title: Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation.
abstract: Deinococcus radiodurans R1 (DEIRA) is a bacterium best known for its extreme resistance to the lethal effects of ionizing radiation, but the molecular mechanisms underlying this phenotype remain poorly understood. To define the repertoire of DEIRA genes responding to acute irradiation (15 kGy), transcriptome dynamics were examined in cells representing early, middle, and late phases of recovery by using DNA microarrays covering approximately 94% of its predicted genes. At least at one time point during DEIRA recovery, 832 genes (28% of the genome) were induced and 451 genes (15%) were repressed 2-fold or more. The expression patterns of the majority of the induced genes resemble the previously characterized expression profile of recA after irradiation. DEIRA recA, which is central to genomic restoration after irradiation, is substantially up-regulated on DNA damage (early phase) and down-regulated before the onset of exponential growth (late phase). Many other genes were expressed later in recovery, displaying a growth-related pattern of induction. Genes induced in the early phase of recovery included those involved in DNA replication, repair, and recombination, cell wall metabolism, cellular transport, and many encoding uncharacterized proteins. Collectively, the microarray data suggest that DEIRA cells efficiently coordinate their recovery by a complex network, within which both DNA repair and metabolic functions play critical roles. Components of this network include a predicted distinct ATP-dependent DNA ligase and metabolic pathway switching that could prevent additional genomic damage elicited by metabolism-induced free radicals.
authors.affiliation: Environmental Sciences and Life Sciences Divisions, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA.
authors.forename: Yongqing
authors.initials: Y
authors.lastname: Liu
authors.forename: Jizhong
authors.initials: J
authors.lastname: Zhou
authors.forename: Marina V
authors.initials: MV
authors.lastname: Omelchenko
authors.forename: Alex S
authors.initials: AS
authors.lastname: Beliaev
authors.forename: Amudhan
authors.initials: A
authors.lastname: Venkateswaran
authors.forename: Julia
authors.initials: J
authors.lastname: Stair
authors.forename: Liyou
authors.initials: L
authors.lastname: Wu
authors.forename: Dorothea K
authors.initials: DK
authors.lastname: Thompson
authors.forename: Dong
authors.initials: D
authors.lastname: Xu
authors.forename: Igor B
authors.initials: IB
authors.lastname: Rogozin
authors.forename: Elena K
authors.initials: EK
authors.lastname: Gaidamakova
authors.forename: Min
authors.initials: M
authors.lastname: Zhai
authors.forename: Kira S
authors.initials: KS
authors.lastname: Makarova
authors.forename: Eugene V
authors.initials: EV
authors.lastname: Koonin
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Daly
mesh_terms: D000595:Amino Acid Sequence; D002455:Cell Division / Q000528:radiation effects; D004260:DNA Repair / Q000235:genetics / Q000528:radiation effects*; D034301:Deinococcus / Q000235:genetics* / Q000254:growth & development / Q000528:radiation effects*; D015964:Gene Expression Regulation, Bacterial / Q000528:radiation effects*; D008969:Molecular Sequence Data; D009876:Operon / Q000528:radiation effects; D011839:Radiation, Ionizing; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid; D014158:Transcription, Genetic / Q000528:radiation effects*