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

Myeong-Gyun Kang, Sanghee Shin, Dong-Gi Jang, Ohyeon Kwon, Song-Yi Lee, Pratyush Kumar Mishra, Minkyo Jung, Ji Young Mun, Jung-Min Kee (), Jong-Seo Kim () and Hyun-Woo Rhee ()
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Myeong-Gyun Kang: Seoul National University
Sanghee Shin: Seoul National University
Dong-Gi Jang: Seoul National University
Ohyeon Kwon: Ulsan National Institute of Science and Technology (UNIST)
Song-Yi Lee: Seoul National University
Pratyush Kumar Mishra: Seoul National University
Minkyo Jung: Korea Brain Research Institute
Ji Young Mun: Korea Brain Research Institute
Jung-Min Kee: Ulsan National Institute of Science and Technology (UNIST)
Jong-Seo Kim: Seoul National University
Hyun-Woo Rhee: Seoul National University

Nature Communications, 2025, vol. 16, issue 1, 1-15

Abstract: Abstract Proximity labeling with engineered ascorbate peroxidase (APEX) has been widely used to identify proteomes within various membrane-enclosed subcellular organelles. However, constructing protein distribution maps between two non-partitioned proximal spaces remains challenging with the current proximity labeling tools. Here, we introduce a proximity labeling approach using isotope-coded phenol probes for APEX labeling (ICAX) that enables the quantitative analysis of the spatial proteome at nanometer resolution between two distinctly localized APEX enzymes. Using this technique, we identify the spatial proteomic architecture of the mitochondrial intracristal space (ICS), which is not physically separated from the peripheral space. ICAX analysis further reveals unexpected dynamics of the mitochondrial spatiome under mitochondrial contact site and cristae organizing system (MICOS) complex inhibition and mitochondrial uncoupling, respectively. Overall, these findings highlight the importance of ICS for mitochondrial quality control under dynamic stress conditions.

Date: 2025
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DOI: 10.1038/s41467-025-62756-0

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