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OrthoID: profiling dynamic proteomes through time and space using mutually orthogonal chemical tools

Author

Listed:
  • Ara Lee

    (Institute for Basic Science (IBS)
    Pohang University of Science and Technology (POSTECH))

  • Gihyun Sung

    (Institute for Basic Science (IBS)
    Pohang University of Science and Technology (POSTECH))

  • Sanghee Shin

    (Institute for Basic Science (IBS)
    Seoul National University)

  • Song-Yi Lee

    (Seoul National University)

  • Jaehwan Sim

    (Institute for Basic Science (IBS)
    Pohang University of Science and Technology (POSTECH))

  • Truong Thi My Nhung

    (Pohang University of Science and Technology (POSTECH))

  • Tran Diem Nghi

    (Pohang University of Science and Technology (POSTECH))

  • Sang Ki Park

    (Pohang University of Science and Technology (POSTECH))

  • Ponnusamy Pon Sathieshkumar

    (Institute for Basic Science (IBS))

  • Imkyeung Kang

    (Korea Brain Research Institute
    University of Ulsan College of Medicine)

  • Ji Young Mun

    (Korea Brain Research Institute)

  • Jong-Seo Kim

    (Institute for Basic Science (IBS)
    Seoul National University)

  • Hyun-Woo Rhee

    (Seoul National University)

  • Kyeng Min Park

    (Daegu Catholic University School of Medicine)

  • Kimoon Kim

    (Institute for Basic Science (IBS)
    Pohang University of Science and Technology (POSTECH)
    Pohang University of Science and Technology (POSTECH)
    Pohang University of Science and Technology (POSTECH))

Abstract

Identifying proteins at organelle contact sites, such as mitochondria-associated endoplasmic reticulum membranes (MAM), is essential for understanding vital cellular processes, yet challenging due to their dynamic nature. Here we report “OrthoID”, a proteomic method utilizing engineered enzymes, TurboID and APEX2, for the biotinylation (Bt) and adamantylation (Ad) of proteins close to the mitochondria and endoplasmic reticulum (ER), respectively, in conjunction with high-affinity binding pairs, streptavidin-biotin (SA-Bt) and cucurbit[7]uril-adamantane (CB[7]-Ad), for selective orthogonal enrichment of Bt- and Ad-labeled proteins. This approach effectively identifies protein candidates associated with the ER-mitochondria contact, including LRC59, whose roles at the contact site were—to the best of our knowledge—previously unknown, and tracks multiple protein sets undergoing structural and locational changes at MAM during mitophagy. These findings demonstrate that OrthoID could be a powerful proteomics tool for the identification and analysis of spatiotemporal proteins at organelle contact sites and revealing their dynamic behaviors in vital cellular processes.

Suggested Citation

  • Ara Lee & Gihyun Sung & Sanghee Shin & Song-Yi Lee & Jaehwan Sim & Truong Thi My Nhung & Tran Diem Nghi & Sang Ki Park & Ponnusamy Pon Sathieshkumar & Imkyeung Kang & Ji Young Mun & Jong-Seo Kim & Hyu, 2024. "OrthoID: profiling dynamic proteomes through time and space using mutually orthogonal chemical tools," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-46034-z
    DOI: 10.1038/s41467-024-46034-z
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    2. Kyung Lock Kim & Gihyun Sung & Jaehwan Sim & James Murray & Meng Li & Ara Lee & Annadka Shrinidhi & Kyeng Min Park & Kimoon Kim, 2018. "Supramolecular latching system based on ultrastable synthetic binding pairs as versatile tools for protein imaging," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
    3. Junji Suzuki & Kazunori Kanemaru & Kuniaki Ishii & Masamichi Ohkura & Yohei Okubo & Masamitsu Iino, 2014. "Imaging intraorganellar Ca2+ at subcellular resolution using CEPIA," Nature Communications, Nature, vol. 5(1), pages 1-13, September.
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