Genome integrity sensing by the broad-spectrum Hachiman antiphage defense complex

Highlights•Hachiman inhibits phage replication by indiscriminate DNA degradation•Cryo-EM structures reveal that HamA is a DNase regulated by complexation with HamB•HamB is a DNA helicase related to archaeal and eukaryotic DNA-repair helicases•Activation in the absence of phage suggests that Hachiman senses genome integritySummaryHachiman is a broad-spectrum antiphage defense system of unknown function. We show here that Hachiman is a heterodimeric nuclease-helicase complex, HamAB. HamA, previously a protein of unknown function, is the effector nuclease. HamB is the sensor helicase. HamB constrains HamA activity during surveillance of intact double-stranded DNA (dsDNA). When the HamAB complex detects DNA damage, HamB helicase activity activates HamA, unleashing nuclease activity. Hachiman activation degrades all DNA in the cell, creating "phantom" cells devoid of both phage and host DNA. We demonstrate Hachiman activation in the absence of phage by treatment with DNA-damaging agents, suggesting that Hachiman responds to aberrant DNA states. Phylogenetic similarities between the Hachiman helicase and enzymes from eukaryotes and archaea suggest deep functional symmetries with other important helicases across domains of life.Graphical abstract