Coordinated repair of nucleobase DNA lesions in a cellular context: an integrated structural and cell biology study – CANDLES

Damage to DNA can have serious consequences in cells, leading to mutagenesis, genome instability and even cell death. Two highly conserved DNA repair pathways, the base excision (BER) and nucleotide excision (NER) repair pathways, are collectively responsible for eliminating DNA modifications occurring at the nucleobase level, notably those caused by ultraviolet (UV) light and ionising radiation. We recently identified direct interactions between bacterial NER and BER factors from the radiation resistant bacterium, Deinococcus radiodurans, and a functional cooperation between these pathways for the elimination of oxidised DNA bases, providing the first evidence for a possible NER-BER interplay in prokaryotes. Moreover, we have strong evidence that the remarkable DNA repair activity of this organism is modulated by the structure and state of compaction of the bacterial nucleoid. Similar observations have previously been made in eukaryotes, but have not so far been reported in bacteria. Building on these important findings, the goals of the CANDLES project are (i) to map the interactions between factors from the NER, BER and an alternative UV damage repair pathway, and structurally characterise these in vitro assembled DNA repair ‘hubs’, (ii) to determine how these three pathways cooperate in vivo to ensure the rapid elimination of damaged nucleobases, and (iii) to investigate the impact of bacterial genome packaging on the distribution and repair of such lesions across the genome. To achieve these goals, our consortium, composed of 3 highly complementary partners, will combine biochemistry, structural biology, advanced fluorescence imaging, analytical chemistry and genome-wide approaches, to address these questions using D. radiodurans as a model system. This fascinating bacterium displays an outstanding DNA repair capacity, and yet possesses a largely ‘classical’ bacterial DNA repair machinery.