The defense island repertoire of the Escherichia coli pan-genome

Author summaryBacteria are commonly infected by viruses called bacteriophages (or phages, for short). To survive phage infection, bacteria employ multiple anti-phage defense systems, many of which were discovered only in recent years. Intriguingly, multiple studies showed that different strains of the same species can encode completely different sets of defense systems, but the reason for the diversification of defense systems among otherwise nearly identical genomes was unknown. Here, we systematically characterized defense systems in >1,300 genomes of the model lab strain Escherichia coli. We find that anti-phage defense systems are almost always carried on mobile genetic elements such as prophages, transposons and conjugative elements. These elements integrate at specific locations, or "hotspots", within the E. coli genome. Different anti-phage defense systems are carried by distinct types of mobile genetic elements that preferentially integrate at specific hotspots, explaining why phage resistance profiles can vary significantly even among closely related E. coli strains. Our findings not only provide a comprehensive view of the distribution of anti-phage defense systems in E. coli genomes, but also shed light on the rapid gain and loss of defense systems in short evolutionary time scale. It has become clear in recent years that anti-phage defense systems cluster non-randomly within bacterial genomes in so-called "defense islands". Despite serving as a valuable tool for the discovery of novel defense systems, the nature and distribution of defense islands themselves remain poorly understood. In this study, we comprehensively mapped the defense system repertoire of >1,300 strains of Escherichia coli, the most widely studied organism for phage-bacteria interactions. We found that defense systems are usually carried on mobile genetic elements including prophages, integrative conjugative elements and transposons, which preferentially integrate at several dozens of dedicated hotspots in the E. coli genome. Each mobile genetic element type has a preferred integration position but can carry a diverse variety of defensive cargo. On average, an E. coli genome has 4.7 hotspots occupied by defense system-containing mobile elements, with some strains possessing up to eight defensively occupied hotspots. Defense systems frequently co-localize with other systems on the same mobile genetic element, in agreement with the observed defense island phenomenon. Our data show that the overwhelming majority of the E. coli pan-immune system is carried on mobile genetic elements, explaining why the immune repertoire varies substantially between different strains of the same species.