Plant Molecular Biology

, Volume 91, Issue 3, pp 341–354 | Cite as

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

  • Maarten DedeckerEmail author
  • Jelle Van Leene
  • Nancy De Winne
  • Dominique Eeckhout
  • Geert Persiau
  • Eveline Van De Slijke
  • Bernard Cannoot
  • Leen Vercruysse
  • Lies Dumoulin
  • Nathalie Wojsznis
  • Kris Gevaert
  • Steven Vandenabeele
  • Geert De JaegerEmail author


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.


Anaphase promoting complex CYCLIN-DEPENDENT KINASE D Oryza sativa (rice) Protein–protein interactions Tandem affinity purification coupled to mass spectrometry (TAP–MS) 



Affinity purification coupled to mass spectrometry


Tandem affinity purification






Protein–protein interaction


Yeast two-hybrid


Open reading frame


Protein complementation analysis






CDK-activating kinase






General transcription factor II H






Streptavidin-binding peptide


Mass spectrometry


Tobacco etch virus


Immunoglobulin G


Rice annotation project


Michigan State University


Calmodulin-binding peptide


Ethylene glycol tetra-acetic acid



Maarten Dedecker is supported by a predoctoral fellowship from the Agency for Innovation by Science and Technology and CropDesign N.V. (‘Baekeland’ funding, IWT 100222). The authors thank Annick Bleys for help in preparing the manuscript.

Author contributions

M.D., S.V. and G.D.J. designed the research. N.D.W., G.P., E.V.D.S, B.C., L.V., L.D. and N.W. performed experiments. M.D., D.E. and G.D.J. analyzed the data. K.G. provided protocols for LC–MS/MS analysis. J.V.L. and K.G. commented on the manuscript. M.D. and G.D.J. wrote the manuscript.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

11103_2016_471_MOESM1_ESM.docx (1.9 mb)
Supplementary material 1 (DOCX 1966 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2016

Authors and Affiliations

  • Maarten Dedecker
    • 1
    • 2
    • 3
    Email author
  • Jelle Van Leene
    • 1
    • 2
  • Nancy De Winne
    • 1
    • 2
  • Dominique Eeckhout
    • 1
    • 2
  • Geert Persiau
    • 1
    • 2
  • Eveline Van De Slijke
    • 1
    • 2
  • Bernard Cannoot
    • 1
    • 2
  • Leen Vercruysse
    • 1
    • 2
  • Lies Dumoulin
    • 3
  • Nathalie Wojsznis
    • 3
  • Kris Gevaert
    • 4
    • 5
  • Steven Vandenabeele
    • 3
  • Geert De Jaeger
    • 1
    • 2
    Email author
  1. 1.Department of Plant Systems BiologyVIBGhentBelgium
  2. 2.Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
  3. 3.CropDesign N.V.GhentBelgium
  4. 4.Department of Medical Protein Research and BiochemistryVIBGhentBelgium
  5. 5.Department of BiochemistryGhent UniversityGhentBelgium

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