title: Comparison of the genomes of deinococcal species using oligonucleotide microarrays.
abstract: The bacterium Deinococcus radiodurans is one of the most resistant organisms to ionizing radiation and other DNAdamaging agents. Although, at present, 30 Deinococcus species have been identified, the whole-genome sequences of most species remain unknown, with the exception of D. radiodurans (DRD), D. geothermalis, and D. deserti. In this study, comparative genomic hybridization (CGH) microarray analysis of three Deinococcus species, D. radiopugnans (DRP), D. proteolyticus (DPL), and D. radiophilus (DRPH), was performed using oligonucleotide arrays based on DRD. Approximately 28%, 14%, and 15% of 3,128 open reading frames (ORFs) of DRD were absent in the genomes of DRP, DPL, and DRPH, respectively. In addition, 162 DRD ORFs were absent in all three species. The absence of 17 randomly selected ORFs was confirmed by a Southern blot. Functional classification showed that the absent genes spanned a variety of functional categories: some genes involved in amino acid biosynthesis, cell envelope, cellular processes, central intermediary metabolism, and DNA metabolism were not present in any of the three deinococcal species tested. Finally, comparative genomic data showed that 120 genes were Deinococcus-specific, not the 230 reported previously. Specifically, ddrD, ddrO, and ddrH genes, previously identified as Deinococcus-specific, were not present in DRP, DPL, or DRPH, suggesting that only a portion of ddr genes are shared by all members of the genus Deinococcus.
authors.affiliation: Radiation Research Division for Biotechnology, Korea Atomic Energy Research Institute, Jeongeup 580-185, Korea.
authors.forename: Sunwook
authors.initials: S
authors.lastname: Jung
authors.forename: Minho
authors.initials: M
authors.lastname: Joe
authors.forename: Seonghun
authors.initials: S
authors.lastname: Im
authors.forename: Dongho
authors.initials: D
authors.lastname: Kim
authors.forename: Sangyong
authors.initials: S
authors.lastname: Lim
mesh_terms: D015139:Blotting, Southern; D055028:Comparative Genomic Hybridization; D004269:DNA, Bacterial / Q000235:genetics*; D034301:Deinococcus / Q000145:classification / Q000235:genetics*; D016680:Genome, Bacterial; D020411:Oligonucleotide Array Sequence Analysis; D016366:Open Reading Frames
chemical_list: D004269:DNA, Bacterial