Genome-wide expression analysis of PTI and ETI responses in wild type and PRR-deficient Arabidopsis plants

Purpose: The goal of this study is to demonstrate the global expression profile of Arabidopsis wild type and PRR mutant plants in response to PTI- and ETI-eliciting strains of Pseudomonas syringae pv tomato (Pst) bacterium. Methods: Four-week-old Arabidopsis plant leaves were infiltrated with sterile water (Mock) or different Pst strains and harvested at 3h or 6h after infiltration for RNA extraction and deep sequencing by Illumina. Raw data were cleaned up and trimmed and reads were mapped to Arabidopsis genome. Gene expression levels were calculated using the TPM method (Transcripts per Kb of exon model per Million mapped reads). Results and Conclusions: This study showed that Pst DC3000 D36E and D36E(avrRpt2) strains both induced significant gene expression changes (with changes of more than 3000 and 7000 genes respectively) in Col-0 plant, and D36E(avrRpt2) strain induced stronger expression changes globally. Furthermore, many genes are differentially regulated in the PRR mutant plants in response to D36E inoculation compared with wild type plant; however, D36E(avrRpt2) inoculation induced very similar expression patterns in two genotypes, suggesting that ETI can largely restore PTI-associated gene expression in the PRR mutant plant. In addition, we also found that ETI can largely induce the expression levels of many key PTI signaling components. Investigation of genome-wide expression profiles of Arabidopsis wildtype and PRR mutants in response to PTI- and ETI-inducing bacterial strains.

研究目的：本研究旨在解析拟南芥野生型与模式识别受体（Pattern Recognition Receptor，PRR）突变体植株，在响应丁香假单胞菌番茄致病变种（Pseudomonas syringae pv tomato，下文简称Pst）的病原相关分子模式触发的免疫（PAMP-triggered immunity，下文简称PTI）与效应因子触发的免疫（Effector-triggered immunity，下文简称ETI）诱导菌株时的全基因组表达谱。
实验方法：选取生长4周的拟南芥叶片，分别以无菌水（Mock对照组）或不同Pst菌株进行叶片浸润接种，于接种后3小时或6小时收取样本，开展RNA提取并通过Illumina测序平台进行深度转录组测序。对原始测序数据进行质控清理与序列修剪，将测序读段比对至拟南芥参考基因组。采用TPM法（Transcripts per Kb of exon model per Million mapped reads，每百万比对读段中外显子模型每千碱基的转录本数）计算基因表达水平。
结果与结论：本研究显示，Pst DC3000 D36E与D36E(avrRpt2)菌株均可在哥伦比亚型（Col-0）拟南芥植株中引发显著的基因表达变化（分别调控超过3000和7000个差异表达基因），且D36E(avrRpt2)菌株在全基因组层面引发更强的表达改变。进一步分析发现，相较于野生型植株，PRR突变体植株在响应D36E接种时存在大量差异调控基因；但D36E(avrRpt2)接种在两种基因型植株中诱导的表达模式高度相似，表明ETI可在很大程度上恢复PRR突变体植株中PTI相关基因的表达。此外，本研究还发现ETI可显著诱导众多关键PTI信号通路组分的转录水平。本数据集覆盖拟南芥野生型与PRR突变体植株响应PTI和ETI诱导型细菌菌株的全基因组表达谱信息。