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Open Access Research article

Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria

Haïtham Sghaier1*, Kaïs Ghedira2, Alia Benkahla2 and Insaf Barkallah1

Author Affiliations

1 Unit of Microbiology and Molecular Biology, National Center for Nuclear Sciences and Technologies (CNSTN), Sidi Thabet Technopark, 2020 Sidi Thabet, Tunisia

2 Group of Bioinformatics and Modelling, Laboratory of Immunology, Vaccinology, and Molecular Genetics, Institute Pasteur of Tunis, 13, place Pasteur BP 74, 1002 Tunis, Tunisia

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BMC Genomics 2008, 9:297  doi:10.1186/1471-2164-9-297

Published: 21 June 2008

Abstract

Background

Ionizing-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.

Results

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. 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.

Conclusion

Our 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.