Aarhus University Seal / Aarhus Universitets segl

Establishment of proximity-dependent biotinylation approaches in different plant model systems

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

DOI

  • Deepanksha Arora, Ghent University, VIB Center for Plant Systems Biology
  • ,
  • Nikolaj B. Abel
  • Chen Liu, Swedish University of Agricultural Sciences
  • ,
  • Petra van Damme, Ghent University, VIB Center for Plant Systems Biology
  • ,
  • Klaas Yperman, Ghent University, VIB Center for Plant Systems Biology
  • ,
  • Dominique Eeckhout, Ghent University, VIB Center for Plant Systems Biology
  • ,
  • Lam Dai Vu, Ghent University, VIB Center for Plant Systems Biology
  • ,
  • Jie Wang, Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB Center for Plant Systems Biology
  • ,
  • Anna Tornkvist, Swedish University of Agricultural Sciences
  • ,
  • Francis Impens, Ghent University, VIB Center for Medical Biotechnology, VIB Proteomics Core
  • ,
  • Barbara Korbei, University of Natural Resources and Life Sciences, Vienna
  • ,
  • Jelle van Leene, Ghent University, VIB Center for Plant Systems Biology
  • ,
  • Alain Goossens, Ghent University, VIB Center for Plant Systems Biology
  • ,
  • Geert de Jaeger, Ghent University, VIB Center for Plant Systems Biology
  • ,
  • Thomas Ott, University of Freiburg
  • ,
  • Panagiotis Nikolaou Moschou, Swedish University of Agricultural Sciences, University of Crete, Foundation for Research and Technology-Hellas
  • ,
  • Daniël van Damme, Ghent University, VIB Center for Plant Systems Biology

Proximity labeling is a powerful approach for detecting protein-protein interactions. Most proximity labeling techniques use a promiscuous biotin ligase or a peroxidase fused to a protein of interest, enabling the covalent biotin labeling of proteins and subsequent capture and identification of interacting and neighboring proteins without the need for the protein complex to remain intact. To date, only a few studies have reported on the use of proximity labeling in plants. Here, we present the results of a systematic study applying a variety of biotin-based proximity labeling approaches in several plant systems using various conditions and bait proteins. We show that TurboID is the most promiscuous variant in several plant model systems and establish protocols that combine mass spectrometry-based analysis with harsh extraction and washing conditions. We demonstrate the applicability of TurboID in capturing membrane-associated protein interactomes using Lotus japonicus symbiotically active receptor kinases as a test case. We further benchmark the efficiency of various promiscuous biotin ligases in comparison with one-step affinity purification approaches. We identified both known and novel interactors of the endocytic TPLATE complex. We furthermore present a straightforward strategy to identify both nonbiotinylated and biotinylated peptides in a single experimental setup. Finally, we provide initial evidence that our approach has the potential to suggest structural information of protein complexes.

OriginalsprogEngelsk
TidsskriftPlant Cell
Vol/bind32
Nummer11
Sider (fra-til)3388-3407
Antal sider20
ISSN1040-4651
DOI
StatusUdgivet - nov. 2020
Eksternt udgivetJa

Bibliografisk note

Funding Information:
We thank Lore Gryffroy (VIB/Ghent University) for providing us with control hairy root cultures. This work was supported by the European Research Council (T-Rex project 682436 to D.V.D. and PROPHECY project 803972 to P.V.D.), the National Science Foundation Flanders (grant G009415N to D.V.D. and G.D.J.), the Deutsche Forschungsgemeinschaft in frame of the Collaborative Research Center 924 (Sonderforschungsbereich 924, grant INST 95/1126-2, Project B4 to T.O. and N.B.A.), the Vetenskapsrådet (VR; grant 21679000 to P.N.M.), the Swedish Research Council Formas (grant 22924-000 to P.N.M.), the Carl Trygger Foundation for Scientific Research (grants 15:336 and 17:317 to P.M.), and from the Foundation of Research and Technology Hellas (IMBB-FORTH; to P.N.M.).

Publisher Copyright:
© 2020 ASPB.

Copyright:
Copyright 2020 Elsevier B.V., All rights reserved.

Se relationer på Aarhus Universitet Citationsformater

ID: 211675479