Upon fungal and bacterial pathogen attack, plants launch pattern-triggered immunity (PTI) by recognizing pathogen-associated molecular patterns (PAMPs) to defend against pathogens. Although PTI-mediated response has been widely studied, a systematic understanding of the reprogrammed cellular processes during PTI by multi-omics analysis is lacking. In this study, we generated metabolome, transcriptome, proteome, ubiquitome and acetylome data to investigate rice (Oryza sativa) PTI responses to two PAMPs, the fungi-derived chitin and the bacteria-derived flg22. Integrative multi-omics analysis uncovered convergence and divergence of rice responses to these PAMPs at multiple regulatory layers. Rice responded to chitin and flg22 in a similar manner at the transcriptome and proteome levels, but distinct at the metabolome level. We found that this was probably due to post-translational regulation including ubiquitination and acetylation, which reshaped gene expression by modulating enzymatic activities, and possibly led to distinct metabolite profiles. We constructed regulatory atlas of metabolic pathways, including the defence-related phenylpropanoid and flavonoid biosynthesis and linoleic acid derivative metabolism. The multi-level regulatory network generated in this study sets the foundation for in-depth mechanistic dissection of PTI in rice and potentially in other related poaceous crop species.

中文翻译：

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水稻模式触发免疫过程中的多层调控景观

在真菌和细菌病原体攻击时，植物通过识别病原体相关分子模式 (PAMP) 来防御病原体，从而启动模式触发免疫 (PTI)。尽管 PTI 介导的反应已被广泛研究，但缺乏通过多组学分析对 PTI 期间重编程细胞过程的系统理解。在这项研究中，我们生成了代谢组、转录组、蛋白质组、泛素组和乙酰组数据来研究水稻（Oryza sativa) PTI 对两种 PAMP 的反应，即真菌衍生的几丁质和细菌衍生的 flg22。综合多组学分析揭示了水稻在多个调控层对这些 PAMP 反应的趋同和分歧。水稻在转录组和蛋白质组水平上对几丁质和 flg22 的反应相似，但在代谢组水平上却不同。我们发现这可能是由于包括泛素化和乙酰化在内的翻译后调控，通过调节酶活性重塑了基因表达，并可能导致不同的代谢物谱。我们构建了代谢途径的调控图谱，包括与防御相关的苯丙素和黄酮类生物合成和亚油酸衍生物代谢。