Bacteria harbour multiple innate defences and adaptive CRISPR–Cas systems that provide immunity against bacteriophages and mobile genetic elements. Although some bacteria modulate defences in response to population density, stress and metabolic state, a lack of high-throughput methods to systematically reveal regulators has hampered efforts to understand when and how immune strategies are deployed. We developed a robust approach called SorTn-seq, which combines saturation transposon mutagenesis, fluorescence-activated cell sorting and deep sequencing to characterize regulatory networks controlling CRISPR–Cas immunity in Serratia sp. ATCC 39006. We applied our technology to assess csm gene expression for ~300,000 mutants and uncovered multiple pathways regulating type III-A CRISPR–Cas expression. Mutation of igaA or mdoG activated the Rcs outer-membrane stress response, eliciting cell-surface-based innate immunity against diverse phages via the transcriptional regulators RcsB and RcsA. Activation of this Rcs phosphorelay concomitantly attenuated adaptive immunity by three distinct type I and III CRISPR–Cas systems. Rcs-mediated repression of CRISPR–Cas defence enabled increased acquisition and retention of plasmids. Dual downregulation of cell-surface receptors and adaptive immunity in response to stress by the Rcs pathway enables protection from phage infection without preventing the uptake of plasmids that may harbour beneficial traits.

细菌具有多种先天防御和适应性 CRISPR-Cas 系统，可提供针对噬菌体和移动遗传元件的免疫力。尽管一些细菌会根据种群密度、压力和代谢状态来调节防御，但缺乏系统地揭示调节器的高通量方法阻碍了了解何时以及如何部署免疫策略的努力。我们开发了一种称为 SorTn-seq 的稳健方法，它结合了饱和转座子诱变、荧光激活细胞分选和深度测序来表征控制沙雷氏菌中 CRISPR-Cas 免疫的调节网络。ATCC 39006. 我们应用我们的技术来评估csm约 300,000 个突变体的基因表达，并揭示了调节 III-A 型 CRISPR-Cas 表达的多种途径。igaA或mdoG的突变激活了 Rcs 外膜应激反应，通过转录调节因子 RcsB 和 RcsA 引发针对多种噬菌体的基于细胞表面的先天免疫。通过三种不同的 I 型和 III 型 CRISPR-Cas 系统激活这种 Rcs 磷酸层同时减弱了适应性免疫。Rcs 介导的 CRISPR-Cas 防御抑制增加了质粒的获取和保留。细胞表面受体的双重下调和响应于 Rcs 途径的压力的适应性免疫能够保护免受噬菌体感染，而不会阻止可能具有有益特征的质粒的摄取。