Abstract
BackgroundIonizing-radiation-resistant bacteria (IRRB) show a surprising capacity for adaptation to ionizing radiation and desiccation. Positive Darwinian selection is expected to play an important role in this trait, but no data are currently available regarding the role of positive adaptive selection in resistance to ionizing-radiation and tolerance of desiccation. We analyzed the four known genome sequences of IRRB (Deinococcus geothermalis, Deinococcus radiodurans, Kineococcus radiotolerans, and Rubrobacter xylanophilus) to determine the role of positive Darwinian selection in the evolution of resistance to ionizing radiation and tolerance of desiccation.ResultsWe used the programs MultiParanoid and DnaSP to deduce the sets of orthologs that potentially evolved due to positive Darwinian selection in IRRB. We find that positive selection targets 689 ortholog sets of IRRB. Among these, 58 ortholog sets are absent in ionizing-radiation-sensitive bacteria (IRSB: Escherichia coli and Thermus thermophilus). The most striking finding is that all basal DNA repair genes in IRRB, unlike many of their orthologs in IRSB, are subject to positive selection.ConclusionOur results provide the first in silico prediction of positively selected genes with potential roles in the molecular basis of resistance to γ-radiation and tolerance of desiccation in IRRB. Identification of these genes provides a basis for future experimental work aimed at understanding the metabolic networks in which they participate.
Highlights
Ionizing-radiation-resistant bacteria (IRRB) show a surprising capacity for adaptation to ionizing radiation and desiccation
The former result based on a collection of ionizing-radiation-sensitive strains of D. radiodurans is consistent with evidence that dried bacterial cells exhibit a substantial number of DNA double-strand breaks (DSBs), single-strand breaks, and DNA crosslinks [11], DNA damage that is observed following exposure to ionizing radiation [12]
Ionizing radiation and desiccation introduce similar types of DNA damage – DNA DSBs – in D. radiodurans [7]. The latter result based on the mutational inactivation of the genes DR_1172 and DR_B0118 considerably strengthens the hypothesis that the D. radiodurans's desiccation tolerance could be a consequence of this organism's adaptation to ionizing radiation, that the origin of ionizing-radiation resistance in bacteria can be explained as an adaptation to environmental radiation [13]
Summary
We used the programs MultiParanoid and DnaSP to deduce the sets of orthologs that potentially evolved due to positive Darwinian selection in IRRB. We find that positive selection targets 689 ortholog sets of IRRB. 58 ortholog sets are absent in ionizing-radiationsensitive bacteria (IRSB: Escherichia coli and Thermus thermophilus). The most striking finding is that all basal DNA repair genes in IRRB, unlike many of their orthologs in IRSB, are subject to positive selection
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