Arbitrium communication controls phage lysogeny through non-lethal activation and inhibition of a bacterial toxin-antitoxin defense system

Bacterial temperate viruses (phages) must decide between a quiescent (lysogenic) and virulent (lytic) lifestyle in the face of a variety of defense systems. Many Bacilli phage families have been shown to use the arbitrium communication system to control these decisions, but the mechanisms by which it functions remain largely unknown. Here we find that the arbitrium system of Bacillus subtilis phage phi3T controls the phage life-cycle through non-lethal activation and inactivation of the host-encoded MazEF toxin-antitoxin system. Upon phage infection, the combined expression of three phage proteins promotes activation of the MazF RNA ribonuclease toxin. When arbitrium signaling levels are low, MazF activity is blocked by phage expression of the arbitrium-dependent AimX protein and a later-expressed phage protein, YosL, both acting as MazE-like antitoxins. When arbitrium levels are high, MazF remains active, strongly restricting lytic propagation. Strikingly, MazF activation occurs without a significant impact on host growth. Specificity of MazF activity towards the phage and the restriction of the lytic state can be explained by low levels of MazF activation and the high density of MazF cleavage sites on phage lytic genes. Continuation of lysogeny is most likely related to the absence of MazF cleavage sites from the phage repressor. The occurrence pattern of MazF cleavage sites is conserved throughout the whole SpBeta-like family of phages. Altogether, our results show how a bacterial toxin-antitoxin defense system has been co-opted by a phage to control lysogeny without affecting host viability.