Understanding the gene regulation of plant pathogens is crucial for pest control and thus global food security. An integrated understanding of bacterial gene regulation in the host is dependent on multi-omic datasets, but these are largely lacking. Here, we simultaneously characterized the transcriptome and proteome of a bacterial pathogen in plants. We found a number of bacterial processes affected by plant immunity at the transcriptome and proteome levels. For instance, salicylic acid-mediated plant immunity suppressed the accumulation of proteins comprising the tip component of the bacterial type III secretion system. Interestingly, there were instances of concordant and discordant regulation of bacterial messenger RNAs and proteins. Gene co-expression analysis uncovered previously unknown gene regulatory modules underlying virulence. This study provides molecular insights into the multiple layers of gene regulation that contribute to bacterial growth in planta, and elucidates the role of plant immunity in affecting pathogen responses.

了解植物病原体的基因调控对于害虫控制和全球粮食安全至关重要。对宿主细菌基因调控的综合理解依赖于多组学数据集，但这些数据在很大程度上是缺乏的。在这里，我们同时表征了植物中细菌病原体的转录组和蛋白质组。我们在转录组和蛋白质组水平上发现了许多受植物免疫影响的细菌过程。例如，水杨酸介导的植物免疫抑制了构成 III 型细菌分泌系统尖端成分的蛋白质的积累。有趣的是，细菌信使 RNA 和蛋白质的调节存在一致和不一致的情况。基因共表达分析揭示了以前未知的潜在毒力基因调控模块。