Supramolecular complex formation in bacterial anti-phage defense and viral immune evasion

Abstract

Bacteria can encode many diverse nuclease-helicase defense systems that protect from viral infection and inhibit phage propagation. An emerging theme in anti-phage defense is the presence of nuclease-helicase operons. However, how nuclease-helicase systems defend against phage infection remains largely unknown. Gabija is one of the most prevalent nuclease-helicase defense systems, occurring in >15% of all sequenced bacterial and archaeal genomes. We discovered that Gabija proteins assemble into an ~500 kDa nuclease-helicase supramolecular complex that degrades phage DNA. Phages evolve diverse immune evasion mechanisms to inhibit host defense systems. We show that a phage-encoded protein, Gabija anti-defense 1 (Gad1), directly binds the Gabija complex by forming an octameric web inhibiting phage DNA recognition and cleavage. Phages can also encode another Gabija inhibitor, Gad2, which does not prevent Gabija DNA targeting in vitro, suggesting that Gad2 works upstream of DNA cleavage during infection. To understand nuclease-helicase system diversity, we biochemically screened 14 nuclease-helicase systems and found that they all form protein complexes of varying oligomeric state and have different phage nucleic acid cleavage specificity. Our results define mechanisms by which bacteria use nuclease-helicase anti-phage defense systems to inhibit viral infection and how phages fight back with unique viral immune evasion mechanisms.