An endonuclease V protects Bacillus subtilis against a deaminase toxin and a uracil-containing phage

Abstract Bacteria deploy polymorphic toxins to inhibit competitors and rely on cognate immunity proteins to prevent self-intoxication. Immunity determinants act by binding and neutralizing incoming toxins, and in the rare cases where toxin-induced damage is also reversed, that activity resides within the immunity protein itself. Whether a conflict system can instead dedicate a separate gene to repairing the damage is unknown. Here we report that an operon in Bacillus subtilis encodes the toxin YwqJ, its cognate immunity protein YwqK, and EndoV Bs an endonuclease that incises DNA at the lesion the toxin creates. YwqJ is a single-stranded DNA cytidine deaminase translocated by the type VIIb secretion system (T7SSb) to mediate contact-dependent interbacterial antagonism. Unexpectedly, EndoV Bs exhibits a preference for uracil over the canonical hypoxanthine, processing genomic uracil in cells and protecting against YwqJ when immunity is absent. Because EndoV Bs acts on the chemical lesion rather than the effector, its protection is indifferent to the source of deamination. EndoV Bs accordingly restricts replication of PBS1, a bacteriophage whose genome naturally substitutes uracil for thymine. These findings establish DNA repair as a novel layer of defense within toxin–immunity loci and reveal a DNA repair mechanism that unifies interbacterial antagonism and antiviral immunity.