Transcription activation mechanism of a non-canonical bacterial DNA damage response pathway

DNA damage repair mechanisms are vital for bacterial survival. Recent studies revealed a non-canonical DNA damage response in Caulobacter crescentus activated by a WYL-domain transcription factor, DriD. DriD binds ssDNA, produced upon DNA damage, within its WYL-domain, and drives expression at multiple promoters. The mechanism behind DriD-mediated transcription activation is, however, unknown. Here we describe cryo-EM structures of DriD-ssDNA bound to RNAP-holoenzyme and three promoters. DriD contains N-terminal DNA-binding domains (DNABDs) connected to WYL-signaling domains by a linker-3-helix-bundle (3HB) module. The three structures reveal a conserved activation mechanism whereby DriD’s 3HBs bind RNAP α-CTD and ß domains, anchoring RNAP on nonoptimal promoters. The 3HBs form autoinhibitory contacts with DNABDs in apo DriD and therefore acts as a ssDNA-driven trigger domain, switching between DNABD-bound apo and RNAP-bound states upon ssDNA-mediated activation. Thus, the structures reveal a unique transcription activation mechanism, likely conserved among the large family of homodimeric WYL-activators.