Activation of the OxyR transcription factor by reversible disulfide bond formation.

The OxyR transcription factor is sensitive to oxidation and activates the expression of antioxidant genes in response to hydrogen peroxide in Escherichia coli. Genetic and biochemical studies revealed that OxyR is activated through the formation of a disulfide bond and is deactivated by enzymatic reduction with glutaredoxin 1 (Grx1). The gene encoding Grx1 is regulated by OxyR, thus providing a mechanism for autoregulation. The redox potential of OxyR was determined to be -185 millivolts, ensuring that OxyR is reduced in the absence of stress. These results represent an example of redox signaling through disulfide bond formation and reduction.

Transcriptional regulator of oxidative stress-inducible genes: direct activation by oxidation.

The oxyR gene positively regulates genes induced by oxidative stress in Salmonella typhimurium and Escherichia coli. Purification of the OxyR protein showed that oxidized but not reduced OxyR activates transcription of oxidative stress-inducible genes in vitro. Conversion between the two forms of OxyR is rapid and reversible. Both the oxidized and the reduced forms of the OxyR protein are capable of binding to three diverse sequences upstream of OxyR-regulated promoters, but the interactions of the two forms of OxyR with the promoter regions are different. The results suggest that direct oxidation of the OxyR protein brings about a conformational change by which OxyR transduces an oxidative stress signal to RNA polymerase.

Bacterial defenses against oxidative stress.

Bacteria treated with low doses of oxidants such as hydrogen peroxide adapt to subsequent high doses of these oxidants by inducing the expression of numerous genes. The study of these genes and the roles they play in defending bacteria against oxidative damage has given general insights into what oxidants are hazardous to cells, what cell constituents are damaged by oxidants, and how cells sense and respond to oxidative stress.

Genomic expression programs in the response of yeast cells to environmental changes.

We explored genomic expression patterns in the yeast Saccharomyces cerevisiae responding to diverse environmental transitions. DNA microarrays were used to measure changes in transcript levels over time for almost every yeast gene, as cells responded to temperature shocks, hydrogen peroxide, the superoxide-generating drug menadione, the sulfhydryl-oxidizing agent diamide, the disulfide-reducing agent dithiothreitol, hyper- and hypo-osmotic shock, amino acid starvation, nitrogen source depletion, and progression into stationary phase. A large set of genes (approximately 900) showed a similar drastic response to almost all of these environmental changes. Additional features of the genomic responses were specialized for specific conditions. Promoter analysis and subsequent characterization of the responses of mutant strains implicated the transcription factors Yap1p, as well as Msn2p and Msn4p, in mediating specific features of the transcriptional response, while the identification of novel sequence elements provided clues to novel regulators. Physiological themes in the genomic responses to specific environmental stresses provided insights into the effects of those stresses on the cell.

Oxidative stress.

Much has been learnt about oxidative stress from studies of Escherichia coli. Key regulators of the adaptive responses in this organism are the SoxRS and OxyR transcription factors, which induce the expression of antioxidant activities in response to O2*- and H2O2 stress, respectively. Recently, a variety of biochemical assays together with the characterization of strains carrying mutations affecting the antioxidant activities and the regulators have given general insights into the sources of oxidative stress, the damage caused by oxidative stress, defenses against the oxidative stress, and the mechanisms by which the stress is perceived. These studies have also shown that the oxidative stress responses are intimately coupled to other regulatory networks in the cell.

Small RNAs in Escherichia coli.

Bacterial cells contain several small RNAs (sRNAs) that are not translated. These stable, abundant RNAs act by multiple mechanisms, such as RNA-RNA basepairing, RNA-protein interactions and intrinsic RNA activity, and regulate diverse cellular functions, including RNA processing, mRNA stability, translation, protein stability and secretion.

Identification and molecular analysis of oxyR-regulated promoters important for the bacterial adaptation to oxidative stress.

The oxyR-encoded regulatory protein, OxyR, acts to induce the synthesis of a family of hydrogen peroxide-inducible proteins in Salmonella typhimurium and Escherichia coli. To further define the mechanism by which oxyR regulates the production of these proteins, we identified, mapped, and characterized oxyR-regulated promoters upstream from the S. typhimurium ahp genes (encoding an alkyl hydroperoxide reductase) and the E. coli katG gene (encoding catalase). A set of ahpC promoter deletions was constructed in vitro and analysis of these deletions revealed the location of sequences that are involved in oxyR-mediated induction of the ahpC gene product. DNase I protection studies of the ahpC promoter region revealed an oxyR-dependent footprint that overlapped the sequences found to be important for oxyR control. E. coli strains containing transcriptional fusions between the katG promoter and the lacZ gene showed strongly increased synthesis of beta-galactosidase in response to hydrogen peroxide treatment. This stimulation was found to be oxyR-dependent. DNase I protection studies of the katG promoter region revealed an oxyR-dependent footprint in the same location relative to the basal promoter elements as was observed with the ahpC promoter. Although both the ahpC and katG promoters were shown to bind the same factor, no strong sequence similarities were found between the two, or between the two and a third oxyR-dependent binding site upstream from the E. coli oxyR gene itself.

Characterization of an unstable allele of the Arabidopsis HY4 locus.

The Arabidopsis HY4 gene encodes the nonessential blue light photoreceptor CRY1. Loss-of-function hy4 mutants have an elongated hypocotyl phenotype after germination under blue light. We previously analyzed 20 independent hy4 alleles produced by fast neutron mutagenesis. These alleles were grouped into two classes based on their genetic behavior and corresponding deletion size: (1) null hy4 alleles that were semidominant over wild type and contained small or moderate-sized deletions at HY4 and (2) null hy4 alleles that were recessive lethal and contained large HY4 deletions. Here we describe one additional fast neutron hy4 mutant, B144, that did not fall into either of these two classes. Mutant B144 was isolated as a heterozygote with an intermediate hy4 phenotype. One allele from this mutant, hy4-B144(Delta), contains a large deletion at HY4 and is recessive lethal. The other allele from this mutant, HY4-B144*, appears to be intact and functional but is unstable and spontaneously converts to a nonfunctional hy4 allele. In addition, HY4-B144* is lethal in homozygotes and suppresses local recombination. We discuss genetic and epigenetic mechanisms that may account for the unusual behavior of the HY4-B144* allele.

Redox sensing by prokaryotic transcription factors.

Prokaryotic cells employ redox-sensing transcription factors to detect elevated levels of reactive oxygen species and regulate expression of antioxidant genes. In Escherichia coli, two such transcription factors, OxyR and SoxR, have been well characterized. The OxyR protein contains a thiol-disulfide redox switch to sense hydrogen peroxide. The SoxR protein uses a 2Fe-2S cluster to sense superoxide generated by redox-cycling agents, as well as to sense nitric oxide. Both proteins are turned on and off with very fast kinetics (approximate minutes), allowing rapid cellular responses to oxidative stress. The mechanisms by which these and other prokaryotic proteins sense redox signals have provided useful paradigms for understanding redox signal transduction in eukaryotic cells.

Transcriptional regulators of oxidative stress-inducible genes in prokaryotes and eukaryotes.

It appears that redox regulation is an important mechanism for the control of transcription factor activation. The role of oxidation-reduction is probably determined in part by the structure of the transcription factors. For example, the presence of cysteine residues within the DNA binding sites may sensitize a transcription factor to ROS. The ROS-mediated regulation of transcription factors is specific, some ROS are more efficient than other ROS in activating defined regulators. While the protective antioxidant responses induced by ROS in prokaryotes and eukaryotes are rather conserved (for example, SOD, HSP...), the regulators for these genes do not appear to be conserved. Further studies designed to fully characterize these regulators and understand the subtle mechanisms involved in redox gene regulation are ongoing, and should provide the theoretical basis for clinical approaches using antioxidant therapies in human diseases in which oxidative stress is implicated.

Transcriptional regulators of the oxidative stress response in prokaryotes and eukaryotes.

Bacteria, yeast and cells of higher eukaryotes specifically induce the expression of genes encoding antioxidant defenses when exposed to reactive oxygen species. Recent studies have also suggested that reactive oxygen intermediates play a role as second messengers in signal transduction pathways. Therefore, cells must possess regulators that sense oxidant signals and transduce the signals into changes in gene expression. This review provides an overview of the transcription factors in Escherichia coli, Saccharomyces cerevisiae and mammalian cells that govern the response to oxidative stress. Some of the regulators function primarily as regulators of antioxidant genes while other regulators of the oxidative stress response also regulate genes important for metal homeostasis or cell metabolism during aerobic or anaerobic growth.

Evaluation of a quantitative solid phase reagent system for determination of blood analytes. Experiences with the analytes: LDH, bilirubin, BUN, glucose, and uric acid.

In the first part of the Seralyzer system evaluation the precision and accuracy was studied with a total of 1245 clinical specimens, various commercial control sera, and pooled human sera. The calculated overall precision (between-run, and within-run) and day-to-day precision (% CV) was found to be within 3.0 to 5.4 for glucose, 2.8 to 7.1 for BUN, 1.5 to 6.2 for uric acid, 5.3 to 7.5 for bilirubin, and 3.2 to 8.6 for LDH. The clinical values are in agreement with values from respective comparative methods, as indicated by the regression statistics. The analysis of Seralyzer accuracy data using quality control sera showed in some cases a between-method difference. Supporting studies simulating additional important clinical situations showed that the clinical values for BUN, glucose, and uric acid of approximately 200 specimens from the emergency ward correlated with the respective comparative method values. In this phase of the study we verified that the instrument calibration was stable for a 24-hour period and that there is no effect of module (test) change on precision of Seralyzer determinations. The intra- and inter-laboratory performance in general practitioners' laboratories could be demonstrated using quality control sera.

Regulating bacterial transcription with small RNAs.

In recent years, the combinations of computational and molecular approaches have led to the identification of an increasing number of small, noncoding RNAs encoded by bacteria and their plasmids and phages. Most of the characterized small RNAs have been shown to operate at a posttranscriptional level, modulating mRNA stability or translation by base-pairing with the 5' regions of the target mRNAs. However, a subset of small RNAs has been found to regulate transcription. One example is the abundant 6S RNA that has been proposed to compete for DNA binding of RNA polymerase by mimicking the open conformation of promoter DNA. Other small RNAs affect transcription termination via base-pairing interactions with sequences in the mRNA. Here, we discuss current understanding and questions regarding the roles of small RNAs in regulating transcription.

Effects of peroxides on susceptibilities of Escherichia coli and Mycobacterium smegmatis to isoniazid.

Escherichia coli strains were previously found to be susceptible to the antituberculosis drug isonicotinic acid hydrazide (isoniazid [INH]) when they carried certain mutations that also sensitize them to peroxides: a deletion in oxyR, a redox-sensitive regulator of hydrogen peroxide-inducible genes, or mutations in both katG and ahpCF, OxyR-regulated genes encoding hydroperoxidase I, and an alkyl hydroperoxide reductase. To test whether INH, like peroxides, activates OxyR, the effect of INH on OxyR regulation was examined. Primer extension assays showed that transcription of the OxyR-regulated oxyS gene was not significantly induced by INH in wild-type cells, indicating that INH does not activate OxyR. However, the INH-susceptible katG ahpCF mutant strain was found to have constitutively high levels of oxyS transcription. This suggested that the lack of peroxidase expression in these strains allows endogenous oxidants to accumulate, and this leads not only to constitutive OxyR activation but also to INH susceptibility. Consistent with this concept, hydrogen peroxide or cumene hydroperoxide potentiated the INH susceptibilities of wild-type cells, while the antioxidant ascorbic acid protected the susceptible katG ahpCF mutant strain from INH. Superoxide radicals, generated by paraquat, did not enhance the INH susceptibilities of wild-type cells. Hydrogen peroxide also potentiated the INH susceptibilities of susceptible and resistant (katG mutant) Mycobacterium smegmatis strains. Our results suggest that INH is converted to a more active drug by reaction with peroxides and that the INH susceptibilities of enterobacteria and mycobacteria are mechanistically related.

Roles of the glutathione- and thioredoxin-dependent reduction systems in the Escherichia coli and saccharomyces cerevisiae responses to oxidative stress.

The glutathione- and thioredoxin-dependent reduction systems are responsible for maintaining the reduced environment of the Escherichia coli and Saccharomyces cerevisiae cytosol. Here we examine the roles of these two cellular reduction systems in the bacterial and yeast defenses against oxidative stress. The transcription of a subset of the genes encoding glutathione biosynthetic enzymes, glutathione reductases, glutaredoxins, thioredoxins, and thioredoxin reductases, as well as glutathione- and thioredoxin-dependent peroxidases is clearly induced by oxidative stress in both organisms. However, only some strains carrying mutations in single genes are hypersensitive to oxidants. This is due, in part, to the redundant effects of the gene products and the overlap between the two reduction systems. The construction of strains carrying mutations in multiple genes is helping to elucidate the different roles of glutathione and thioredoxin, and studies with such strains have recently revealed that these two reduction systems modulate the activities of the E. coli OxyR and SoxR and the S. cerevisiae Yap1p transcriptional regulators of the adaptive responses to oxidative stress.

OxyR: a regulator of antioxidant genes.

The study of the bacterial response to hydrogen peroxide has given general insights into how cells defend against deleterious oxidants. Treatment of Salmonella typhimurium and Escherichia coli cells with low doses of hydrogen peroxide results in the induction of 30 proteins and resistance to killing by higher doses of hydrogen peroxide. The expression of nine of the hydrogen peroxide-inducible proteins, including the antioxidant enzymes catalase, glutathione reductase and an alkyl hydroperoxide reductase, is controlled by the positive regulator oxyR. Strains carrying deletions of the oxyR gene are hypersensitive to hydrogen peroxide and have increased levels of spontaneous mutagenesis during aerobic growth. The OxyR protein is homologous to the LysR-NodD family of bacterial regulatory proteins and binds to the promoters of oxyR-regulated genes. The oxidized, but not the reduced, form of the OxyR protein activates transcription of oxyR-regulated genes in vitro, suggesting that direct oxidation of the OxyR protein brings about a conformation change by which OxyR senses an oxidative stress signal and then activates the expression of defense activities.

6S RNA regulates E. coli RNA polymerase activity.

The E. coli 6S RNA was discovered more than three decades ago, yet its function has remained elusive. Here, we demonstrate that 6S RNA associates with RNA polymerase in a highly specific and efficient manner. UV crosslinking experiments revealed that 6S RNA directly contacts the sigma70 and beta/beta' subunits of RNA polymerase. 6S RNA accumulates as cells reach the stationary phase of growth and mediates growth phase-specific changes in RNA polymerase. Stable association between sigma70 and core RNA polymerase in extracts is only observed in the presence of 6S RNA. We show 6S RNA represses expression from a sigma70-dependent promoter during stationary phase. Our results suggest that the interaction of 6S RNA with RNA polymerase modulates sigma70-holoenzyme activity.

High intensity and blue light regulated expression of chimeric chalcone synthase genes in transgenic Arabidopsis thaliana plants.

To establish a genetic system for dissection of light-mediated signal transduction in plants, we analyzed the light wavelengths and promoter sequences responsible for the light-induced expression of the Arabidopsis thaliana chalcone synthase (CHS) promoter fused to the beta-glucuronidase (GUS) marker gene. Transgenic A. thaliana lines carrying 1975, 523, 186, and 17 bp of the CHS promoter fused to the GUS gene were generated, and the expression of these chimeric genes was monitored in response to high intensity light in mature plants and to different wavelengths of light in seedlings. Fusion constructs containing 1975 and 523 bp of CHS promoter sequence behaved identically to the endogenous CHS gene under all conditions. Expression of these constructs was induced specifically in response to high intensity white light and blue light. The response to blue light was seen in the presence of the Pfr form of phytochrome. Fusion constructs containing 186 bp of promoter sequence showed reduced basal levels of expression and only weak stimulation by blue light but were induced significantly by high intensity white light. These analyses showed that the expression of the A. thaliana CHS gene is responsive to a specific blue light receptor and that sequences between -523 and -186 bp are required for optimal basal and blue light-induced expression of this gene. The experiments lay the foundation for a simple genetic screen for light response mutants.