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Mechanisms and evolutionary consequences of host immunosuppression by anti-CRISPR phages

抗 CRISPR 噬菌体抑制宿主免疫的机制和进化后果

基本信息

批准号：
BB/S017674/1
负责人：
Stineke Van Houte
金额：
$ 65.29万
依托单位：
UNIVERSITY OF EXETER
依托单位国家：
英国
项目类别：
Research Grant
财政年份：
2020
资助国家：
英国
起止时间：
2020 至无数据
项目状态：
未结题

来源：
https://gtr.ukri.org/projects?ref=BB%2FS017674%2F1
关键词：
Mechanisms evolutionary consequences host immunosuppression

项目摘要

CRISPR-Cas is an immune system present in many bacteria that protects them against infections with bacterial viruses, called phages. Several years ago researchers made the exciting discovery that phages have evolved ways to counteract this immune response, by producing small proteins that bind to CRISPR-Cas immunity complexes and thereby block their activity. These molecules, named anti-CRISPRs (Acr), are produced immediately upon phage infection, but our earlier work has shown that Acr production is often 'too little, too late" so that phages are outpaced by the CRISPR-Cas complexes in the bacterial host cell. However, our work also shows that Acr linger on in the cell and keeps blocking CRISPR-Cas immunity complexes, even when the initial phage infection has been cleared. This opens the door to a second phage that can now successfully infect this immunosuppressed host. Some Acrs are "stronger" than others, i.e. they are better at blocking CRISPR-Cas, but we do not understand what factors determine how strong an Acr is and the associated immunosuppression. Being able to strongly immunosuppress is not necessarily better for the phage; when different phage species compete with each other (which is very common in many environments), phages that do not produce Acr can exploit those that produce strong Acr molecules. Our data indicate that Acr are costly to produce (for example, because it takes energy to produce them) and this exploitation risk could therefore mean that during phage-phage competition the fitness of the phage producing Acrs is lowered. In the proposed project we wish to understand the mechanism by which Acr-phages immunosuppress their hosts, and the evolutionary consequences of host immunosuppression on maintenance of Acr genes in the absence and presence of phage-phage competition. We will do this by integrating research on the molecular level (how do Acr bind to CRISPR-Cas immunity complexes?), the single-cell level (how does the ability to immunosuppress influence the infection success of phage in individual bacteria? How does this change when phages that infect the same bacterium compete with each other?) and the population level (are Acr molecules costly? is it always better for a phage to produce multiple different Acrs over one Acr? and how does phage-phage competition influence phage fitness and therefore Acr gene maintenance in the long term?). The research outcomes are important for several reasons. Understanding how Acrs interact with CRISPR-Cas complexes and how natural selection acts on them is important for our fundamental understanding of CRISPR-Cas biology. CRISPR-Cas also has extremely important applications, as they are extremely useful tools in a technique called gene editing, where specific mutations or genes can be removed or introduced in the DNA of an organism. This has major potential in healthcare, where the technique could be used to repair mutations that cause genetic diseases in human, such as Cystic Fibrosis, Duchenne muscular dystrophy and Huntington's disease. But CRISPR-Cas is also used for ecological engineering, for example to reduce the spread of infectious diseases by insects, and for microbiome engineering to remove antimicrobial resistance and/or pathogenic bacteria. For these applications, it would very useful to have ways to control CRISPR-Cas activity (for example, because we only want it to be active during a certain time period or in specific tissues or cells). Currently, we have no ways to control CRISPR-Cas activity on protein level, but using Acr molecules would be an extremely reliable way of temporal inactivation of CRISPR-Cas as required. This research will give us new, exciting and important insights in the mechanisms underlying Acr - CRISPR-Cas interactions and the evolutionary consequences of these interactions, which will be crucial for successfully applying Acrs as a CRISPR-Cas regulating tool in healthcare, life sciences research and agriculture.

CRISPR-Cas是一种存在于许多细菌中的免疫系统，可以保护它们免受细菌病毒（称为CRISPR）的感染。几年前，研究人员发现了一个令人兴奋的发现，他们已经进化出了抵消这种免疫反应的方法，通过产生与CRISPR-Cas免疫复合物结合的小蛋白，从而阻止它们的活性。这些分子被称为抗CRISPR（Acr），在噬菌体感染后立即产生，但我们早期的工作表明Acr的产生往往“太少、太晚”，因此噬菌体被细菌宿主细胞中的CRISPR-Cas复合物超越。然而，我们的工作还表明，Acr在细胞中停留并持续阻断CRISPR-Cas免疫复合物，即使最初的噬菌体感染已经被清除。这为第二个噬菌体打开了大门，它现在可以成功地感染这种免疫抑制的宿主。一些Acr比其他Acr“更强”，即它们更擅长阻断CRISPR-Cas，但我们不知道是什么因素决定了Acr的强度以及相关的免疫抑制。能够强烈的免疫抑制并不一定对噬菌体更好;当不同的噬菌体物种相互竞争时（这在许多环境中非常常见），不产生Acr的噬菌体可以利用产生强Acr分子的噬菌体。我们的数据表明，Acr的生产成本很高（例如，因为生产它们需要能量），因此这种利用风险可能意味着在噬菌体-噬菌体竞争期间，产生Acr的噬菌体的适应性降低。在所提出的项目中，我们希望了解Acr免疫抑制其宿主的机制，以及宿主免疫抑制在存在和不存在噬菌体-噬菌体竞争的情况下对Acr基因维持的进化后果。我们将通过整合分子水平上的研究（Acr如何与CRISPR-Cas免疫复合物结合？）单细胞水平（免疫抑制能力如何影响噬菌体在单个细菌中的感染成功？当感染同一种细菌的细菌相互竞争时，这种情况会发生什么变化？）和人口水平（Acr分子昂贵吗？噬菌体产生多个不同的Acr总是比产生一个Acr更好吗？以及噬菌体-噬菌体竞争如何影响噬菌体适应性并因此影响Acr基因的长期维持？研究结果之所以重要，有几个原因。了解Acr如何与CRISPR-Cas复合物相互作用以及自然选择如何作用于它们对于我们对CRISPR-Cas生物学的基本理解非常重要。CRISPR-Cas也有非常重要的应用，因为它们是一种称为基因编辑的技术中非常有用的工具，可以在生物体的DNA中删除或引入特定的突变或基因。这在医疗保健领域具有巨大潜力，该技术可用于修复导致人类遗传性疾病的突变，例如囊性纤维化、杜氏肌营养不良症和亨廷顿舞蹈症。但CRISPR-Cas也可用于生态工程，例如减少昆虫传播传染病，以及用于微生物组工程以消除抗菌素耐药性和/或病原菌。对于这些应用，控制CRISPR-Cas活性的方法将非常有用（例如，因为我们只希望它在特定时间段内或在特定组织或细胞中具有活性）。目前，我们还没有方法在蛋白质水平上控制CRISPR-Cas活性，但使用Acr分子将是根据需要暂时灭活CRISPR-Cas的非常可靠的方法。这项研究将为我们提供关于Acr-CRISPR-Cas相互作用的机制以及这些相互作用的进化后果的新的、令人兴奋的和重要的见解，这对于成功地将Acrs作为CRISPR-Cas调节工具应用于医疗保健、生命科学研究和农业至关重要。

项目成果

期刊论文数量（10）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Antibiotics that affect translation can antagonize phage infectivity by interfering with the deployment of counter-defenses.

DOI：
10.1073/pnas.2216084120
发表时间：
2023-01-24
期刊：
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
影响因子：
11.1
作者：
Pons, Benoit J.;Dimitriu, Tatiana;Westra, Edze R.;van Houte, Stineke
通讯作者：
van Houte, Stineke

Determination of Acr-mediated immunosuppression in Pseudomonas aeruginosa.