Proximity labeling of protein complexes and cell type-specific organellar proteomes in Arabidopsis enabled by TurboID

  1. Andrea Mair
  2. Shou-ling Xu
  3. Tess C Branon
  4. Alice Y Ting
  5. Dominique C Bergmann  Is a corresponding author
  1. Stanford University, United States
  2. Carnegie Institution for Science, United States

Abstract

Defining specific protein interactions and spatially or temporally restricted local proteomes improves our understanding of all cellular processes, but obtaining such data is challenging, especially for rare proteins, cell types, or events. Proximity labeling enables discovery of protein neighborhoods defining functional complexes and/or organellar protein compositions. Recent technological improvements, namely two highly active biotin ligase variants (TurboID and miniTurbo), allowed us to address two challenging questions in plants: (1) what are in vivo partners of a low abundant key developmental transcription factor and (2) what is the nuclear proteome of a rare cell type? Proteins identified with FAMA-TurboID include known interactors of this stomatal transcription factor and novel proteins that could facilitate its activator and repressor functions. Directing TurboID to stomatal nuclei enabled purification of cell type- and subcellular compartment-specific proteins. Broad tests of TurboID and miniTurbo in Arabidopsis and N. benthamiana and versatile vectors enable customization by plant researchers.

Data availability

MS data have been depositedProteomeXchange Consortium (http://proteomecentral.proteomexchange.org) via the PRIDE partner repository (Vizcaino et al. 2013) and can be accessed through a reviewer account.Proximity labeling datasest:Dataset identifier: PXD013596FAMA-CFP AP-MS datasets:Dataset identifier: PXD013595

The following data sets were generated

Article and author information

Author details

  1. Andrea Mair

    Department of Biology, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-2492-4318
  2. Shou-ling Xu

    Department of Plant Biology, Carnegie Institution for Science, Stanford, United States
    Competing interests
    No competing interests declared.
  3. Tess C Branon

    Department of Biology, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.
  4. Alice Y Ting

    Department of Biology, Stanford University, Stanford, United States
    Competing interests
    No competing interests declared.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8277-5226
  5. Dominique C Bergmann

    Department of Biology, Stanford University, Stanford, United States
    For correspondence
    bergmann@stanford.edu
    Competing interests
    Dominique C Bergmann, Reviewing editor, eLife.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-0873-3543

Funding

Howard Hughes Medical Institute

  • Dominique C Bergmann

Austrian Science Fund (J4019-B29)

  • Andrea Mair

National Institutes of Health (RO1-CA186568)

  • Alice Y Ting

Carnegie Institution of Washington

  • Shou-ling Xu

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

Reviewing Editor

  1. Frank LH Menke, The Sainsbury Laboratory, United Kingdom

Version history

  1. Received: April 22, 2019
  2. Accepted: September 15, 2019
  3. Accepted Manuscript published: September 19, 2019 (version 1)
  4. Version of Record published: October 14, 2019 (version 2)
  5. Version of Record updated: September 28, 2020 (version 3)

Copyright

© 2019, Mair 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. Andrea Mair
  2. Shou-ling Xu
  3. Tess C Branon
  4. Alice Y Ting
  5. Dominique C Bergmann
(2019)
Proximity labeling of protein complexes and cell type-specific organellar proteomes in Arabidopsis enabled by TurboID
eLife 8:e47864.
https://doi.org/10.7554/eLife.47864

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https://doi.org/10.7554/eLife.47864

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