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

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Standard

Establishment of proximity-dependent biotinylation approaches in different plant model systems. / Arora, Deepanksha; Abel, Nikolaj B.; Liu, Chen; van Damme, Petra; Yperman, Klaas; Eeckhout, Dominique; Vu, Lam Dai; Wang, Jie; Tornkvist, Anna; Impens, Francis; Korbei, Barbara; van Leene, Jelle; Goossens, Alain; de Jaeger, Geert; Ott, Thomas; Moschou, Panagiotis Nikolaou; van Damme, Daniël.

I: Plant Cell, Bind 32, Nr. 11, 11.2020, s. 3388-3407.

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

Harvard

Arora, D, Abel, NB, Liu, C, van Damme, P, Yperman, K, Eeckhout, D, Vu, LD, Wang, J, Tornkvist, A, Impens, F, Korbei, B, van Leene, J, Goossens, A, de Jaeger, G, Ott, T, Moschou, PN & van Damme, D 2020, 'Establishment of proximity-dependent biotinylation approaches in different plant model systems', Plant Cell, bind 32, nr. 11, s. 3388-3407. https://doi.org/10.1105/TPC.20.00235

APA

Arora, D., Abel, N. B., Liu, C., van Damme, P., Yperman, K., Eeckhout, D., Vu, L. D., Wang, J., Tornkvist, A., Impens, F., Korbei, B., van Leene, J., Goossens, A., de Jaeger, G., Ott, T., Moschou, P. N., & van Damme, D. (2020). Establishment of proximity-dependent biotinylation approaches in different plant model systems. Plant Cell, 32(11), 3388-3407. https://doi.org/10.1105/TPC.20.00235

CBE

Arora D, Abel NB, Liu C, van Damme P, Yperman K, Eeckhout D, Vu LD, Wang J, Tornkvist A, Impens F, Korbei B, van Leene J, Goossens A, de Jaeger G, Ott T, Moschou PN, van Damme D. 2020. Establishment of proximity-dependent biotinylation approaches in different plant model systems. Plant Cell. 32(11):3388-3407. https://doi.org/10.1105/TPC.20.00235

MLA

Vancouver

Arora D, Abel NB, Liu C, van Damme P, Yperman K, Eeckhout D o.a. Establishment of proximity-dependent biotinylation approaches in different plant model systems. Plant Cell. 2020 nov;32(11):3388-3407. https://doi.org/10.1105/TPC.20.00235

Author

Arora, Deepanksha ; Abel, Nikolaj B. ; Liu, Chen ; van Damme, Petra ; Yperman, Klaas ; Eeckhout, Dominique ; Vu, Lam Dai ; Wang, Jie ; Tornkvist, Anna ; Impens, Francis ; Korbei, Barbara ; van Leene, Jelle ; Goossens, Alain ; de Jaeger, Geert ; Ott, Thomas ; Moschou, Panagiotis Nikolaou ; van Damme, Daniël. / Establishment of proximity-dependent biotinylation approaches in different plant model systems. I: Plant Cell. 2020 ; Bind 32, Nr. 11. s. 3388-3407.

Bibtex

@article{6c59ee3bdfe749b4b5723b0736acba70,
title = "Establishment of proximity-dependent biotinylation approaches in different plant model systems",
abstract = "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.",
author = "Deepanksha Arora and Abel, {Nikolaj B.} and Chen Liu and {van Damme}, Petra and Klaas Yperman and Dominique Eeckhout and Vu, {Lam Dai} and Jie Wang and Anna Tornkvist and Francis Impens and Barbara Korbei and {van Leene}, Jelle and Alain Goossens and {de Jaeger}, Geert and Thomas Ott and Moschou, {Panagiotis Nikolaou} and {van Damme}, Dani{\"e}l",
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 Vetenskapsr{\aa}det (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: {\textcopyright} 2020 ASPB. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.",
year = "2020",
month = nov,
doi = "10.1105/TPC.20.00235",
language = "English",
volume = "32",
pages = "3388--3407",
journal = "Plant Cell",
issn = "1040-4651",
publisher = "American Society of Plant Biologists",
number = "11",

}

RIS

TY - JOUR

T1 - Establishment of proximity-dependent biotinylation approaches in different plant model systems

AU - Arora, Deepanksha

AU - Abel, Nikolaj B.

AU - Liu, Chen

AU - van Damme, Petra

AU - Yperman, Klaas

AU - Eeckhout, Dominique

AU - Vu, Lam Dai

AU - Wang, Jie

AU - Tornkvist, Anna

AU - Impens, Francis

AU - Korbei, Barbara

AU - van Leene, Jelle

AU - Goossens, Alain

AU - de Jaeger, Geert

AU - Ott, Thomas

AU - Moschou, Panagiotis Nikolaou

AU - van Damme, Daniël

N1 - 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.

PY - 2020/11

Y1 - 2020/11

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=85095460832&partnerID=8YFLogxK

U2 - 10.1105/TPC.20.00235

DO - 10.1105/TPC.20.00235

M3 - Journal article

C2 - 32843435

AN - SCOPUS:85095460832

VL - 32

SP - 3388

EP - 3407

JO - Plant Cell

JF - Plant Cell

SN - 1040-4651

IS - 11

ER -