1. Biochemistry and Chemical Biology
  2. Cell Biology

AirID, a novel proximity biotinylation enzyme, for analysis of protein-protein interactions

  1. Kohki Kido
  2. Satoshi Yamanaka
  3. Shogo Nakano
  4. Kou Motani
  5. Souta Shinohara
  6. Akira Nozawa
  7. Hidetaka Kosako
  8. Sohei Ito
  9. Tatsuya Sawasaki  Is a corresponding author
  1. Ehime University, Japan
  2. University of Shizuoka, Japan
  3. Tokushima University, Japan
https://doi.org/10.7554/eLife.54983
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Cite this article
  1. Kohki Kido
  2. Satoshi Yamanaka
  3. Shogo Nakano
  4. Kou Motani
  5. Souta Shinohara
  6. Akira Nozawa
  7. Hidetaka Kosako
  8. Sohei Ito
  9. Tatsuya Sawasaki
(2020)
AirID, a novel proximity biotinylation enzyme, for analysis of protein-protein interactions
eLife 9:e54983.
https://doi.org/10.7554/eLife.54983
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Abstract

Proximity biotinylation based on Escherichia coli BirA enzymes like BioID (BirA*) and TurboID is a key technology for identifying proteins interacting with a target protein in a cell or organism. However, there have been some improvements in the enzymes for that purpose. Here, we demonstrate a novel BirA enzyme, AirID (ancestral BirA for proximity-dependent biotin identification), which was designed de novo using an ancestral enzyme reconstruction algorithm and metagenome data. AirID-fusion proteins like AirID-p53 or AirID-IκBα indicated biotinylation of MDM2 or RelA, respectively, in vitro and in cells, respectively. AirID-CRBN showed the pomalidomide-dependent biotinylation of IKZF1 and SALL4 in vitro. AirID-IκBα biotinylated the endogenous CUL4 and RBX1 in the CRL4CRBN complex based on the streptavidin pull-down assay. LC-MS/MS analysis of cells stably expressing AirID-IκBα showed top-level biotinylation of RelA proteins. These results indicate that AirID is a novel enzyme for analysing protein–protein interactions.

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All data generated or analysed during this study are included in the manuscript and supporting files. Source data files have been provided for Figures 3, 4, and 6.

Article and author information

Author details

  1. Kohki Kido

    Proteo-Science Center, Ehime University, Matsuyama, Japan
    Competing interests
    The authors declare that no competing interests exist.

  2. Satoshi Yamanaka

    Proteo-Science Center, Ehime University, Matsuyama, Japan
    Competing interests
    The authors declare that no competing interests exist.

  3. Shogo Nakano

    Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
    Competing interests
    The authors declare that no competing interests exist.

  4. Kou Motani

    Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, Japan
    Competing interests
    The authors declare that no competing interests exist.

  5. Souta Shinohara

    Proteo-Science Center, Ehime University, Matsuyama, Japan
    Competing interests
    The authors declare that no competing interests exist.

  6. Akira Nozawa

    Proteo-Science Center, Ehime University, Matsuyama, Japan
    Competing interests
    The authors declare that no competing interests exist.

  7. Hidetaka Kosako

    Fujii Memorial Institute of Medical Sciences, Tokushima University, Tokushima, Japan
    Competing interests
    The authors declare that no competing interests exist.

  8. Sohei Ito

    Graduate School of Integrated Pharmaceutical and Nutritional Sciences, University of Shizuoka, Shizuoka, Japan
    Competing interests
    The authors declare that no competing interests exist.

  9. Tatsuya Sawasaki

    Proteo-Science Center, Ehime University, Matsuyama, Japan
    For correspondence
    sawasaki@ehime-u.ac.jp
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7952-0556

Funding

Japan Agency for Medical Research and Development (JP19am0101077)

  • Tatsuya Sawasaki

Japan Society for the Promotion of Science (JP16H06579)

  • Tatsuya Sawasaki

Japan Society for the Promotion of Science (JP16H04729)

  • Tatsuya Sawasaki

Japan Society for the Promotion of Science (JP19H03218)

  • Tatsuya Sawasaki

Japan Society for the Promotion of Science (18KK0229)

  • Hidetaka Kosako

Japan Society for the Promotion of Science (19H04966)

  • Hidetaka Kosako

Takeda Science Foundation

  • Tatsuya Sawasaki

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Volker Dötsch, Goethe University, Germany

Publication history

  1. Received: January 8, 2020
  2. Accepted: May 7, 2020
  3. Accepted Manuscript published: May 11, 2020 (version 1)
  4. Version of Record published: June 18, 2020 (version 2)

Copyright

© 2020, Kido et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Kohki Kido
  2. Satoshi Yamanaka
  3. Shogo Nakano
  4. Kou Motani
  5. Souta Shinohara
  6. Akira Nozawa
  7. Hidetaka Kosako
  8. Sohei Ito
  9. Tatsuya Sawasaki
(2020)
AirID, a novel proximity biotinylation enzyme, for analysis of protein-protein interactions
eLife 9:e54983.
https://doi.org/10.7554/eLife.54983

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