In vivo proteomic mapping through GFP-directed proximity-dependent biotin labelling in zebrafish

  1. Zherui Xiong
  2. Harriet P Lo
  3. Kerrie-Ann McMahon
  4. Nick Martel
  5. Alun Jones
  6. Michelle M Hill
  7. Robert G Parton  Is a corresponding author
  8. Thomas E Hall  Is a corresponding author
  1. Institute for Molecular Bioscience, University of Queensland, Australia
  2. QIMR Berghofer Medical Research Institute, Australia

Abstract

Protein interaction networks are crucial for complex cellular processes. However, the elucidation of protein interactions occurring within highly specialised cells and tissues is challenging. Here we describe the development, and application, of a new method for proximity-dependent biotin labelling in whole zebrafish. Using a conditionally stabilised GFP-binding nanobody to target a biotin ligase to GFP-labelled proteins of interest, we show tissue-specific proteomic profiling using existing GFP-tagged transgenic zebrafish lines. We demonstrate the applicability of this approach, termed BLITZ (Biotin Labelling In Tagged Zebrafish), in diverse cell types such as neurons and vascular endothelial cells. We applied this methodology to identify interactors of caveolar coat protein, cavins, in skeletal muscle. Using this system, we defined specific interaction networks within in vivo muscle cells for the closely related but functionally distinct Cavin4 and Cavin1 proteins.

Data availability

All data generated or analysed during this study are included in the manuscript and supplementary files. Source data files have been provided for Figures 1, 2, 4 and 5

Article and author information

Author details

  1. Zherui Xiong

    Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-5038-5629
  2. Harriet P Lo

    Department of Cell and Developmental Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
    Competing interests
    The authors declare that no competing interests exist.
  3. Kerrie-Ann McMahon

    Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
    Competing interests
    The authors declare that no competing interests exist.
  4. Nick Martel

    Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
    Competing interests
    The authors declare that no competing interests exist.
  5. Alun Jones

    Mass Spectrometry Facility, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
    Competing interests
    The authors declare that no competing interests exist.
  6. Michelle M Hill

    Precision & Systems Biomedicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, Australia
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-1134-0951
  7. Robert G Parton

    Mass Spectrometry Facility, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
    For correspondence
    r.parton@imb.uq.edu.au
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7494-5248
  8. Thomas E Hall

    Cell Biology and Molecular Medicine, Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
    For correspondence
    thomas.hall@imb.uq.edu.au
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7718-7614

Funding

National Health and Medical Research Council (569542)

  • Robert G Parton

National Health and Medical Research Council (1045092)

  • Robert G Parton

National Health and Medical Research Council (APP1044041)

  • Robert G Parton

National Health and Medical Research Council (APP1099251)

  • Robert G Parton
  • Thomas E Hall

Australian Research Council (DP200102559)

  • Robert G Parton
  • Thomas E Hall

Australian Research Council Centre of Excellence in Convergent Bio-Nano Science and Technology (CE140100036)

  • Robert G Parton

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

Ethics

Animal experimentation: This study was approved by Institutional Biosafety Committee, Office of the Gene Technology Regulator, Australian Government Department of Health, and Molecular Biosciences Animal Ethics Committees, the University of Queensland. The ethics approval numbers are IMB/271/19/BREED and IMB/326/17. IBC/OGTR approval number are IBC/1080/IMB/2017.

Reviewing Editor

  1. Lilianna Solnica-Krezel, Washington University School of Medicine, United States

Publication history

  1. Received: November 5, 2020
  2. Accepted: February 15, 2021
  3. Accepted Manuscript published: February 16, 2021 (version 1)
  4. Version of Record published: February 22, 2021 (version 2)

Copyright

© 2021, Xiong 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. Zherui Xiong
  2. Harriet P Lo
  3. Kerrie-Ann McMahon
  4. Nick Martel
  5. Alun Jones
  6. Michelle M Hill
  7. Robert G Parton
  8. Thomas E Hall
(2021)
In vivo proteomic mapping through GFP-directed proximity-dependent biotin labelling in zebrafish
eLife 10:e64631.
https://doi.org/10.7554/eLife.64631

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