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Intracristal space proteome mapping using super-resolution proximity labeling with isotope-coded probes.

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  • 1Department of Chemistry, Seoul National University, Seoul, Korea.

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This study introduces ICAX, a new method for mapping proteins in subcellular spaces. It reveals the mitochondrial intracristal space proteome and its dynamics under stress.

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Area of Science:

  • Cell biology
  • Proteomics
  • Biochemistry

Background:

  • Proximity labeling using engineered ascorbate peroxidase (APEX) is crucial for identifying organelle proteomes.
  • Mapping protein distribution in non-partitioned proximal spaces remains a challenge.

Purpose of the Study:

  • To develop a novel proximity labeling method for quantitative spatial proteome analysis at nanometer resolution.
  • To investigate the proteomic architecture of the mitochondrial intracristal space (ICS).

Main Methods:

  • Introduction of isotope-coded phenol probes for APEX labeling (ICAX).
  • Quantitative analysis of spatial proteomes between two distinct APEX enzyme localizations.
  • Application to the mitochondrial ICS, a non-physically separated compartment.

Main Results:

  • Identification of the spatial proteomic architecture of the mitochondrial ICS.
  • Revealed unexpected dynamics of the mitochondrial spatiome under MICOS complex inhibition and mitochondrial uncoupling.
  • Demonstrated ICAX's capability for nanometer-resolution spatial proteome analysis.

Conclusions:

  • ICAX enables quantitative spatial proteome analysis in challenging subcellular environments.
  • The mitochondrial ICS plays a vital role in mitochondrial quality control during stress.
  • The study provides new insights into mitochondrial spatiome dynamics.