Radiation-response in Deinococcus bacteria: characterization of the transient IrrE–DdrO heterodimer complex

Abstract Radiation resistance in Deinococcus requires an SOS-independent response mechanism, controlled by M78 family (COG2856) metallopeptidase IrrE and XRE family transcriptional repressor DdrO, to induce expression of DNA repair genes after exposure to radiation. DdrO must form dimers to bind target DNA sites. IrrE inactivates DdrO by cleaving the C-terminal dimerization domain of DdrO. However, the molecular basis of the interaction between IrrE and DdrO is still unknown. Here, we showed that IrrE is monomeric in solution and forms heterodimers with DdrO, with the N-terminal DNA-binding domain of DdrO contributing to the interaction. We further revealed that the initially isolated radiation-sensitive irrE mutant strain encodes an oxidation-sensitive IrrE protein affected in DdrO cleavage. Predicted COG2856/XRE regulatory protein pairs are present in many environmental, pathogenic, and industrial bacteria. Single-stranded DNA enhanced the cleavage activity of IrrE from Deinococcus as well as from closely related Marinithermus and Oceanithermus species, but not of the distant homologs ImmA from Bacillus subtilis and Rir from Streptococcus thermophilus. The formation of a heterotrimer containing IrrE, DdrO, and single-stranded DNA was also demonstrated. Together, these findings provide new insights into the molecular interplay between the key regulators IrrE and DdrO.