Broad and specific anti-defense genes in bacteriophage genomes

Bacteria and bacteriophages have been engaged in a relentless evolutionary arms race, driving a rapid evolution of bacterial defense mechanisms and leading to their scattered distribution across genomes. We hypothesized that the variability in defense systems presence in bacterial genomes leads to equally variable counter-defense repertoires in phage genomes. To test this, we analyzed the variable regions in Pseudomonas model phages of the Pbunavirus genus, uncovering five anti-defense genes inhibiting Zorya type I, RADAR, Hypnos, Druantia type I and III, and Thoeris type III. Remarkably, a typical Pbunavirus encodes up to five known anti-defense genes, some inhibiting four unrelated defense systems with distinct nucleic acid-targeting mechanisms. Structural searches revealed that these broad-acting inhibitors are encoded across diverse phage taxa infecting multiple bacterial hosts. The presence of both broad and specific inhibitors suggests that defense systems exert a strong selective pressure, and their utility presents opportunities to improve phage-based therapeutics.