Table 5_The crucial role of mitochondrial/chloroplast-related genes in viral genome replication and host defense: integrative systems biology analysis in plant-virus interaction.xlsx

Plant viruses participate as biotrophic parasites in complex interactions with their hosts, resulting in the regulation of a diverse range of chloroplast/mitochondria-related genes that are essential for mediating immune responses. In this study, integrative systems biology approaches were applied to identify chloroplast/mitochondrial genes during viral infections caused by a wide number of viruses in Arabidopsis thaliana, tobacco (Nicotiana tabacum L.), and rice (Oryza sativa L.). These findings indicated that 1.5% of the DEGs were common between Arabidopsis/tobacco and Arabidopsis/rice, whereas 0.1% of the DEGs were shared among all species. Approximately 90% of common DEGs are uniquely associated with chloroplasts and mitochondria in the host defense against viral infection and replication. The functions of WRKY, NAC, and MYB transcription factors in imparting resistance to viral infections can be established. Promoter analysis revealed that AP2/EREBP, DOF, and C2H2 zinc finger factors included the most frequent binding sites and played a more important role in plant-viral interactions. Comparative analysis revealed several miRNAs with defensive functions including miRNA156, miRNA160, and miRNA169. The PPI network revealed several key hub genes mostly related to chloroplasts/mitochondria, including ZAT6, CML37, CHLI, DREB, F27B13.20, and ASP2 with upregulation, also PLGG1, PSBY, APO2, POR, ERF, and CSP with downregulation. Moreover, novel hub genes with unknown functions, such as AT2G41640 and AT3G57380 have been identified. This study represents the first preliminary systems biology approach to elucidate the roles of chloroplast/mitochondria-related genes in Arabidopsis, tobacco, and rice against viral challenges by introducing valuable candidate genes for enhanced genetic engineering programs to develop virus-resistant crop varieties.

植物病毒作为活体营养型寄生物，与宿主形成复杂的互作关系，进而调控参与免疫应答介导的多种叶绿体/线粒体相关基因。本研究采用整合系统生物学方法，在拟南芥（Arabidopsis thaliana）、普通烟草（Nicotiana tabacum L.）以及水稻（Oryza sativa L.）受多种病毒侵染的过程中，鉴定叶绿体/线粒体相关基因。研究结果显示，拟南芥与烟草、拟南芥与水稻的共有的差异表达基因（Differentially Expressed Genes, DEGs）占比达1.5%，而三类物种共有的差异表达基因占比仅为0.1%。约90%的共有差异表达基因仅与叶绿体和线粒体相关，参与宿主对抗病毒侵染与复制的防御过程。WRKY、NAC与MYB转录因子赋予植物抗病毒侵染能力的功能得以证实。启动子分析结果显示，AP2/EREBP、DOF及C2H2锌指转录因子家族拥有最为频繁的结合位点，在植物-病毒互作过程中发挥更为关键的作用。比较分析还鉴定出多种具有防御功能的微RNA（microRNA, miRNA），涵盖miRNA156、miRNA160与miRNA169。蛋白质相互作用（Protein-Protein Interaction, PPI）网络分析显示，多个与叶绿体/线粒体密切相关的关键枢纽基因被鉴定：其中ZAT6、CML37、CHLI、DREB、F27B13.20及ASP2呈上调表达，而PLGG1、PSBY、APO2、POR、ERF及CSP则呈下调表达。此外，本研究还鉴定出若干功能未知的新型枢纽基因，例如AT2G41640与AT3G57380。本研究首次采用系统生物学方法，阐明了拟南芥、普通烟草与水稻中叶绿体/线粒体相关基因在抵御病毒侵染时的功能，并筛选出一批具有应用潜力的候选基因，可为优化基因工程策略、培育抗病毒作物新品种提供重要参考依据。