Spatial-proteomics reveals phospho-signaling dynamics at subcellular resolution

Nat Commun. 2021 Dec 7;12(1):7113. doi: 10.1038/s41467-021-27398-y.

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 .

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Biological Phenomena
  • Cell Fractionation
  • HeLa Cells
  • Humans
  • Male
  • Mass Spectrometry
  • Mice
  • Mice, Inbred C57BL
  • Osmotic Pressure
  • Phosphorylation
  • Proteome / metabolism*
  • Proteomics*
  • Signal Transduction*
  • Subcellular Fractions / metabolism
  • Workflow

Substances

  • Proteome