Bacteriophage defences are divided into innate and adaptive systems. Serratia sp. ATCC 39006 has three CRISPR-Cas adaptive immune systems, but its innate immune repertoire is unknown. Here, we re-sequenced and annotated the Serratia genome and predicted its toxin–antitoxin (TA) systems. TA systems can provide innate phage defence through abortive infection by causing infected cells to ‘shut down’, limiting phage propagation. To assess TA system function on a genome-wide scale, we utilized transposon insertion and RNA sequencing. Of the 32 TA systems predicted bioinformatically, 4 resembled pseudogenes and 11 were demonstrated to be functional based on transposon mutagenesis. Three functional systems belonged to the poorly characterized but widespread, AbiE, abortive infection/TA family. AbiE is a type IV TA system with a predicted nucleotidyltransferase toxin. To investigate the mode of action of this toxin, we measured the transcriptional response to AbiEii expression. We observed dysregulated levels of tRNAs and propose that the toxin targets tRNAs resulting in bacteriostasis. A recent report on a related toxin shows this occurs through addition of nucleotides to tRNA(s). This study has demonstrated the utility of functional genomics for probing TA function in a high-throughput manner, defined the TA repertoire in Serratia and shown the consequences of AbiE induction.

中文翻译：

---

功能基因组学揭示沙雷氏菌的毒素-抗毒素库和 AbiE 活性


噬菌体防御分为先天系统和适应性系统。沙雷氏菌属ATCC 39006 具有三个 CRISPR-Cas 适应性免疫系统，但其先天免疫系统尚不清楚。在这里，我们对沙雷氏菌基因组进行了重新测序和注释，并预测了其毒素-抗毒素（TA）系统。 TA 系统可以通过流产感染提供先天噬菌体防御，使受感染的细胞“关闭”，限制噬菌体繁殖。为了在全基因组范围内评估 TA 系统功能，我们利用了转座子插入和 RNA 测序。在生物信息学预测的 32 个 TA 系统中，4 个类似假基因，11 个基于转座子诱变被证明具有功能。三个功能系统属于特征不明但分布广泛的 AbiE、流产感染/TA 家族。 AbiE 是一种 IV 型 TA 系统，具有预测的核苷酸转移酶毒素。为了研究这种毒素的作用模式，我们测量了对 AbiEii 表达的转录反应。我们观察到 tRNA 水平失调，并提出该毒素以 tRNA 为目标，从而导致抑菌。最近一份有关相关毒素的报告表明，这是通过向 tRNA 添加核苷酸来实现的。这项研究证明了功能基因组学以高通量方式探测 TA 功能的实用性，定义了沙雷氏菌中的 TA 库，并显示了 AbiE 诱导的后果。