Mutations in Escherichia coli that effect sensitivity to oxygen

Aerobic Conditions and Endogenous Reactive Oxygen Species Reduce the Production of Infectious MS2 Phage by Escherichia coli

Most of the defective/non-infectious enteric phages and viruses that end up in wastewater originate in human feces. Some of the causes of this high level of inactivity at the host stage are unknown. There is a significant gap between how enteric phages are environmentally transmitted and how we might design molecular tools that would only detect infectious ones. Thus, there is a need to explain the low proportion of infectious viral particles once replicated. By analyzing lysis plaque content, we were able to confirm that, under aerobic conditions, Escherichia coli produce low numbers of infectious MS2 phages (I) than the total number of phages indicated by the genome copies (G) with an I/G ratio of around 2%. Anaerobic conditions of replication and ROS inhibition increase the I/G ratio to 8 and 25%, respectively. These data cannot only be explained by variations in the total numbers of MS2 phages produced or in the metabolism of E. coli. We therefore suggest that oxidative damage impacts the molecular replication and assembly of MS2 phages.

A second class I ribonucleotide reductase in Enterobacteriaceae: characterization of the Salmonella typhimurium enzyme

The nrdA and nrdB genes of Escherichia coli and Salmonella typhimurium encode the R1 and R2 proteins that together form an active class I ribonucleotide reductase. Both organisms contain two additional chromosomal genes, nrdE and nrdF, whose corresponding protein sequences show some homology to the products of the genes nrdA and nrdB. When present on a plasmid, nrdE and nrdF together complement mutations in nrdA or nrdB. We have now obtained in nearly homogeneous form the two proteins encoded by the S. typhimurium nrdE and nrdF genes (R1E and R2F). They correspond to the R1 and R2 proteins. Each protein is a homodimer. Together they catalyze the reduction of CDP to dCDP, using dithiothreitol or reduced glutaredoxin, but not thioredoxin, as an electron donor. CDP reduction is strongly stimulated by low concentrations of dATP, presumably acting as an allosteric effector. Protein R2F contains an antiferromagnetically coupled dinuclear iron center and a tyrosyl free radical. The E. coli and S. typhimurium chromosome thus have maintained the information for a potentially active additional class I ribonucleotide reductase, whose role in vivo is as yet unknown. The allosteric regulation of this enzyme differs from that of the normally expressed reductase.

Functions of the gene products of Escherichia coli

A list of currently identified gene products of Escherichia coli is given, together with a bibliography that provides pointers to the literature on each gene product. A scheme to categorize cellular functions is used to classify the gene products of E. coli so far identified. A count shows that the numbers of genes concerned with small-molecule metabolism are on the same order as the numbers concerned with macromolecule biosynthesis and degradation. One large category is the category of tRNAs and their synthetases. Another is the category of transport elements. The categories of cell structure and cellular processes other than metabolism are smaller. Other subjects discussed are the occurrence in the E. coli genome of redundant pairs and groups of genes of identical or closely similar function, as well as variation in the degree of density of genetic information in different parts of the genome.

Escherichia coli genes involved in cell survival during dormancy: role of oxidative stress

When Escherichia coli cells reach stationary phase of growth, specific gene products are synthesized that protect cells while dormant. "Aged" cells may remain viable in cultures for years. For example, agar cultures stored for 38 years still had more than 10(5) viable cells/ml. However, when specific mutants were cultured, the population of these mutants dropped sharply after 4-10 days. This defect is termed "Stationary-Phase-Death". Each mutant strain was hypersensitive to near-ultraviolet radiation and other oxidative agents. Bovine catalase rescued many of the mutants from death in dormancy, suggesting that specific gene products protect "aged" cells against oxidative damage.

Oxygen sensitivity of an Escherichia coli mutant

Genetic evidence indicates that Oxys-6, an oxygen-sensitive mutant of Escherichia coli AB1157, is defective in the region of the hemB locus. Oxys-6 is capable of growth under aerobic conditions only if cultures are initiated at low-inoculum levels. Aerobic liquid cultures are limited to a cell density of 10(7) cells per ml by the accumulation of a metabolically produced, low-molecular-weight, heat-stable material in complex organic media. Both Oxys-6 and AB1157 cells produce the material, but only aerobic cultures of the mutant are inhibited by it. The material is produced by both intact cells and cell extracts in complex media. This reaction also occurs when the amino acid L-lysine is substituted for complex media.

Oxidative stress responses in Escherichia coli and Salmonella typhimurium

Oxidative stress is strongly implicated in a number of diseases, such as rheumatoid arthritis, inflammatory bowel disorders, and atherosclerosis, and its emerging as one of the most important causative agents of mutagenesis, tumorigenesis, and aging. Recent progress on the genetics and molecular biology of the cellular responses to oxidative stress, primarily in Escherichia coli and Salmonella typhimurium, is summarized. Bacteria respond to oxidative stress by invoking two distinct stress responses, the peroxide stimulon and the superoxide stimulon, depending on whether the stress is mediated by peroxides or the superoxide anion. The two stimulons each contain a set of more than 30 genes. The expression of a subset of genes in each stimulon is under the control of a positive regulatory element; these genes constitute the OxyR and SoxRS regulons. The schemes of regulation of the two regulons by their respective regulators are reviewed in detail, and the overlaps of these regulons with other stress responses such as the heat shock and SOS responses are discussed. The products of Oxy-R- and SoxRS-regulated genes, such as catalases and superoxide dismutases, are involved in the prevention of oxidative damage, whereas others, such as endonuclease IV, play a role in the repair of oxidative damage. The potential roles of these and other gene products in the defense against oxidative damage in DNA, proteins, and membranes are discussed in detail. A brief discussion of the similarities and differences between oxidative stress responses in bacteria and eukaryotic organisms concludes this review.

The anaerobic ribonucleoside triphosphate reductase from Escherichia coli requires S-adenosylmethionine as a cofactor

Extracts from anaerobically grown Escherichia coli contain an oxygen-sensitive activity that reduces CTP to dCTP in the presence of NADPH, dithiothreitol, Mg2+ ions, and ATP, different from the aerobic ribonucleoside diphosphate reductase (2'-deoxyribonucleoside-diphosphate: oxidized-thioredoxin 2'-oxidoreductase, EC 1.17.4.1) present in aerobically grown E. coli. After fractionation, the activity required at least five components, two heat-labile protein fractions and several low molecular weight fractions. One protein fraction, suggested to represent the actual ribonucleoside triphosphate reductase was purified extensively and on denaturing gel electrophoresis gave rise to several defined protein bands, all of which were stained by a polyclonal antibody against one of the two subunits (protein B1) of the aerobic reductase but not by monoclonal anti-B1 antibodies. Peptide mapping and sequence analyses revealed partly common structures between two types of protein bands but also suggested the presence of an additional component. Obviously, the preparations are heterogeneous and the structure of the reductase is not yet established. The second, crude protein fraction is believed to contain several ancillary enzymes required for the reaction. One of the low molecular weight components is S-adenosylmethionine; a second component is a loosely bound metal. We propose that S-adenosylmethionine together with a metal participates in the generation of the radical required for the reduction of carbon 2' of the ribosyl moiety of CTP.

Measurement of in vivo expression of nrdA and nrdB genes of Escherichia coli by using lacZ gene fusions

By using a promoter probe plasmid we investigated expression of the linked nrdA and nrdB genes coding for the two different subunits of the ribonucleoside diphosphate reductase enzyme of Escherichia coli. For this reason, nrdA-lacZ, nrdAB-lacZ and nrdB-lacZ fusions were constructed. Results obtained indicate that the nrdB gene has a promoter from which it may be transcribed independently of the nrdA gene. Furthermore, the nrdB gene may also be transcribed from the nrdA promoter. The expression of the nrdB gene is about 14-fold higher from the nrdA promoter than from its own promoter. The induction of both nrdA and nrdB genes by DNA-damaging agents in the wild-type strain as well as in several SOS mutants was also studied; nrdA gene expression was increased by these treatments in RecA+, RecA-, and LexAInd- strains, although in both RecA- and LexAInd- mutants the nrdA gene expression was considerably lower than that in RecA+ cells. nrdB gene expression was stimulated by DNA damage only when its transcription was from the nrdA promoter, but there was no effect when nrdB was transcribed from its own promoter. In addition, the basal level of nrdA-lacZ and nrdAB-lacZ fusions was reduced in strains containing either RecA- and LexAInd- mutations or a multicopy plasmid carrying the lexA+ gene, whereas the presence of a LexA51Def mutation increased the constitutive expression of both fusions. On the contrary, the basal level of the nrdB-lacZ fusion remained constant in all these strains. Together these results indicate that induction of the SOS response enhances expression of the nrd genes from the nrdA promoter.

The use of microbial membranes to achieve anaerobiosis

The cytoplasmic membranes of many aerobic and facultative bacteria contain enzymes that catalyze the reduction of dissolved oxygen to water. Preparations of small particles derived from such membranes can be filter sterilized without loss of the oxygen-reducing enzymes. These particle preparations can be used to produce anaerobic conditions in a variety of biological environments. They have been shown to stimulate the growth of many anaerobic bacteria and can also be used to stabilize oxygen-sensitive chemical reagents. The particle preparations are stable for long periods of time. They are functional over a pH range and temperature range frequently encountered in biological systems. Various techniques for using the particles are presented. The advantages and limitations of this new approach to achieving oxygen-free conditions are discussed.

Microbial stress proteins

There is general agreement that a function, perhaps the major function, of stress proteins under normal physiological conditions is to help assembly and disassembly of protein complexes and to catalyse protein-translocation processes. It remains unclear, however, as to what role these processes play in stressed cells. It could be that cells under stress produce abnormal, misfolded or otherwise damaged proteins and that increased synthesis of stress proteins is required to counter protein modifications. A role for stress proteins in recovery of cells from stress, as opposed to a role in helping cells to withstand a lethal stress, is thus suggested. The intracellular location of stress proteins, in the unstressed and stressed cell, is worthy of further studies. Members of the hsp70 family are associated with the cytosol, mitochondria and endoplasmic reticulum. There is evidence, particularly from studies on mammalian cells (Tanguay, 1985; Welch and Mizzen, 1988; Arrigo et al., 1988), that following stress hsps migrate to various cellular compartments and subsequently delocalize after stress. However, there is little comparable data from microbial systems for this phenomenon (e.g. Rossi and Lindquist, 1989). The question as to the role of stress proteins in the transient acquisition of thermotolerance remains to be answered. It is insufficient to equate the kinetics of stress-protein synthesis with acquisition of thermotolerance. Quantitative data on the amount of stress protein present at various times, including the recovery period, is required. The demonstration that microbial stress proteins are important antigenic determinants of micro-organisms causing major debilitating diseases in the world is an exciting observation. Studies on the interplay of pathogen and host, both carrying similar antigenic hsp determinants, will be a challenging area for future research. It is likely that E. coli and Sacch. cerevisiae, with their well-established biochemical and genetic properties, will continue to be the experimental systems of choice for studies on stress proteins. On the other hand, it is encouraging that studies on other micro-organisms have expanded in the past few years and have made substantial contributions towards our understanding of the stress response. The ubiquitous nature of the stress response and the remarkable evolutionary conservation of the stress proteins continue to be attractive areas for research.

Characterization of the oxygen-dependent promoter of the Vitreoscilla hemoglobin gene in Escherichia coli

The gene coding for the Vitreoscilla hemoglobin (VHb) molecule has been cloned and functionally expressed in Escherichia coli. By using a plasmid-encoded gene as well as single-copy integrants, the oxygen-dependent VHb gene (VHb) promoter was shown to be functional in E. coli. The promoter was maximally induced under microaerobic conditions (dissolved oxygen levels of less than 2% air saturation). Direct analysis of mRNA levels as well as the use of gene fusions with lacZ showed that oxygen-dependent regulation occurred at the level of transcription. Transcriptional activity decreased substantially under anaerobic conditions, suggesting the presence of a regulatory mechanism that is maximally induced under hypoxic but not completely anaerobic conditions in E. coli. Primer extension analysis was used to identify the existence of two overlapping promoters within a 150-base-pair region upstream of the structural VHb gene. The oxygen-dependent activity of both promoters was qualitatively similar, suggesting the existence of a common mechanism by which available oxygen concentrations influence expression from the two promoters. Analysis of promoter activity in crp and cya mutants showed that both cyclic AMP and catabolite activator protein were required for full activity of the promoter. The VHb promoter contained a region of significant homology to the catabolite activator protein-binding site near the E. coli lac promoter.

General method for site-directed mutagenesis in Escherichia coli O18ac:K1:H7: deletion of the inducible superoxide dismutase gene, sodA, does not diminish bacteremia in neonatal rats

A defined deletion in the Escherichia coli K-12 sodA gene (encoding manganese-superoxide dismutase) linked to a nontransposable selectable marker was generated by transposon Tn5 insertion in combination with in vitro mutagenesis. This mutant allele was used to replace the wild-type sodA gene in an E. coli clinical isolate of serotype O18ac:K1:H7 by bacteriophage P1 transduction. The O18ac:K1:H7 sodA mutant contained no manganese-superoxide dismutase and no hybrid manganese-iron-superoxide dismutase. The sodA mutant was more sensitive to paraquat toxicity than were the parental strain and an isogenic mutant bearing an analogously constructed sodA+ Tn5 insertion allele. In a suckling rat model for bacteremia following oral inoculation of E. coli K1, the sodA mutant was undiminished in its capabilities both to colonize the gastrointestinal tract and, surprisingly, to cause bacteremia. In conjunction with the rat model for E. coli K1 pathogenesis, the method for site-directed mutagenesis described in this paper permits determination of the role played in colonization and bacteremia by any K1 gene which either has a homolog in E. coli K-12 or can be cloned and manipulated therein.

Oxygen-sensitive ribonucleoside triphosphate reductase is present in anaerobic Escherichia coli

Ribonucleoside diphosphate reductase from Escherichia coli and mammalian cells provides the deoxyribonucleoside triphosphates for DNA synthesis. The active enzyme contains a tyrosyl free radical whose formation requires oxygen. Earlier genetic evidence suggested that the enzyme is not required for anaerobic growth of E. coli, implicating the activity of a different enzyme or enzyme system for deoxyribonucleotide synthesis in the absence of oxygen. We now conclude from isotope incorporation experiments that E. coli during anaerobiosis obtains its deoxyribonucleotides by reduction of ribonucleotides. Extracts from anaerobically grown bacteria contain a different enzyme activity capable of reducing CTP to dCTP. To obtain an active enzyme, strict anaerobiosis must be maintained during extract preparation and during assay of the enzyme. The reaction is stimulated by NADPH, Mg2+, and ATP. Inhibition by deoxyribonucleoside triphosphates suggests that the anaerobic enzyme has allosteric properties. Antibodies raised against the aerobic enzyme do not inhibit the new activity, and hydroxyurea, a potent scavenger of the tyrosyl radical of the aerobic enzyme, only weakly inhibits the anaerobic enzyme. The anaerobic enzyme has interesting evolutionary aspects since it might reflect on an activity that in the absence of oxygen made possible the transition from an "RNA world" into a "DNA world."

Bacterial genes involved in response to near-ultraviolet radiation

A model of the possible pathways of activities following NUV treatment was presented in Section I and in Fig. 1. Some of the components are firmly established, some are speculative, and many are difficult to evaluate because of insufficient experimental information. Perhaps the most relevant experiments, especially concerning ozone depletion, would be to determine the mutational specificity of NUV. By selecting lacI mutants after exposing cells to NUV, and sequencing the bases of this gene, this is now feasible. There are some problems, however. The mutation frequency is normally so low that it might be difficult to distinguish NUV mutants from spontaneous mutants. However, by irradiating cells having a uvrA or uvrB mutation, the frequency of mutation above background can be increased considerably. There remains the problem as to what fraction of the observed mutations results from oxidative damage. Some of this could be clarified by comparing mutation spectra of cells treated with NUV and cells subjected to excess oxidative damage and determining what fraction results from other avenues of lesion formation in DNA. Different species of reactive oxygen could cause different kinds of DNA lesions, and, fortunately, use of appropriate mutants should allow us to sort out any differences in specificity of lesions. Also, by appropriate manipulation of quantities of endogenous photosensitizers, it might be possible to sort out the specific mutations that are caused by photodynamic action. Another avenue of research is to explore the pathways by which NUV lesions are repaired, and whether such repair is error prone or error free. Again, the use of mutants such as xthA, uvr, and polA should assist in our understanding of the specificity of the mutational events. There are now a number of examples of global control mechanisms whereby cells abruptly shift their protein synthesis pattern under environmental stress. It is important to understand whether NUV stress results in induction of one or more of the known regulatory genes, or whether another regulon might be involved. One particular aspect of regulation that remains unsolved is the role of the katF gene, which is known to regulate the xthA and katE, but it may also regulate other genes as well. A number of striking physiological events occur even at very low fluences of NUV irradiation of cells. In part, this may be related to regulon induction. However, some of these events are in need of special exploration, such as changes at the membrane level.(ABSTRACT TRUNCATED AT 400 WORDS)

Evidence for a new ribonucleotide reductase in anaerobic E. coli

E. coli conditional iron-containing ribonucleotide reductase (Fe-RR) mutant and wild type strains grew anaerobically under conditions when Fe-RR was absent or inhibited. Furthermore, a B12-independent, hydroxyurea-resistant RR activity, unaffected by monoclonal antibodies against either subunit B1 or B2 of Fe-RR, was partially purified from anaerobically grown mutant and wild-type E. coli. These findings indicate that E. coli has a second RR representative of a new class of RRs and that this is the first report where both in vivo and in vitro evidence is presented. It is probable that other facultative anaerobes also have two different RRs such that an optimal supply of deoxyribonucleotides is maintained under all growth conditions.

Molecular genetics of superoxide dismutases

Molecular genetics of SOD has been recently developed primarily due to the new biotechnologies. Different types of isoenzymes have now been cloned and sequenced from several species ranging from bacteria to human and plants. Knowledge of the nucleotide sequences permitted refinement of structural models and provided information on subcellular locations. Cloned genes allowed the production of large amounts of SOD. They have been used for physiological and regulation studies, structural and enzymatic analyses, and are vital tools for the isolation of mutants. Isolation of mutants is generally essential to the understanding of the biological function of the gene in question. Indeed, SOD deficient mutants have now been isolated in bacteria and yeast. Their properties support, at numerous levels, a major role of SOD in cellular defense against oxygen toxicity. Few data are presently available on the molecular basis of mechanisms that regulate the expression of SOD.