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; Ginny G Farias

doi:10.1038/s41467-024-55052-w

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
, Ginny G Farias

Research output: Contribution to Journal › Article › Academic › peer-review

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.

Original language	English
Article number	10829
Pages (from-to)	1-19
Number of pages	19
Journal	Nature Communications
Volume	15
Issue number	1
Early online date	30 Dec 2024
DOIs	https://doi.org/10.1038/s41467-024-55052-w
Publication status	Published - 2024

Bibliographical note

Funding

We thank Ha Nguyen (Farias lab) for providing RUSH-SYT1 constructs. We thank Mirjam Damen and Cristina Trueba Sanchez (Utrecht University) for their advice on proteomic sample preparation, data acquisition, and analysis. We thank Professor Dr. Judith Klumperman (University Medical Center Utrecht, NL) for providing critical feedback and discussion during the project. This work was supported by the European Research Council (ERC-StG 950617), the Netherlands Organization of Scientific Research (0.16.VIDI.189.019) to G.G.F., and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement (ITN-SAND 860035) to GGF, and the Netherlands Organization of Scientific Research (OCENW.KLEIN.236) to G.G.F. & J.K.

Funders	Funder number
Horizon 2020 Framework Programme
European Research Council	ERC-StG 950617
Nederlandse Organisatie voor Wetenschappelijk Onderzoek	0.16
H2020 Marie Skłodowska-Curie Actions	OCENW.KLEIN.236, ITN-SAND 860035

Keywords

Neurons/metabolism
Proteomics/methods
Animals
Lysosomes/metabolism
Protein Transport
Axons/metabolism
Mice
Lysosomal Membrane Proteins/metabolism
Humans

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title = "Spatiotemporal proteomics reveals the biosynthetic lysosomal membrane protein interactome in neurons",

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.",

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AU - Koppers, Max

AU - Post, Harm

AU - Altelaar, Maarten

AU - Farias, Ginny G

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AB - 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.

KW - Neurons/metabolism

KW - Proteomics/methods

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KW - Protein Transport

KW - Axons/metabolism

KW - Mice

KW - Lysosomal Membrane Proteins/metabolism

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JF - Nature Communications

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ER -

Spatiotemporal proteomics reveals the biosynthetic lysosomal membrane protein interactome in neurons

Abstract

Bibliographical note

Funding

Keywords

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