Ring-Like Nucleoids and DNA Repair through Error-Free Nonhomologous End Joining in Deinococcus radiodurans

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Shortly after its isolation from canned ground meat in 1956, the bacterium Micrococcus radiodurans, later reclassified as Deinococcus radiodurans, was found to be capable of withstanding radioactive irradiation in doses that are 2 to 3 orders of magnitude higher than those most other organisms can cope with. Following exposure to these irradiation doses as well as to other assaults, such as extreme desiccation, that damage chromatin, each of the genome copies in D. radiodurans is shattered into 150 to 200 fragments (1, 4). The ability to reconstitute the whole genome from multiple fragments in an error-free process is remarkable because homologous recombination pathways of DNA repair cannot occur in the absence of an intact chromosome that acts as a template. The mystery surrounding the resilience of D. radiodurans was intensified following the complete sequencing of its genome, which failed to clarify the genetic elements that promote accurate DNA mending of hundreds of fragments. Specifically, the annotated sequence implied that most of the typical complements of DNA repair proteins are present in D. radiodurans (2, 29). In 2003, we reported our high-resolution electron microscopy results, which indicated that chromosomes in D. radiodurans cells adopt highly condensed ring-like organizations (14). We proposed that within this particularly stable mode of tight DNA packaging, DNA ends generated by double-strand breaks are kept in close spatial proximity, allowing for accurate DNA repair through nonhomologous end joining (NHEJ) (6, 14, 18). This proposal was supported by our observation that, under particular growth conditions that sustain normal proliferation of D. radiodurans cells but completely abolish radioresistance, the ring-like shape of the genome is no longer detected, being instead replaced by a dispersed, irregular conformation (14). In their recent article, Eltsov and Dubochet used cryoelectron microscopy of vitreous sections (CEMOVIS) to examine the structure of D. radiodurans (5). By using this method, the authors found that the nucleoids of exponentially growing cells appear to adopt a diffuse shape, whereas in stationary-phase cells, some local order was detected. Eltsov and Dubochet argue that dense toroidal DNA packaging probably does not exist in D. radiodurans, in contrast to our previous results. On the basis of these observations, it was concluded that the structure of the nucleoid in D. radiodurans does not directly contribute to DNA repair in this bacterium. We do not agree with the interpretation of the experimental data presented in the Eltsov and Dubochet article, nor do we accept the final conclusion. Specifically, we claim that nucleoids in D. radiodurans as well as those in other highly resistant bacterial species do adopt unique conformations and that these conformations represent a sine qua non factor of DNA repair by directly promoting the efficiency and accuracy of NHEJ processes in these organisms. In the following sections, we analyze the experimental data reported in the Eltsov and Dubochet article (5) and juxtapose these data with results derived from other structural techniques. We then proceed to examine the interpretation of the data in light of recently reported findings that directly pertain to the structural basis of DNA repair in D. radiodurans.