Spatiotemporal proteomics reveals the biosynthetic lysosomal membrane protein interactome in neurons

Chun Hei Li, Noortje Kersten, Nazmiye Özkan, Dan T. M. Nguyen, Max Koppers, Harm Post, Maarten Altelaar and Ginny G. Farias ()
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Chun Hei Li: Utrecht University
Noortje Kersten: Utrecht University
Nazmiye Özkan: Utrecht University
Dan T. M. Nguyen: Utrecht University
Max Koppers: Utrecht University
Harm Post: Utrecht University
Maarten Altelaar: Utrecht University
Ginny G. Farias: Utrecht University

Nature Communications, 2024, vol. 15, issue 1, 1-19

Abstract: Abstract Lysosomes are membrane-bound organelles critical for maintaining cellular homeostasis. Delivery of biosynthetic lysosomal proteins to lysosomes is crucial to orchestrate proper lysosomal function. However, it remains unknown how the delivery of biosynthetic lysosomal proteins to lysosomes is ensured in neurons, which are highly polarized cells. Here, we developed Protein Origin, Trafficking And Targeting to Organelle Mapping (POTATOMap), by combining trafficking synchronization and proximity-labelling based proteomics, to unravel the trafficking routes and interactome of the biosynthetic lysosomal membrane protein LAMP1 at specified time points. This approach, combined with advanced microscopy, enables us to identify the neuronal domain-specific trafficking machineries of biosynthetic LAMP1. We reveal a role in replenishing axonal lysosomes, in delivery of newly synthesized axonal synaptic proteins, and interactions with RNA granules to facilitate hitchhiking in the axon. POTATOMap offers a robust approach to map out dynamic biosynthetic protein trafficking and interactome from their origin to destination.

Date: 2024
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DOI: 10.1038/s41467-024-55052-w

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