Bacteriophages and genetic elements such as cryptic prophages or pathogenicity islands make up a considerable amount of the bacterial genome. It is through their transfer and subsequent activity within the host's genetic circuitry that bacterial evolution has been significantly shaped. A physiologically important but often unnoted phenomenon is the spontaneous activation of these elements in single cells of bacterial populations even in the absence of an external trigger, a phenomenon dubbed 'spontaneous prophage induction' (SPI) (1).
In our studies, we use the Gram-positive soil bacterium Corynebacterium glutamicum ATCC 13032, which contains three genomically integrated prophage elements (CGP1-3), as a model organism to study the trigger and physiological consequence of spontaneous prophage induction. Promoter fusions of prominent phage and stress response genes (e.g. Pintegrase, PrecA) to genes encoding fluorescent proteins were constructed to observe the activity of C. glutamicum prophages in single bacterial cells using flow cytometry and time-lapse fluorescence microscopy (2). This approach revealed that the spontaneous induction of the SOS response is partly responsible for the spontaneous activity of prophage CGP3, but also showed a considerable fraction of SOS-independent prophage induction. Using time-lapse fluorescence microscopy of cells grown in microfluidic chip devices we visualized the dynamics of the SOS response and prophage induction in bacterial microcolonies.
Current efforts focus on the identification of molecular factors influencing CGP3 SPI in C. glutamicum. Recently, we identified a small nucleoid-associated protein (CgpS), which is essential due to its function as a silencer of cryptic prophages in C. glutamicum. Genome-wide profiling using ChIP-Seq revealed the binding of CgpS to AT-rich DNA regions, including the large prophage CGP3, thereby counter-acting prophage induction. This example nicely demonstrates how silencing proteins are required to adjust the activity of foreign DNA to a tolerable level for the host cell.

1. Nanda, A., K. Thormann & J. Frunzke (2015), J Bacteriol 197: 410-419.

2. Helfrich, Pfeifer et al. (2015) Mol Microbiol 98: 636-50.