WYL-family protein DdaA mediates DNA damage response in Moraxellales. A new pipeline Novel-Sample identifies a novel WYL-Family protein mediating global DNA damage response in Moraxellales

The family Moraxellales contains clinically significant species including multidrug-resistant strains, yet their potential global DNA damage response (DDR) systems has not been identified. By developing a bioinformatic pipeline Novel-Sample we found a conserved and well-palindrome DNA damage response related cis-element. We confirmed that a WYL domain-containing protein binds to the predicted cis-element, we named the protein 'the DNA damage response of Acinetobacter A' (DdaA). DdaA regulated gene transcriptional network is distinct from the three well-studied global DDR systems currently known in bacteria. The knockout of ddaA significantly reduced the viability of Acinetobacter baumanni under UV radiation and MMC treatment. Transcriptomics and molecular experiments confirmed that DdaA is a transcriptional activator binding to a palindromic sequence upstreaming of essential DDR genes, including recA, uvrA, uvrC, and ruvAB. Interestingly, DdaA also regulates a large portion of the CRISPR proteins found in Moracellaceae, implying DdaA also takes part in phage infection responses. Phylogenetic analysis revealed that DdaA belongs to a novel subgroup of the WYL family, which is functionally distinct from the known DNA damage response protein PafBC and DriD, or phage infection response protein BrxR and CapW. This study answers the long-lasting question of the global DNA damage response system adopted in Moraxellales and expands our understanding of WYL family proteins. We also demo our pipeline on biophysics.zju.edu.cn to facilitate future studies of microbial transcriptional regulators in general.