Exploring the role of diversity in bacteria-phage ecology and evolution.

根际的细菌可以为植物提供营养，从而对农业有益。然而，它们的有益作用被认为受到土壤中病毒（噬菌体）的限制。细菌的CRISPR-Cas适应性免疫系统提供噬菌体抗性，但细菌通常很难进化出这种类型的噬菌体抗性，并且当它进化时，噬菌体很容易通过点突变逃避CRISPR-Cas。最近的研究表明，当适应性免疫系统与先天免疫系统（称为限制性修饰（RM））相结合时，噬菌体抗性可能会得到改善。然而，CRISPR和RM之间的协同作用尚未得到明确证明，而且由于RM系统高度多样化，这种协同作用是否适用于所有或仅适用于部分RM系统也尚不清楚。因此，本项目的主要目的是研究不同类型的RM和CRISPR-Cas之间是否存在协同作用，并研究这种协同作用如何影响细菌-噬菌体的共同进化。我们已经有了一种细菌宿主，它进化出了高水平的CRISPR免疫，以应对一些噬菌体，但不是所有的噬菌体。我们将使用该实验系统首先检查当细菌配备不同类型的RM系统时，进化的CRISPR免疫水平是否会增加，以揭示假定的RM-CRISPR协同相互作用。然后，我们将比较在RM存在和不存在的情况下伴随CRISPR免疫进化的遗传变化，以重建RM-CRISPR协同相互作用的机制基础。这将辅以体外生化研究，研究纯化的RM成分如何消化DNA分子。最后，我们将研究整合的RM-CRISPR免疫反应如何影响细菌-噬菌体的共同进化，特别是噬菌体克服免疫的能力，与携带单一免疫机制的细菌相比，并检查编码多种免疫机制相关的权衡。学生将接受实验进化、生物化学、分子微生物学和遗传学方面的培训。这个跨学科项目整合了CRISPR-Cas（韦斯特拉，埃克塞特），RM （Sczcelkun，布里斯托尔）和细菌噬菌体共同进化（屈曲，埃克塞特）的专业知识。

Bacteria in the rhizosphere can benefit agriculture by making nutrients available to plants. However, their beneficial effect is thought to be limited by viruses (phage) in soil. CRISPR-Cas adaptive immune systems of bacteria provide phage resistance but it is frequently very difficult to have bacteria evolve this type of phage resistance, and when it evolves, phage can readily escape CRISPR-Cas by point mutation. Recent studies suggest phage resistance may be improved when the adaptive immune system is integrated with an innate immune system, known as restriction-modification (RM). However, synergism between CRISPR and RM has not been clearly demonstrated yet, and because RM systems are highly diverse, it is also unclear whether such synergism would apply to all or only some RM systems. The key aim of this project is therefore to investigate the existence of synergy between different types of RM and CRISPR-Cas, and examine how this synergistic interaction affects bacteria-phage co-evolution. We already have a bacterial host that evolves high levels of CRISPR immunity in response to some, but not all phages. We will use this experimental system to first examine if levels of evolved CRISPR immunity increase when bacteria are equipped with different types of RM systems, to reveal putative synergistic RM-CRISPR interactions. We will then compare the genetic changes that accompany the evolution of CRISPR immunity in the presence and absence of RM, in order to reconstruct the mechanistic basis underlying the synergistic RM-CRISPR interactions. This will be complemented with in vitro biochemical studies that examine how purified RM components digest DNA molecules. Finally, we will investigate how an integrated RM-CRISPR immune response impacts bacteria-phage co-evolution, specifically the ability of phage to overcome immunity, compared to bacteria carrying a single immune mechanism and examine trade-offs associated with encoding multiple immune mechanisms. The student will receive training in experimental evolution, biochemistry, molecular microbiology and genetics. This interdisciplinary project integrates expertise on CRISPR-Cas (Westra, Exeter), RM (Sczcelkun, Bristol) and bacteria-phage co-evolution (Buckling, Exeter).