The genome-wide transcription profile of Escherichia coli cells treated with hydrogen peroxide was examined with a DNA microarray composed of 4,169 E. coli open reading frames. By measuring gene expression in isogenic wild-type and oxyR deletion strains, we confirmed that the peroxide response regulator OxyR activates most of the highly hydrogen peroxide-inducible genes. The DNA microarray measurements allowed the identification of several new OxyR-activated genes, including the hemH heme biosynthetic gene; the six-gene suf operon, which may participate in Fe-S cluster assembly or repair; and four genes of unknown function. We also identified several genes, including uxuA, encoding mannonate hydrolase, whose expression might be repressed by OxyR, since their expression was elevated in the ⌬oxyR mutant strain. In addition, the induction of some genes was found to be OxyR independent, indicating the existence of other peroxide sensors and regulators in E. coli. For example, the isc operon, which specifies Fe-S cluster formation and repair activities, was induced by hydrogen peroxide in strains lacking either OxyR or the superoxide response regulators SoxRS. These results expand our understanding of the oxidative stress response and raise interesting questions regarding the nature of other regulators that modulate gene expression in response to hydrogen peroxide.

We examined the genomewide transcriptional responses of Escherichia coli treated with nitrosylated glutathione or the nitric oxide (NO)-generator acidified sodium nitrite (NaNO 2) during aerobic growth. These assays showed that NorR, a homolog of NOresponsive transcription factors in Ralstonia eutrophus, and Fur, the global repressor of ferric ion uptake, are major regulators of the response to reactive nitrogen species. In contrast, SoxR and OxyR, regulators of the E. coli defenses against superoxide-generating compounds and hydrogen peroxide, respectively, have minor roles. Moreover, additional regulators of the E. coli response to reactive nitrogen species remain to be identified because several of the induced genes were regulated normally in norR, fur, soxRS, and oxyR mutant strains. We propose that the E. coli transcriptional response to reactive nitrogen species is a composite response mediated by the modification of multiple transcription factors containing iron or redox-active cysteines, some specifically designed to sense NO and its derivatives and others that are collaterally activated by the reactive nitrogen species.

A nearly complete collection of 4,290Escherichia coli open reading frames was amplified and arrayed in high density on glass slides. To exploit this reagent, conditions for RNA isolation from E. coli cells, cDNA production with attendant fluorescent dye incorporation, DNA-DNA hybridization, and hybrid quantitation have been established. A brief isopropyl-␤-D-thiogalactopyranoside (IPTG) treatment elevated lacZ, lacY, and lacA transcript content about 30-fold; in contrast, most other transcript titers remained unchanged. Distinct RNA expression patterns between E. coli cultures in the exponential and transitional phases of growth were catalogued, as were differences associated with culturing in minimal and rich media. The relative abundance of each transcript was estimated by using hybridization of a genomic DNA-derived, fluorescently labeled probe as a correction factor. This inventory provided a quantitative view of the steady-state level of each mRNA species. Genes the expression of which was detected by this method were enumerated, and results were compared with the current understanding of E. coli physiology.Escherichia coli K-12 has been exhaustively studied for over 50 years. Early experiments measured the molecular fluxes from small compounds into macromolecular constituents (33). These studies were followed by others in which small molecule pools of central metabolic building blocks (21), nucleotides (3), and amino acids were enumerated. The levels of several macromolecular components, including individual species of proteins (26), have been measured. Such measurements of the steady state provide a census of the cellular content, while changes upon imposition of a stress catalogue the cell's fight for survival. This response to an insulting or adverse condition can take many forms, from relieving end product inhibition to derepressing transcription (20).In E. coli, experiments to define stress-related, global regulatory responses have often relied upon either the isolation of operon fusions induced by a particular stress (16) or proteomic measures in which the protein fractions from stressed and unstressed cultures are separated by a two-dimensional method prior to comparison (37). Each method has an inherent technological hurdle; the map location of responsive gene fusions must be ascertained precisely, while induced or repressed proteins excised from the two-dimensional gels must be correctly identified.Alternatively, mRNA measurements utilizing techniques such as hybridization to DNA and primer extension have allowed the monitoring of individual gene's expression profiles. Recently, expression profiling of most yeast genes has been reported (8, 40); such measurements were facilitated by highdensity arrays of individual genes and specific labeling of cDNA copies of eukaryotic mRNA by using poly(A) tail-specific primers. Thus, the lack of a poly(A) tail and the extremely short bacterial mRNA half-life represent hurdles for the application of DNA microarray technology to prokaryotic research. Nonetheless...