Department of Viticulture & Enology, University of California Davis, Davis, CA, USA.
BMC Genomics. 2013 Mar 12;14:166. doi: 10.1186/1471-2164-14-166.
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).
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.
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.
尽管小麦作为主要粮食作物的重要性以及疾病对其全球产量的负面影响，但人们对小麦抗性反应中涉及的遗传机制和基因相互作用仍知之甚少。水稻基因组的完整序列为小麦的遗传和基因组学研究提供了一条极其有用的平行路线图。最近在水稻中构建的防御反应相互作用网络有可能进一步增强将水稻的进展转化为小麦和其他禾本科植物的能力。本研究的目的是确定水稻和小麦防御反应相互作用网络中蛋白质-蛋白质相互作用的保守程度。作为切入点，我们选择了作为水稻防御反应关键调节剂的蛋白质：RAR1/SGT1/HSP90 蛋白复合物、NPR1、XA21 和 XB12（XA21 相互作用蛋白 12）。
利用现有的小麦序列数据库和系统发育分析，我们鉴定并克隆了这四种水稻蛋白的小麦同源物，包括最近复制的同源物，以及它们已知的直接相互作用物，并使用酵母双杂交（Y2H）测定法测试了 86 个二元蛋白相互作用。使用植物体内双分子荧光互补（BiFC）进一步测试了所有小麦蛋白之间的相互作用。当用水稻相互作用物测试小麦蛋白时，已知的 83%的水稻相互作用得到了证实，而使用小麦蛋白对时，有 76%的相互作用得到了证实。在所鉴定的同源小麦蛋白中，RAR1/SGT1/HSP90、NPR1 和 XB12 节点中的所有相互作用均得到了证实，而在以 XA21 为中心的相互作用网络中，只有 44%的相互作用得到了证实。我们假设这种减少可能与小麦和水稻谱系分化后该基因家族发生的多次复制的不同亚功能化历史有关。
作为水稻防御反应关键调节剂的蛋白质之间相互作用的高保守性表明，现有的水稻相互作用网络可用于预测小麦中的相互作用。对于在两个谱系中经历了不同复制和亚功能化历史的节点，这种预测的可靠性较低。
