Regulators of oxidative stress response genes in Escherichia coli and their functional conservation in bacteria

Transcriptional signatures associated with the survival of Escherichia coli biofilm during treatment with plasma-activated water

Biofilm formation on surfaces, tools and equipment can damage their quality and lead to high repair or replacement costs. Plasma-activated water (PAW), a new technology, has shown promise in killing biofilm and non-biofilm bacteria due to reactive oxygen and nitrogen species (RONS), particularly superoxide. However, the exact genetic mechanisms behind PAW's effectiveness against biofilms remain unclear. Here, we examined the stress responses of Escherichia coli biofilms exposed to sub-lethal PAW treatment using bulk RNA sequencing and transcriptomics. We compared gene expression in PAW-treated E. coli biofilms with and without superoxide removal, achieved by adding the scavenger Tiron. Biofilms treated with PAW exhibited a 40 % variation in gene expression compared to those treated with PAW-Tiron and controls. Specifically, PAW treatment resulted in 478 upregulated genes (>1.5 log2FC) and 186 downregulated genes (<-1.5 log2FC) compared to the control. Pathway and biological process enrichment analysis revealed significant upregulation of genes involved in sulfur metabolism, ATP-binding transporter, amino acid metabolism, hypochlorite response systems and oxidative phosphorylation in PAW-treated biofilms compared to control. Biofilm viability and intracellular RONS accumulation were tested for E. coli mutants lacking key genes from these pathways. Knockout mutants of thioredoxin (trxC), thiosulfate-binding proteins (cysP), and NADH dehydrogenase subunit (nuoM) showed significantly reduced biofilm viability after PAW treatment. Notably, ΔtrxC biofilms had the highest intracellular ROS accumulation, as revealed by 2',7'-dichlorofluorescin diacetate staining after PAW treatment. This confirms the importance of these genes in managing oxidative stress caused by PAW and highlights the significance of superoxide in PAW's bactericidal effects. Overall, our findings shed light on the specific genes and pathways that help E. coli biofilms survive and respond to PAW treatment, offering a new understanding of plasma technology and its anti-biofilm mechanisms.

Disinfectants and one health review: The role of reactive oxygen species in the bactericidal activity of chlorine against Salmonella

Salmonella are among the most common foodborne pathogens in humans, and they are associated with mild to severe diseases commonly referred to as salmonellosis. The genus resides in various animals' intestinal tracts, including humans. It is one of the most diverse genera of bacteria, including over 2500 serovars. Consumption of poultry products contaminated with Salmonella is a significant source of disease transmission in humans. Because of this food safety concern, the poultry industry and governments spend billions of dollars on Salmonella containment methods. However, a completely effective strategy is yet to be established. Chlorine has been commonly used as a disinfectant in the poultry industry. In humans, antibiotic therapy is the primary means for managing Salmonella infection. However, widespread use of both compounds at sub-inhibitory concentrations has allowed resistant strains to emerge and rapidly spread globally. Both antimicrobial compounds involve generating reactive oxygen species (ROS) as a bactericidal mechanism of action. However, ROS generation and its association with bacterial survival and growth inhibition have not been widely explored. Thus, a better understanding of ROS generation during antimicrobial treatments may help devise better Salmonella containment strategies.

Antibiotic-induced stress responses in Gram-negative bacteria and their role in antibiotic resistance

Bacteria adapt to changes in their natural environment through a network of stress responses that enable them to alter their gene expression to survive in the presence of stressors, including antibiotics. These stress responses can be specific to the type of stress and the general stress response can be induced in parallel as a backup mechanism. In Gram-negative bacteria, various envelope stress responses are induced upon exposure to antibiotics that cause damage to the cell envelope or result in accumulation of toxic metabolic by-products, while the heat shock response is induced by antibiotics that cause misfolding or accumulation of protein aggregates. Antibiotics that result in the production of reactive oxygen species (ROS) induce the oxidative stress response and those that cause DNA damage, directly and through ROS production, induce the SOS response. These responses regulate the expression of various proteins that work to repair the damage that has been caused by antibiotic exposure. They can contribute to antibiotic resistance by refolding, degrading or removing misfolded proteins and other toxic metabolic by-products, including removal of the antibiotics themselves, or by mutagenic DNA repair. This review summarizes the stress responses induced by exposure to various antibiotics, highlighting their interconnected nature, as well the roles they play in antibiotic resistance, most commonly through the upregulation of efflux pumps. This can be useful for future investigations targeting these responses to combat antibiotic-resistant Gram-negative bacterial infections.

Role of organophosphorus pesticides in facilitating plasmid-mediated conjugative transfer: Efficiency and mechanisms

Non-antibiotic conditions, including organophosphorus pesticides (OPPs), have been implicated in the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) to varying degrees. While most studies focus on the toxicity of OPPs to humans and animals, their roles in ARG dissemination remain largely unexplored. In this study, we investigate the effects and involved molecular mechanisms of environmentally relevant concentrations of malathion and dimethoate, two representative OPPs, on plasmid-mediated conjugal transfer. By detecting reactive oxygen species (ROS) production and cell membrane permeability, we gained insights into the underlying processes. Furthermore, we substantiated the role of ROS and cell membrane permeability in plasmid-mediated conjugative transfer through the analysis of relevant antioxidant enzyme activities, cell membrane-related indices, and RNA sequences. Additionally, our examination of proton motive force and adenosine triphosphate content provided evidence that OPPs create conditions conducive to plasmid-mediated conjugative transfer from an energetic perspective. The findings of the present study highlight the potential risk of OPPs in promoting ARG spread, which could ultimately provide new theoretical support and direction for future research on the impacts of pesticides on ARG propagation.

A transcription factor from the cryptic Escherichia coli Rac prophage controls both phage and host operons

Bacterial genomes are shaped by cryptic prophages, which are viral genomes integrated into the bacterial chromosome. Escherichia coli genomes have 10 prophages on average. Though usually inactive, prophage genes can profoundly impact host cell physiology. Among the phage genes in the E. coli chromosome, there are several putative transcription factors (TFs). These prophage TFs are predicted to control only phage promoters; however, their regulatory functions are not well characterized. The cohabitation of prophages and bacteria has led to conditions under which the majority of prophage genes are unexpressed, at least under normal growth conditions. We characterized a Rac prophage TF, YdaT, expression of which is normally inhibited by Rac TFs and, surprisingly, by the host global regulator OxyR. YdaT, when expressed, leads to a toxic phenotype manifested by drastic cell filamentation and cell death. We determined the binding sites and regulatory action for YdaT, finding two sites within the Rac locus, and one upstream of the host rcsA gene, which codes for the global regulator RcsA. The resulting increase in RcsA strongly impacts the bacterial RcsA/B regulon, which includes operons related to motility, capsule biosynthesis, colanic acid production, biofilm formation, and cell division. Our results provide novel insights into the host's genetic network, which appears to integrate YdaT in a complex manner, favoring its maintenance in the silenced state. The fact that the potentially toxic YdaT locus remains unmutated suggests its importance and potential benefits for the host, which may appear under stress conditions that are not yet known.

The transcription factor YbdO attenuates the pathogenicity of avian pathogenic Escherichia coli by regulating oxidative stress response

Avian pathogenic Escherichia coli (APEC) is a significant pathogen infecting poultry that is responsible for high mortality, morbidity and severe economic losses to the poultry industry globally, posing a substantial risk to the health of poultry. APEC encounters reactive oxygen species (ROS) during the infection process and thus has evolved antioxidant defense mechanisms to protect against oxidative damage. The imbalance of ROS production and antioxidant defenses is known as oxidative stress, which results in oxidative damage to proteins, lipids and DNA, and even bacterial cell death. APEC uses transcription factors (TFs) to handle oxidative stress. While many TFs in E. coli have been well characterized, the mechanism of the YbdO TF on protecting against oxidative damage and regulating the virulence and pathogenicity of APEC has not been clarified. Here we focus on the regulatory mechanism of YbdO on the pathogenicity of APEC. The results from this study showed that YbdO attenuated the pathogenicity of APEC in chicks infection models by inhibiting the expression of virulence genes fepG and ycgV using quantitative real-time reverse transcription PCR (RT-qPCR) experiments. The electrophoretic mobility shift assays (EMSA) confirmed that YbdO specifically bound to the promoters of fepG and ycgV. Additionally, YbdO increases H2O2-induced oxidative damage to APEC via repressing the expression of oxidative stress response genes sodA, soxR, ahpC, ahpF, katG, and oxyR by binding to their promoter regions. The repression effect facilitates host immune response to eliminate APEC and to generate beneficial immune protection to the body, thereby indirectly attenuating the pathogenicity of APEC. These findings might provide further insights into the mechanism of oxidative damage to APEC and offer new perspectives for further studies on the prevention and control of APEC infections.

Antibiofilm, Anti-Inflammatory, and Regenerative Properties of a New Stable Ozone-Gel Formulation

Background/Objectives: Chronic skin wounds are characterized by inflammation, persistent infections, and tissue necrosis. The presence of bacterial biofilms prolongs the inflammatory response and delays healing. Ozone is a potent antimicrobial molecule, and many formulations have been used in the advanced therapeutic treatment of chronic wounds. The aim of this work was to determine the antimicrobial, anti-inflammatory, and regenerative activity of a stable ozone-gel formulation over time. Methods: The antimicrobial property was assessed by measuring the minimal inhibitory concentration and the antibiofilm activity. The anti-inflammatory effect was evaluated by TNF-α determination, and the regenerative effect was measured by scratch assay. Results: The ozone gel demonstrated antimicrobial and antibiofilm activity in all ATCC microorganisms examined and on most clinical isolates. Higher concentrations of the ozone gel were also useful in the dispersion of preformed biofilm. The ozone gel also showed anti-inflammatory activity by reducing the production of TNF-α and regenerative activity in human fibroblasts and keratinocytes. Conclusions: Given all these antimicrobial, anti-inflammatory, and regenerative characteristics, the ozone gel could be, in this formulation, used in the treatment of wounds. The ozone-gel formulation described here retains stability for over 30 months, which facilitates its use compared to formulations that lose efficacy quickly.

Expression of Rhodococcus erythropolis stress genes in planctonic culture supplemented with various hydrocabons

Studying Rhodococcus erythropolis stress response is of significant scientific interest, since this microorganism is widely used for bioremediation of oil-contaminated sites and is essential for environmental biotechnology. In addition, much less data was published on molecular mechanisms of stress resistance and adaptation to effects of pollutants for Gram-positive oil degraders compared to Gram-negative ones. This study provided an assessment of changes in the transcription level of the soxR, sodA, sodC, oxyR, katE, katG, recA, dinB, sigF, sigH genes in the presence of decane, hexadecane, cyclohexane, benzene, naphthalene, anthracene and diesel fuel. Judging by the changes in the expression of target genes, hydrocarbons as the main carbon source caused oxidative stress in R. erythropolis cells, which resulted in DNA damage. It was documented by enhanced transcription of genes encoding antioxidant enzymes (superoxide dismutase and catalase), SOS response, DNA polymerase IV, and sigma factors of RNA polymerase SigH and SigF. At this, it was likely that in the presence of hydrocarbons, transcription of catalase genes (katE and katG) was coordinated primarily by the sigF regulator.

Biological characterization of lipoic acid- and heme-dependent Escherichia coli small colony variants isolated from sheep in Xinjiang, China

Escherichia coli (E. coli) small colony variants (SCVs) have garnered attention due to their heightened antibiotic resistance and enhanced cell retention, posing significant risks to public health and food safety. However, understanding of SCVs derived from sheep remains limited. This study aimed to detect the biological characterization of sheep-derived E. coli SCVs and investigate the factors contributing to SCV development with preliminary genomic data. In this study, a lipoic acid-dependent SCV (LA-SCV) and a wild-type (WT) strain were isolated from sheep bile. Then, a heme-dependent SCV (HD-SCV) was induced from WT using amikacin. Initially, we examined factors contributing to SCV formation via comparative genomics. Subsequent comparisons between WT and two SCV strains encompassed antibiotic resistance, hemolytic activity, biofilm formation, motility, and metabolism. Genomic analyses identified a frameshift deletion mutation in the lipA gene in LA-SCV and a stopgain mutation in the hemG gene in HD-SCV, hypothesized as potential triggers for lipoic acid- and heme-dependent SCV development, respectively. Physiological, biochemical, and cultural traits exhibited notable differences between WT and SCVs, including increased antibiotic resistance, hemolytic activity, and biofilm formation, but alongside non-fermentative acetate utilization, slow growth, reduced intracellular ATP, and decreased motility (P < 0.01). The energy and amino acid metabolism were suppressed during the logarithmic phase in LA-SCV, while both logarithmic and stable phases in HD-SCV. These alterations in biological characteristics present significant challenges in managing E. coli pathogenicity and antibiotic resistance.

The master regulator OxyR orchestrates bacterial oxidative stress response genes in space and time

Bacteria employ diverse gene regulatory networks to survive stress, but deciphering the underlying logic of these complex networks has proved challenging. Here, we use time-resolved single-cell imaging to explore the functioning of the E. coli regulatory response to oxidative stress. We observe diverse gene expression dynamics within the network. However, by controlling for stress-induced growth-rate changes, we show that these patterns involve just three classes of regulation: downregulated genes, upregulated pulsatile genes, and gradually upregulated genes. The two upregulated classes are distinguished by differences in the binding of the transcription factor, OxyR, and appear to play distinct roles during stress protection. Pulsatile genes activate transiently in a few cells for initial protection of a group of cells, whereas gradually upregulated genes induce evenly, generating a lasting protection involving many cells. Our study shows how bacterial populations use simple regulatory principles to coordinate stress responses in space and time. A record of this paper's transparent peer review process is included in the supplemental information.

Transcriptomic response of wetland microbes to root influence

Wetlands are hotspots for carbon and nutrient cycling. The important role of plant-microbe interactions in driving wetland biogeochemistry is widely acknowledged, prompting research into their molecular biological basis for a deeper understanding of these processes. We analyzed transcriptomic responses of soil microbes to root exudates in coastal wetland soils using 13CO2 pulse labeling. Metatranscriptomics revealed 388 upregulated and 11 downregulated genes in response to root exudates. The Wood-Ljungdahl pathway and dissimilatory sulfate reduction/oxidation were the most active microbial pathways independent of root influence, whereas pathways with the strongest upregulation in response to root influence were related to infection, stress response, and motility. We demonstrate shifts within the active community toward higher relative abundances of Betaproteobacteria, Campylobacterota, Kiritimatiellota, Lentisphaerota, and Verrucomicrobiota in response to exudates. Overall, this study improves our mechanistic understanding of wetland plant-soil microbe interactions by revealing the phylogenetic and transcriptional response of soil microorganisms to root influence and exudate input.

Vibrio natriegens: Application of a Fast-Growing Halophilic Bacterium

The fast growth accompanied with high substrate consumption rates and a versatile metabolism paved the way to exploit Vibrio natriegens as unconventional host for biotechnological applications. Meanwhile, a wealth of knowledge on the physiology, the metabolism, and the regulation in this halophilic marine bacterium has been gathered. Sophisticated genetic engineering tools and metabolic models are available and have been applied to engineer production strains and first chassis variants of V. natriegens. In this review, we update the current knowledge on the physiology and the progress in the development of synthetic biology tools and provide an overview of recent advances in metabolic engineering of this promising host. We further discuss future challenges to enhance the application range of V. natriegens.

Oxidative stress response in avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) leads to significant economic losses in the poultry industry worldwide and restricts the development of the poultry industry. Oxidative stress, through the production of reactive oxygen species (ROS), damage iron‑sulfur (FeS) clusters, cysteine and methionine protein residues, and DNA, and then result in bacterial cells death. APEC has evolved a series of regulation systems to sense and quickly and appropriately respond to oxidative stress. Quorum sensing (QS), second messenger (SM), transcription factors (TFs), small regulatory RNAs (sRNAs), and two-component system (TCS) are important regulation systems ubiquitous in bacteria. It is of great significance to control APEC infection through investigating the molecular regulation mechanism on APEC adapting to oxidative stress. However, how the cross-talk among these regulation systems co-regulates transcription of oxidative stress-response genes in APEC has not been reported. This review suggests exploring connector proteins that co-regulate these regulation systems that co-activate transcription of oxidative stress-response genes to disrupt bacterial antioxidative defense mechanism in APEC, and then using these connector proteins as drug targets to control APEC infection. This review might contribute to illustrating the functional mechanism of APEC adapting to oxidative stress and exploring potential drug targets for the prevention and treatment of APEC infection.

Transcription factor AbrB regulates ROS generation and clearance in Bacillus licheniformis

Oxidative damage caused by the accumulation of reactive oxygen species (ROS) is one of the main obstacles to the improvement of microbial cell growth and fermentation characteristics under adverse environments. And the antioxidant capacity of cells will increase with the cell growth. Here, we found that a transition state transcription factor AbrB related to changes in cell growth status could regulate the accumulation of ROS and antioxidant capacity in Bacillus licheniformis. The results showed that the accumulation of intracellular ROS was reduced by 23.91 % and the cell survival rates were increased by 1.77-fold under 0.5 mM H2O2 when AbrB was knocked out. We further mapped regulatory target genes of AbrB related to ROS generation or clearance based on our previously analyzed transcriptome sequencing. It proved that AbrB could promote ROS generation via upregulating the synthesis of oxidase and siderophores, and negatively regulating the synthesis of iron chelators (pulcherriminic acid, and H2S). Additionally, AbrB could inhibit ROS clearance by negatively regulating the synthesis of antioxidase (superoxide dismutase, catalase, peroxidase, thioredoxin, thioredoxin reductase) and cysteine. Those results illustrated that the inactivation of AbrB during the stationary phase, along with its control over ROS generation and clearance, might represent a vital self-protection mechanism during cell evolution. Overall, the systematic investigation of the multi-pathway regulation network of ROS generation and clearance highlights the important function of AbrB in maintaining intracellular redox balance.

Reactive Oxygen Species Mediate the Bactericidal Activity of Chlorine Against Salmonella

Chlorine and its derivatives have been used as an antibacterial agent to reduce Salmonella contamination in poultry meat during processing. We evaluated the survival of 4 different Salmonella serotypes (Typhimurium, Enteritidis, Heidelberg, and Gaminara) in the presence of 50 ppm sodium hypochlorite (NaOCl) alone or with the addition of thiourea (radical scavenger) or Dip (iron chelator) to determine the contribution of reactive oxygen species (ROS) in the bactericidal activity of NaOCl. The result showed that for all four serotypes the addition of thiourea or Dip significantly increased the % survival as compared to the respective NaOCl treatment groups, while it was significantly higher with thiourea as compared to Dip (P < 0.05). We also evaluated the survival of 11 deletion mutants of S. Typhimurium, which were demonstrated to increase (∆atpC, ∆cyoA, ∆gnd, ∆nuoG, ∆pta, ∆sdhC, and ∆zwf) or decrease the production of ROS (∆edd, ∆fumB, ∆pykA, and ∆tktB) in Escherichia coli (E. coli), in the presence of 50 ppm. The results showed that only two (∆sdhC and ∆zwf) out of 7 ROS-increasing mutants showed reduced % survival as compared to the wild-type (P < 0.05), while all four deletion ROS-decreasing mutants showed significantly higher % survival as compared to the wild-type (P < 0.05). This work suggests that the production of ROS is a major component of the bactericidal activity of NaOCl against Salmonella serotypes and there might be a significant difference in the metabolic pathways involved in ROS production between Salmonella and E. coli.

Scalable, robust, high-throughput expression & purification of nanobodies enabled by 2-stage dynamic control

Nanobodies are single-domain antibody fragments that have garnered considerable use as diagnostic and therapeutic agents as well as research tools. However, obtaining pure VHHs, like many proteins, can be laborious and inconsistent. High level cytoplasmic expression in E. coli can be challenging due to improper folding and insoluble aggregation caused by reduction of the conserved disulfide bond. We report a systems engineering approach leveraging engineered strains of E. coli, in combination with a two-stage process and simplified downstream purification, enabling improved, robust, soluble cytoplasmic nanobody expression, as well as rapid cell autolysis and purification. This approach relies on the dynamic control over the reduction potential of the cytoplasm, incorporates lysis enzymes for purification, and can also integrate dynamic expression of protein folding catalysts. Collectively, the engineered system results in more robust growth and protein expression, enabling efficient scalable nanobody production, and purification from high throughput microtiter plates, to routine shake flask cultures and larger instrumented bioreactors. We expect this system will expedite VHH development.

Characterization of a Novel Oxidative Stress Responsive Transcription Regulator in Mycobacterium bovis

The antioxidant defense is critical for the survival of intracellular pathogens such as Mycobacterium tuberculosis complex (MTBC) species, including Mycobacterium bovis, which are often exposed to an oxidative environment caused by reactive oxygen species (ROS) in hosts. However, the signaling pathway in mycobacteria for sensing and responding to oxidative stress remains largely unclear. In this study, we characterize a TetR-type transcription regulator BCG_3893c, designated AotM, as a novel redox sensor in Mycobacterium bovis that increases mycobacterial tolerance to oxidative stress. AotM is required for the growth of M. bovis in the presence of 1 mM hydrogen peroxide. Loss of the aotM gene leads to altered transcriptional profiles with 352 genes significantly up-regulated and 25 genes significantly down-regulated. AotM recognizes a 14-bp palindrome sequence motif and negatively regulates the expression of a FAD-dependent oxidoreductase encoded by bcg_3892c. Overexpression of BCG_3892c increases intracellular ROS production and reduces the growth of M. bovis. In summary, we propose that AotM enhances the mycobacterial resistance against oxidative stress probably by inhibiting intracellular ROS production. Our findings reveal a novel underlying regulatory mechanism behind mycobacterial oxidative stress adaptation.

Integrative transcriptomic and metabolomic analysis to elucidate the effect of gossypol on Enterobacter sp. GD5

Gossypol, a yellow polyphenolic compound found in the Gossypium genus, is toxic to animals that ingest cotton-derived feed materials. However, ruminants display a notable tolerance to gossypol, attributed to the pivotal role of ruminal microorganisms in its degradation. The mechanisms of how rumen microorganisms degrade and tolerate gossypol remain unclear. Therefore, in this study, Enterobacter sp. GD5 was isolated from rumen fluid, and the effects of gossypol on its metabolism and gene expression were investigated using liquid chromatography-mass spectrometry (LC-MS) and RNA analyses. The LC-MS results revealed that gossypol significantly altered the metabolic profiles of 15 metabolites (eight upregulated and seven downregulated). The Kyoto Encyclopedia of Genes and Genomes analysis results showed that significantly different metabolites were associated with glutathione metabolism in both positive and negative ion modes, where gossypol significantly affected the biosynthesis of amino acids in the negative ion mode. Transcriptomic analysis indicated that gossypol significantly affected 132 genes (104 upregulated and 28 downregulated), with significant changes observed in the expression of catalase peroxidase, glutaredoxin-1, glutathione reductase, thioredoxin 2, thioredoxin reductase, and alkyl hydroperoxide reductase subunit F, which are related to antioxidative stress. Furthermore, Gene Ontology analysis revealed significant changes in homeostatic processes following gossypol supplementation. Overall, these results indicate that gossypol induces oxidative stress, resulting in the increased expression of antioxidative stress-related genes in Enterobacter sp. GD5, which may partially explain its tolerance to gossypol.

Chemical mixture effects on the simplified human intestinal microbiota: Assessing xenobiotics at environmentally realistic concentrations

The microbial community present in our intestines is pivotal for converting indigestible substances into vital nutrients and signaling molecules such as short-chain fatty acids (SCFAs). These compounds have considerable influence over our immune system and the development of diverse human diseases. However, ingested environmental contaminants, known as xenobiotics, can upset the delicate balance of the microbial gut community and enzymatic processes, consequently affecting the host organism. In our study, we employed an in vitro bioreactor model system based on the simplified human microbiome model (SIHUMIx) to investigate the direct effects of specific xenobiotics, such as perfluorooctanoic acid (PFOA), perfluorohexanoic acid (PFHxA) and perfluorobutanoic acid (PFBA) or bisphenol S (BPS) and bisphenol F (BPF), either individually or in combination, on the microbiota. We observed increased SCFA production, particularly acetate and butyrate, with PFAS exposure. Metaproteomics revealed pathway alterations across treatments, including changes in vitamin synthesis and fatty acid metabolism with BPX. This study underscores the necessity of assessing the combined effects of xenobiotics to better safeguard public health. It emphasizes the significance of considering adverse effects on the microbiome in the risk assessment of environmental chemicals.

Unravelling the key steps impairing the metabolic state of Xanthomonas cells undergoing programmed cell death

Programmed cell death (PCD) has been reported in Xanthomonas axonopodis pv. glycines (Xag) wild type earlier and was indirectly shown to be induced by metabolic stress; however, deciphering the key proteins regulating the metabolic stress remained unrevealed. In this study, transcriptomic and proteomic analyses were performed to investigate the prominent pathways, having a role in the induction of metabolic stress in Xag cells undergoing PCD. A comprehensive analysis of transcriptome and proteome data revealed the major involvement of metabolic pathways related to branched chain amino acid degradation, such as acyl-CoA dehydrogenase and energy-yielding, ubiquinol:cytochrome c oxidoreductase complex, in Xag cells undergoing PCD. Consequently, oxidative stress response genes showed major upregulation in Xag cells in PCD-inducing medium; however, no such upregulation was observed at the protein level, indicative of depleted protein levels under excessive stress conditions. Activation of stress response and DNA repair proteins was also observed in Xag cells grown in PCD-inducing medium, which is indicative of excessive cellular damage. Thus, the findings indicate that programmed cell death in Xag is an outcome of metabolic stress in nutrient condition not suitable for a plant pathogen like Xanthomonas, which is more acclimatised with altogether a different nutritional requirement predominantly having an enriched carbohydrate source.

Complete genome sequence and transcriptome response to vitamin C supplementation of Novacetimonas hansenii SI1 - producer of highly-stretchable cellulose

Novacetimonas hansenii SI1, previously known as Komagataeibacter hansenii, produces bacterial nanocellulose (BNC) with unique ability to stretch. The addition of vitamin C in the culture medium increases the porosity of the membranes and their stretchability making them highly moldable. To better understand the genetic background of this strain, we obtained its complete genome sequence using a hybrid sequencing and assembly strategy. We described the functional regions in the genome which are important for the synthesis of BNC and acetan-like II polymer. We next investigated the effect of 1% vitamin C supplementation on the global gene expression profile using RNA sequencing. Our transcriptomic readouts imply that vitamin C functions mainly as a reducing agent. We found that the changes in cellular redox status are balanced by strong repression of the sulfur assimilation pathway. Moreover, in the reduced conditions, glucose oxidation is decreased and alternative pathways for energy generation, such as acetate accumulation, are activated. The presence of vitamin C negatively influences acetan-like II polymer biosynthesis, which may explain the lowered yield and changed mechanical properties of BNC. The results of this study enrich the functional characteristics of the genomes of the efficient producers of the N. hansenii species. Improved understanding of the adaptation to the presence of vitamin C at the molecular level has important guiding significance for influencing the biosynthesis of BNC and its morphology.

OxyR is required for oxidative stress resistance of the entomopathogenic bacterium Xenorhabdus nematophila and has a minor role during the bacterial interaction with its hosts

Xenorhabdus nematophila is a Gram-negative bacterium, mutualistically associated with the soil nematode Steinernema carpocapsae, and this nemato-bacterial complex is parasitic for a broad spectrum of insects. The transcriptional regulator OxyR is widely conserved in bacteria and activates the transcription of a set of genes that influence cellular defence against oxidative stress. It is also involved in the virulence of several bacterial pathogens. The aim of this study was to identify the X. nematophila OxyR regulon and investigate its role in the bacterial life cycle. An oxyR mutant was constructed in X. nematophila and phenotypically characterized in vitro and in vivo after reassociation with its nematode partner. OxyR plays a major role during the X. nematophila resistance to oxidative stress in vitro. Transcriptome analysis allowed the identification of 59 genes differentially regulated in the oxyR mutant compared to the parental strain. In vivo, the oxyR mutant was able to reassociate with the nematode as efficiently as the control strain. These nemato-bacterial complexes harbouring the oxyR mutant symbiont were able to rapidly kill the insect larvae in less than 48 h after infestation, suggesting that factors other than OxyR could also allow X. nematophila to cope with oxidative stress encountered during this phase of infection in insect. The significantly increased number of offspring of the nemato-bacterial complex when reassociated with the X. nematophila oxyR mutant compared to the control strain revealed a potential role of OxyR during this symbiotic stage of the bacterial life cycle.

Reactive Oxygen Species (ROS)-Mediated Antibacterial Oxidative Therapies: Available Methods to Generate ROS and a Novel Option Proposal

The increasing emergence of multidrug-resistant (MDR) pathogens causes difficult-to-treat infections with long-term hospitalizations and a high incidence of death, thus representing a global public health problem. To manage MDR bacteria bugs, new antimicrobial strategies are necessary, and their introduction in practice is a daily challenge for scientists in the field. An extensively studied approach to treating MDR infections consists of inducing high levels of reactive oxygen species (ROS) by several methods. Although further clinical investigations are mandatory on the possible toxic effects of ROS on mammalian cells, clinical evaluations are extremely promising, and their topical use to treat infected wounds and ulcers, also in presence of biofilm, is already clinically approved. Biochar (BC) is a carbonaceous material obtained by pyrolysis of different vegetable and animal biomass feedstocks at 200-1000 °C in the limited presence of O2. Recently, it has been demonstrated that BC's capability of removing organic and inorganic xenobiotics is mainly due to the presence of persistent free radicals (PFRs), which can activate oxygen, H2O2, or persulfate in the presence or absence of transition metals by electron transfer, thus generating ROS, which in turn degrade pollutants by advanced oxidation processes (AOPs). In this context, the antibacterial effects of BC-containing PFRs have been demonstrated by some authors against Escherichia coli and Staphylococcus aureus, thus giving birth to our idea of the possible use of BC-derived PFRs as a novel method capable of inducing ROS generation for antimicrobial oxidative therapy. Here, the general aspects concerning ROS physiological and pathological production and regulation and the mechanism by which they could exert antimicrobial effects have been reviewed. The methods currently adopted to induce ROS production for antimicrobial oxidative therapy have been discussed. Finally, for the first time, BC-related PFRs have been proposed as a new source of ROS for antimicrobial therapy via AOPs.

Phaseolotoxin: Environmental Conditions and Regulatory Mechanisms Involved in Its Synthesis

Phaseolotoxin is an antimetabolite toxin produced by diverse pathovars of Pseudomonas syringae which affects various plants, causing diseases of economic importance. Phaseolotoxin contributes to the systemic dissemination of the pathogen in the plant, therefore it is recognized as a major virulence factor. Genetic traits such as the Pht cluster, appear defining to the toxigenic strains phaseolotoxin producers. Extensive research has contributed to our knowledge concerning the regulation of phaseolotoxin revealing a complex regulatory network that involves processes at the transcriptional and posttranscriptional levels, in which specific and global regulators participate. Even more, significant advances in understanding how specific signals, including host metabolites, nutrient sources, and physical parameters such as the temperature, can affect phaseolotoxin production have been made. A general overview of the phaseolotoxin regulation, focusing on the chemical and physical cues, and regulatory pathways involved in the expression of this major virulence factor will be given in the present work.

Identification of the mutual gliding locus as a factor for gut colonization in non-native bee hosts using the ARTP mutagenesis

BACKGROUND

The gut microbiota and their hosts profoundly affect each other's physiology and evolution. Identifying host-selected traits is crucial to understanding the processes that govern the evolving interactions between animals and symbiotic microbes. Current experimental approaches mainly focus on the model bacteria, like hypermutating Escherichia coli or the evolutionary changes of wild stains by host transmissions. A method called atmospheric and room temperature plasma (ARTP) may overcome the bottleneck of low spontaneous mutation rates while maintaining mild conditions for the gut bacteria.

RESULTS

We established an experimental symbiotic system with gnotobiotic bee models to unravel the molecular mechanisms promoting host colonization. By in vivo serial passage, we tracked the genetic changes of ARTP-treated Snodgrassella strains from Bombus terrestris in the non-native honeybee host. We observed that passaged isolates showing genetic changes in the mutual gliding locus have a competitive advantage in the non-native host. Specifically, alleles in the orphan mglB, the GTPase activating protein, promoted colonization potentially by altering the type IV pili-dependent motility of the cells. Finally, competition assays confirmed that the mutations out-competed the ancestral strain in the non-native honeybee gut but not in the native host.

CONCLUSIONS

Using the ARTP mutagenesis to generate a mutation library of gut symbionts, we explored the potential genetic mechanisms for improved gut colonization in non-native hosts. Our findings demonstrate the implication of the cell mutual-gliding motility in host association and provide an experimental system for future study on host-microbe interactions. Video Abstract.

CYP116B5-SOX: An artificial peroxygenase for drug metabolites production and bioremediation

CYP116B5 is a class VII P450 in which the heme domain is linked to a FMN and 2Fe2S-binding reductase. Our laboratory has proved that the CYP116B5 heme domain (CYP116B5-hd) is capable of catalyzing the oxidation of substrates using H2O2. Recently, the Molecular Lego approach was applied to join the heme domain of CYP116B5 to sarcosine oxidase (SOX), which provides H2O2 in-situ by the sarcosine oxidation. In this work, the chimeric self-sufficient fusion enzyme CYP116B5-SOX was heterologously expressed, purified, and characterized for its functionality by absorbance and fluorescence spectroscopy. Differential scanning calorimetry (DSC) experiments revealed a TM of 48.4 ± 0.04 and 58.3 ± 0.02°C and a enthalpy value of 175,500 ± 1850 and 120,500 ± 1350 cal mol-1 for the CYP116B5 and SOX domains respectively. The fusion enzyme showed an outstanding chemical stability in presence of up to 200 mM sarcosine or 5 mM H2O2 (4.4 ± 0.8 and 11.0 ± 2.6% heme leakage respectively). Thanks to the in-situ H2O2 generation, an improved kcat/KM for the p-nitrophenol conversion was observed (kcat of 20.1 ± 0.6 min-1 and KM of 0.23 ± 0.03 mM), corresponding to 4 times the kcat/KM of the CYP116B5-hd. The aim of this work is the development of an engineered biocatalyst to be exploited in bioremediation. In order to tackle this challenge, an E. coli strain expressing CYP116B5-SOX was employed to exploit this biocatalyst for the oxidation of the wastewater contaminating-drug tamoxifen. Data show a 12-fold increase in tamoxifen N-oxide production-herein detected for the first time as CYP116B5 metabolite-compared to the direct H2O2 supply, equal to the 25% of the total drug conversion.

Redox active plant phenolic, acetosyringone, for electrogenetic signaling

Redox is a unique, programmable modality capable of bridging communication between biology and electronics. Previous studies have shown that the E. coli redox-responsive OxyRS regulon can be re-wired to accept electrochemically generated hydrogen peroxide (H2O2) as an inducer of gene expression. Here we report that the redox-active phenolic plant signaling molecule acetosyringone (AS) can also induce gene expression from the OxyRS regulon. AS must be oxidized, however, as the reduced state present under normal conditions cannot induce gene expression. Thus, AS serves as a "pro-signaling molecule" that can be activated by its oxidation-in our case by application of oxidizing potential to an electrode. We show that the OxyRS regulon is not induced electrochemically if the imposed electrode potential is in the mid-physiological range. Electronically sliding the applied potential to either oxidative or reductive extremes induces this regulon but through different mechanisms: reduction of O2 to form H2O2 or oxidation of AS. Fundamentally, this work reinforces the emerging concept that redox signaling depends more on molecular activities than molecular structure. From an applications perspective, the creation of an electronically programmed "pro-signal" dramatically expands the toolbox for electronic control of biological responses in microbes, including in complex environments, cell-based materials, and biomanufacturing.

RpoS and the bacterial general stress response

SUMMARYThe general stress response (GSR) is a widespread strategy developed by bacteria to adapt and respond to their changing environments. The GSR is induced by one or multiple simultaneous stresses, as well as during entry into stationary phase and leads to a global response that protects cells against multiple stresses. The alternative sigma factor RpoS is the central GSR regulator in E. coli and conserved in most γ-proteobacteria. In E. coli, RpoS is induced under conditions of nutrient deprivation and other stresses, primarily via the activation of RpoS translation and inhibition of RpoS proteolysis. This review includes recent advances in our understanding of how stresses lead to RpoS induction and a summary of the recent studies attempting to define RpoS-dependent genes and pathways.

Polyhydroxyalkanoate involvement in stress-survival of two psychrophilic bacterial strains from the High Arctic

An ever-growing body of literature evidences the protective role of polyhydroxyalkanoates (PHAs) against a plethora of mostly physical stressors in prokaryotic cells. To date, most of the research done involved bacterial strains isolated from habitats not considered to be life-challenging or extremely impacted by abiotic environmental factors. Polar region microorganisms experience a multitude of damaging factors in combinations rarely seen in other of Earth's environments. Therefore, the main objective of this investigation was to examine the role of PHAs in the adaptation of psychrophilic, Arctic-derived bacteria to stress conditions. Arctic PHA producers: Acidovorax sp. A1169 and Collimonas sp. A2191, were chosen and their genes involved in PHB metabolism were deactivated making them unable to accumulate PHAs (ΔphaC) or to utilize them (Δi-phaZ) as a carbon source. Varying stressors were applied to the wild-type and the prepared mutant strains and their survival rates were assessed based on CFU count. Wild-type strains with a functional PHA metabolism were best suited to survive the freeze-thaw cycle - a common feature of polar region habitats. However, the majority of stresses were best survived by the ΔphaC mutants, suggesting that the biochemical imbalance caused by the lack of PHAs induced a permanent cell-wide stress response thus causing them to better withstand the stressor application. Δi-phaZ mutants were superior in surviving UV irradiation, hinting that PHA granule presence in bacterial cells is beneficial despite it being biologically inaccessible. Obtained data suggests that the ability to metabolize PHA although important for survival, probably is not the most crucial mechanism in the stress-resistance strategies arsenal of cold-loving bacteria. KEY POINTS: • PHA metabolism helps psychrophiles survive freezing • PHA-lacking psychrophile mutants cope better with oxidative and heat stresses • PHA granule presence enhances the UV resistance of psychrophiles.

OxyR-regulated T6SS functions in coordination with siderophore to resist oxidative stress

The formation of reactive oxygen species is harmful and can destroy intracellular macromolecules such as lipids, proteins, and DNA, even leading to bacterial death. To cope with this situation, microbes have evolved a variety of sophisticated mechanisms, including antioxidant enzymes, siderophores, and the type VI secretion system (T6SS). However, the mechanism of oxidative stress resistance in Cupriavidus pinatubonensis is unclear. In this study, we identified Reut_A2805 as an OxyR ortholog in C. pinatubonensis, which positively regulated the expression of T6SS1 by directly binding to its operon promoter region. The study revealed that OxyR-regulated T6SS1 combats oxidative stress by importing iron into bacterial cells. Moreover, the T6SS1-mediated outer membrane vesicles-dependent iron acquisition pathway played a crucial role in the oxidative stress resistance process. Finally, our study demonstrated that the T6SS1 and siderophore systems in C. pinatubonensis exhibit different responses in combating oxidative stress under low-iron conditions, providing a comprehensive understanding of how bacterial iron acquisition systems function in diverse conditions.IMPORTANCEThe ability to eliminate reactive oxygen species is crucial for bacterial survival. Continuous formation of hydroperoxides can damage metalloenzymes, disrupt DNA integrity, and even result in cell death. While various mechanisms have been identified in other bacterial species to combat oxidative stress, the specific mechanism of oxidative stress resistance in C. pinatubonensis remains unclear. The importance of this study is that we elucidate the mechanism that OxyR-regulated T6SS1 combats oxidative stress by importing iron with the help of bacterial outer membrane vesicle. Moreover, the study highlights the contrasting responses of T6SS1- and siderophore-mediated iron acquisition systems to oxidative stress. This study provides a comprehensive understanding of bacterial iron acquisition and its role in oxidative stress resistance in C. pinatubonensis under low-iron conditions.

The etherase system of Novosphingobium sp. MBES04 functions as a sensor of lignin fragments through phenylpropanone production to induce specific transcriptional responses

The MBES04 strain of Novosphingobium accumulates phenylpropanone monomers as end-products of the etherase system, which specifically and reductively cleaves the β-O-4 ether bond (a major bond in lignin molecules). However, it does not utilise phenylpropanone monomers as an energy source. Here, we studied the response to the lignin-related perturbation to clarify the physiological significance of its etherase system. Transcriptome analysis revealed two gene clusters, each consisting of four tandemly linked genes, specifically induced by a lignin preparation extracted from hardwood (Eucalyptus globulus) and a β-O-4-type lignin model biaryl compound, but not by vanillin. The most strongly induced gene was a 2,4'-dihydroxyacetophenone dioxygenase-like protein, which leads to energy production through oxidative degradation. The other cluster was related to multidrug resistance. The former cluster was transcriptionally regulated by a common promoter, where a phenylpropanone monomer acted as one of the effectors responsible for gene induction. These results indicate that the physiological significance of the etherase system of the strain lies in its function as a sensor for lignin fragments. This may be a survival strategy to detect nutrients and gain tolerance to recalcitrant toxic compounds, while the strain preferentially utilises easily degradable aromatic compounds with lower energy demands for catabolism.

Co-PATHOgenex web application for assessing complex stress responses in pathogenic bacteria

IMPORTANCE

Unveiling gene co-expression networks in bacterial pathogens has the potential for gaining insights into their adaptive strategies within the host environment. Here, we developed Co-PATHOgenex, an interactive and user-friendly web application that enables users to construct networks from gene co-expressions using custom-defined thresholds (https://avicanlab.shinyapps.io/copathogenex/). The incorporated search functions and visualizations within the tool simplify the usage and facilitate the interpretation of the analysis output. Co-PATHOgenex also includes stress stimulons for various bacterial species, which can help identify gene products not previously associated with a particular stress condition.

Exploring Metabolic and Gut Microbiome Responses to Paraquat Administration in Male Wistar Rats: Implications for Oxidative Stress

In this study, we examined the metabolic and gut microbiome responses to paraquat (PQ) in male Wistar rats, focusing on oxidative stress effects. Rats received a single intraperitoneal injection of PQ at 15 and 30 mg/kg, and various oxidative stress parameters (i.e., MDA, SOD, ROS, 8-isoprostanes) were assessed after three days. To explore the omic profile, GC-qTOF and UHPLC-qTOF were performed to assess the plasma metabolome; 1H-NMR was used to assess the urine metabolome; and shotgun metagenomics sequencing was performed to study the gut microbiome. Our results revealed reductions in body weight and tissue changes, particularly in the liver, were observed, suggesting a systemic effect of PQ. Elevated lipid peroxidation and reactive oxygen species levels in the liver and plasma indicated the induction of oxidative stress. Metabolic profiling revealed changes in the tricarboxylic acid cycle, accumulation of ketone body, and altered levels of key metabolites, such as 3-hydroxybutyric acid and serine, suggesting intricate links between energy metabolism and redox reactions. Plasma metabolomic analysis revealed alterations in mitochondrial metabolism, nicotinamide metabolism, and tryptophan degradation. The gut microbiome showed shifts, with higher PQ doses influencing microbial populations (e.g., Escherichia coli and Akkermansia muciniphila) and metagenomic functions (pyruvate metabolism, fermentation, nucleotide and amino acid biosynthesis). Overall, this study provides comprehensive insights into the complex interplay between PQ exposure, metabolic responses, and gut microbiome dynamics. These findings enhance our understanding of the mechanisms behind oxidative stress-induced metabolic alterations and underscore the connections between xenobiotic exposure, gut microbiota, and host metabolism.

A singular PpaA/AerR-like protein in Rhodospirillum rubrum rules beyond the boundaries of photosynthesis in response to the intracellular redox state

IMPORTANCE

Rhodospirillum rubrum vast metabolic versatility places it as a remarkable model bacterium and an excellent biotechnological chassis. The key component of photosynthesis (PS) studied in this work (HP1) stands out among the other members of PpaA/AerR anti-repressor family since it lacks the motif they all share: the cobalamin B-12 binding motif. Despite being reduced and poorly conserved, HP1 stills controls PS as the other members of the family, allowing a fast response to changes in the redox state of the cell. This work also shows that HP1 absence affects genes from relevant biological processes other than PS, including nitrogen fixation and stress response. From a biotechnological perspective, HP1 could be manipulated in approaches where PS is not necessary, such as hydrogen or polyhydroxyalkanoates production, to save energy.

Aminoglycoside uptake, stress, and potentiation in Gram-negative bacteria: new therapies with old molecules

SUMMARYAminoglycosides (AGs) are long-known molecules successfully used against Gram-negative pathogens. While their use declined with the discovery of new antibiotics, they are now classified as critically important molecules because of their effectiveness against multidrug-resistant bacteria. While they can efficiently cross the Gram-negative envelope, the mechanism of AG entry is still incompletely understood, although this comprehension is essential for the development of new therapies in the face of the alarming increase in antibiotic resistance. Increasing antibiotic uptake in bacteria is one strategy to enhance effective treatments. This review aims, first, to consolidate old and recent knowledge about AG uptake; second, to explore the connection between AG-dependent bacterial stress and drug uptake; and finally, to present new strategies of potentiation of AG uptake for more efficient antibiotic therapies. In particular, we emphasize on the connection between sugar transport and AG potentiation.

DegS protease regulates antioxidant capacity and adaptability to oxidative stress environment in Vibrio cholerae

Adaptation to oxidative stress is critical for survival of Vibrio cholerae in aquatic ecosystems and hosts. DegS activates the σE envelope stress response. We have previously revealed that DegS may be involved in regulating the oxidative stress response. In this study, we demonstrated that deletion of the degS gene attenuates the antioxidant capacity of V. cholerae. In addition, our results further revealed that the regulation of antioxidant capacity by DegS in V. cholerae could involve the cAMP-CRP complex, which regulates rpoS. XthA is an exonuclease that repairs oxidatively damaged cells and affects the bacterial antioxidant capacity. qRT-PCR showed that DegS, σE, cAMP, CRP, and RpoS positively regulate xthA gene transcription. XthA overexpression partially compensates for antioxidant deficiency in the degS mutant. These results suggest that DegS affects the antioxidant capacity of V.cholerae by regulating xthA expression via the cAMP-CRP-RpoS pathway. In a mouse intestinal colonization experiment, our data showed that V.cholerae degS, rpoE, and rpoS gene deletions were associated with significantly reduced resistance to oxidative stress and the ability to colonize the mouse intestine. In conclusion, these findings provide new insights into the regulation of antioxidant activity by V.cholerae DegS.

Ahp deficiency-induced redox imbalance leads to metabolic alterations in E.coli

Alkyl hydroperoxide reductase (Ahp) is the primary scavenger of endogenous hydrogen peroxide in Escherichia coli (E. coli). Ahp-deficient strains have been found to have high reactive oxygen species (ROS) levels, sufficient to cause cell damage. However, the exact role and underlying mechanisms of Ahp deficiency-induced cell damage remain largely unknown. Here, the E. coli MG1655 ΔAhp mutant strain was constructed as a model of deficiency to assess its role. The cells of the ΔAhp strain were found to be significantly longer than those of the wild strain, with elevated ROS and hydrogen peroxide (H2O2) levels. Proteome, redox proteome and metabolome analyses were performed to systematically present a global and quantitative profile and delineate the redox signaling and metabolic alterations at the proteome, metabolome, and cysteine oxidation site levels. The multiomics data revealed that Ahp deficiency disrupted the redox balance, activated the OxyR system, upregulated oxidative defense proteins and inhibited the TCA cycle to some extent. Surprisingly, the mutant strain shifted from aerobic respiration to anaerobic respiration and fermentation during the logarithmic phase in the presence of sufficient O2. The acid resistance system was activated to mitigate the effect of excessive acid produced by fermentation. Taken together, the results of this study demonstrated that Ahp deficiency triggered cellular redox imbalance and regulated metabolic pathways to confer resistance to submicromolar intracellular H2O2 levels in E. coli.

Transcription factor OxyR regulates sulfane sulfur removal and L-cysteine biosynthesis in Corynebacterium glutamicum

Sulfane sulfur, a collective term for hydrogen polysulfide and organic persulfide, often damages cells at high concentrations. Cells can regulate intracellular sulfane sulfur levels through specific mechanisms, but these mechanisms are unclear in Corynebacterium glutamicum. OxyR is a transcription factor capable of sensing oxidative stress and is also responsive to sulfane sulfur. In this study, we found that OxyR functioned directly in regulating sulfane sulfur in C. glutamicum. OxyR binds to the promoter of katA and nrdH and regulates its expression, as revealed via in vitro electrophoretic mobility shift assay analysis, real-time quantitative PCR, and reporting systems. Overexpression of katA and nrdH reduced intracellular sulfane sulfur levels by over 30% and 20% in C. glutamicum, respectively. RNA-sequencing analysis showed that the lack of OxyR downregulated the expression of sulfur assimilation pathway genes and/or sulfur transcription factors, which may reduce the rate of sulfur assimilation. In addition, OxyR also affected the biosynthesis of L-cysteine in C. glutamicum. OxyR overexpression strain Cg-2 accumulated 183 mg/L of L-cysteine, increased by approximately 30% compared with the control (142 mg/L). In summary, OxyR not only regulated sulfane sulfur levels by controlling the expression of katA and nrdH in C. glutamicum but also facilitated the sulfur assimilation and L-cysteine synthesis pathways, providing a potential target for constructing robust cell factories of sulfur-containing amino acids and their derivatives. IMPORTANCE C. glutamicum is an important industrial microorganism used to produce various amino acids. In the production of sulfur-containing amino acids, cells inevitably accumulate a large amount of sulfane sulfur. However, few studies have focused on sulfane sulfur removal in C. glutamicum. In this study, we not only revealed the regulatory mechanism of OxyR on intracellular sulfane sulfur removal but also explored the effects of OxyR on the sulfur assimilation and L-cysteine synthesis pathways in C. glutamicum. This is the first study on the removal of sulfane sulfur in C. glutamicum. These results contribute to the understanding of sulfur regulatory mechanisms and may aid in the future optimization of C. glutamicum for biosynthesis of sulfur-containing amino acids.

Deionococcus proteotlycius Genomic Library Exploration Enhances Oxidative Stress Resistance and Poly-3-hydroxybutyrate Production in Recombinant Escherichia coli

Cell growth is inhibited by abiotic stresses during industrial processes, which is a limitation of microbial cell factories. Microbes with robust phenotypes are critical for its maximizing the yield of the target products in industrial biotechnology. Currently, there are several reports on the enhanced production of industrial metabolite through the introduction of Deinococcal genes into host cells, which confers cellular robustness. Deinococcus is known for its unique genetic function thriving in extreme environments such as radiation, UV, and oxidants. In this study, we established that Deinococcus proteolyticus showed greater resistance to oxidation and UV-C than commonly used D. radiodurans. By screening the genomic library of D. proteolyticus, we isolated a gene (deipr_0871) encoding a response regulator, which not only enhanced oxidative stress, but also promoted the growth of the recombinant E. coli strain. The transcription analysis indicated that the heterologous expression of deipr_0871 upregulated oxidative-stress-related genes such as ahpC and sodA, and acetyl-CoA-accumulation-associated genes via soxS regulon. Deipr_0871 was applied to improve the production of the valuable metabolite, poly-3-hydroxybutyrate (PHB), in the synthetic E. coli strain, which lead to the remarkably higher PHB than the control strain. Therefore, the stress tolerance gene from D. proteolyticus should be used in the modification of E. coli for the production of PHB and other biomaterials.

An RNA modification enzyme directly senses reactive oxygen species for translational regulation in Enterococcus faecalis

Bacteria possess elaborate systems to manage reactive oxygen and nitrogen species (ROS) arising from exposure to the mammalian immune system and environmental stresses. Here we report the discovery of an ROS-sensing RNA-modifying enzyme that regulates translation of stress-response proteins in the gut commensal and opportunistic pathogen Enterococcus faecalis. We analyze the tRNA epitranscriptome of E. faecalis in response to reactive oxygen species (ROS) or sublethal doses of ROS-inducing antibiotics and identify large decreases in N²-methyladenosine (m²A) in both 23 S ribosomal RNA and transfer RNA. This we determine to be due to ROS-mediated inactivation of the Fe-S cluster-containing methyltransferase, RlmN. Genetic knockout of RlmN gives rise to a proteome that mimics the oxidative stress response, with an increase in levels of superoxide dismutase and decrease in virulence proteins. While tRNA modifications were established to be dynamic for fine-tuning translation, here we report the discovery of a dynamically regulated, environmentally responsive rRNA modification. These studies lead to a model in which RlmN serves as a redox-sensitive molecular switch, directly relaying oxidative stress to modulating translation through the rRNA and the tRNA epitranscriptome, adding a different paradigm in which RNA modifications can directly regulate the proteome.

The Arsenal of Leptospira Species against Oxidants

Reactive oxygen species (ROS) are byproducts of oxygen metabolism produced by virtually all organisms living in an oxic environment. ROS are also produced by phagocytic cells in response to microorganism invasion. These highly reactive molecules can damage cellular constituents (proteins, DNA, and lipids) and exhibit antimicrobial activities when present in sufficient amount. Consequently, microorganisms have evolved defense mechanisms to counteract ROS-induced oxidative damage. Leptospira are diderm bacteria form the Spirochaetes phylum. This genus is diverse, encompassing both free-living non-pathogenic bacteria as well as pathogenic species responsible for leptospirosis, a widespread zoonotic disease. All leptospires are exposed to ROS in the environment, but only pathogenic species are well-equipped to sustain the oxidative stress encountered inside their hosts during infection. Importantly, this ability plays a pivotal role in Leptospira virulence. In this review, we describe the ROS encountered by Leptospira in their different ecological niches and outline the repertoire of defense mechanisms identified so far in these bacteria to scavenge deadly ROS. We also review the mechanisms controlling the expression of these antioxidants systems and recent advances in understanding the contribution of Peroxide Stress Regulators in Leptospira adaptation to oxidative stress.

Bacterial antioxidant mechanism in calcium peroxide aided sludge anaerobic fermentation

Although calcium peroxide (CaO₂) can enhance the short-chain fatty acids (SCFAs) production in sludge anaerobic fermentation, the microbiological mechanisms underlying this process remain unclear. In this study, it is aimed to elucidate the bacterial protective mechanisms in response to the oxidative stress induced by CaO₂. Results show that extracellular polymeric substance (EPS) and anti-oxidant enzymes play vital roles in protecting bacterial cells from CaO₂. The addition of CaO₂ resulted in increased relative abundances of genes exoP and SRP54, which are associated with EPS secretion and transportation. Superoxide dismutase (SOD) played a crucial in alleviating oxidative stress. The dosage of CaO₂ significantly influences the succession of the bacterial community in the anaerobic fermentation system. With 0.3 g CaO₂/g VSS, the net income was approximately 4 USD/ton of sludge treated. The CaO₂-assisted anaerobic fermentation process has the potential to recover more resources from sludge and thus, benefit the environment.

RNAs as Sensors of Oxidative Stress in Bacteria

Oxidative stress is an important and pervasive physical stress encountered by all kingdoms of life, including bacteria. In this review, we briefly describe the nature of oxidative stress, highlight well-characterized protein-based sensors (transcription factors) of reactive oxygen species that serve as standards for molecular sensors in oxidative stress, and describe molecular studies that have explored the potential of direct RNA sensitivity to oxidative stress. Finally, we describe the gaps in knowledge of RNA sensors-particularly regarding the chemical modification of RNA nucleobases. RNA sensors are poised to emerge as an essential layer of understanding and regulating dynamic biological pathways in oxidative stress responses in bacteria and, thus, also represent an important frontier of synthetic biology.

Susceptibility of Campylobacter jejuni to Stressors in Agrifood Systems and Induction of a Viable-but-Nonculturable State

Many bacteria can become viable but nonculturable (VBNC) in response to stressors commonly identified in agrifood systems. Campylobacter is able to enter the VBNC state to evade unfavorable environmental conditions, but how food processing can induce Campylobacter jejuni to enter this state and the potential role of foods in inducing the VBNC state in C. jejuni remains largely unknown. In this study, the culturability and viability of C. jejuni cells were investigated under chlorine treatment (25 ppm), aerobic stress (atmospheric condition), and low-temperature (4°C) conditions that mimicked food processing. In addition, the behaviors of C. jejuni cells in ultrahigh-temperature (UHT) and pasteurized milk were also monitored during refrigerated storage. The numbers of viable and culturable C. jejuni cells in both the pure bacterial culture and food matrices were separately determined by propidium monoazide (PMA)-quantitative PCR (qPCR) and plating assay. The C. jejuni cells lost their culturability but partially retained their viability (1% to 10%) once mixed with chlorine. In comparison, ~10% of C. jejuni cells were induced to enter the VBNC state after 24 h and 20 days under aerobic and low-temperature conditions, respectively. The viability of the C. jejuni cells remained stable during the induction process in UHT (>10%) and pasteurized (>10%) milk. The number of culturable C. jejuni cells decreased quickly in pasteurized milk, but culturable cells could still be detected in the end (day 21). In contrast, the number of culturable C. jejuni cells slowly decreased, and they became undetectable after >42 days in UHT milk. The C. jejuni cells responded differently to various stress conditions and survived in high numbers in the VBNC state in agrifood systems. IMPORTANCE The VBNC state of pathogens can pose risks to food safety and public health because the pathogens cannot be detected using conventional microbiological culture-based methods but can resuscitate under favorable conditions to develop virulence. As a leading cause of human gastroenteritis worldwide, C. jejuni can enter the VBNC state to survive in the environment and food-processing chain with high prevalence. In this study, the effect of food-processing conditions and food products on the development of VBNC state in C. jejuni was investigated, providing a better understanding of the interaction between C. jejuni and the agroecosystem. The knowledge elicited from this study can aid in developing novel intervention strategies to reduce the food safety risks associated with this microbe.

Oxidative Stress Response and E. coli Biofilm Formation under the Effect of Pristine and Modified Carbon Nanotubes

The article investigates the expression of oxyR and soxS oxidative stress genes in E. coli under the effect of pristine multi-walled carbon nanotubes (MWCNTs) and pristine single-walled carbon nanotubes (SWCNTs), MWCNTs and SWCNTs functionalized with carboxyl groups (MWCNTs-COOH and SWCNTs-COOH, respectively), SWCNTs functionalized with amino groups (SWCNTs-NH₂) and SWCNTs functionalized with octadecylamine (SWCNTs-ODA). Significant differences were found in the expression of the soxS gene, while no changes were observed in the expression level of the oxyR gene. The pro-oxidant effect of SWCNTs, SWCNTs-COOH, SWCNTs-NH₂, and SWCNTs-ODA is presented, and the contrary antioxidant effect of pristine MWCNTs and MWCNTs-COOH in the presence of methyl viologen hydrate (paraquat) is shown. The article shows that SWCNTs-COOH, SWCNTs-NH₂, and SWCNTs-ODA added to the medium generate the production of reactive oxygen species (ROS) in bacterial cells. SWCNTs-COOH intensified the E. coli biofilm formation, and the biofilm biomass exceeded the control by 25 times. Additionally, it is shown that the rpoS expression increased in response to MWCNTs-COOH and SWCNTs-COOH, and the effect of SWCNTs-COOH was more significant. SWCNTs-COOH and SWCNTs-NH₂ initiated an increase in ATP concentration in the planktonic cells and a decrease in the biofilm cells. The atomic force microscopy (AFM) method showed that the volume of E. coli planktonic cells after the exposure to carbon nanotubes (CNTs) decreased compared to that without exposure, mainly due to a decrease in cell height. The absence of a strong damaging effect of functionalized SWCNTs on E. coli K12 cells, both in suspension and in biofilms, is shown. Contact with functionalized SWCNTs initiated the aggregation of the polymeric substances of the biofilms; however, the cells did not lyse. Among the studied CNTs, SWCNTs-COOH caused an increased expression of the soxS and rpoS, the formation of ROS, and stimulation of the biofilm formation.

A novel bidirectional regulation mechanism of mancozeb on the dissemination of antibiotic resistance

The high abundance of antibiotic resistance genes (ARGs) in the fungicide residual environment, posing a threat to the environment and human health, raises the question of whether and how fungicide promotes the prevalence and dissemination of antibiotic resistance. Here, we reported a novel mechanism underlying bidirectional regulation of a typical heavy-metal-containing fungicide mancozeb on the horizontal transfer of ARGs. Our findings revealed that mancozeb exposure significantly exerted oxidative and osmotic stress on the microbes and facilitated plasmid-mediated ARGs transfer, but its metallic portions (Mn and Zn) were potentially utilized as essential ions by microbes for metalating enzymes to deal with cellular stress and thus reduce the transfer. The results of transcriptome analysis with RT-qPCR confirmed that the expression levels of cellular stress responses and conjugation related genes were drastically altered. It can be concluded mancozeb bidirectionally regulated the ARGs dissemination which may be attributed to the diverse effects on the microbes by its different portions. This novel mechanism provides an updated understanding of neglected fungicide-triggered ARGs dissemination and crucial insight for comprehensive risk assessment of fungicides.

Repairing of rutin to the toxicity of combined F-53B and chromium pollution on the biofilm formed by Pseudomonas aeruginosa

The wastewater discharge from the process of chrome plating, which contains 6:2 chlorinated polyfluorinated ether sulfonate (F-53B) and chromium (Cr), may be toxic to biofilm. In this study we found that the biofilm formed by Pseudomonas aeruginosa PAO1 was inhibited by exposure to a combination of F-53B and Cr(VI). The combined pollution damaged the cell membranes and the structure of the biofilm, and inhibited the production of the Pseudomonas quinolone-based signal, which affected biofilm formation. Moreover, the secretion of extracellular polymeric substances decreased as a result of this combined exposure. Exposure to F-53B and Cr(VI) individually or in combination could induce the excessive accumulation of intracellular reactive oxygen species (ROS), and the ROS positive rate of the bacteria increased under the treatment with 0.2 mmol/L of Cr(VI) and 250 nmol/L of F-53B, respectively. In addition, the activities of superoxide dismutase (SOD) and catalase (CAT) were enhanced for scavenging ROS in the bacteria that were exposed to Cr(VI) and F-53B. As an antioxidant, rutin was used to repair the toxicity of Cr(VI) and F-53B towards the biofilm formed by the bacteria. When rutin was added to the bacteria medium, with either Cr(VI) or F-53B as pollutant, or with the combined pollutants, the extracellular protein content of the bacteria recovered to 0.84, 0.94, and 0.85 times that of the control, respectively. Meanwhile, the accumulation of ROS and the activities of SOD and CAT decreased, which indicated that the addition of rutin can alleviate the oxidative stress and promote the antioxidant stress system.

Global Transcriptional Response of Escherichia coli Exposed In Situ to Different Low-Dose Ionizing Radiation Sources

Characterization of biological and chemical responses to ionizing radiation by various organisms is essential for potential applications in bioremediation, alternative modes of detecting nuclear material, and national security. Escherichia coli DH10β is an optimal system to study the microbial response to low-dose ionizing radiation at the transcriptional level because it is a well-characterized model bacterium and its responses to other environmental stressors, including those to higher radiation doses, have been elucidated in prior studies. In this study, RNA sequencing with downstream transcriptomic analysis (RNA-seq) was employed to characterize the global transcriptional response of stationary-phase E. coli subjected to 239Pu, 3H (tritium), and 55Fe, at an approximate absorbed dose rate of 10 mGy day-1 for 1 day and 15 days. Differential expression analysis identified significant changes in gene expression of E. coli for both short- and long-term exposures. Radionuclide source exposure induced differential expression in E. coli of genes involved in biosynthesis pathways of nuclear envelope components, amino acids, and siderophores, transport systems such as ABC transporters and type II secretion proteins, and initiation of stress response and regulatory systems of temperature stress, the RpoS regulon, and oxidative stress. These findings provide a basic understanding of the relationship between low-dose exposure and biological effect of a model bacterium that is critical for applications in alternative nuclear material detection and bioremediation. IMPORTANCE Escherichia coli strain DH10β, a well-characterized model bacterium, was subjected to short-term (1-day) and long-term (15-day) exposures to three different in situ radiation sources comprised of radionuclides relevant to nuclear activities to induce a measurable and identifiable genetic response. We found E. coli had both common and unique responses to the three exposures studied, suggesting both dose rate- and radionuclide-specific effects. This study is the first to provide insights into the transcriptional response of a microorganism in short- and long-term exposure to continuous low-dose ionizing radiation with multiple in situ radionuclide sources and the first to examine microbial transcriptional response in stationary phase. Moreover, this work provides a basis for the development of biosensors and informing more robust dose-response relationships to support ecological risk assessment.

Phenotypic heterogeneity in the bacterial oxidative stress response is driven by cell-cell interactions

Genetically identical bacterial cells commonly display different phenotypes. This phenotypic heterogeneity is well known for stress responses, where it is often explained as bet hedging against unpredictable environmental threats. Here, we explore phenotypic heterogeneity in a major stress response of Escherichia coli and find it has a fundamentally different basis. We characterize the response of cells exposed to hydrogen peroxide (H2O2) stress in a microfluidic device under constant growth conditions. A machine-learning model reveals that phenotypic heterogeneity arises from a precise and rapid feedback between each cell and its immediate environment. Moreover, we find that the heterogeneity rests upon cell-cell interaction, whereby cells shield each other from H2O2 via their individual stress responses. Our work shows how phenotypic heterogeneity in bacterial stress responses can emerge from short-range cell-cell interactions and result in a collective phenotype that protects a large proportion of the population.

The role of oxidative stress in genome destabilization and adaptive evolution of bacteria

The review is devoted to bacterial genome destabilization by oxidative stress. The article discusses the main groups of substances causing such stress. Stress regulons involved in destabilization of genetic material and mechanisms enhancing mutagenesis, bacterial genome rearrangements, and horizontal gene transfer, induced by oxidative damage to cell components are also considered. Based on the analysis of publications, it can be claimed that rapid development of new food substrates and ecological niches by microorganisms occurs due to acceleration of genetic changes induced by oxidative stress, mediated by several stress regulons (SOS, RpoS and RpoE) and under selective pressure. The authors conclude that non-lethal oxidative stress is probably-one of the fundamental processes that guide evolution of prokaryotes and a powerful universal trigger for adaptive destabilization of bacterial genome under changing environmental conditions.