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

Authors
  • Dedecker, Maarten1, 2, 3
  • Van Leene, Jelle4, 5
  • De Winne, Nancy4, 5
  • Eeckhout, Dominique4, 5
  • Persiau, Geert4, 5
  • Van De Slijke, Eveline4, 5
  • Cannoot, Bernard4, 5
  • Vercruysse, Leen4, 5
  • Dumoulin, Lies6
  • Wojsznis, Nathalie6
  • Gevaert, Kris7, 8
  • Vandenabeele, Steven6
  • De Jaeger, Geert9, 10
  • 1 Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium. [email protected]
  • 2 Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium. [email protected]
  • 3 CropDesign N.V., Technologiepark 21, 9052, Ghent, Belgium. [email protected]
  • 4 Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium.
  • 5 Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
  • 6 CropDesign N.V., Technologiepark 21, 9052, Ghent, Belgium.
  • 7 Department of Medical Protein Research and Biochemistry, VIB, Albert Baertsoenkaai 3, 9000, Ghent, Belgium.
  • 8 Department of Biochemistry, Ghent University, Albert Baertsoenkaai 3, 9000, Ghent, Belgium.
  • 9 Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium. [email protected]
  • 10 Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium. [email protected]
Type
Published Article
Journal
Plant molecular biology
Publication Date
June 2016
Volume
91
Issue
3
Pages
341–354
Identifiers
DOI: 10.1007/s11103-016-0471-x
PMID: 27003905
Source
Medline
Keywords
License
Unknown

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.

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