Structural and functional analysis of YopR and identification of an additional key component of the SPβ phage lysis-lysogeny management system

Prophages need to tightly control their lifestyle to either be maintained within the host genome or enter the lytic cycle. The SP{beta} prophage present in the genome of Bacillus subtilis 168 was recently shown to possess an arbitrium system defining its replication stage. Using an historic B. subtilis strain harboring the heat-sensitive SP{beta} c2 mutant, we analyzed a key component of the lysis-lysogeny decision system called YopR, which is critical for maintenance of lysogeny. Here, we demonstrate that the heat-sensitive SP{beta} c2 phenotype is due to a single nucleotide exchange in the yopR gene, rendering the encoded YopRG136E protein temperature sensitive. Structural characterization of YopR revealed that the protein is a DNA-binding protein with an overall fold like tyrosine recombinases. Biochemical and functional analyses indicate that YopR has lost the recombinase function and the G136E exchange impairs its higher order structure and DNA binding activity. We further show that the heat-inducible SP{beta} excision of the c2 mutant still depends on the serine recombinase SprA. Finally, an evolution experiment identified the YosL protein of unknown function as a novel component of the lysis-lysogeny management system, as the presence of yosL is crucial for the induction of the lytic cycle of SP{beta}.