An Analysis of Bipyrimidine Limitations as Photoprotective Genome Strategies in Halophilic Archaea

Haloarchaea experience high levels of ultraviolet (UV) light in their environments and demonstrate resistance to UV irradiation under laboratory conditions, yet the mechanisms underlying haloarchaeal photoprotection remain unclear. Herein, we consider genomic signatures as a potential photoprotective strategy. One of the predominant forms of UV-induced DNA damage is cyclobutane pyrimidine dimer (CPD) formation at pyrimidine dinucleotides, particularly at thymine-thymine (TT) and thymine-cytosine (TC) sites. A survey of all haloarchaea genomes available in the NCBI database demonstrates that on average, haloarchaea feature higher proportions of guanine (G) and C nucleotides within their genomes than non-halophilic microorganisms. Altogether, these notions have led us, among others, to consider whether the high G+C content seen in haloarchaea serves a photoprotective function through limiting T nucleotides. We reason that if halophiles have evolved a genomic strategy to attenuate the damaging effects of UV radiation, then the incidences of the most photoreactive dinucleotide species should be limited in their genomes. Therefore, we designed a program to determine the frequencies of the four pyrimidine dinucleotides (TT, TC, CT, and CC) for samples of haloarchaea, archaea, and bacteria (n=29 each). The outputs were used to generate a single metric quantifying the “genomic photoreactivity” of each sample; we then employed statistical methods to compare results between the three sample groups. Our findings do not support the notion that the UV resistance seen in haloarchaea can be attributed to a genomic strategy.