Consequences of phage resistance elicited by CRISPR-Cas in Pectobacterium atrosepticum

Abstract

Phages are abundant and diverse, outnumbering bacteria ten-fold in most environments. Consequently, bacteria have developed various strategies to prevent phage predation, that act at different stages of the phage infection cycle. Additionally, the phage resistance mechanisms lead to different outcomes, for both individual cells and the population. CRISPR-Cas systems provide protection against phages, and other mobile genetic elements, by capturing memories of infections in the form of short DNA sequences. These memories can direct nuclease-mediated degradation of the invader DNA upon reinfection. Due to their biotechnological applications, the mechanisms of CRISPR-Cas immunity have been investigated extensively. However, few studies have focused on how CRISPR-Cas-mediated phage resistance affects the fate of both the host and the phages, at a cellular level, as well as for bacterial populations. In this thesis, the influence of CRISPR-Cas immunity on different aspects of phage-host interactions was investigated for the type I-F CRISPR-Cas system in Pectobacterium atrosepticum. The CRISPR-Cas system was shown to act through an abortive infection-like mechanism in response to phage infection, whereby infected cells did not survive infection, but reduced the phage burden in the population to protect uninfected cells. Phages were able to overcome CRISPR-Cas targeting without mutations that abolished targeting, albeit phage infectivity was reduced. In addition, phages with genomic alterations were detected, including large deletions in structural genes, showing that CRISPR-Cas can select for phage structural diversity. Finally, the ability of the system to reduce the population phage burden promoted the spread of bacterial genes between cells via transduction. These studies in P. atrosepticum provided novel insights into how CRISPR-Cas immunity influences the fate of both phages and bacteria, at both individual and population levels.