon & Jun Qi & Katharina Blatt & Mark Wunderlich & Meredith J. Taylor & Christopher Johns & A, 2011. "RNAi screen identifies Brd4 as a therapeutic target in acute myeloid leukaemia," Nature, Nature, vol. 478(7370), pages 524-528, October.
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    Cited by:

    1. Ziqi Ren & Wei Tang & Luxin Peng & Peng Zou, 2023. "Profiling stress-triggered RNA condensation with photocatalytic proximity labeling," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

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