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

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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.