Background Mutational Features of the Radiation-Resistant Bacterium Deinococcus radiodurans

Abstract

Deinococcus bacteria are extremely resistant to radiation, oxidation, and desiccation. Resilience to these factors has been suggested to be due to enhanced damage prevention and repair mechanisms, as well as highly efficient antioxidant protection systems. Here, using mutation-accumulation experiments, we find that the GC-rich Deinococcus radiodurans has an overall background genomic mutation rate similar to that of E. coli, but differs in mutation spectrum, with the A/T to G/C mutation rate (based on a total count of 88 A:T → G:C transitions and 82 A:T → C:G transversions) per site per generation higher than that in the other direction (based on a total count of 157 G:C → A:T transitions and 33 G:C → T:A transversions). We propose that this unique spectrum is shaped mainly by the abundant uracil DNA glycosylases reducing G:C → A:T transitions, adenine methylation elevating A:T → C:G transversions, and absence of cytosine methylation decreasing G:C → A:T transitions. As opposed to the greater than 100× elevation of the mutation rate in MMR(-) (DNA Mismatch Repair deficient) strains of most other organisms, MMR(-) D. radiodurans only exhibits a 4-fold elevation, raising the possibility that other DNA repair mechanisms compensate for a relatively low-efficiency DNA MMR pathway. As D. radiodurans has plentiful insertion sequence (IS) elements in the genome and the activities of IS elements are rarely directly explored, we also estimated the insertion (transposition) rate of the IS elements to be 2.50 × 10(-3) per genome per generation in the wild-type strain; knocking out MMR did not elevate the IS element insertion rate in this organism.

Keywords: DNA mismatch repair; Deinococcus radiodurans; mutation accumulation; mutation rate; mutation spectrum.