Abstract

Many species of bacteria harbor multiple prophages in their genomes. Prophages often carry genes that confer a selective advantage to the bacterium, typically during host colonization. Prophages can convert to infectious viruses through a process known as induction, which is relevant to the spread of bacterial virulence genes. The paradigm of prophage induction, as set by the phage Lambda model, sees the process initiated by the RecA-stimulated self-proteolysis of the phage repressor. Here we show that a large family of lambdoid prophages found in Salmonella genomes employs an alternative induction strategy. The repressors of these phages are not cleaved upon induction; rather, they are inactivated by the binding of small antirepressor proteins. Formation of the complex causes the repressor to dissociate from DNA. The antirepressor genes lie outside the immunity region and are under direct control of the LexA repressor, thus plugging prophage induction directly into the SOS response. GfoA and GfhA, the antirepressors of Salmonella prophages Gifsy-1 and Gifsy-3, each target both of these phages' repressors, GfoR and GfhR, even though the latter proteins recognize different operator sites and the two phages are heteroimmune. In contrast, the Gifsy-2 phage repressor, GtgR, is insensitive to GfoA and GfhA, but is inactivated by an antirepressor from the unrelated Fels-1 prophage (FsoA). This response is all the more surprising as FsoA is under the control of the Fels-1 repressor, not LexA, and plays no apparent role in Fels-1 induction, which occurs via a Lambda CI-like repressor cleavage mechanism. The ability of antirepressors to recognize non-cognate repressors allows coordination of induction of multiple prophages in polylysogenic strains. Identification of non-cleavable gfoR/gtgR homologues in a large variety of bacterial genomes (including most Escherichia coli genomes in the DNA database) suggests that antirepression-mediated induction is far more common than previously recognized. Author Summary Many viruses that infect bacteria (bacteriophages) can direct the integration of their DNA into the bacterial chromosome. This condition, known as lysogeny, is relevant to bacterial evolution, as it is one of the main pathways leading to the incorporation of foreign DNA in nature. Indeed, bacteriophages often carry genes that escape lysogenic repression and benefit the bacterium. This symbiotic association can come to an end if bacteria suffer DNA damage. A mechanism mediated by the host's RecA protein causes the relief of repression, viral DNA excision, and replication. This process, known as prophage induction, kills the host and results in the release of viral particles. In this work, we have analyzed the mechanism responsible for induction in a large family of prophages naturally present in the genomes of Salmonella bacteria. We found that, unlike in best-studied model phages, the repressors of these Salmonella phages do not undergo RecA-mediated proteolysis; rather, they are inactivated by the binding of small antirepressor proteins. We show that some antirepressors can act on both cognate and non-cognate repressors, allowing separate prophages within a given strain to be induced simultaneously. We discuss evidence suggesting that antirepressor-mediated prophage induction is quite common in the bacterial world.