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 Ϸ94% 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.T he Gram-positive aerobic bacterium Deinococcus radiodurans R1 (DEIRA) has an extraordinary resistance to ␥-radiation and a wide range of other DNA-damaging conditions, including desiccation and oxidizing agents (1, 2). Ionizing radiation induces DNA double-stranded breaks (DSBs) that are the most lethal form of DNA damage (3). After acute exposures to 10 kGy, early stationary phase (ESP) DEIRA can reassemble its 3.285-Mbp genome, which consists of four haploid genomic copies per cell (4), from hundreds of DNA DSB fragments without lethality or induced mutagenesis (5, 6). Also remarkable is DEIRA's ability to grow at 60 Gy͞h without any discernable effect on its growth rate (7). Because most organisms, generally, can tolerate so few DSBs (8), radiationinduced DSBs and their repair have been difficult to study. In DEIRA, however, there are so many DSBs in fully viable irradiated cells after high-dose irradiation that the steps in DSB repair can be monitored directly in mass culture (5, 9-11). This characteristic has been exploited and used to examine the timing of DNA recombination (5, 10, 12) after high-dose irradiation and has revealed the sequential action of RecA-independent and -dependent pathways during repair (11).Comparative genomic and experimental analyses support the view that DEIRA's extreme radiation resistance phenotype is complex, likely determined collectively by an assortment o...

To determine the potential of DNA array technology for assessing functional gene diversity and distribution, a prototype microarray was constructed with genes involved in nitrogen cycling: nitrite reductase (nirS and nirK) genes, ammonia mono-oxygenase (amoA) genes, and methane mono-oxygenase (pmoA) genes from pure cultures and those cloned from marine sediments. In experiments using glass slide microarrays, genes possessing less than 80 to 85% sequence identity were differentiated under hybridization conditions of high stringency (65°C). The detection limit for nirS genes was approximately 1 ng of pure genomic DNA and 25 ng of soil community DNA using our optimized protocol. A linear quantitative relationship (r 2 ‫؍‬ 0.89 to 0.94) was observed between signal intensity and target DNA concentration over a range of 1 to 100 ng for genomic DNA (or genomic DNA equivalent) from both pure cultures and mixed communities. However, the quantitative capacity of microarrays for measuring the relative abundance of targeted genes in complex environmental samples is less clear due to divergent target sequences. Sequence divergence and probe length affected hybridization signal intensity within a certain range of sequence identity and size, respectively. This prototype functional gene array did reveal differences in the apparent distribution of nir and amoA and pmoA gene families in sediment and soil samples. Our results indicate that glass-based microarray hybridization has potential as a tool for revealing functional gene composition in natural microbial communities; however, more work is needed to improve sensitivity and quantitation and to understand the associated issue of specificity.