Molecular mechanism of a single stranded DNA-stimulated bacterial immune peptidase

Bacteria encode hundreds of immune pathways that protect host cells against infection by bacteriophages. While immune pathways possess exquisite mechanisms for self-regulation to avoid aberrant activation, many are also tightly regulated at the level of transcription. Many immune operons are regulated by CapP+CapH, a two-protein transcriptional regulator system that triggers immune operon expression in response to DNA damage, by sensing the presence of single-stranded DNA byproducts of DNA damage repair. Here we define how the CapP peptidase is activated by single-stranded DNA. DNA binding in a conserved inter-domain groove in CapP triggers rearrangement of the autoregulatory "cysteine switch loop", opening the active site and allowing binding and cleavage of CapH, which in turn leads to transcriptional activation of an associated immune operon. Our data define a conserved molecular mechanism for sensing bacteriophage infection via DNA damage, and for triggering increased expression of immune operons in response.