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Transferring an optimized TAP-toolbox for the isolation of protein complexes to a portfolio of rice tissues

Maarten Dedecker, Jelle Van Leene UGent, Nancy De Winne UGent, Dominique Eeckhout UGent, Geert Persiau UGent, Eveline Van De Slijke UGent, Bernard Cannoot UGent, Leen Vercruysse, Lies Dumoulin, Nathalie Wojsznis, et al. (2016) PLANT MOLECULAR BIOLOGY. 91(3). p.341-354
abstract
Proteins are the cell's functional entities. Rather than operating independently, they interact with other proteins. Capturing in vivo protein complexes is therefore crucial to gain understanding of the function of a protein in a cellular context. Affinity purification coupled to mass spectrometry has proven to yield a wealth of information about protein complex constitutions for a broad range of organisms. For Oryza sativa, the technique has been initiated in callus and shoots, but has not been optimized ever since. We translated an optimized tandem affinity purification (TAP) approach from Arabidopsis thaliana toward Oryza sativa, and demonstrate its applicability in a variety of rice tissues. A list of non-specific and false positive interactors is presented, based on re-occurrence over more than 170 independent experiments, to filter bona fide interactors. We demonstrate the sensitivity of our approach by isolating the complexes for the rice ANAPHASE PROMOTING COMPLEX SUBUNIT 10 (APC10) and CYCLIN-DEPENDENT KINASE D (CDKD) proteins from the proliferation zone of the emerging fourth leaf. Next to APC10 and CDKD, we tested several additional baits in the different rice tissues and reproducibly retrieved at least one interactor for 81.4 % of the baits screened for in callus tissue and T1 seedlings. By transferring an optimized TAP tag combined with state-of-the-art mass spectrometry, our TAP protocol enables the discovery of interactors for low abundance proteins in rice and opens the possibility to capture complex dynamics by comparing tissues at different stages of a developing rice organ.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
MONOCULM 1, CYCLE, KINASES, TRANSCRIPTION FACTOR, ARABIDOPSIS-THALIANA, ANAPHASE-PROMOTING COMPLEX, TANDEM AFFINITY PURIFICATION, Tandem affinity purification coupled to mass spectrometry (TAP-MS), Protein-protein interactions, Oryza sativa (rice), CYCLIN-DEPENDENT KINASE D, Anaphase promoting complex, INTERACTOME, REVEALS, SUBUNIT
journal title
PLANT MOLECULAR BIOLOGY
Plant Mol.Biol.
volume
91
issue
3
pages
341 - 354
Web of Science type
Article
Web of Science id
000377025200008
JCR category
PLANT SCIENCES
JCR impact factor
3.356 (2016)
JCR rank
31/211 (2016)
JCR quartile
1 (2016)
ISSN
0167-4412
DOI
10.1007/s11103-016-0471-x
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
7775145
handle
http://hdl.handle.net/1854/LU-7775145
date created
2016-06-27 13:20:49
date last changed
2017-05-04 14:01:22
@article{7775145,
  abstract     = {Proteins are the cell's functional entities. Rather than operating independently, they interact with other proteins. Capturing in vivo protein complexes is therefore crucial to gain understanding of the function of a protein in a cellular context. Affinity purification coupled to mass spectrometry has proven to yield a wealth of information about protein complex constitutions for a broad range of organisms. For Oryza sativa, the technique has been initiated in callus and shoots, but has not been optimized ever since. We translated an optimized tandem affinity purification (TAP) approach from Arabidopsis thaliana toward Oryza sativa, and demonstrate its applicability in a variety of rice tissues. A list of non-specific and false positive interactors is presented, based on re-occurrence over more than 170 independent experiments, to filter bona fide interactors. We demonstrate the sensitivity of our approach by isolating the complexes for the rice ANAPHASE PROMOTING COMPLEX SUBUNIT 10 (APC10) and CYCLIN-DEPENDENT KINASE D (CDKD) proteins from the proliferation zone of the emerging fourth leaf. Next to APC10 and CDKD, we tested several additional baits in the different rice tissues and reproducibly retrieved at least one interactor for 81.4 \% of the baits screened for in callus tissue and T1 seedlings. By transferring an optimized TAP tag combined with state-of-the-art mass spectrometry, our TAP protocol enables the discovery of interactors for low abundance proteins in rice and opens the possibility to capture complex dynamics by comparing tissues at different stages of a developing rice organ.},
  author       = {Dedecker, Maarten and Van Leene, Jelle and De Winne, Nancy and Eeckhout, Dominique and Persiau, Geert and Van De Slijke, Eveline and Cannoot, Bernard and Vercruysse, Leen and Dumoulin, Lies and Wojsznis, Nathalie and Gevaert, Kris and Vandenabeele, Steven and De Jaeger, Geert},
  issn         = {0167-4412},
  journal      = {PLANT MOLECULAR BIOLOGY},
  keyword      = {MONOCULM 1,CYCLE,KINASES,TRANSCRIPTION FACTOR,ARABIDOPSIS-THALIANA,ANAPHASE-PROMOTING COMPLEX,TANDEM AFFINITY PURIFICATION,Tandem affinity purification coupled to mass spectrometry (TAP-MS),Protein-protein interactions,Oryza sativa (rice),CYCLIN-DEPENDENT KINASE D,Anaphase promoting complex,INTERACTOME,REVEALS,SUBUNIT},
  language     = {eng},
  number       = {3},
  pages        = {341--354},
  title        = {Transferring an optimized TAP-toolbox for the isolation of protein complexes to a portfolio of rice tissues},
  url          = {http://dx.doi.org/10.1007/s11103-016-0471-x},
  volume       = {91},
  year         = {2016},
}

Chicago
Dedecker, Maarten, Jelle Van Leene, Nancy De Winne, Dominique Eeckhout, Geert Persiau, Eveline Van De Slijke, Bernard Cannoot, et al. 2016. “Transferring an Optimized TAP-toolbox for the Isolation of Protein Complexes to a Portfolio of Rice Tissues.” Plant Molecular Biology 91 (3): 341–354.
APA
Dedecker, M., Van Leene, J., De Winne, N., Eeckhout, D., Persiau, G., Van De Slijke, E., Cannoot, B., et al. (2016). Transferring an optimized TAP-toolbox for the isolation of protein complexes to a portfolio of rice tissues. PLANT MOLECULAR BIOLOGY, 91(3), 341–354.
Vancouver
1.
Dedecker M, Van Leene J, De Winne N, Eeckhout D, Persiau G, Van De Slijke E, et al. Transferring an optimized TAP-toolbox for the isolation of protein complexes to a portfolio of rice tissues. PLANT MOLECULAR BIOLOGY. 2016;91(3):341–54.
MLA
Dedecker, Maarten, Jelle Van Leene, Nancy De Winne, et al. “Transferring an Optimized TAP-toolbox for the Isolation of Protein Complexes to a Portfolio of Rice Tissues.” PLANT MOLECULAR BIOLOGY 91.3 (2016): 341–354. Print.