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

根际的细菌可以使植物获得营养，从而使农业受益。然而，它们的有益作用被认为受到土壤中的病毒(噬菌体)的限制。细菌的CRISPR-Cas适应性免疫系统提供噬菌体抵抗力，但细菌往往很难进化出这种类型的噬菌体抵抗力，当它进化时，噬菌体可以通过点突变很容易逃脱CRISPR-Cas。最近的研究表明，当适应性免疫系统与先天免疫系统整合时，噬菌体的抵抗力可能会得到改善，这被称为限制修饰(RM)。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，也不清楚这种协同作用是适用于所有RM系统还是仅适用于某些RM系统。因此，该项目的主要目的是研究不同类型的RM和CRISPR-CA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。我们已经有一个细菌宿主，它对某些噬菌体但不是所有噬菌体都能进化出高水平的CRISPR免疫。我们将使用这个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免疫水平是否增加，以揭示假定的协同RM-CRISPR相互作用。然后，我们将比较在存在和不存在RM的情况下伴随CRISPR免疫进化的遗传变化，以重建协同RM-CRISPR相互作用的机制基础。这将与体外生化研究相辅相成，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，特别是与携带单一免疫机制的细菌相比，噬菌体克服免疫的能力，并研究与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。这一跨学科项目整合了CRISPR-CAS(Westra，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)方面的专业知识。

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).