Spatiotemporal-resolved protein networks profiling with photoactivation dependent proximity labeling

Yansheng Zhai, Xiaoyan Huang, Keren Zhang, Yuchen Huang, Yanlong Jiang, Jingwei Cui, Zhe Zhang, Cookson K. C. Chiu, Weiye Zhong and Gang Li ()
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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
Cookson K. C. Chiu: Shenzhen Bay Laboratory
Weiye Zhong: Shenzhen Bay Laboratory
Gang Li: Shenzhen Bay Laboratory

Nature Communications, 2022, vol. 13, issue 1, 1-12

Abstract: 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.

Date: 2022
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DOI: 10.1038/s41467-022-32689-z

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