Many bacterial members are provided with a nonhomologous end joining system (NHEJ) responsible for repairing double strand breaks (DSB), the most hazardous DNA lesions as they are lethal to dividing cells if they are not repaired in a timely fashion. Such a repair pathway is constituted by a Ku homodimer and a dedicated and multifunctional ATP-dependent Ligase (LigD). Previous biochemical analysis of bacterial LigD allowed the identification of polymerization, ligase and fosfoesterase activities. We have recently characterized the additional presence of an unexpected 5’-2-deoxyribose-5-phosphate (dRP) lyase activity in the ligase domain (LigDom) of the LigD from B. subtilis and P.aeruginosa. This activity coordinates with the polymerization and ligase activities to allow efficient repairing of an AP site-containing DNA in an in vitro reconstituted Base Excision Repair (BER) reaction. Therefore, LigD has in the same polypeptidic chain the three activities required in the last steps of BER, suggesting that its DNA repair role is not restricted to the NHEJ pathway, but expands beyond, being potentially active in additional repair pathways. Additionaly we have identified a novel AP-lyase activity in the PolDom of LigD that cleaves AP sites specifically when they are proximal to recessive 5’-ends and through the formation of a preternary precatalytic complex with Mn2+ ions and an incoming ribonucleotide complementary to the templating nucleotide opposite the AP site, guaranteeing the coupling of AP sites removal to the end-joining reaction by the bacterial LigD.
We have recently characterized a protein called Insertion Sequence excision enhancer, specifically present in enteropathogenic E. coli bacteria, and belonging to the Archaeal/Eukaryotic primase superfamily. Our studies have demonstrated that this is a novel DNA polymerase capable of carrying out microhomology-mediated end joining, possessing biochemical characteristics typical of DNA polymerases involved in DNA lesion repair.