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Abstract:

Recently, mining of bacterial and archaeal genomes for antivirus defense systems has revealed a remarkable diversity of defense mechanisms. Each bacterial genome carries multiple defense systems. Thus, Escherichia coli isolates carry, on average, 5-7 defense per genome that are effective again various phages and act on different stages of infection. In many cases, components of different defense systems are encoded in close proximity to each other, within defense islands. The repertoires composition of defense systems varies significantly even among closely related bacterial strains, but the causes of this variation remain poorly understood. Understanding functional and evolutionary connections between various defense systems is crucial for the reconstruction of the bigger picture of host-virus coevolution. We investigated the patterns of co-occurrence of 110 diverse defense systems in 26,362 complete E. coli genomes and identified many significant positive and negative correlations between the occurrences of pairs of defense systems. We show that some groups of E. coli strains such as those in the phylogroup E, have strong preference for retaining some defense systems, such as Zorya II, Druantia III, and PsyrTA that are rarely present in other phylogroups. Furthermore, we show that negative correlations do not result from antagonistic effects of the respective defense systems, but instead, even if partially redundant, such negatively correlated systems can act in synergy and provide better defense when present together in the cell. Collectively, our results complex interaction between defense systems in bacteria that require further investigation.