Dual RNA-seq of Xanthomonas oryzae pv. oryzicola infecting rice reveals novel insights into bacterial-plant interaction

The Gram-negative bacterium Xanthomonas oryzae pv. oryzicola (Xoc) is the causal agent of rice bacterial leaf streak (BLS), one of the most destructive diseases of rice (Oryza sativa L.) that is the important staple crop. Xoc can invade host leaves via stomata and wounds and its type three secretion system (T3SS) is pivotal to its pathogenic lifestyle. In this study, using a novel dual RNA-seq approach, we examined transcriptomes of rice and Xoc in samples inoculated with wild type Xoc GX01 and its T3SS defective strain (T3SD), to investigate the global transcriptional changes in both organisms. Compared with T3SD strain, rice inoculated with wild type Xoc GX01 resulted in significant expression changes of a series of plant defence related genes, including ones altered in plant signalling pathway, and downregulated in phenylalanine metabolism, flavonoid and momilactone biosynthesis, suggesting repression of plant defence response and reduction in both callose deposition and phytoalexin accumulation. Also, some known transcription activator-like effector (TALE) targets were induced by Xoc GX01, e.g. OsSultr3;6 which contributes to rice susceptibility. Some cell elongation related genes, including several expansin genes, were induced by GX01 too, suggesting that Xoc may exploit this pathway to weaken cell wall strength, beneficial for bacterial infection. On the other hand, compared with wild type, the T3SD strain transcriptome in planta was characterized by downregulation of ATP, protein and polysaccharide synthesis, and upregulation of antioxidation and detoxification related genes, revealing that T3SD strain faced serious starvation and oxidation stresses in planta without a functional T3SS. In addition, comparative global transcript profiles of Xoc in planta and in medium revealed an upregulation of virulence factor synthesis and secretion in planta in favour of bacterial infection. Collectively, this study provides a comprehensive representation of cross talk between the host and bacterial pathogen, revealing insights into the Xoc-rice pathogenic dynamic and reveals novel strategies exploited by this important pathogen to cause disease.

革兰氏阴性杆菌稻黄单胞菌稻生致病变种（Xanthomonas oryzae pv. oryzicola，以下简称Xoc）是水稻细菌性条斑病（BLS）的病原菌，而水稻（Oryza sativa L.）作为重要主粮作物，其最具破坏性的病害之一便包含该病害。Xoc可通过气孔与伤口侵染寄主叶片，其三型分泌系统（type three secretion system，T3SS）是其致病生活方式的关键因子。本研究采用新型双RNA测序（dual RNA-seq）技术，对接种野生型Xoc GX01及其T3SS缺陷菌株（T3SD）的样本开展转录组分析，以解析寄主与病原菌双方的全局转录组变化。与T3SD菌株相比，接种野生型Xoc GX01的水稻样本中，一系列植物防御相关基因出现显著表达变化，包括植物信号通路相关基因的表达改变，以及苯丙氨酸代谢、类黄酮与稻叶内酯（momilactone）生物合成相关基因的下调，这提示Xoc可抑制植物防御响应，并降低胼胝质沉积与植保素积累。此外，Xoc GX01还可诱导部分已报道的转录激活因子样效应蛋白（transcription activator-like effector，以下简称TALE）靶标基因的表达，例如OsSultr3;6，该基因可增强水稻的感病性。GX01同时还诱导了一批细胞伸长相关基因（包括多个膨胀素基因）的表达，这表明Xoc可能通过调控该通路削弱寄主细胞壁强度，以利于自身侵染。另一方面，与野生型菌株相比，植物体内的T3SD菌株转录组呈现出ATP、蛋白质与多糖合成相关基因的下调，以及抗氧化与解毒相关基因的上调特征，这说明缺失功能型T3SS的T3SD菌株在植物体内会面临严重的饥饿与氧化胁迫。此外，对比植物体内与培养基中Xoc的全局转录谱发现，植物体内的Xoc会上调毒力因子的合成与分泌通路，以适配侵染过程。综上，本研究全面解析了寄主与病原菌之间的交叉互作，为解析Xoc与水稻的致病动态提供了全新视角，并揭示了该重要病原菌致病所依赖的新型策略。