BREX phage defence: expanding the role of cyclic nucleotide signalling in the prokaryotic immune system

“基因编辑”已经从科幻领域转移到了主流生物技术领域。我们有能力编辑生物体的基因，以操纵它们的外观、生长、行为和治疗疾病。这是通过“CRISPR-cas”实现的，这个工具现在经常在报纸甚至流行电视和流媒体节目中被提及。不常被提及的是，CRISPR-cas是基于围绕着我们日常生活的一场古老而持续的战争的武器。地球上的细菌数量是天文数字，而一种叫做噬菌体的病毒的数量是它们的10倍。细菌和噬菌体已经共同进化了数百万年。谢天谢地，这些噬菌体不会伤害人类。但就像我们的免疫系统对感染做出反应一样，细菌被迫进化出保护自己免受噬菌体侵害的系统。这些防御系统通常有特定的活动，比如切割DNA。因此，我们的许多生物技术都是从这些系统的应用中产生的，包括CRISPR-cas。最近，人们发现了细菌用来防御噬菌体的系统。因此，将我们自身的免疫系统与细菌的免疫系统进行类比已经成为现实。哺乳动物的抗病毒反应和细菌的噬菌体防御之间的进化和功能联系现已得到证实。此外，我们可以扭转这种关系，利用细菌中新系统的发现来预测和识别哺乳动物免疫系统中的新系统！这一发现表明，也许我们应该将细菌中的噬菌体防御视为一种“免疫系统”。因此，不同的防御系统将被期望进行沟通和共同监管。鼓风机实验室的工作已经确定了共同调节多种防御系统的蛋白质。其他实验室的工作已经确定了一系列被称为环核苷酸的分子，它们在防御系统的组成部分之间移动，并打开或关闭防御系统。回到我们的类比，我们知道这些环核苷酸在人类中被用来控制免疫网络。因此，环状核苷酸也可能是控制细菌免疫系统的关键。我们已经确定了一种防御蛋白，它可以降解环核苷酸，作为称为噬菌体排斥（BREX）的防御机制的一部分。目前尚不清楚为什么会出现这种活动，以及它如何影响BREX。BREX的整体机制也不清楚。我们的目的是研究环核苷酸在BREX背景下的使用。我们将描述降解环核苷酸的蛋白质的活性，以及它更喜欢靶向的核苷酸形式。我们将研究组成BREX的各种蛋白质（有六种）如何相互作用，以及环核苷酸的存在如何改变这些相互作用。然后，我们将通过了解如何设计它来修改DNA，来研究如何在生物技术上使用BREX。BREX添加了一种对控制DNA在衰老和疾病等过程中的使用非常重要的修饰。有针对性的修饰方法将为生物医学研究提供另一种工具。总体产出将为具有凝聚力的细菌免疫系统提供进一步的证据，并将我们对BREX的理解推进到潜在的生物技术开发。

"Gene-editing" has transferred from the realms of sci-fi to mainstream biotechnology. We have the ability to edit the genes of organisms in order to manipulate how they look, grow, behave, and to cure disease. This has been made possible through "CRISPR-cas", a tool that now regularly gets name-checked in newspapers and even popular TV and streaming shows. What is not often mentioned is that CRISPR-cas is based upon the weaponry of an ancient and ongoing war that surrounds our everyday lives.The Earth is home to truly astronomical numbers of bacteria, and they are outnumbered 10-to-1 by viruses called bacteriophages. Bacteria and bacteriophages have been co-evolving for millions of years. These bacteriophages thankfully don't harm humans. But in the same way that our immune system responds to infections, bacteria have been forced to evolve systems that protect from bacteriophages. These defence systems often have specific activities, such as cutting DNA. As a result, many of our biotechnologies have arisen from the applications of these systems, including CRISPR-cas.There has been a recent explosion in the discovery of systems bacteria use for defence against bacteriophages. As a result, the analogy comparing our own immune system with that of bacteria has become reality. There are now proven evolutionary and functional links between the antiviral response in mammals and bacteriophage defence in bacteria. Furthermore, we can reverse this relationship, using the discovery of new systems in bacteria to predict forward and identify new systems in the mammalian immune system!This finding suggests that perhaps we should consider bacteriophage defence in bacteria as an "immune system". As such, the varied defence systems would be expected to communicate and be co-regulated. Work in the Blower lab has already identified proteins that co-regulate diverse defence systems. Work in other labs has identified a series of molecules called cyclic nucleotides that move between component parts of defence systems and switch them on or off. Going back to our analogy, we know that these cyclic nucleotides are used in humans to control networks of immunity. It follows that cyclic nucleotides might also therefore be key to control within the bacterial immune system.We have identified a defence protein that degrades cyclic nucleotides as part of a defence mechanism called Bacteriophage Exclusion (BREX). It is not currently understood why this activity is present, and how it impacts BREX. The overall mechanism for BREX is also not understood. Our objective is to investigate cyclic nucleotide usage in the context of BREX. We will characterise the activity of the protein that degrades cyclic nucleotides, and which forms of nucleotides it prefers to target. We will look at how the varied proteins that make up BREX (there are six), interact, and how the presence of cyclic nucleotides might alter these interactions. We will then look at how to use BREX biotechnologically by understanding how to engineer it to make modifications in DNA. BREX adds a modification that is important for controlling use of DNA in processes such as aging and disease. Having a targeted method of modification will provide another tool for biomedical research.The overall outputs will be to provide further evidence towards a cohesive bacterial immune system and progress our understanding of BREX towards potential biotechnological exploitation.