A DNA damage-activated kinase phosphorylates a transcriptional repressor to control bacterial immune pathway expression

Bacteria encode numerous stress-response pathways that protect their hosts against both internal and external threats. A key question is how these pathways are regulated, especially anti-phage immune pathways that mediate host-cell killing. Here, we identify two proteins termed CapK and CapS that are encoded upstream of diverse immune operons, and regulate these operons' expression in response to DNA damage. CapK resembles bacterial anti-sigma factor kinases, and CapS resembles STAS-domain antagonists of these proteins. CapS is a DNA-binding transcriptional repressor, and phosphorylation of CapS by CapK results in dissociation of a CapS homodimer and de-repression of transcription. The CapK kinase is directly activated by single-stranded DNA generated as a byproduct of DNA repair. Finally, we show that CapK and CapS-like proteins have been co-opted into an anti-phage toxin-antitoxin system with a VapC-like protein, where they similarly respond to DNA damage to activate VapC nuclease activity. Overall, our results reveal how a kinase-substrate pair can regulate expression of an adjacent operon in response to DNA damage, and highlight the modularity of immune and other stress-response pathways.