Kataria Raghav, Kaundal Rakesh
Department of Plants, Soils, and Climate, College of Agriculture and Applied Sciences, Utah State University, Logan, UT, United States.
Bioinformatics Facility, Center for Integrated BioSystems, Utah State University, Logan, UT, United States.
Front Plant Sci. 2022 Jun 21;13:895480. doi: 10.3389/fpls.2022.895480. eCollection 2022.
(wheat), a major staple food grain, is affected by various biotic stresses. Among these, fungal diseases cause about 15-20% of yield loss, worldwide. In this study, we performed a comparative analysis of protein-protein interactions between two races ( 21-0 and Ug99) that cause stem (black) rust in wheat. The available molecular techniques to study the host-pathogen interaction mechanisms are expensive and labor-intensive. We implemented two computational approaches (interolog and domain-based) for the prediction of PPIs and performed various functional analysis to determine the significant differences between the two pathogen races. The analysis revealed that - 21-0 and - Ug99 interactomes consisted of ∼90M and ∼56M putative PPIs, respectively. In the predicted PPIs, we identified 115 21-0 and 34 Ug99 potential effectors that were highly involved in pathogen virulence and development. Functional enrichment analysis of the host proteins revealed significant GO terms and KEGG pathways such as -methyltransferase activity (GO:0008171), regulation of signal transduction (GO:0009966), lignin metabolic process (GO:0009808), plastid envelope (GO:0009526), plant-pathogen interaction pathway (ko04626), and MAPK pathway (ko04016) that are actively involved in plant defense and immune signaling against the biotic stresses. Subcellular localization analysis anticipated the host plastid as a primary target for pathogen attack. The highly connected host hubs in the protein interaction network belonged to protein kinase domain including Ser/Thr protein kinase, MAPK, and cyclin-dependent kinase. We also identified 5,577 transcription factors in the interactions, associated with plant defense during biotic stress conditions. Additionally, novel host targets that are resistant to stem rust disease were also identified. The present study elucidates the functional differences between 21-0 and Ug99, thus providing the researchers with strain-specific information for further experimental validation of the interactions, and the development of durable, disease-resistant crop lines.
小麦作为一种主要的主食谷物，受到各种生物胁迫的影响。其中，真菌病害在全球范围内导致约15%-20%的产量损失。在本研究中，我们对导致小麦茎（黑）锈病的两个小种（21-0和Ug99）之间的蛋白质-蛋白质相互作用进行了比较分析。用于研究宿主-病原体相互作用机制的现有分子技术昂贵且 labor-intensive。我们实施了两种计算方法（同源互作和基于结构域）来预测蛋白质-蛋白质相互作用，并进行了各种功能分析，以确定这两个病原体小种之间的显著差异。分析表明，21-0和Ug99的相互作用组分别由约90M和约56M个推定的蛋白质-蛋白质相互作用组成。在预测的蛋白质-蛋白质相互作用中，我们鉴定出115个21-0和34个Ug99潜在效应子，它们高度参与病原体的毒力和发育。宿主蛋白质的功能富集分析揭示了显著的基因本体（GO）术语和京都基因与基因组百科全书（KEGG）途径，如甲基转移酶活性（GO:0008171）、信号转导调控（GO:0009966）、木质素代谢过程（GO:0009808）、质体包膜（GO:0009526）、植物-病原体相互作用途径（ko04626）和丝裂原活化蛋白激酶（MAPK）途径（ko04016），这些途径积极参与植物对生物胁迫的防御和免疫信号传导。亚细胞定位分析预测宿主质体是病原体攻击的主要目标。蛋白质相互作用网络中高度连接的宿主中心属于蛋白质激酶结构域，包括丝氨酸/苏氨酸蛋白激酶、MAPK和细胞周期蛋白依赖性激酶。我们还在相互作用中鉴定出5577个转录因子，它们与生物胁迫条件下的植物防御相关。此外，还鉴定出了对茎锈病具有抗性的新的宿主靶点。本研究阐明了21-0和Ug99之间的功能差异，从而为研究人员提供了菌株特异性信息，以便对相互作用进行进一步的实验验证，并开发持久的抗病作物品系。
