ssDNA is an allosteric regulator of the C. crescentus SOS-independent DNA damage response transcription activator, DriD

DNA damage repair systems are critical for genomic integrity. However, they must be coordinated with DNA replication and cell division to ensure accurate genomic transmission. In most bacteria this coordination is mediated by the SOS response through LexA , which triggers a halt in cell division until repair is completed. Recently, an SOS-independent damage response system was revealed in Caulobacter crescentus. This pathway is controlled by the transcription activator, DriD, but how DriD senses and signals DNA damage is unknown. To address this question we performed biochemical, cellular, and structural studies. We show that DriD binds a specific promoter DNA site via its N-terminal HTH domain to activate transcription of genes including the cell division inhibitor didA. A structure of the C-terminal portion of DriD revealed a  WYL-motif domain linked to a WCX dimerization domain. Strikingly, we found that DriD binds ssDNA between the WYL and WCX domains. Comparison of apo and ssDNA-bound DriD reveals that ssDNA binding orders and orients the DriD domains, indicating a mechanism for ssDNA-mediated DNA-binding activation. Biochemical and in vivo studies support the structural model. Our data indicate this as a conserved mechanism of signaling for WYL-containing regulators. Chromatin-immunoprecipitation with deep sequencing experiments (ChIP-seq) were performed on mid exponential-phase Caulobacter crescentus treated with and without DNA damage (see the Materials and Methods for the exact treatment that were applied to each strain).