title: Deinococcus geothermalis: the pool of extreme radiation resistance genes shrinks.
abstract: Bacteria of the genus Deinococcus are extremely resistant to ionizing radiation (IR), ultraviolet light (UV) and desiccation. The mesophile Deinococcus radiodurans was the first member of this group whose genome was completely sequenced. Analysis of the genome sequence of D. radiodurans, however, failed to identify unique DNA repair systems. To further delineate the genes underlying the resistance phenotypes, we report the whole-genome sequence of a second Deinococcus species, the thermophile Deinococcus geothermalis, which at its optimal growth temperature is as resistant to IR, UV and desiccation as D. radiodurans, and a comparative analysis of the two Deinococcus genomes. Many D. radiodurans genes previously implicated in resistance, but for which no sensitive phenotype was observed upon disruption, are absent in D. geothermalis. In contrast, most D. radiodurans genes whose mutants displayed a radiation-sensitive phenotype in D. radiodurans are conserved in D. geothermalis. Supporting the existence of a Deinococcus radiation response regulon, a common palindromic DNA motif was identified in a conserved set of genes associated with resistance, and a dedicated transcriptional regulator was predicted. We present the case that these two species evolved essentially the same diverse set of gene families, and that the extreme stress-resistance phenotypes of the Deinococcus lineage emerged progressively by amassing cell-cleaning systems from different sources, but not by acquisition of novel DNA repair systems. Our reconstruction of the genomic evolution of the Deinococcus-Thermus phylum indicates that the corresponding set of enzymes proliferated mainly in the common ancestor of Deinococcus. Results of the comparative analysis weaken the arguments for a role of higher-order chromosome alignment structures in resistance; more clearly define and substantially revise downward the number of uncharacterized genes that might participate in DNA repair and contribute to resistance; and strengthen the case for a role in survival of systems involved in manganese and iron homeostasis.
authors: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA. makarova@ncbi.nlm.nih.gov
authors: Kira S
authors: KS
authors: Makarova
authors: Marina V
authors: MV
authors: Omelchenko
authors: Elena K
authors: EK
authors: Gaidamakova
authors: Vera Y
authors: VY
authors: Matrosova
authors: Alexander
authors: A
authors: Vasilenko
authors: Min
authors: M
authors: Zhai
authors: Alla
authors: A
authors: Lapidus
authors: Alex
authors: A
authors: Copeland
authors: Edwin
authors: E
authors: Kim
authors: Miriam
authors: M
authors: Land
authors: Konstantinos
authors: K
authors: Mavrommatis
authors: Samuel
authors: S
authors: Pitluck
authors: Paul M
authors: PM
authors: Richardson
authors: Chris
authors: C
authors: Detter
authors: Thomas
authors: T
authors: Brettin
authors: Elizabeth
authors: E
authors: Saunders
authors: Barry
authors: B
authors: Lai
authors: Bruce
authors: B
authors: Ravel
authors: Kenneth M
authors: KM
authors: Kemner
authors: Yuri I
authors: YI
authors: Wolf
authors: Alexander
authors: A
authors: Sorokin
authors: Anna V
authors: AV
authors: Gerasimova
authors: Mikhail S
authors: MS
authors: Gelfand
authors: James K
authors: JK
authors: Fredrickson
authors: Eugene V
authors: EV
authors: Koonin
authors: Michael J
authors: MJ
authors: Daly
mesh_terms: D000595:Amino Acid Sequence; D002876:Chromosomes, Bacterial / Q000235:genetics / Q000528:radiation effects; D004269:DNA, Bacterial / Q000235:genetics; D034301:Deinococcus / Q000235:genetics* / Q000528:radiation effects*; D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial; D007259:Infrared Rays; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction; D017386:Sequence Homology, Amino Acid; D013052:Spectrometry, X-Ray Emission; D014466:Ultraviolet Rays
chemical_list: D004269:DNA, Bacterial