UV irradiation induces homologous recombination genes in the model archaeon, Halobacterium sp. NRC-1

Abstract

Background: A variety of strategies for survival of UV irradiation are used by cells, ranging from repair of UV-damaged DNA, cell cycle arrest, tolerance of unrepaired UV photoproducts, and shielding from UV light. Some of these responses involve UV-inducible genes, including the SOS response in bacteria and an array of genes in eukaryotes. To address the mechanisms used in the third branch of life, we have studied the model archaeon, Halobacterium sp. strain NRC-1, which tolerates high levels of solar radiation in its natural hypersaline environment.

Results: Cells were irradiated with 30-70 J/m(2) UV-C and an immunoassay showed that the resulting DNA damage was largely repaired within 3 hours in the dark. Under such conditions, transcriptional profiling showed the most strongly up-regulated gene was radA1, the archaeal homolog of rad51/recA, which was induced 7-fold. Additional genes involved in homologous recombination, such as arj1 (recJ-like exonuclease), dbp (eukaryote-like DNA binding protein of the superfamily I DNA and RNA helicases), and rfa3 (replication protein A complex), as well as nrdJ, encoding for cobalamin-dependent ribonucleotide reductase involved in DNA metabolism, was also significantly induced in one or more of our experimental conditions. Neither prokaryotic nor eukaryotic excision repair gene homologs were induced and there was no evidence of an SOS-like response.

Conclusion: These results show that homologous recombination plays an important role in the cellular response of Halobacterium sp. NRC-1 to UV damage. Homologous recombination may permit rescue of stalled replication forks, and/or facilitate recombinational repair. In either case, this provides a mechanism for the observed high-frequency recombination among natural populations of halophilic archaea.

Figure 1

Survival of model organisms exposed to UV-C radiation. The percent survival (y axis logarithmic scale) is plotted versus dose of UV radiation (x axis linear scale) for human fibroblasts [41], Escherichia coli [42], Saccharomyces cerevisiae [43], Halobacterium sp. NRC-1 (in the dark or in presence of visible light) [11], and Deinococcus radiodurans [44].

Figure 2

Repair of the two principle UV-induced photoproducts in Halobacterium sp. Repair of cyclobutane pyrimidine dimers (CPDs) and 6-4 photoproducts (6-4 pp) was measured after a UV-C dose of 50 J/m². About 55 % of CPDs and 25 % of 6-4 pp remain unrepaired after 1 hour; after 3 hours, the percentages are 28% and 2% respectively.

Figure 3

Whole genome microarray hybridization results comparing UV-irradiated cells to control cells. Irradiated cells received a UV-C dose of 30 J/m² and incubated in the dark for 1 h (upper panel) and 3 h (lower panel). Control cells were treated exactly the same except for UV-irradiation. For each ORF represented on the array, the logarithm of the hybridization ratio of UV-irradiated cells (Cy5-labeled cDNA) to control cells (Cy3-labeled cDNA) is displayed in black marks on the y axis. The location of ORFs within the entire 2.6-megabase genome maps on the x axis. Expression ratios of selected genes are indicated.