Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution

Ana Martinez-Val, Dorte B. Bekker-Jensen, Sophia Steigerwald, Claire Koenig, Ole Østergaard, Adi Mehta, Trung Tran, Krzysztof Sikorski, Estefanía Torres-Vega, Ewa Kwasniewicz, Sólveig Hlín Brynjólfsdóttir, Lisa B. Frankel, Rasmus Kjøbsted, Nicolai Krogh, Alicia Lundby, Simon Bekker-Jensen, Fridtjof Lund-Johansen, Jesper V. Olsen

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Abstract

Dynamic change in subcellular localization of signaling proteins is a general concept that eukaryotic cells evolved for eliciting a coordinated response to stimuli. Mass spectrometry-based proteomics in combination with subcellular fractionation can provide comprehensive maps of spatio-temporal regulation of protein networks in cells, but involves laborious workflows that does not cover the phospho-proteome level. Here we present a high-throughput workflow based on sequential cell fractionation to profile the global proteome and phospho-proteome dynamics across six distinct subcellular fractions. We benchmark the workflow by studying spatio-temporal EGFR phospho-signaling dynamics in vitro in HeLa cells and in vivo in mouse tissues. Finally, we investigate the spatio-temporal stress signaling, revealing cellular relocation of ribosomal proteins in response to hypertonicity and muscle contraction. Proteomics data generated in this study can be explored through https://SpatialProteoDynamics.github.io .

Original languageEnglish
Article number7113
JournalNature Communications
Volume12
Issue number1
Number of pages17
ISSN2041-1723
DOIs
Publication statusPublished - 2021

Bibliographical note

© 2021. The Author(s).

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