A phage repressor involved in the DNA-damage response of Francisella

Members of the S24 family of serine peptidases play central roles in bacterial and phage regulatory networks that respond to DNA damage. In most bacteria, the S24-family peptidase LexA functions as the master repressor of the SOS response, regulating the activity of genes involved in DNA repair and mutagenesis. LexA is known to be absent in some bacterial lineages, including genera of intracellular bacteria with substantial genomic reduction, but it has been shown that other S24-family peptidases can uptake its regulatory functions. In this work, we combine experimental and computational approaches to define the response to DNA damage in Francisella, a genus of facultative intracellular bacteria with moderate genome reduction that encodes a highly diverged LexA family protein. We use RNA sequencing to investigate the transcriptional response of Francisella hispaniensis to the DNA-damaging agent ciprofloxacin and reveal that canonical SOS genes are not induced upon DNA damage. Among the differentially expressed genes, we identify a gene encoding an S24-family peptidase that we term FddR (Francisella DNA-damage regulator). Electrophoretic mobility shift assays demonstrate that the product of this gene specifically binds to the palindromic sequence GTG-N₁₁-CAC present in its promoter region, resulting in autoregulation. In silico analyses reveal that this S24-family peptidase is most likely a co-opted phage repressor that implements a DNA-damage response across the Francisella genus, regulating itself and divergently transcribed genes. Our results provide insights into the SOS repair system of the Francisella genus and its evolution, putting forward a mechanism for the gradual reconstruction of an SOS response network from self-contained divergently transcribed units.