Recognition of a pathogen by the plant immune system often triggers a form of regulated cell death traditionally known as the hypersensitive response (HR). This type of cell death occurs precisely at the site of pathogen recognition, and it is restricted to a few cells. Extensive research has shed light on how plant immune receptors are mechanistically activated. However, two central key questions remain largely unresolved: how does cell death zonation take place, and what are the mechanisms that underpin this phenomenon? Consequently, bona fide transcriptional indicators of HR are lacking, which prevents deeper insight into its mechanisms before cell death becomes macroscopic and precludes early or live observation. In this study, to identify the transcriptional indicators of HR we used the paradigmatic Arabidopsis thaliana–Pseudomonas syringae pathosystem and performed a spatiotemporally resolved gene expression analysis that compared infected cells that will undergo HR upon pathogen recognition with bystander cells that will stay alive and activate immunity. Our data revealed unique and time-dependent differences in the repertoire of differentially expressed genes, expression profiles, and biological processes derived from tissue undergoing HR and that of its surroundings. Furthermore, we generated a pipeline based on concatenated pairwise comparisons between time, zone, and treatment that enabled us to define 13 robust transcriptional HR markers. Among these genes, the promoter of an uncharacterized AAA-ATPase was used to obtain a fluorescent reporter transgenic line that displays a strong spatiotemporally resolved signal specifically in cells that will later undergo pathogen-triggered cell death. This valuable set of genes can be used to define cells that are destined to die upon infection with HR-triggering bacteria, opening new avenues for specific and/or high-throughput techniques to study HR processes at a single-cell level.

植物免疫系统对病原体的识别通常会触发一种传统上称为过敏反应 (HR) 的受调节细胞死亡形式。这种类型的细胞死亡恰好发生在病原体识别部位，并且仅限于少数细胞。广泛的研究揭示了植物免疫受体是如何被机械激活的。然而，两个核心关键问题在很大程度上仍未得到解决：细胞死亡分区是如何发生的，以及支持这种现象的机制是什么？因此，缺乏真正的HR 转录指标，这阻碍了在细胞死亡变得宏观之前对其机制的更深入了解，并排除了早期或现场观察。在这项研究中，为了识别 HR 的转录指标，我们使用了范式拟南芥——丁香假单胞菌pathosystem 并进行了时空分辨的基因表达分析，该分析将在病原体识别后经历 HR 的感染细胞与将保持活力并激活免疫的旁观者细胞进行比较。我们的数据揭示了来自经历 HR 的组织及其周围环境的差异表达基因、表达谱和生物学过程的独特和时间依赖性差异。此外，我们基于时间、区域和治疗之间的串联成对比较生成了一个管道，这使我们能够定义 13 个稳健的转录 HR 标记。在这些基因中，未表征的 AAA-ATP 酶的启动子用于获得荧光报告基因转基因系，该系在随后将经历病原体触发的细胞死亡的细胞中显示出强烈的时空分辨信号。这组有价值的基因可用于定义在感染 HR 触发细菌时注定要死亡的细胞，为在单细胞水平上研究 HR 过程的特定和/或高通量技术开辟了新途径。