Photoproximity labeling of endogenous receptors in the live mouse brain in minutes

Takato, Mikiko; Sakamoto, Seiji; Nonaka, Hiroshi; Tanimura Valor, Fátima Yuri; Tamura, Tomonori; Hamachi, Itaru

doi:10.1038/s41589-024-01692-4

Nat Chem Biol

2024

DOI: 10.1038/s41589-024-01692-4

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Photoproximity labeling of endogenous receptors in the live mouse brain in minutes

Mikiko Takato,

Seiji Sakamoto,

Hiroshi Nonaka

et al.

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Cited by 2 publications

References 64 publications

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Lipid- and protein-directed photosensitizer proximity labeling captures the cholesterol interactome

Becker,

Biletch,

Kennelly

et al. 2024

Preprint

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The physical properties of cellular membranes, including fluidity and function, are influenced by protein and lipid interactions. In situ labeling chemistries, most notably proximity-labeling interactomics are well suited to characterize these dynamic and often fleeting interactions. Established methods require distinct chemistries for proteins and lipids, which limits the scope of such studies. Here we establish a singlet-oxygen-based photocatalytic proximity labeling platform (POCA) that reports intracellular interactomes for both proteins and lipids with tight spatiotemporal resolution using cell-penetrant photosensitizer reagents. Using both physiologically relevant lipoprotein-complexed probe delivery and genetic manipulation of cellular cholesterol handling machinery, cholesterol-directed POCA captured established and unprecedented cholesterol binding proteins, including protein complexes sensitive to intracellular cholesterol levels and proteins uniquely captured by lipoprotein uptake. Protein-directed POCA accurately mapped known intracellular membrane complexes, defined sterol-dependent changes to the non-vesicular cholesterol transport protein interactome, and captured state-dependent changes in the interactome of the cholesterol transport protein Aster-B. More broadly, we find that POCA is a versatile interactomics platform that is straightforward to implement, using the readily available HaloTag system, and fulfills unmet needs in intracellular singlet oxygen-based proximity labeling proteomics. Thus, we expect widespread utility for POCA across a range of interactome applications, spanning imaging to proteomics.

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Lipid- and protein-directed photosensitizer proximity labeling captures the cholesterol interactome

Becker,

Biletch,

Kennelly

et al. 2024

Preprint

View full text Add to dashboard Cite

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Silicon-rhodamine-enabled Identification (SeeID) for Near-Infrared Light Controlled Proximity Labeling In Vitro and In Vivo

Wang,

Guo,

Yan

et al. 2024

Preprint

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Advancement in fluorescence imaging techniques enables the study of protein dynamics and localization with unprecedented spatiotemporal resolution. However, current imaging tools are unable to elucidate dynamic protein interactomes underlying imaging observations. In contrast, proteomics tools such as proximity labeling enable the analysis of protein interactomes at a single time point but lack information about protein dynamics. We herein developed Silicon-rhodamine-enabled Identification (SeeID) for near-infrared light controlled proximity labeling that could bridge the gap between imaging and proximity labeling. SeeID was benchmarked through characterization of various organelle-specific proteomes and the KRAS protein interactome. The fluorogenic nature of SiR allows for intracellular proximity labeling with high subcellular specificity. Leveraging SiR as both a fluorophore and a photocatalyst, we developed a protocol that allows the study of dynamic protein interactomes of Parkin during mitophagy. We discovered the association of the proteasome complex with Parkin at early time points, indicating the involvement of the ubiquitin-proteasome system for protein degradation in the early phase of mitophagy. In addition, by virtue of the deep tissue penetration of near-infrared light, we achieved spatiotemporally controlled proximity labeling in vivo across the mouse brain cortex with a labeling depth of ~2 mm using an off-the-shelf 660 nm LED light set-up.

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Photoproximity labeling of endogenous receptors in the live mouse brain in minutes

Cited by 2 publications

References 64 publications

Lipid- and protein-directed photosensitizer proximity labeling captures the cholesterol interactome

Lipid- and protein-directed photosensitizer proximity labeling captures the cholesterol interactome

Silicon-rhodamine-enabled Identification (SeeID) for Near-Infrared Light Controlled Proximity Labeling In Vitro and In Vivo

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