Identifying factors that drive CRISPR-Cas-dependent phage resistance in bacteria

所有的生物，包括人类、植物、昆虫，甚至细菌，都会受到病毒的感染。了解细菌如何保护自己免受病毒感染很重要，原因有几个。首先，一些细菌会导致人类患病，而病毒被认为是一种有希望治愈患者的方法，即噬菌体疗法。其次，细菌在工业中被广泛使用，例如用于生产酸奶，而在这些工业过程中感染病毒会导致产品降级和巨大的经济损失。因此，了解有助于保护细菌或使细菌对病毒感染敏感的因素至关重要。例如，在食品行业，细菌需要受到病毒的保护，而感染患者、动物或农作物的病原体需要对病毒感染敏感。CRISPR-CA是一种广泛存在的原核适应性免疫系统，可以保护细菌免受病毒感染。然而，我们对导致CRISPR-Cas介导的免疫因应病毒而进化的因素了解有限。我们假设，当细菌暴露于触发CRISPR-Cas适应性免疫系统表达(活性)的化学或环境因素时，CRISPR-Cas免疫进化水平可能会增加。因此，在我们的研究中，我们将首先研究CRISPR-CAS免疫系统是如何开启和关闭的。具体地说，我们的目标是了解细菌释放的化学信号在细菌群体中触发CRISPR-CA同步表达的作用。其次，我们假设侵袭性(毒力)病毒的速度可能超过细菌的CRISPR-Cas适应性免疫系统。我们将通过将病毒毒力水平与细菌进化CRISPR-Cas介导的免疫的能力相关联来检验这一假设。最后，我们将利用我们对化学和环境因素如何开启和关闭CRISPR-Cas的理解，来操纵CRISPR-Cas在病毒感染时的免疫进化程度。具体地说，我们将使细菌暴露在增加或减少CRISPR-Cas表达的因素中。控制CRISPR-Cas免疫进化的水平对于对抗细菌病原体是重要的。我们将使用一种重要的人类病原体铜绿假单胞菌进行实验分析。这种病原体感染的患者包括烧伤创面、囊性纤维化或癌症。目前，噬菌体治疗试验正在进行中，感染铜绿假单胞菌的烧伤创面患者接受病毒治疗以杀死病原体。我们认为，如果CRISPR-CA等病毒免疫系统被抑制，很可能对患者有利。我们的研究旨在使这类抑制剂的开发更近一步。

All organisms, including humans, plants, insects and even bacteria, experience infections by viruses. Understanding how bacteria protect themselves against their viruses is important for several reasons. First, some bacteria cause disease in humans, and viruses are recognised as a promising method to cure patients, known as phage therapy. Second, bacteria are widely used in industry, for example for the production of yoghurt, and virus infections during these industrial processes cause product downgrades and large financial losses. It is therefore of key importance to understand the factors that help to protect or sensitize bacteria to virus infections. For example, in the food industry, bacteria need to be protected against viruses, whereas pathogenic bacteria that infect patients, animals or crops need to be sensitised to virus infections. CRISPR-Cas are widespread prokaryotic adaptive immune systems that can protect bacteria against infections by viruses. However, we have a limited understanding of the factors that cause CRISPR-Cas-mediated immunity to evolve in response to viruses. We hypothesise that the level of CRISPR-Cas immunity evolution may be increased when bacteria are exposed to chemical or environmental factors that trigger expression (activity) of the CRISPR-Cas adaptive immune system. In our research we will therefore first examine how CRISPR-Cas immune systems are switched on and off. Specifically, we aim to understand the role of chemical signals that are released by bacteria to trigger synchronous expression of CRISPR-Cas in bacterial populations. Secondly, we hypothesise that aggressive (virulent) viruses may outpace the CRISPR-Cas adaptive immune system of bacteria. We will examine this hypothesis by correlating virus virulence levels with the ability of bacteria to evolve CRISPR-Cas-mediated immunity. Finally, we will use our understanding of how chemical and environmental factors switch CRISPR-Cas on and off, to manipulate the extent of CRISPR-Cas immunity evolution upon virus infection. Specifically, we will expose bacteria to factors that increase or decrease CRISPR-Cas expression. Manipulating the level of CRISPR-Cas immunity that evolves is important for combatting bacterial pathogens. We will use an important human pathogen, Pseudomonas aeruginosa, for our experimental analyses. This pathogen infects amongst others patients suffering from burn wounds, cystic fibrosis, or cancer. Currently, phage therapy trials are running where burn wound patients infected with P. aeruginosa are treated with virus to kill the pathogen. We believe that it is likely to benefit the patient if virus immune systems such as CRISPR-Cas are inhibited. Our study aims to bring the development of such inhibitors one step closer.