1. Plant Biology
Download icon

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
Tools and Resources
  • Cited 8
  • Views 9,558
  • Annotations
Cite this article as: eLife 2019;8:e47864 doi: 10.7554/eLife.47864

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.

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

Publication 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)

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.

Metrics

  • 9,558
    Page views
  • 1,660
    Downloads
  • 8
    Citations

Article citation count generated by polling the highest count across the following sources: Crossref, Scopus, PubMed Central.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Download citations (links to download the citations from this article in formats compatible with various reference manager tools)

Open citations (links to open the citations from this article in various online reference manager services)

Further reading

    1. Biochemistry and Chemical Biology
    2. Plant Biology
    Pengxiang Fan et al.
    Research Article Updated

    Plants produce phylogenetically and spatially restricted, as well as structurally diverse specialized metabolites via multistep metabolic pathways. Hallmarks of specialized metabolic evolution include enzymatic promiscuity and recruitment of primary metabolic enzymes and examples of genomic clustering of pathway genes. Solanaceae glandular trichomes produce defensive acylsugars, with sidechains that vary in length across the family. We describe a tomato gene cluster on chromosome 7 involved in medium chain acylsugar accumulation due to trichome specific acyl-CoA synthetase and enoyl-CoA hydratase genes. This cluster co-localizes with a tomato steroidal alkaloid gene cluster and is syntenic to a chromosome 12 region containing another acylsugar pathway gene. We reconstructed the evolutionary events leading to this gene cluster and found that its phylogenetic distribution correlates with medium chain acylsugar accumulation across the Solanaceae. This work reveals insights into the dynamics behind gene cluster evolution and cell-type specific metabolite diversity.

    1. Plant Biology
    Kasey Markel
    Short Report

    Gagliano et al. (Learning by association in plants, 2016) reported associative learning in pea plants. Associative learning has long been considered a behavior performed only by animals, making this claim particularly newsworthy and interesting. In the experiment, plants were trained in Y-shaped mazes for 3 days with fans and lights attached at the top of the maze. Training consisted of wind consistently preceding light from either the same or the opposite arm of the maze. When plant growth forced a decision between the two arms of the maze, fans alone were able to influence growth direction, whereas the growth direction of untrained plants was not affected by fans. However, a replication of their protocol failed to demonstrate the same result, calling for further verification and study before mainstream acceptance of this paradigm-shifting phenomenon. This replication attempt used a larger sample size and fully blinded analysis.