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An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations

Author

Listed:
  • Xiaonan Liu

    (University of Helsinki
    University of Helsinki)

  • Kari Salokas

    (University of Helsinki
    University of Helsinki)

  • Fitsum Tamene

    (University of Helsinki
    University of Helsinki
    University of Helsinki)

  • Yaming Jiu

    (University of Helsinki
    University of Helsinki)

  • Rigbe G. Weldatsadik

    (University of Helsinki
    University of Helsinki
    University of Helsinki)

  • Tiina Öhman

    (University of Helsinki
    University of Helsinki
    University of Helsinki)

  • Markku Varjosalo

    (University of Helsinki
    University of Helsinki
    University of Helsinki)

Abstract

Protein-protein interactions govern almost all cellular functions. These complex networks of stable and transient associations can be mapped by affinity purification mass spectrometry (AP-MS) and complementary proximity-based labeling methods such as BioID. To exploit the advantages of both strategies, we here design and optimize an integrated approach combining AP-MS and BioID in a single construct, which we term MAC-tag. We systematically apply the MAC-tag approach to 18 subcellular and 3 sub-organelle localization markers, generating a molecular context database, which can be used to define a protein’s molecular location. In addition, we show that combining the AP-MS and BioID results makes it possible to obtain interaction distances within a protein complex. Taken together, our integrated strategy enables the comprehensive mapping of the physical and functional interactions of proteins, defining their molecular context and improving our understanding of the cellular interactome.

Suggested Citation

  • Xiaonan Liu & Kari Salokas & Fitsum Tamene & Yaming Jiu & Rigbe G. Weldatsadik & Tiina Öhman & Markku Varjosalo, 2018. "An AP-MS- and BioID-compatible MAC-tag enables comprehensive mapping of protein interactions and subcellular localizations," Nature Communications, Nature, vol. 9(1), pages 1-16, December.
  • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-03523-2
    DOI: 10.1038/s41467-018-03523-2
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    Cited by:

    1. Helka Göös & Matias Kinnunen & Kari Salokas & Zenglai Tan & Xiaonan Liu & Leena Yadav & Qin Zhang & Gong-Hong Wei & Markku Varjosalo, 2022. "Human transcription factor protein interaction networks," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    2. Hankum Park & Frances V. Hundley & Qing Yu & Katherine A. Overmyer & Dain R. Brademan & Lia Serrano & Joao A. Paulo & Julia C. Paoli & Sharan Swarup & Joshua J. Coon & Steven P. Gygi & J. Wade Harper, 2022. "Spatial snapshots of amyloid precursor protein intramembrane processing via early endosome proteomics," Nature Communications, Nature, vol. 13(1), pages 1-21, December.
    3. Eva Nývltová & Jonathan V. Dietz & Javier Seravalli & Oleh Khalimonchuk & Antoni Barrientos, 2022. "Coordination of metal center biogenesis in human cytochrome c oxidase," Nature Communications, Nature, vol. 13(1), pages 1-17, December.

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