IDENTIFYING NEW COMPOUNDS CAPABLE OF INDUCING MODEL PHAGES

Abstract

Prophages are the genomes of bacteriophages (phages, bacterial viruses) that integrate into the chromosome of their host upon infection, lying dormant until conditions favour their reactivation. A cell harbouring a prophage is called a lysogen, as, upon exposure to certain signals, the prophage will initiate a replicative cycle ending in lysis of the host bacterium and release of phages. This process is known as induction. Canonically, induction occurs through activation of the bacterial SOS-response, a DNA repair cascade initiated by detection of DNA damage. Studies of prophage induction have almost exclusively relied on challenges with compounds that result in the initiation of the host SOS response. Recent studies have identified some signals that affect prophage induction independently of the SOS response, but these approaches have not been systematic. To identify non-canonical triggers of prophage induction, I screened 3,936 compounds against two model lysogens. The first, carrying phage HK97, is a model for induction. The second, carrying phage Mu—a prophage thought to be uninducible—serves as a control. Any compound which inhibited bacterial growth in only our HK97 lysogen was considered to have resulted in a phage-mediated response. The 171 compounds identified in this screen were then used to re-challenge the lysogen at a range of concentrations and monitor the resulting release of free phages associated with induction. Increases in phage counts were seen for 86 compounds. While 38 of these were known SOS activators, 49 were novel, ‘non-canonical’ inducers. Unexpectedly, the screening also revealed seven unique chemical inducers for the supposedly un-inducible model prophage, Mu. The 56 new phage-inducers identified by this work include compounds likely to be driving phage induction through non-canonical pathways. As prophages are thought to respond to bacterial stress, these may reflect stressors acting through new mechanisms. Using these compounds as tools opens up an avenue to probe other stress pathways in bacteria, and, as evidenced by induction of Mu, potentially help discover new phages that don’t respond to canonical inducers.