PAMP-triggered genetic reprogramming involves widespread alternative transcription initiation and an immediate transcription factor wave

Immune responses triggered by pathogen-associated molecular patterns (PAMPs) are key to pathogen defense, but drivers and stabilizers of the growth-to-defense genetic reprogramming remain incompletely understood in plants. Here, we report a time-course study of the establishment of PAMP-triggered immunity (PTI) using cap analysis of gene expression. We show that around 15% of all transcription start sites (TSSs) rapidly induced during PTI define alternative transcription initiation events. From these, we identify clear examples of regulatory TSS change via alternative inclusion of target peptides or domains in encoded proteins, or of upstream open reading frames in mRNA leader sequences. We also find that 60% of PAMP response genes respond earlier than previously thought. In particular, a cluster of rapidly and transiently PAMP-induced genes is enriched in transcription factors (TFs) whose functions, previously associated with biological processes as diverse as abiotic stress adaptation and stem cell activity, appear to converge on growth restriction. Furthermore, examples of known potentiators of PTI, in one case under direct mitogen-activated protein kinase control, support the notion that the rapidly induced TFs could constitute direct links to PTI signaling pathways and drive gene expression changes underlying establishment of the immune state. RNA-seq sequencing of 14-day old whole Arabidopsis thaliana Col-0 wild type seedlings that underwent flg22 peptide treatment at 0 minutes (control), 10, 30, and 60 minutes.

由病原体相关分子模式（pathogen-associated molecular patterns, PAMPs）触发的免疫反应是植物抵御病原体的核心环节，但植物中介导生长向防御遗传重编程的驱动因子与稳定因子仍未得到充分阐释。本研究采用基因表达帽分析（cap analysis of gene expression, CAGE）技术，对PAMP触发的免疫（PAMP-triggered immunity, PTI）的建立过程开展时间序列研究。结果显示，PTI期间快速诱导的全部转录起始位点（transcription start sites, TSSs）中，约15%属于可变转录起始事件。通过此类事件，我们明确鉴定到多例通过在编码蛋白中可变包含目标肽段或结构域，或在mRNA前导序列中可变引入上游开放阅读框（upstream open reading frames, uORFs）以实现调控性TSS改变的案例。此外，我们发现60%的PAMP响应基因的响应时间早于既往认知。尤为关键的是，一个快速且瞬时受PAMP诱导的基因簇显著富集转录因子（transcription factors, TFs）；这类转录因子的功能此前被证实参与非生物胁迫适应、干细胞活性等多种迥异的生物学过程，而其核心功能似乎均指向生长抑制。进一步，已知的PTI增强因子（其中一例直接受丝裂原活化蛋白激酶（mitogen-activated protein kinase, MAPK）调控）的相关案例，支持了快速诱导的转录因子可直接连接PTI信号通路，并驱动免疫状态建立相关的基因表达变化这一观点。本数据集来源于14日龄拟南芥Col-0野生型整株幼苗，分别在0分钟（对照组）、10分钟、30分钟及60分钟用flg22肽段处理后进行RNA-seq测序。