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Chemical proteomic analysis of 6-benzylaminopurine molecular partners in wheat grains

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Abstract

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An affinity-based chemical proteomic technique enabled direct identification of BAP-interacting proteins in wheat, including the well-known cytokinin-binder, cytokinin-binding protein 1.

Abstract

In this work, we show the development of a chemical proteomic technique for the identification of proteins binding to natural aromatic cytokinins (CKs). 6-benzylaminopurine (BAP) and documented CK-binder, wheat germ-allocated cytokinin-binding protein 1 (CBP-1), were suggested as an ideal proof-of concept affinity pair. Therefore, wheat grains were chosen as a model plant material. The BAP affinity beads were prepared by the immobilization of synthesized BAP-derived ligand to a commercial, pre-activated resin and used to isolate target proteins. The proteomic analysis of complex plant extracts is often complicated by the presence of highly abundant background proteins; in this case, the omnipresent alpha-amylase inhibitors (AAIs). To cope with this problem, we included SDS–PAGE, in-gel trypsin digestion and fraction pooling prior to shotgun analysis, which brought about an obvious drop in the signals belonging to the obstructing proteins. This was accompanied by a sharp increase in the number of identified BAP targets in comparison to a conventional in-solution digestion approach. To distinguish specific CK-binding proteins from those having a general affinity for nucleotide-like compounds, competitive pull-downs with natural nucleotides and free BAP were included in every affinity experiment. By this approach, we were able to identify a group of BAP-interacting proteins, which were subsequently found to be related to biological processes affected by CKs. Moreover, the selected affinity enrichment strategy was verified by the detection of the aforementioned CK-interacting protein, CBP-1. We propose that the developed method represents a promising tool for appealing research of as yet unknown CK molecular partners in plants.

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Abbreviations

AAI:

Alpha-amylase inhibitor

BAP:

6-Benzylaminopurine

C2-AHA-BAP:

2-(6-Aminohexyl)-6-benzyl-9H-purine-2,6-diamine

CBP-1:

Cytokinin-binding protein 1

CK:

Cytokinin

DMSO:

Dimethylsulfoxide

EDTA:

Ethylenediaminetetraacetic acid

FDR:

False discovery rate

GO:

Gene ontology

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Acknowledgements

We thank David A. Morris for helpful discussions, advices, careful reading and critical remarks on the manuscript. We are grateful to Petr Galuszka and David Kopečný for their help with the TIGR database. This work was supported by the Grant LO1204 from the National Program of Sustainability I by the Ministry of Education, Youth and Sports, Czech Republic.

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Author notes

  1. Jindřich Kania

    Present address: R&D, Production, Polypure AS, Oslo Research Park, Gaustadallen 21, 0349, Oslo, Norway

  2. Radim Simerský and Ivo Chamrád contributed equally to this work.

Authors and Affiliations

  1. Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Šlechtitelů 241/27, 783 71, Olomouc, Czech Republic

    Radim Simerský, Ivo Chamrád, Marek Šebela & René Lenobel

  2. Laboratory of Growth Regulators, Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University, Šlechtitelů 241/27, 783 71, Olomouc, Czech Republic

    Jindřich Kania & Miroslav Strnad

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  1. Radim Simerský
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Correspondence to Ivo Chamrád.

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Communicated by Vincent Thijs.

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Simerský, R., Chamrád, I., Kania, J. et al. Chemical proteomic analysis of 6-benzylaminopurine molecular partners in wheat grains. Plant Cell Rep 36, 1561–1570 (2017). https://doi.org/10.1007/s00299-017-2174-4

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  • DOI: https://doi.org/10.1007/s00299-017-2174-4

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