Reassembly of shattered chromosomes in Deinococcus radiodurans

Abstract

Deinococcus radiodurans, isolated in the 1950s from canned meat that had gone off despite being sterilized by high-dose radiation, can recover from radiation exposure even though the DNA damage caused completely fragments the genome. How does it achieve this remarkable feat? It is known to carry multiple copies of its genome and quick and effective DNA repair mechanisms. A new study now shows that first, DNA fragments with regions of complementary sequence find each other and initiate synthesis by a DNA polymerase to form long single-stranded ends on the fragments. Then, complementary single-strand tails pair, to regenerate long double-stranded DNA molecules that are processed into the original circular genome. Deinococcus radiodurans is able to withstand high doses of radiation, despite the DNA damage caused. Genome fragments with regions of complementary sequence meet and initiate synthesis by a DNA polymerase to form long single-stranded ends on the fragments. The complementary single-strand tails then pair and regenerate long double-stranded DNA molecules that are processed into the original circular genome. Dehydration or desiccation is one of the most frequent and severe challenges to living cells1. The bacterium Deinococcus radiodurans is the best known extremophile among the few organisms that can survive extremely high exposures to desiccation and ionizing radiation, which shatter its genome into hundreds of short DNA fragments2,3,4,5. Remarkably, these fragments are readily reassembled into a functional 3.28-megabase genome. Here we describe the relevant two-stage DNA repair process, which involves a previously unknown molecular mechanism for fragment reassembly called ‘extended synthesis-dependent strand annealing’ (ESDSA), followed and completed by crossovers. At least two genome copies and random DNA breakage are requirements for effective ESDSA. In ESDSA, chromosomal fragments with overlapping homologies are used both as primers and as templates for massive synthesis of complementary single strands, as occurs in a single-round multiplex polymerase chain reaction. This synthesis depends on DNA polymerase I and incorporates more nucleotides than does normal replication in intact cells. Newly synthesized complementary single-stranded extensions become ‘sticky ends’ that anneal with high precision, joining together contiguous DNA fragments into long, linear, double-stranded intermediates. These intermediates require RecA-dependent crossovers to mature into circular chromosomes that comprise double-stranded patchworks of numerous DNA blocks synthesized before radiation, connected by DNA blocks synthesized after radiation.