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Open Access Research article

Comparative analysis of protein-protein interactions in the defense response of rice and wheat

Dario Cantu1, Baoju Yang23, Randy Ruan4, Kun Li5, Virginia Menzo26, Daolin Fu5, Mawsheng Chern4, Pamela C Ronald47* and Jorge Dubcovsky289*

Author Affiliations

1 Department of Viticulture & Enology, University of California Davis, Davis, CA, USA

2 Department of Plant Sciences, University of California Davis, Davis, CA, USA

3 Northwest A&F University, Yangling, Shaanxi, China

4 Department of Plant Pathology, University of California Davis, Davis, CA, USA

5 College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, China

6 CRA, Experimental Institute for Cereal Research of Foggia, Foggia, Italy

7 Genome Center, University of California Davis, Davis, CA, USA

8 Howard Hughes Medical Institute, Chevy Chase, MD, USA

9 Gordon & Betty Moore Foundation, Palo Alto, CA, USA

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BMC Genomics 2013, 14:166  doi:10.1186/1471-2164-14-166

Published: 12 March 2013

Abstract

Background

Despite the importance of wheat as a major staple crop and the negative impact of diseases on its production worldwide, the genetic mechanisms and gene interactions involved in the resistance response in wheat are still poorly understood. The complete sequence of the rice genome has provided an extremely useful parallel road map for genetic and genomics studies in wheat. The recent construction of a defense response interactome in rice has the potential to further enhance the translation of advances in rice to wheat and other grasses. The objective of this study was to determine the degree of conservation in the protein-protein interactions in the rice and wheat defense response interactomes. As entry points we selected proteins that serve as key regulators of the rice defense response: the RAR1/SGT1/HSP90 protein complex, NPR1, XA21, and XB12 (XA21 interacting protein 12).

Results

Using available wheat sequence databases and phylogenetic analyses we identified and cloned the wheat orthologs of these four rice proteins, including recently duplicated paralogs, and their known direct interactors and tested 86 binary protein interactions using yeast-two-hybrid (Y2H) assays. All interactions between wheat proteins were further tested using in planta bimolecular fluorescence complementation (BiFC). Eighty three percent of the known rice interactions were confirmed when wheat proteins were tested with rice interactors and 76% were confirmed using wheat protein pairs. All interactions in the RAR1/SGT1/ HSP90, NPR1 and XB12 nodes were confirmed for the identified orthologous wheat proteins, whereas only forty four percent of the interactions were confirmed in the interactome node centered on XA21. We hypothesize that this reduction may be associated with a different sub-functionalization history of the multiple duplications that occurred in this gene family after the divergence of the wheat and rice lineages.

Conclusions

The observed high conservation of interactions between proteins that serve as key regulators of the rice defense response suggests that the existing rice interactome can be used to predict interactions in wheat. Such predictions are less reliable for nodes that have undergone a different history of duplications and sub-functionalization in the two lineages.