Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America.
Innovative Genomics Institute, Berkeley, California, United States of America.
PLoS Biol. 2020 Oct 13;18(10):e3000877. doi: 10.1371/journal.pbio.3000877. eCollection 2020 Oct.
Bacteriophages (phages) are critical players in the dynamics and function of microbial communities and drive processes as diverse as global biogeochemical cycles and human health. Phages tend to be predators finely tuned to attack specific hosts, even down to the strain level, which in turn defend themselves using an array of mechanisms. However, to date, efforts to rapidly and comprehensively identify bacterial host factors important in phage infection and resistance have yet to be fully realized. Here, we globally map the host genetic determinants involved in resistance to 14 phylogenetically diverse double-stranded DNA phages using two model Escherichia coli strains (K-12 and BL21) with known sequence divergence to demonstrate strain-specific differences. Using genome-wide loss-of-function and gain-of-function genetic technologies, we are able to confirm previously described phage receptors as well as uncover a number of previously unknown host factors that confer resistance to one or more of these phages. We uncover differences in resistance factors that strongly align with the susceptibility of K-12 and BL21 to specific phage. We also identify both phage-specific mechanisms, such as the unexpected role of cyclic-di-GMP in host sensitivity to phage N4, and more generic defenses, such as the overproduction of colanic acid capsular polysaccharide that defends against a wide array of phages. Our results indicate that host responses to phages can occur via diverse cellular mechanisms. Our systematic and high-throughput genetic workflow to characterize phage-host interaction determinants can be extended to diverse bacteria to generate datasets that allow predictive models of how phage-mediated selection will shape bacterial phenotype and evolution. The results of this study and future efforts to map the phage resistance landscape will lead to new insights into the coevolution of hosts and their phage, which can ultimately be used to design better phage therapeutic treatments and tools for precision microbiome engineering.
噬菌体（phages）是微生物群落动态和功能的关键参与者，它们驱动着从全球生物地球化学循环到人类健康等各种过程。噬菌体往往是精细调整的捕食者，专门攻击特定的宿主，甚至细化到菌株水平，而宿主则使用一系列机制来保护自己。然而，迄今为止，快速而全面地识别在噬菌体感染和抗性中起重要作用的细菌宿主因素的努力尚未完全实现。在这里，我们使用两种具有已知序列差异的模式大肠杆菌菌株（K-12 和 BL21），对 14 种具有不同进化关系的双链 DNA 噬菌体的宿主遗传决定因素进行了全球映射，以证明菌株特异性差异。通过全基因组功能丧失和功能获得遗传技术，我们能够确认先前描述的噬菌体受体，并发现许多以前未知的宿主因子，这些因子赋予了对一种或多种噬菌体的抗性。我们发现了抗性因子的差异，这些差异与 K-12 和 BL21 对特定噬菌体的敏感性强烈一致。我们还确定了噬菌体特异性机制，例如环状二鸟苷酸在宿主对噬菌体 N4 的敏感性中的意外作用，以及更通用的防御机制，例如产生大量的荚膜多糖，该多糖可以抵御广泛的噬菌体。我们的结果表明，宿主对噬菌体的反应可以通过多种细胞机制发生。我们系统和高通量的遗传工作流程来描述噬菌体-宿主相互作用决定因素，可以扩展到不同的细菌，生成数据集，从而可以预测噬菌体介导的选择将如何塑造细菌表型和进化。这项研究的结果以及未来绘制噬菌体抗性图谱的努力，将使我们对宿主与其噬菌体的共同进化有新的认识，最终可以用于设计更好的噬菌体治疗方法和精确微生物组工程的工具。
