[Low-Molecular Thiols as a Factor Improving the Sensitivity of Escherichia coli Mutants with Impaired ADP-Heptose Synthesis to Antibiotics].

Low molecular-weight thiols as glutathione and cysteine are an important part of the cell's redox regulation system. Previously, we have shown that inactivation of ADP-heptose synthesis in Escherichia coli with a gmhA deletion induces the oxidative stress. It is accompanied by rearrangement of thiol homeostasis and increased sensitivity to antibiotics. In our study, we found that restriction of cysteine metabolism (ΔcysB and ΔcysE) and inhibition of glutathione synthesis (ΔgshAB) lead to a decrease in the sensitivity of the ΔgmhA mutant to antibiotics but not to its expected increase. At the same time, blocking of the export of cysteine (ΔeamA) or increasing import (Ptet-tcyP) into cells of the oxidized form of cysteine-cystine leads to an even greater increase in the sensitivity of gmhA-deleted cells to antibiotics. In addition, there is no correlation between the cytotoxic effect of antibiotics and the level of reactive oxygen species (ROS), the total pool of thiols, or the viability of the initial cell population. However, a correlation between the sensitivity to antibiotics and the level of oxidized glutathione in cells was found in our study. Apparently, a decrease in the content of low-molecular-weight thiols saves NADPH equivalents and limits the processes of protein redox modification. This leads to increasing of resistance of the ΔgmhA strain to antibiotics. An increase in low-molecular-weight thiols levels requires a greater expenditure of cell resources, leads to an increase in oxidized glutathione and induces to greater increase in sensitivity of the ΔgmhA strain to antibiotics.

Enhancement of the Bactericidal Effect of Antibiotics by Inhibition of Enzymes Involved in Production of Hydrogen Sulfide in Bacteria.

Counteraction of the origin and distribution of multidrug-resistant pathogens responsible for intra-hospital infections is a worldwide issue in medicine. In this brief review, we discuss the results of our recent investigations, which argue that many antibiotics, along with inactivation of their traditional biochemical targets, can induce oxidative stress (ROS production), thus resulting in increased bactericidal efficiency. As we previously showed, hydrogen sulfide, which is produced in the cells of different pathogens protects them not only against oxidative stress but also against bactericidal antibiotics. Next, we clarified the interplay of oxidative stress, cysteine metabolism, and hydrogen sulfide production. Finally, demonstrated that small molecules, which inhibit a bacterial enzyme involved in hydrogen sulfide production, potentiate bactericidal antibiotics including quinolones, beta-lactams, and aminoglycosides against bacterial pathogens in in vitro and in mouse models of infection. These inhibitors also suppress bacterial tolerance to antibiotics by disrupting the biofilm formation and substantially reducing the number of persister bacteria, which survive the antibiotic treatment. We hypothesise that agents which limit hydrogen sulfide biosynthesis are effective tools to counteract the origin and distribution of multidrug-resistant pathogens.

[Enhancement of the Bactericidal Effect of Antibiotics by Inhibition of Enzymes Involved in Production of Hydrogen Sulfide in Bacteria].

Counteraction of the origin and distribution of multidrug-resistant pathogens responsible for intra-hospital infections is a worldwide issue in medicine. In this brief review, we discuss the results of our recent investigations, which argue that many antibiotics, along with inactivation of their traditional biochemical targets, can induce oxidative stress (ROS production), thus resulting in increased bactericidal efficiency. As we previously showed, hydrogen sulfide, which is produced in the cells of different pathogens protects them not only against oxidative stress but also against bactericidal antibiotics. Next, we clarified the interplay of oxidative stress, cysteine metabolism, and hydrogen sulfide production. Finally, demonstrated that small molecules, which inhibit a bacterial enzyme involved in hydrogen sulfide production, potentiate bactericidal antibiotics including quinolones, beta-lactams, and aminoglycosides against bacterial pathogens in in vitro and in mouse models of infection. These inhibitors also suppress bacterial tolerance to antibiotics by disrupting the biofilm formation and substantially reducing the number of persister bacteria, which survive the antibiotic treatment. We hypothesise that agents which limit hydrogen sulfide biosynthesis are effective tools to counteract the origin and distribution of multidrug-resistant pathogens.

[Inactivation of Terminal Oxidase bd-I Leads to Supersensitivity of E. coli to Quinolone and Beta-Lactam Antibiotics].

In cells of Escherichia coli, terminal oxidase bd-I encoded by the cydAB gene catalyzes the reduction of O2 to water using hydroquinone as an electron donor. In addition to the cydAB operon, two other genes, cydC and cydD, encoding the heterodimeric ATP-binding cassette-type transporter are essential for the assembly of cytochrome bd-I. It was shown that inactivation of cytochrome bd-I by the introduction of cydB or cydD deletions into the E. coli chromosome leads to supersensitivity of the bacteria to antibiotics of the quinolone and beta-lactam classes. The sensitivity of these mutants to antibiotics is partially suppressed by introduction of a constitutively expressed gene katG under the control of the Ptet promoter into their genome. The increased level of hydrogen sulfide resulting from the introduction of the mstA gene, encoding 3-mercaptopyruvate sulfurtransferase, under the control of the Ptet promoter, leads to the same effect. These data demonstrate the important role of cytochrome bd-I in the defense of bacteria from oxidative stress and bactericidal antibiotics.

[Biotechnological Potential of the Bacillus subtilis 20 Strain].

Bacillus subtilis bacteria play an important role in veterinary medicine, medicine, and biotechnology, and the permanently growing demand for biotechnological products fuels the improvement of the properties of biotechnological strains. B. subtilis strains with improved characteristics maybe obtained by rational design and the directed evolution technologies, or be found among newly described strains. In the course of the long-term microbiome composition studies in the Russian segment of the International Space Station, the B. subtilis 20 strain was isolated, this strain shows the capacity for rapid growth and considerable biomass accumulation, as well as increased resistance to acidification of the environment in comparison to the "terrestrial" B. subtilis 168 strain. What is more, B. subtilis 20 is hyperresistant to the DNA and protein damaging factors that are linked to the overexpression of the genes controlling DNA repair, hydrogen sulfide production, and reactive oxygen species neutralization. The described properties of B. subtilis 20 are indicative of its considerable potential as a promising producer of biologically active compounds.

[Bacillus subtilis ypaA gene regulation mechanism involves FMN-binding sensor RNA].

We studied the regulation of the Bacillus subtilis ypaA gene-encoding riboflavin-transporter protein involving FMN-dependent sensor RNA. Using translational fusions of the wild-type ypaA gene with the lacZ-reporter gene in the leader region we showed that in vivo ypaA gene expression decreased more than 10-fold in the presence of endogenous FMN. Introduction of two nucleotide substitutions providing stabilization of the sequester hairpins results in almost complete repression of reporter gene expression. Using toeprint assay in vitro it has been shown that FMN presence inhibits the formation of the 30S initiation complexint the ypaA gene leader mRNA. Our results support the model of ypaA gene regulation whereby FMN binding with the ypaA gene leader sequence results in translation suppression through the sequestering of the SD-sequence.

Possible Function of the ribT Gene of Bacillus subtilis: Theoretical Prediction, Cloning, and Expression.

The complete decipherment of the functions and interactions of the elements of the riboflavin biosynthesis operon (rib operon) of Bacillus subtilis are necessary for the development of superproducers of this important vitamin. The function of its terminal ribT gene has not been established to date. In this work, a search for homologs of the hypothetical amino acid sequence of the gene product through databases, as well as an analysis of the homolgs, was performed; the distribution of secondary structure elements was theoretically predicted; and the tertiary structure of the RibT protein was proposed. The ribT gene nucleotide sequence was amplified and cloned into the standard high-copy expression vector pET15b and then expressed after induction with IPTG in E. coli BL21 (DE3) strain cells containing the inducible phage T7 RNA polymerase gene. The ribT gene expression was confirmed by SDS-PAGE. The protein product of the expression was purified by affinity chromatography. Therefore, the real possibility of RibT protein production in quantities sufficient for further investigation of its structure and functional activity was demonstrated.

[RPN4 the yeast transcription factor promotes the complex defence against methyi, methanesulfonate].

Methyl methanesulfonate (MMS) is an alkylating agent commonly used in models of genotoxic stress. It methylates bases in DNA but also leads to oxidative stress. The transcription factor Rpn4 protects yeast cells from toxic effect of MMS. Although Rpn4 is a major regulator of ubiquitin-proteasome system (UPS), a number of data points to its participation in the stress response regardless of the UPS. We have demonstrated that under the methyl methanesulfonate stress Rpn4 promotes the regulation of several genes involved in DNA repair, antioxidant response and glucose metabolism. We suggest a mechanism of complex action of Rpn4 in the stress response.

[Role of reactive oxygen species in the bactericidal action of quinolones--inhibitors of DNA gyrase].

Quinolone antibiotics inhibit DNA gyrase, but the induced degradation of chromosomal DNA is determined by a complex process of joint action quinolones and hydroxyl radical OH'. To quantify the level of stress responses and their time dependence in bacterial cells the induced specific lux-biosensors--the bacterium Escherichia coli, containing hybrid plasmids pColD'::lux; pSoxS'::lux; pKatG'::lux were used in this study. It is shown that quinolones (nalidixic acid, norfloxacin) induce SOS-response and oxidative stress with the formation of superoxide anion O2(-) in E. coli cells. The main parameters of SOS-response and oxidative stress, which depend on the quinolone concentration, are determined. Formation of superoxide anion O2(-) occurs almost simultaneously with the SOS-response. The mutant strain of E. coli sodA sodB, which do not contain active forms of superoxide dismutases SodA and SodB, is characterized by an increased resistance to quinolones as compared to the wild type cells. At high concentrations of quinolones (nalidixic acid-->20 µg/mL; norfloxacin-->500 ng/mL) their bactericidal effect is partially caused by conversion of the superoxide anion to hydrogen peroxide H2O2, conducted by superoxide dismutases SodA and SodB, which is followed by the Fenton reaction and the formation of toxic hydroxyl radical OH'. At low concentrations of quinolones (nalidixic acid--<20 µg/mL; norfloxacin--<500 ng/mL), the role of active oxygen species in the antimicrobial effect is practically nonexistent.

Acadesine Triggers Non-apoptotic Death in Tumor Cells.

We studied the cytotoxicity of acadesine (5-aminoimidazole-4-carboxamide-1-ß-D-ribofuranoside) for tumor and normal cells of various species and tissue origin. In tumor cells, acadesine triggered non-apoptotic death; the potency of the compound to normal cells was substantially lower. Acadesine was toxic for tumor cells with multidrug resistant phenotypes caused by the transmembrane transporter Р-glycoprotein or lack of proapoptotic p53. Activity of adenosine receptors was required for acadesine-induced cell death, whereas functioning of АМР-dependent protein kinase was not required. A more pronounced cytotoxicity for tumor cells, as well as the non-canonical death mechanism(s), makes acadesine a promising candidate for antitumor therapy.

[The characterization of internal promoters in the Bacillus subtilis riboflavin biosynthesis operon].

The transcription start sites of two internal promoters, the P2 and P3 promoters, in the Bacillus subtilis riboflavin biosynthesis operon were identified by primer extension. Putative -35 and -10 sequences that are recognized by the vegetative delta(70) subunit of RNA polymerase have been found upstream of the P2 and P3 transcription start sites. The relative strengths of the P1, P2, and P3 promoters were determined by cloning these promoters into the pDG268 expression vector. It was shown that the transcriptional activity of the P3 promoter is approximately fivefold higher as compared with P1, the major promoter, whereas P2 promoter activity is lower by almost two orders of magnitude. Real-time PCR demonstrated that unlike the P1 promoter, P2- and P3-driven expression is not regulated by flavins.

[Butanol as a regulatory factor of ompC gene expression in E. coli cells].

The influence of butanol on the expression of ompC gene encoding synthesis of OmpC porin in the MG 1655 strain of E. coli and butanol-tolerant mutant ButR was studied. It was shown that in the case of wild bacteria, the addition of butanol to the growth medium results in an increased level of ompC transcription. However, OmpC porin is not detected in the membrane fraction of cells. ButR mutant exhibits a higher level of ompC gene expression. A direct correlation is observed between the level of OmpC porin expression and its content in the membrane fraction of ButR mutant cells. In the regulatory region of the ompC gene of the ButR mutant, three nucleotide substitutions located in the binding sites of OmpR and CpxR activator proteins were identified. It was shown that mutations in the regulatory region of the ompC gene in the ButR mutant are responsible for the decreased level of OmpC porin expression under normal growth conditions. However, these mutations lead to an increased level of OmpC porin synthesis in the presence of butanol. These data suggest an additional mechanism of ompC gene regulation with the participation of butanol as a positive transcription effector.

[Mutation analysis of the purine operon leader region in Bacillus subtilis].

Expression of Bacillus subtilis purine (purE) operon is a subject of double negative control involving repressor protein PurR and a transcription terminator located in the operon leader region. We have performed site-directed mutagenesis of the specific motives, which are involved in formation of alternative hairpin structures, one of which produces transcription termination at the leader region ofpurEoperon. In vivo and in vitro analyses of the generated mutants have shown that purine bases, guanine and hypoxantine, serve as effector metabolites capable of increasing stability of terminating hairpin within the leader mRNA. Therefore, the leader RNA of purE operon serves as a sensor towards these metabolites and a riboswitch that provides premature termination of the operon transcription. The synergistic effect of the PurR repressor protein and a transcription terminator located at the leader region on the expression of purE operon was also revealed.

[Mutational analysis of the ribC gene of Bacillus subtilis].

The nucleotide sequence of the ribC gene encoding the synthesis ofbifunctional flavokinase/flavine adenine nucleotide (FAD) synthetase in Bacillus subtilis have been determined in a family of riboflavin-constitutive mutants. Two mutations have been found in the proximal region of the gene, which controls the transferase (FAD synthase) activity. Three point mutations and one double mutation have been found (in addition to the two mutations that were detected earlier) in the distal region of the gene, which controls the flavokinase (flavin mononucleotide (FMN) synthase) activity. On the basis of all data known to date, it has been concluded that the identified mutations affect riboflavin and ATP binding sites. No mutations have been found in the PTAN conserved sequence, which forms the magnesium and ATP common binding site and is identical for organisms of all organizational levels, from bacteria too humans.

[Regulation of bacterial transcription elongation].

The elongation complex, which involves RNA polymerase, DNA template and nascent RNA, is a central intermediate in transcription cycle. It is elongation complex that represents the main target for the action of different regulatory factors. Over the past several years, many structural and biochemical data have been obtained that shed light upon the molecular details of RNA polymerase function. Cooperation between RNA polymerase elongation complex and translating ribosome was established recently. Here we discuss the mechanisms of the regulation of bacterial transcription elongation.

Reconstruction of Purine Metabolism in Bacillus subtilis to Obtain the Strain Producer of AICAR: A New Drug with a Wide Range of Therapeutic Applications.

AICAR is a natural compound, an analogue and precursor of adenosine. As activator of AMP-activated protein kinase (AMPK), AICAR has a broad therapeutic potential, since it normalizes the carbohydrate and lipid metabolism and inhibits the proliferation of tumor cells. The synthesis of AICAR inBacillus subtiliscells is controlled by the enzymes of purine biosynthesis; their genes constituting purine operon (pur-operon). Reconstruction of purine metabolism inB. subtiliswas performed to achieve overproduction of AICAR. For this purpose, the genepurH, which encodes formyltransferase/IMP-cyclohydrolase, an enzyme that controls the conversion of AICAR to IMP, was removed from theB. subtilisgenome, ensuring the accumulation of AICAR. An insertion inactivating the genepurRthat encodes the negative transcriptional regulator of the purine biosynthesis operon was introduced into theB.subtilischromosome in order to boost the production of AICAR; the transcription attenuator located in the leader sequence ofpur-operon was deleted. Furthermore, the expression integrative vector carrying a strong promoter of therpsFgene encoding the ribosomal protein S6 was designed. The heterologousEscherichia coligenepurFencoding the first enzyme of the biosynthesis of purines with impaired allosteric regulation, as well as the modifiedE.coligeneprsresponsible for the synthesis of the precursor of purines - phosphoribosyl pyrophosphate (PRPP) - was cloned into this vector under the control of therpsFgene promoter. The modifiedpurFandprsgenes were inserted into the chromosome of theB. subtilisstrain.B. subtilisstrain obtained by these genetic manipulations accumulates 11-13 g/L of AICAR in the culture fluid.

[Multifunctional regulatory mutation in Bacillus subtilis flavinogenesis system].

Among Bacillus subtilis riboflavin-resistant mutants we identified one, which differed from other regulatory mutants by overproduction of riboflavin and simultaneous upregulation of the rib C gene encoding flavokinase/FAD-synthase. Genetic and biochemical analysis showed that the ribU1 mutation determines a trans-acting factor that simultaneously regulates activity of riboflavin and truB-ribC-rpsO operons. Regulatory activity of the ribU1 mutation comprises about 10% of Rfn element activity on interaction with flavins. The ribUl mutation can be presumably ascribed to a gene of the transcriptional regulators family.

[Gene yddG of Escherichia coli encoding the putative exporter of aromatic amino acids: constitutive transcription and dependence of the expression level on the cell growth rate].

Gene yddG of Escherichia coli encodes a protein of the inner membrane. Data obtained earlier demonstrated that under conditions of oversynthesis of aromatic amino acids, YddG promotes their export from E. coli cells. In this work, a method of primer extension was used to localize the P(yddG) promoter, which corresponds to E. coli promoters recognized by RNA polymerase in complex with sigma70 or sigma(S) subunits. By constructing a gene of the hybrid protein YddG'-LacZ at the intrinsic site of gene yddG location in the E. coli chromosome and analyzing the activity of beta-galactosidase in cells growing on laboratory media LB and M9, the constitutive type of yddG expression at a low level was demonstrated (the activity reached approximately 3 to 4% of the level of LacZ in E. coli wild-type cells under induction of the lac operon). The expression of yddG had a twofold increase under conditions of retarded cell growth upon the stress caused by the high NaCl content (0.6 M) or by the presence of phenylalanine excess quantities (> 1 mM) in the culture medium.