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

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.