RNA-seq for polyphenols treated Pseudomonas syringae. RNA-seq for polyphenols treated Pseudomonas syringae

Bacteria use a variety of mechanisms, such as two‐component regulatory systems (TCSs), to rapidly sense and respond to distinct conditions and signals in their host organisms. For example, a type III secretion system (T3SS) is the key determinant of the virulence of the model plant pathogen Pseudomonas syringae and contains the TCS RhpRS as a key regulator. However, the signal sensed by RhpRS remains unknown. We found that RhpRS directly senses plant-generated polyphenols and responds by switching off P. syringae T3SS via crosstalk with alternative histidine kinases. Through a chemical screen, we identified three natural polyphenols (tannic acid, 1,2,3,4,6-pentagalloylglucose and epigallocatechin gallate) that induced the expression of the rhpRS operon in a RhpS-dependent manner. Overall design: RNA-seq for polyphenols treated Pseudomonas syringae and microbiota analysis for Arabidopsis thaliana Both 'Psph-wt-MM*' and 'PSPH-WT-MM*' are wild-type Pseudomonas savastanoi pv. phaseolicola 1448A strain that grown in minimal media but belong to different sequencing batches. The *MM* and *mock samples are also the same cases, they are all wild-type stain cultured in minimal media. In the submitted RNA-seq data, Psph-wt-MM is the control group for L13-NAR500-MM; PSPH-WT-mock is the control group for PSPH-WT-EGCG-10; PSPH-WT-MM is the wild type sample for rhpS mutant and rhpS/3550/3736/5115

细菌借助多种信号感知与响应机制，例如双组分调控系统（two-component regulatory systems, TCSs），可快速感知并响应宿主内的各类环境条件与信号分子。例如，III型分泌系统（type III secretion system, T3SS）是模式植物病原菌丁香假单胞菌（Pseudomonas syringae）毒力的关键决定因子，其核心调控元件为双组分系统RhpRS。但目前RhpRS所感知的具体信号分子仍未明确。
本研究发现，RhpRS可直接识别植物产生的多酚类物质，并通过与其他组氨酸激酶的交叉调控通路，抑制丁香假单胞菌的III型分泌系统表达。通过化学筛选实验，我们鉴定出鞣酸、1,2,3,4,6-五没食子酰葡萄糖和表没食子儿茶素没食子酸酯这三种天然多酚类物质，它们可通过依赖RhpS的方式诱导rhpRS操纵子的转录表达。
整体实验设计：对经多酚处理的丁香假单胞菌进行RNA测序（RNA-seq），并对拟南芥（Arabidopsis thaliana）开展微生物组分析。
其中，"Psph-wt-MM*"与"PSPH-WT-MM*"均为在基础培养基中培养的野生型晕疫病假单胞菌菜豆致病变种（Pseudomonas savastanoi pv. phaseolicola）1448A菌株，但分属不同的测序批次。所有标注为*MM*和*mock*的样本均为同一类样本，即均为在基础培养基中培养的野生型菌株。
在本次提交的RNA测序数据中，Psph-wt-MM为L13-NAR500-MM的对照组；PSPH-WT-mock为PSPH-WT-EGCG-10的对照组；PSPH-WT-MM则作为rhpS突变体以及rhpS/3550/3736/5115菌株的野生型对照样本。