Intracristal space proteome mapping using super-resolution proximity labeling with isotope-coded probes
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.
Authors
- Ji Young Mun (ORCID: https://orcid.org/0000-0003-0820-6233)
- Pratyush Kumar Mishra (ORCID: https://orcid.org/0000-0002-7202-5093)
- Jung‐Min Kee (ORCID: https://orcid.org/0000-0001-9985-5436)
- Sanghee Shin (ORCID: https://orcid.org/0000-0002-8786-6995)
- Hyun‐Woo Rhee (ORCID: https://orcid.org/0000-0002-3817-3455)
- Dong-Gi Jang (ORCID: https://orcid.org/0009-0005-0861-188X)
- Ohyeon Kwon
- Jong‐Seo Kim (ORCID: https://orcid.org/0000-0002-8909-8440)
- Song-Yi Lee
- Myeong‐Gyun Kang (ORCID: https://orcid.org/0009-0006-4395-1537)
- Minkyo Jung
Institutions
- Seoul National University (KR)
- Daegu Gyeongbuk Institute of Science and Technology (KR)
- New Generation University College (ET)
- The Seoul Institute (KR)
- Institute for Basic Science (KR)
- Dana-Farber Cancer Institute (US)
- National University College (PR)
- Korea Brain Research Institute (KR)
- Ulsan National Institute of Science and Technology (KR)
Publication Details
- Journal
- Nature Communications
- Published
- 2025-08-20
- DOI
- https://doi.org/10.1038/s41467-025-62756-0
- Citations
- 3
- Primary Topic
- Biotin and Related Studies
- Type
- article
- Field-Weighted Citation Impact
- 3.45
Funders
- Korea Brain Research Institute
- National Research Foundation
- Pohang University of Science and Technology
- Seoul National University
- Korea Health Industry Development Institute
- National Research Foundation of Korea
- Daegu Gyeongbuk Institute of Science and Technology
- Institute for Basic Science
- Ministry of Science and ICT, South Korea
- Samsung Science and Technology Foundation
- Samsung
- Korea National Institute of Health