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

Abstract
Data availability
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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

1. Mair A
2. Bergmann DC
(2019) Proximity labeling datasest
ProteomeXchange Consortium, PXD013596.

http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD013596
1. Mair A
2. Bergmann DC
(2019) FAMA-CFP AP-MS datasets
ProteomeXchange Consortium, PXD013595.

http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD013595

Article and author information

Author details

Andrea Mair

Department of Biology, Stanford University, Stanford, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-2492-4318
Shou-ling Xu

Department of Plant Biology, Carnegie Institution for Science, Stanford, United States

Competing interests
No competing interests declared.
Tess C Branon

Department of Biology, Stanford University, Stanford, United States

Competing interests
No competing interests declared.
Alice Y Ting

Department of Biology, Stanford University, Stanford, United States

Competing interests
No competing interests declared.

"This ORCID iD identifies the author of this article:" 0000-0002-8277-5226
Dominique C Bergmann

Department of Biology, Stanford University, Stanford, United States

For correspondence
bergmann@stanford.edu

Competing interests
Dominique C Bergmann, Reviewing editor, eLife.

"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.

Copyright

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.