How Microbes Defend Themselves From Incoming Hydrogen Peroxide

Short-term supplementation with uncoated and encapsulated Enterococcus faecium affected growth performance, gut microbiome and intestinal barrier integrity in broiler chickens

Enterococcus faecium (E. faecium) is an alternative to antibiotics, while the probiotic effect of short-term application in mature broiler chickens remains unclear. In the current study, 48 Arbor Acres male broilers were chosen to investigate the effects of E. faecium on growth performance, the gut microbiome and intestinal health during the finishing period. Forty-eight birds were randomly allocated to 4 treatment groups that were fed a corn-soybean meal basal diet (Con), a basal diet supplemented with 1 g/kg amoxicillin (ABX), 5×106 CFU/g encapsulated E. faecium (cEF), or 5×106 CFU/g uncoated E. faecium (EF) from d 33 to 42. The results showed that 10 d of antibiotic treatment decreased the growth performance of the broilers (P < 0.05). The feed conversion ratio of the cEF and EF groups were lower than that of the Con group by 0.13 and 0.07, respectively (P > 0.05). The abundance of viable ileal and cecal E. faecium in the cEF group was greater than that in the EF group (P < 0.05), and both groups were markedly greater than those in the Con and ABX groups (P < 0.05). The ABX treatment decreased the Shannon and Chao1 indices of the cecal microbiota, while the dietary E. faecium treatment resulted in significant differences in the β diversity of the ileal and cecal microbiota (P < 0.05). Mantel correlation revealed that the ileal microbiota at the genus level was significantly correlated with the growth performance of broilers, with Lactobacillus, Bacillus and Escherichia-Shigella showing positive and strong correlations (P < 0.05). In the ileum, the crypt depth was lower in the cEF group than in the Con group, but the villi height-to-crypt depth ratio was greater in the cEF group than in the other groups (P = 0.037). However, the expression of the ZO-2 and Occludin genes was downregulated in the E. faecium-fed birds (P < 0.05). In the cecum, the acetate, butyrate and total SCFA levels were greater in the EF group (P < 0.05), while the propionate, isobutyrate and isovalerate levels were lower in the ABX group (P < 0.05). In summary, 10 d of dietary supplementation with E. faecium markedly increased colonization in mature broilers and potentially improved growth performance by modulating the ileal microbiota. Encapsulation techniques could enable a slow release of E. faecium in the intestine, thereby reducing the negative impacts of rapid expansion of E. faecium on the intestinal epithelium.

Stealing survival: Iron acquisition strategies of Mycobacteriumtuberculosis

Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis (TB), faces iron scarcity within the host due to immune defenses. This review explores the importance of iron for Mtb and its strategies to overcome iron restriction. We discuss how the host limits iron as an innate immune response and how Mtb utilizes various iron acquisition systems, particularly the siderophore-mediated pathway. The review illustrates the structure and biosynthesis of mycobactin, a key siderophore in Mtb, and the regulation of its production. We explore the potential of targeting siderophore biosynthesis and uptake as a novel therapeutic approach for TB. Finally, we summarize current knowledge on Mtb's iron acquisition and highlight promising directions for future research to exploit this pathway for developing new TB interventions.

Antioxidants are ineffective at quenching reactive oxygen species inside bacteria and should not be used to diagnose oxidative stress

A wide variety of stresses have been proposed to exert killing effects upon bacteria by stimulating the intracellular formation of reactive oxygen species (ROS). A key part of the supporting evidence has often been the ability of antioxidant compounds to protect the cells. In this study, some of the most-used antioxidants-thiourea, glutathione, N-acetylcysteine, and ascorbate-have been examined. Their ability to quench superoxide and hydrogen peroxide was verified in vitro, but the rate constants were orders of magnitude too slow for them to have an impact upon superoxide and peroxide concentrations in vivo, where these species are already scavenged by highly active enzymes. Indeed, the antioxidants were unable to protect the growth and ROS-sensitive enzymes of E. coli strains experiencing authentic oxidative stress. Similar logic posits that antioxidants cannot substantially quench hydroxyl radicals inside cells, which contain abundant biomolecules that react with them at diffusion-limited rates. Indeed, antioxidants were able to protect cells from DNA damage only if they were applied at concentrations that slow metabolism and growth. This protective effect was apparent even under anoxic conditions, when ROS could not possibly be involved, and it was replicated when growth was similarly slowed by other means. Experimenters should discard the use of antioxidants as a way of detecting intracellular oxidative stress and should revisit conclusions that have been based upon such experiments. The notable exception is that these compounds can effectively degrade hydrogen peroxide from environmental sources before it enters cells.

Functional Analysis of Stress Resistance of Bacillus cereus SCL10 Strain Based on Whole-Genome Sequencing

A Gram-positive, rod-shaped, aerobic, motile, and spore-forming bacterium, designated SCL10, was isolated from Acaudina molpadioides exposure to Co-60 radiation. In this study, whole-genome sequencing was performed to identify the strain as Bacillus cereus and functional characterization, with a focus on stress resistance. The genome of the B. cereus SCL10 strain was sequenced and assembled, revealing a size of 4,979,182 bp and 5167 coding genes. The genes involved in biological functions were annotated by using the GO, COG, KEGG, NR, and Swiss-Prot databases. The results showed that genes related to alkyl hydroperoxide reductase (ahpC, ahpF), DNA-binding proteins from starved cells (dps), spore and biofilm formation (spoVG, spo0A, gerP), cold shock-like protein (cspC, cspE), ATP-dependent chaperone (clpB), and photolyase, small, acid-soluble spore protein (SASP) and DNA repair protein (recA, radD) could explain the stress resistance. These findings suggest that antioxidant activity, sporulation, biofilm formation, and DNA protection may be considered as the main resistance mechanisms under exposure to radiation in the B. cereus SCL10 strain.

Microbes vary strategically in their metalation of mononuclear enzymes

Studies have determined that nonredox enzymes that are cofactored with Fe(II) are the most oxidant-sensitive targets inside Escherichia coli. These enzymes use Fe(II) cofactors to bind and activate substrates. Because of their solvent exposure, the metal can be accessed and oxidized by reactive oxygen species, thereby inactivating the enzyme. Because these enzymes participate in key physiological processes, the consequences of stress can be severe. Accordingly, when E. coli senses elevated levels of H2O2, it induces both a miniferritin and a manganese importer, enabling the replacement of the iron atom in these enzymes with manganese. Manganese does not react with H2O2 and thereby preserves enzyme activity. In this study, we examined several diverse microbes to identify the metal that they customarily integrate into ribulose-5-phosphate 3-epimerase, a representative of this enzyme family. The anaerobe Bacteroides thetaiotaomicron, like E. coli, uses iron. In contrast, Bacillus subtilis and Lactococcus lactis use manganese, and Saccharomyces cerevisiae uses zinc. The latter organisms are therefore well suited to the oxidizing environments in which they dwell. Similar results were obtained with peptide deformylase, another essential enzyme of the mononuclear class. Strikingly, heterologous expression experiments show that it is the metal pool within the organism, rather than features of the protein itself, that determine which metal is incorporated. Further, regardless of the source organism, each enzyme exhibits highest turnover with iron and lowest turnover with zinc. We infer that the intrinsic catalytic properties of the metal cannot easily be retuned by evolution of the polypeptide.

Dissolved organic matter accelerates microbial degradation of 17 alpha-ethinylestradiol in the presence of iron mineral

Dissolved organic matter (DOM) and iron minerals widely existing in the natural aquatic environment can mediate the migration and transformation of organic pollutants. However, the mechanism of interaction between DOM and iron minerals in the microbial degradation of pollutants deserves further investigation. In this study, the mechanism of 17 alpha-ethinylestradiol (EE2) biodegradation mediated by humic acid (HA) and three kinds of iron minerals (goethite, magnetite, and pyrite) was investigated. The results found that HA and iron minerals significantly accelerated the biodegradation process of EE2, and the highest degradation efficiency of EE2 (48%) was observed in the HA-mediated microbial system with pyrite under aerobic conditions. Furthermore, it had been demonstrated that hydroxyl radicals (HO•) was the main active substance responsible for the microbial degradation of EE2. HO• is primarily generated through the reaction between hydrogen peroxide secreted by microorganisms and Fe(II), with aerobic conditions being more conducive. The presence of iron minerals and HA could change the microbial communities in the EE2 biodegradation system. These findings provide new information for exploring the migration and transformation of pollutants by microorganisms in iron-rich environments.

The long-chain flavodoxin FldX1 improves the biodegradation of 4-hydroxyphenylacetate and 3-hydroxyphenylacetate and counteracts the oxidative stress associated to aromatic catabolism in Paraburkholderia xenovorans

BACKGROUND

Bacterial aromatic degradation may cause oxidative stress. The long-chain flavodoxin FldX1 of Paraburkholderia xenovorans LB400 counteracts reactive oxygen species (ROS). The aim of this study was to evaluate the protective role of FldX1 in P. xenovorans LB400 during the degradation of 4-hydroxyphenylacetate (4-HPA) and 3-hydroxyphenylacetate (3-HPA).

METHODS

The functionality of FldX1 was evaluated in P. xenovorans p2-fldX1 that overexpresses FldX1. The effects of FldX1 on P. xenovorans were studied measuring growth on hydroxyphenylacetates, degradation of 4-HPA and 3-HPA, and ROS formation. The effects of hydroxyphenylacetates (HPAs) on the proteome (LC-MS/MS) and gene expression (qRT-PCR) were quantified. Bioaugmentation with strain p2-fldX1 of 4-HPA-polluted soil was assessed, measuring aromatic degradation (HPLC), 4-HPA-degrading bacteria, and plasmid stability.

RESULTS

The exposure of P. xenovorans to 4-HPA increased the formation of ROS compared to 3-HPA or glucose. P. xenovorans p2-fldX1 showed an increased growth on 4-HPA and 3-HPA compared to the control strain WT-p2. Strain p2-fldX1 degraded faster 4-HPA and 3-HPA than strain WT-p2. Both WT-p2 and p2-fldX1 cells grown on 4-HPA displayed more changes in the proteome than cells grown on 3-HPA in comparison to glucose-grown cells. Several enzymes involved in ROS detoxification, including AhpC2, AhpF, AhpD3, KatA, Bcp, CpoF1, Prx1 and Prx2, were upregulated by hydroxyphenylacetates. Downregulation of organic hydroperoxide resistance (Ohr) and DpsA proteins was observed. A downregulation of the genes encoding scavenging enzymes (katE and sodB), and gstA and trxB was observed in p2-fldX1 cells, suggesting that FldX1 prevents the antioxidant response. More than 20 membrane proteins, including porins and transporters, showed changes in expression during the growth of both strains on hydroxyphenylacetates. An increased 4-HPA degradation by recombinant strain p2-fldX1 in soil microcosms was observed. In soil, the strain overexpressing the flavodoxin FldX1 showed a lower plasmid loss, compared to WT-p2 strain, suggesting that FldX1 contributes to bacterial fitness. Overall, these results suggest that recombinant strain p2-fldX1 is an attractive bacterium for its application in bioremediation processes of aromatic compounds.

CONCLUSIONS

The long-chain flavodoxin FldX1 improved the capability of P. xenovorans to degrade 4-HPA in liquid culture and soil microcosms by protecting cells against the degradation-associated oxidative stress.

The role of metals in hypothiocyanite resistance in Escherichia coli

The innate immune system employs a variety of antimicrobial oxidants to control and kill host-associated bacteria. Hypothiocyanite/hypothiocyanous acid (-OSCN/HOSCN) is one such antimicrobial oxidant that is synthesized by lactoperoxidase, myeloperoxidase, and eosinophil peroxidase at sites throughout the human body. HOSCN has potent antibacterial activity while being largely non-toxic towards human cells. The molecular mechanisms by which bacteria sense and defend themselves against HOSCN have only recently begun to be elaborated, notably by the discovery of bacterial HOSCN reductase (RclA), an HOSCN-degrading enzyme widely conserved among bacteria that live on epithelial surfaces. In this paper, I show that Ni2+ sensitizes Escherichia coli to HOSCN by inhibiting glutathione reductase, and that inorganic polyphosphate protects E. coli against this effect, probably by chelating Ni2+ ions. I also found that RclA is very sensitive to inhibition by Cu2+ and Zn2+, metals that are accumulated to high levels by innate immune cells, and that, surprisingly, thioredoxin and thioredoxin reductase are not involved in HOSCN stress resistance in E. coli. These results advance our understanding of the contribution of different oxidative stress response and redox buffering pathways to HOSCN resistance in E. coli and illustrate important interactions between metal ions and the enzymes bacteria use to defend themselves against oxidative stress.

Effects of OxyR regulator on oxidative stress, Apx toxin secretion and virulence of Actinobacillus pleuropneumoniae

Introduction

Actinobacillus pleuropneumoniae, the causative agent of porcine pleuropneumonia, poses a significant threat to global swine populations due to its high prevalence, mortality rates, and substantial economic ramifications. Understanding the pathogen's defense mechanisms against host-produced reactive oxygen species is crucial for its survival, with OxyR, a conserved bacterial transcription factor, being pivotal in oxidative stress response.

Methods

This study investigated the presence and role of OxyR in A. pleuropneumoniae serovar 1-12 reference strains. Transcriptomic analysis was conducted on an oxyR disruption mutant to delineate the biological activities influenced by OxyR. Additionally, specific assays were employed to assess urease activity, catalase expression, ApxI toxin secretion, as well as adhesion and invasion abilities of the oxyR disruption mutant on porcine 3D4/21 and PT cells. A mice challenge experiment was also conducted to evaluate the impact of oxyR inactivation on A. pleuropneumoniae virulence.

Results

OxyR was identified as a conserved regulator present in A. pleuropneumoniae serovar 1-12 reference strains. Transcriptomic analysis revealed the involvement of OxyR in multiple biological activities. The oxyR disruption resulted in decreased urease activity, elevated catalase expression, enhanced ApxI toxin secretion-attributed to OxyR binding to the apxIBD promoter-and reduced adhesion and invasion abilities on porcine cells. Furthermore, inactivation of oxyR reduced the virulence of A. pleuropneumoniae in a mice challenge experiment.

Discussion

The findings highlight the pivotal role of OxyR in influencing the virulence mechanisms of A. pleuropneumoniae. The observed effects on various biological activities underscore OxyR as an essential factor contributing to the pathogenicity of this bacterium.

How a natural antibiotic uses oxidative stress to kill oxidant-resistant bacteria

Natural products that possess antibiotic and antitumor qualities are often suspected of working through oxidative mechanisms. In this study, two quinone-based small molecules were compared. Menadione, a classic redox-cycling compound, was confirmed to generate high levels of reactive oxygen species inside Escherichia coli. It inactivated iron-cofactored enzymes and blocked growth. However, despite the substantial levels of oxidants that it produced, it was unable to generate significant DNA damage and was not lethal. Streptonigrin, in contrast, was poorer at redox cycling and did not inactivate enzymes or block growth; however, even in low doses, it damaged DNA and killed cells. Its activity required iron and oxygen, and in vitro experiments indicated that its quinone moiety transferred electrons through the adjacent iron atom to oxygen. Additionally, in vitro experiments revealed that streptonigrin was able to damage DNA without inhibition by catalase, indicating that hydrogen peroxide was not involved. We infer that streptonigrin can reduce bound oxygen directly to a ferryl species, which then oxidizes the adjacent DNA, without release of superoxide or hydrogen peroxide intermediates. This scheme allows streptonigrin to kill a bacterial cell without interference by scavenging enzymes. Moreover, its minimal redox-cycling behavior avoids alerting either the OxyR or the SoxRS systems, which otherwise would block killing. This example highlights qualities that may be important in the design of oxidative drugs. These results also cast doubt on proposals that bacteria can be killed by stressors that merely stimulate intracellular O2- and H2O2 formation.

Evidence that protein thiols are not primary targets of intracellular reactive oxygen species in growing Escherichia coli

The oxidizability of cysteine residues is exploited in redox chemistry and as a source of stabilizing disulfide bonds, but it also raises the possibility that these side chains will be oxidized when they should not be. It has often been suggested that intracellular oxidative stress from hydrogen peroxide or superoxide may result in the oxidation of the cysteine residues of cytoplasmic proteins. That view seemed to be supported by the discovery that one cellular response to hydrogen peroxide is the induction of glutaredoxin 1 and thioredoxin 2. In this study we used model compounds as well as alkaline phosphatase to test this idea. Our results indicate that molecular oxygen, superoxide, and hydrogen peroxide are very poor oxidants of N-acetylcysteine and of the protein thiols of alkaline phosphatase in vitro. Copper could accelerate thiol oxidation, but iron did not. When alkaline phosphatase was engineered to remain in the cytoplasm of live cells, unnaturally high concentrations of hydrogen peroxide were required to oxidize it to its active, disulfide-dependent form, and toxic levels of superoxide had no effect. At the same time, far lower concentrations of these oxidants were sufficient to poison key metalloenzymes. The elimination of glutaredoxin 1 and thioredoxin 2 did not change these results, raising the question of why E. coli induces them during peroxide stress. In fact, when catalase/peroxidase mutants were chronically stressed with hydrogen peroxide, the absence of glutaredoxin 1 and thioredoxin 2 did not impair growth at all, even in a minimal medium over many generations. We conclude that physiological levels of reduced oxygen species are not potent oxidants of typical protein thiols. Glutaredoxin and thioredoxin must either have an alternative purpose or else play a role under culture conditions that differ from the ones we tested.

Phenomic and transcriptomic analyses reveal the sequential synthesis of Fe3O4 nanoparticles in Acidithiobacillus ferrooxidans BYM

IMPORTANCE

As the most important non-magnetotactic magnetosome-producing bacteria, Acidithiobacillus ferrooxidans only requires very mild conditions to produce Fe3O4 nanoparticles, thus conferring greater flexibility and potential application in biomagnetic nanoparticle production. However, the available information cannot explain the mechanism of Fe3O4 nanoparticle formation in A. ferrooxidans. In this study, we applied phenomic and transcriptomic analyses to reveal this mechanism. We found that different treatment condition factors notably affect the phenomic data of Fe3O4 nanoparticle in A. ferrooxidans. Using transcriptomic analyses, the gene network controlling/regulating Fe3O4 nanoparticle biogenesis in A. ferrooxidans was proposed, excavating the candidate hub genes for Fe3O4 nanoparticle formation in A. ferrooxidans. Based on this information, a sequential model for Fe3O4 nanoparticle synthesis in A. ferrooxidans was hypothesized. It lays the groundwork for further clarifying the feature of Fe3O4 nanoparticle synthesis.

Byproducts of inflammatory radical metabolism provide transient nutrient niches for microbes in the inflamed gut

Louis Pasteur's experiments on tartaric acid laid the foundation for our understanding of molecular chirality, but major questions remain. By comparing the optical activity of naturally-occurring tartaric acid with chemically-synthesized paratartaric acid, Pasteur realized that naturally-occurring tartaric acid contained only L-tartaric acid while paratartaric acid consisted of a racemic mixture of D- and L-tartaric acid. Curiously, D-tartaric acid has no known natural source, yet several gut bacteria specifically degrade D-tartaric acid. Here, we investigated the oxidation of monosaccharides by inflammatory reactive oxygen and nitrogen species. We found that this reaction yields an array of alpha hydroxy carboxylic acids, including tartaric acid isomers. Utilization of inflammation- derived D- and L-tartaric acid enhanced colonization by Salmonella Typhimurium and E. coli in murine models of gut inflammation. Our findings suggest that byproducts of inflammatory radical metabolism, such as tartrate and other alpha hydroxy carboxylic acids, create transient nutrient niches for enteric pathogens and other potentially harmful bacteria. Furthermore, this work illustrates that inflammatory radicals generate a zoo of molecules, some of which may erroneously presumed to be xenobiotics.

A novel ruthenium-silver based antimicrobial potentiates aminoglycoside activity against Pseudomonas aeruginosa

The rapid dissemination of antibiotic resistance combined with the decline in the discovery of novel antibiotics represents a major challenge for infectious disease control that can only be mitigated by investments in novel treatment strategies. Alternative antimicrobials, including silver, have regained interest due to their diverse mechanisms of inhibiting microbial growth. One such example is AGXX, a broad-spectrum antimicrobial that produces highly cytotoxic reactive oxygen species (ROS) to inflict extensive macromolecular damage. Due to the connections identified between ROS production and antibiotic lethality, we hypothesized that AGXX could potentially increase the activity of conventional antibiotics. Using the gram-negative pathogen Pseudomonas aeruginosa, we screened possible synergistic effects of AGXX on several antibiotic classes. We found that the combination of AGXX and aminoglycosides tested at sublethal concentrations led to a rapid exponential decrease in bacterial survival and restored the sensitivity of a kanamycin-resistant strain. ROS production contributes significantly to the bactericidal effects of AGXX/aminoglycoside treatments, which is dependent on oxygen availability and can be reduced by the addition of ROS scavengers. Additionally, P. aeruginosa strains deficient in ROS detoxifying/repair genes were more susceptible to AGXX/aminoglycoside treatment. We further demonstrate that this synergistic interaction was associated with a significant increase in outer and inner membrane permeability, resulting in increased antibiotic influx. Our study also revealed that AGXX/aminoglycoside-mediated killing requires an active proton motive force across the bacterial membrane. Overall, our findings provide an understanding of cellular targets that could be inhibited to increase the activity of conventional antimicrobials. IMPORTANCE The emergence of drug-resistant bacteria coupled with the decline in antibiotic development highlights the need for novel alternatives. Thus, new strategies aimed at repurposing conventional antibiotics have gained significant interest. The necessity of these interventions is evident especially in gram-negative pathogens as they are particularly difficult to treat due to their outer membrane. This study highlights the effectiveness of the antimicrobial AGXX in potentiating aminoglycoside activities against P. aeruginosa. The combination of AGXX and aminoglycosides not only reduces bacterial survival rapidly but also significantly re-sensitizes aminoglycoside-resistant P. aeruginosa strains. In combination with gentamicin, AGXX induces increased endogenous oxidative stress, membrane damage, and iron-sulfur cluster disruption. These findings emphasize AGXX's potential as a route of antibiotic adjuvant development and shed light on potential targets to enhance aminoglycoside activity.

A double-negative feedback loop between NtrBC and a small RNA rewires nitrogen metabolism in legume symbionts

The nitrogen (N) status transduced via the NtrBC two-component system is a major signaling cue in the root nodule endosymbiosis of diazotrophic rhizobia with legumes. NtrBC is upregulated in the N-limiting rhizosphere environment at the onset of nodulation but silenced in nodules to favor the assimilation of the fixed N into plant biomass. We reported that the trans-acting sRNA NfeR1 (Nodule Formation Efficiency RNA) broadly influences the symbiotic performance of the α-rhizobium Sinorhizobium meliloti. Here, we show that NfeR1 is indeed an N-responsive sRNA that fine-tunes NtrBC output during the symbiotic transition. Biochemical and genetic approaches unveiled that NtrC and the LysR-type symbiotic regulator LsrB bind at distinct nearby sites in the NfeR1 promoter, acting antagonistically as repressor and activator of transcription, respectively. This complex transcriptional control specifies peak NfeR1 steady-state levels in N-starved and endosymbiotic bacteria. Furthermore, NfeR1 base pairs the translation initiation region of the histidine kinase coding mRNA ntrB, causing a decrease in both NtrB and NtrC abundance as assessed by double-plasmid genetic assays. In the context of endogenous regulation, NfeR1-mediated ntrBC silencing most likely amends the effective strength of the known operon autorepression exerted by NtrC. Accordingly, a lack of NfeR1 shifts the wild-type NtrBC output, restraining the fitness of free-living rhizobia under N stress and plant growth upon nodulation. The mixed NtrBC-NfeR1 double-negative feedback loop is thus an unprecedented adaptive network motif that helps α-rhizobia adjust N metabolism to the demands of an efficient symbiosis with legume plants. IMPORTANCE Root nodule endosymbioses between diazotrophic rhizobia and legumes provide the largest input of combined N to the biosphere, thus representing an alternative to harmful chemical fertilizers for sustainable crop production. Rhizobia have evolved intricate strategies to coordinate N assimilation for their own benefit with N2 fixation to sustain plant growth. The rhizobial N status is transduced by the NtrBC two-component system, the seemingly ubiquitous form of N signal transduction in Proteobacteria. Here, we show that the regulatory sRNA NfeR1 (nodule formation efficiency RNA) of the alfalfa symbiont Sinorhizobium meliloti is transcribed from a complex promoter repressed by NtrC in a N-dependent manner and feedback silences ntrBC by complementary base-pairing. These findings unveil a more prominent role of NtrC as a transcriptional repressor than hitherto anticipated and a novel RNA-based mechanism for NtrBC regulation. The NtrBC-NfeR1 double-negative feedback loop accurately rewires symbiotic S. meliloti N metabolism and is likely conserved in α-rhizobia.

In vitro activity of hypochlorous acid generating electrochemical bandage against monospecies and dual-species bacterial biofilms

AIMS

As antimicrobial resistance is on the rise, treating chronic wound infections is becoming more complex. The presence of biofilms in wound beds contributes to this challenge. Here, the activity of a novel hypochlorous acid (HOCl) producing electrochemical bandage (e-bandage) against monospecies and dual-species bacterial biofilms formed by bacteria commonly found in wound infections was assessed.

METHODS AND RESULTS

The system was controlled by a wearable potentiostat powered by a 3V lithium-ion battery and maintaining a constant voltage of + 1.5V Ag/AgCl, allowing continuous generation of HOCl. A total of 19 monospecies and 10 dual-species bacterial biofilms grown on polycarbonate membranes placed on tryptic soy agar (TSA) plates were used as wound biofilm models, with HOCl producing e-bandages placed over the biofilms. Viable cell counts were quantified after e-bandages were continuously polarized for 2, 4, 6, and 12 hours. Time-dependent reductions in colony forming units (CFUs) were observed for all studied isolates. After 12 hours, average CFU reductions of 7.75 ± 1.37 and 7.74 ± 0.60 log10 CFU/cm2 were observed for monospecies and dual-species biofilms, respectively.

CONCLUSIONS

HOCl producing e-bandages reduce viable cell counts of in vitro monospecies and dual-species bacterial biofilms in a time-dependent manner in vitro. After 12 hours, >99.999% reduction in cell viability was observed for both monospecies and dual-species biofilms.

The oxidative stress response, in particular the katY gene, is temperature-regulated in Yersinia pseudotuberculosis

Pathogenic bacteria, such as Yersinia pseudotuberculosis encounter reactive oxygen species (ROS) as one of the first lines of defense in the mammalian host. In return, the bacteria react by mounting an oxidative stress response. Previous global RNA structure probing studies provided evidence for temperature-modulated RNA structures in the 5'-untranslated region (5'-UTR) of various oxidative stress response transcripts, suggesting that opening of these RNA thermometer (RNAT) structures at host-body temperature relieves translational repression. Here, we systematically analyzed the transcriptional and translational regulation of ROS defense genes by RNA-sequencing, qRT-PCR, translational reporter gene fusions, enzymatic RNA structure probing and toeprinting assays. Transcription of four ROS defense genes was upregulated at 37°C. The trxA gene is transcribed into two mRNA isoforms, of which the most abundant short one contains a functional RNAT. Biochemical assays validated temperature-responsive RNAT-like structures in the 5'-UTRs of sodB, sodC and katA. However, they barely conferred translational repression in Y. pseudotuberculosis at 25°C suggesting partially open structures available to the ribosome in the living cell. Around the translation initiation region of katY we discovered a novel, highly efficient RNAT that was primarily responsible for massive induction of KatY at 37°C. By phenotypic characterization of catalase mutants and through fluorometric real-time measurements of the redox-sensitive roGFP2-Orp1 reporter in these strains, we revealed KatA as the primary H2O2 scavenger. Consistent with the upregulation of katY, we observed an improved protection of Y. pseudotuberculosis at 37°C. Our findings suggest a multilayered regulation of the oxidative stress response in Yersinia and an important role of RNAT-controlled katY expression at host body temperature.

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.

Neutrophil defect and lung pathogen selection in cystic fibrosis

Cystic fibrosis is a life-threatening genetic disorder caused by mutations in the CFTR chloride channel. Clinically, over 90% of patients with cystic fibrosis succumb to pulmonary complications precipitated by chronic bacterial infections, predominantly by Pseudomonas aeruginosa and Staphylococcus aureus. Despite the well-characterized gene defect and clearly defined clinical sequelae of cystic fibrosis, the critical link between the chloride channel defect and the host defense failure against these specific pathogens has not been established. Previous research from us and others has uncovered that neutrophils from patients with cystic fibrosis are defective in phagosomal production of hypochlorous acid, a potent microbicidal oxidant. Here we report our studies to investigate if this defect in hypochlorous acid production provides P. aeruginosa and S. aureus with a selective advantage in cystic fibrosis lungs. A polymicrobial mixture of cystic fibrosis pathogens (P. aeruginosa and S. aureus) and non-cystic fibrosis pathogens (Streptococcus pneumoniae, Klebsiella pneumoniae, and Escherichia coli) was exposed to varied concentrations of hypochlorous acid. The cystic fibrosis pathogens withstood higher concentrations of hypochlorous acid than did the non-cystic fibrosis pathogens. Neutrophils derived from F508del-CFTR HL-60 cells killed P. aeruginosa less efficiently than did the wild-type counterparts in the polymicrobial setting. After intratracheal challenge in wild-type and cystic fibrosis mice, the cystic fibrosis pathogens outcompeted the non-cystic fibrosis pathogens and exhibited greater survival in the cystic fibrosis lungs. Taken together, these data indicate that reduced hypochlorous acid production due to the absence of CFTR function creates an environment in cystic fibrosis neutrophils that provides a survival advantage to specific microbes-namely, S. aureus and P. aeruginosa-in the cystic fibrosis lungs.

A panel of visual bacterial biosensors for the rapid detection of genotoxic and oxidative damage: A proof of concept study

The emergence of new compounds during the past decade requires a high-throughput screening method for toxicity assay. The stress-responsive whole-cell biosensor is a powerful tool to evaluate direct or indirect damages of biological macromolecules induced by toxic chemicals. In this proof-of-concept study, nine well-characterized stress-responsive promoters were first selected to assemble a set of blue indigoidine-based biosensors. The PuspA-based, PfabA-based, and PgrpE-based biosensors were eliminated due to their high background. A dose-dependent increase of visible blue signal was observed in PrecA-, PkatG-, and PuvrA-based biosensors, responsive to potent mutagens, including mitomycin and nalidixic acid, but not to genotoxic lead and cadmium. The PrecA, PkatG, and Ppgi gene promoters were further fused to a purple deoxyviolacein synthetic enzyme cluster. Although high basal production of deoxyviolacein is unavoidable, an enhanced visible purple signal in response to mitomycin and nalidixic acid was observed as dose-dependent, especially in PkatG-based biosensors. The study shows that a set of stress-responsive biosensors employing visible pigment as a reporter is pre-validating in detecting extensive DNA damage and intense oxidative stress. Unlike widely-used fluorescent and bioluminescent biosensors, the visual pigment-based biosensor can become a novel, low-cost, mini-equipment, and high-throughput colorimetric device for the toxicity assessment of chemicals. However, combining multiple improvements can further improve the biosensing performance in future studies.

Meddling with Metal Sensors: Fur-Family Proteins as Signaling Hubs

The ferric uptake regulator (Fur) protein is the founding member of the FUR superfamily of metalloregulatory proteins that control metal homeostasis in bacteria. FUR proteins regulate metal homeostasis in response to the binding of iron (Fur), zinc (Zur), manganese (Mur), or nickel (Nur). FUR family proteins are generally dimers in solution, but the DNA-bound complex can involve a single dimer, a dimer-of-dimers, or an extended array of bound protein. Elevated FUR levels due to changes in cell physiology increase DNA occupancy and may also kinetically facilitate protein dissociation. Interactions between FUR proteins and other regulators are commonplace, often including cooperative and competitive DNA-binding interactions within the regulatory region. Further, there are many emerging examples of allosteric regulators that interact directly with FUR family proteins. Here, we focus on newly uncovered examples of allosteric regulation by diverse Fur antagonists (Escherichia coli YdiV/SlyD, Salmonella enterica EIIANtr, Vibrio parahaemolyticus FcrX, Acinetobacter baumannii BlsA, Bacillus subtilis YlaN, and Pseudomonas aeruginosa PacT) as well as one Zur antagonist (Mycobacterium bovis CmtR). Small molecules and metal complexes may also serve as regulatory ligands, with examples including heme binding to Bradyrhizobium japonicum Irr and 2-oxoglutarate binding to Anabaena FurA. How these protein-protein and protein-ligand interactions act in conjunction with regulatory metal ions to facilitate signal integration is an active area of investigation.

Excess copper catalyzes protein disulfide bond formation in the bacterial periplasm but not in the cytoplasm

Copper avidly binds thiols and is redox active, and it follows that one element of copper toxicity may be the generation of undesirable disulfide bonds in proteins. In the present study, copper oxidized the model thiol N-acetylcysteine in vitro. Alkaline phosphatase (AP) requires disulfide bonds for activity, and copper activated reduced AP both in vitro and when it was expressed in the periplasm of mutants lacking their native disulfide-generating system. However, AP was not activated when it was expressed in the cytoplasm of copper-overloaded cells. Similarly, this copper stress failed to activate OxyR, a transcription factor that responds to the creation of a disulfide bond. The elimination of cellular disulfide-reducing systems did not change these results. Nevertheless, in these cells, the cytoplasmic copper concentration was high enough to impair growth and completely inactivate enzymes with solvent-exposed [4Fe-4S] clusters. Experiments with N-acetylcysteine determined that the efficiency of thiol oxidation is limited by the sluggish pace at which oxygen regenerates copper(II) through oxidation of the thiyl radical-Cu(I) complex. We conclude that this slow step makes copper too inefficient a catalyst to create disulfide stress in the thiol-rich cytoplasm, but it can still impact the few thiol-containing proteins in the periplasm. It also ensures that copper accumulates intracellularly in the Cu(I) valence.

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.

Identification of a Small Molecule Compound Active against Antibiotic-Tolerant Staphylococcus aureus by Boosting ATP Synthesis

Antibiotic tolerance poses a threat to current antimicrobial armamentarium. Bacteria at a tolerant state survive in the presence of antibiotic treatment and account for persistence, relapse and recalcitrance of infections. Antibiotic treatment failure may occur due to antibiotic tolerance. Persistent infections are difficult to treat and are often associated with poor prognosis, imposing an enormous burden on the healthcare system. Effective strategies targeting antibiotic-tolerant bacteria are therefore highly warranted. In this study, small molecule compound SA-558 was identified to be effective against Staphylococcus aureus that are tolerant to being killed by conventional antibiotics. SA-558 mediated electroneutral transport across the membrane and led to increased ATP and ROS generation, resulting in a reduction of the population of antibiotic-tolerant bacteria. In a murine chronic infection model, of which vancomycin treatment failed, we demonstrated that SA-558 alone and in combination with vancomycin caused significant reduction of MRSA abundance. Our results indicate that SA-558 monotherapy or combinatorial therapy with vancomycin is an option for managing persistent S. aureus bacteremia infection and corroborate that bacterial metabolism is an important target for counteracting antibiotic tolerance.

Hypothiocyanite and host-microbe interactions

The pseudohypohalous acid hypothiocyanite/hypothiocyanous acid (OSCN^- /HOSCN) has been known to play an antimicrobial role in mammalian immunity for decades. It is a potent oxidant that kills bacteria but is non-toxic to human cells. Produced from thiocyanate (SCN^- ) and hydrogen peroxide (H₂ O₂ ) in a variety of body sites by peroxidase enzymes, HOSCN has been explored as an agent of food preservation, pathogen killing, and even improved toothpaste. However, despite the well-recognized antibacterial role HOSCN plays in host-pathogen interactions, little is known about how bacteria sense and respond to this oxidant. In this work, we will summarize what is known and unknown about HOSCN in innate immunity and recent advances in understanding the responses that both pathogenic and non-pathogenic bacteria mount against this antimicrobial agent, highlighting studies done with three model organisms, Escherichia coli, Streptococcus spp., and Pseudomonas aeruginosa.

H2 O2 feeding enables LPMO-assisted cellulose saccharification during simultaneous fermentative production of lactic acid

Simultaneous saccharification and fermentation (SSF) is a well-known strategy for valorization of lignocellulosic biomass. Because the fermentation process typically is anaerobic, oxidative enzymes found in modern commercial cellulase cocktails, such as lytic polysaccharide monooxygenases (LPMOs), may be inhibited, limiting the overall efficiency of the enzymatic saccharification. Recent discoveries, however, have shown that LPMOs are active under anoxic conditions if they are provided with H₂ O₂ at low concentrations. In this study, we build on this concept and investigate the potential of using externally added H₂ O₂ to sustain oxidative cellulose depolymerization by LPMOs during an SSF process for lactic acid production. The results of bioreactor experiments with 100 g/L cellulose clearly show that continuous addition of small amounts of H₂ O₂ (at a rate of 80 µM/h) during SSF enables LPMO activity and improves lactic acid production. While further process optimization is needed, the present proof-of-concept results show that modern LPMO-containing cellulase cocktails such as Cellic CTec2 can be used in SSF setups, without sacrificing the LPMO activity in these cocktails.

Self-cloning of the Catalase Gene in Environmental Isolates Improves Their Colony-forming Abilities on Agar Media

Hydrogen peroxide (H₂O₂) inhibits microbial growth at a specific concentration. However, we previously isolated two environmental bacterial strains that exhibited sensitivity to a lower H₂O₂ concentration in agar plates. Putative catalase genes, which degrade H₂O₂, were detected in their genomes. We herein elucidated the characteristics of these putative genes and their products using a self-cloning technique. The products of the cloned genes were identified as functional catalases. The up-regulation of their expression increased the colony-forming ability of host cells under H₂O₂ pressure. The present results demonstrated high sensitivity to H₂O₂ even in microbes possessing functional catalase genes.

Critical Effect of H2O2 in the Agar Plate on the Growth of Laboratory and Environmental Strains

We previously showed that autoclaving in preparing agar media is one of the sources of hydrogen peroxide (H2O2) in the medium. This medium-embedded H2O2 was shown to lower the total colony count of environmental microorganisms. However, the critical concentrations of H2O2 detrimental to colony formation on the agar plate remain largely undetermined. Herein, we elucidated the specific effect of H2O2 on microbial colony formation on solid agar medium by external supplementation of varying amounts of H2O2. While common laboratory strains (often called domesticated microbes) formed colonies in the presence of high H2O2 concentrations (48.8 μM or higher), microbes from a freshwater sample demonstrated greatly decreased colony counts in the presence of 8.3 μM H2O2. This implies that environmental microbes are susceptible to much lower concentrations of H2O2 than laboratory strains. Among the emergent colonies on agar plates supplemented with different H2O2 concentrations, the relative abundance of betaproteobacterial colonies was found to be lower on plates containing higher amounts of H2O2. Further, the growth of the representative betaproteobacterial isolates was completely inhibited in the presence of 7.2 μM H2O2. Therefore, our study clearly demonstrates that low micromolar levels of H2O2 in agar plates critically affect growth of environmental microbes, and large portions of those are far more susceptible to the same than laboratory strains. IMPORTANCE It is well-known that most of environmental microorganisms do not form colonies on agar medium despite that agar medium is the commonly used solidified medium. We previously demonstrated the negative effects of H2O2 generation during agar medium preparation on colony formation. In the present study, we investigated the independent effect of H2O2 on microbial growth by adding different concentrations of H2O2 to agar medium. Our results demonstrate for the first time that even low micromolar levels of H2O2 in agar plates, that are far lower than previously recognized as significant, adversely affect colony number obtained from freshwater inoculum.

To Be or Not to Be? Are Reactive Oxygen Species, Antioxidants, and Stress Signalling Universal Determinants of Life or Death?

In the environmental and organism context, oxidative stress is complex and unavoidable. Organisms simultaneously cope with a various combination of stress factors in natural conditions. For example, excess light stress is accompanied by UV stress, heat shock stress, and/or water stress. Reactive oxygen species (ROS) and antioxidant molecules, coordinated by electrical signalling (ES), are an integral part of the stress signalling network in cells and organisms. They together regulate gene expression to redirect energy to growth, acclimation, or defence, and thereby, determine cellular stress memory and stress crosstalk. In plants, both abiotic and biotic stress increase energy quenching, photorespiration, stomatal closure, and leaf temperature, while toning down photosynthesis and transpiration. Locally applied stress induces ES, ROS, retrograde signalling, cell death, and cellular light memory, then acclimation and defence responses in the local organs, whole plant, or even plant community (systemic acquired acclimation, systemic acquired resistance, network acquired acclimation). A simplified analogy can be found in animals where diseases vs. fitness and prolonged lifespan vs. faster aging, are dependent on mitochondrial ROS production and ES, and body temperature is regulated by sweating, temperature-dependent respiration, and gene regulation. In this review, we discuss the universal features of stress factors, ES, the cellular production of ROS molecules, ROS scavengers, hormones, and other regulators that coordinate life and death.

The Functional Characteristics of Goat Cheese Microbiota from a One-Health Perspective

Goat cheese is an important element of the Mediterranean diet, appreciated for its health-promoting features and unique taste. A pivotal role in the development of these characteristics is attributed to the microbiota and its continuous remodeling over space and time. Nevertheless, no thorough study of the cheese-associated microbiota using two metaomics approaches has previously been conducted. Here, we employed 16S rRNA gene sequencing and metaproteomics to explore the microbiota of a typical raw goat milk cheese at various ripening timepoints and depths of the cheese wheel. The 16S rRNA gene-sequencing and metaproteomics results described a stable microbiota ecology across the selected ripening timepoints, providing evidence for the microbiologically driven fermentation of goat milk products. The important features of the microbiota harbored on the surface and in the core of the cheese mass were highlighted in both compositional and functional terms. We observed the rind microbiota struggling to maintain the biosafety of the cheese through competition mechanisms and/or by preventing the colonization of the cheese by pathobionts of animal or environmental origin. The core microbiota was focused on other biochemical processes, supporting its role in the development of both the health benefits and the pleasant gustatory nuances of goat cheese.

The vulnerability of radical SAM enzymes to oxidants and soft metals

Radical S-adenosylmethionine enzymes (RSEs) drive diverse biological processes by catalyzing chemically difficult reactions. Each of these enzymes uses a solvent-exposed [4Fe-4S] cluster to coordinate and cleave its SAM co-reactant. This cluster is destroyed during oxic handling, forcing investigators to work with these enzymes under anoxic conditions. Analogous substrate-binding [4Fe-4S] clusters in dehydratases are similarly sensitive to oxygen in vitro; they are also extremely vulnerable to reactive oxygen species (ROS) in vitro and in vivo. These observations suggested that ROS might similarly poison RSEs. This conjecture received apparent support by the observation that when E. coli experiences hydrogen peroxide stress, it induces a cluster-free isozyme of the RSE HemN. In the present study, surprisingly, the purified RSEs viperin and HemN proved quite resistant to peroxide and superoxide in vitro. Furthermore, pathways that require RSEs remained active inside E. coli cells that were acutely stressed by hydrogen peroxide and superoxide. Viperin, but not HemN, was gradually poisoned by molecular oxygen in vitro, forming an apparent [3Fe-4S]+ form that was readily reactivated. The modest rate of damage, and the known ability of cells to repair [3Fe-4S]+ clusters, suggest why these RSEs remain functional inside fully aerated organisms. In contrast, copper(I) damaged HemN and viperin in vitro as readily as it did fumarase, a known target of copper toxicity inside E. coli. Excess intracellular copper also impaired RSE-dependent biosynthetic processes. These data indicate that RSEs may be targets of copper stress but not of reactive oxygen species.

Transposon-Directed Insertion-Site Sequencing Reveals Glycolysis Gene gpmA as Part of the H2O2 Defense Mechanisms in Escherichia coli

Hydrogen peroxide (H₂O₂) is a common effector of defense mechanisms against pathogenic infections. However, bacterial factors involved in H₂O₂ tolerance remain unclear. Here we used transposon-directed insertion-site sequencing (TraDIS), a technique allowing the screening of the whole genome, to identify genes implicated in H₂O₂ tolerance in Escherichia coli. Our TraDIS analysis identified 10 mutants with fitness defect upon H₂O₂ exposure, among which previously H₂O₂-associated genes (oxyR, dps, dksA, rpoS, hfq and polA) and other genes with no known association with H₂O₂ tolerance in E. coli (corA, rbsR, nhaA and gpmA). This is the first description of the impact of gpmA, a gene involved in glycolysis, on the susceptibility of E. coli to H₂O₂. Indeed, confirmatory experiments showed that the deletion of gpmA led to a specific hypersensitivity to H₂O₂ comparable to the deletion of the major H₂O₂ scavenger gene katG. This hypersensitivity was not due to an alteration of catalase function and was independent of the carbon source or the presence of oxygen. Transcription of gpmA was upregulated under H₂O₂ exposure, highlighting its role under oxidative stress. In summary, our TraDIS approach identified gpmA as a member of the oxidative stress defense mechanism in E. coli.

In-situ generation of H2O2 by zero valent iron to control depolymerization of lignocellulose in composting niche

Lignocellulosic degradation is a bottleneck of bioconversion during the composting process. In-situ generation of H₂O₂ in the composting system was an ideal method for efficiently promoting lignocellulase degradation, and zero valent iron (ZVI) was concerned because it can generate H₂O₂ by reducing dissolved oxygen. This study focused on the effects of ZVI treatment on lignocellulose degradation, microbial communities, and carbohydrate-active enzymes (CAZymes) genes during composting. Its results indicated that ZVI increased H₂O₂ content during composting, accompanied by the formation of •OH. The degradation rates of lignin, cellulose and hemicellulose in ZVI group (20.77%, 30.35% and 44.7%) were significantly higher than in CK group (17.01%, 26.12% and 38.5%). Metagenomic analysis showed that ZVI induced microbial growth that favored lignocellulose degradation, which increased the abundance of Actinobacteria and Firmicutes but reduced Proteobacteria. At the genus level, the abundance of Thermomonospora, Streptomyces, and Bacillus significantly increased. In addition, glycoside hydrolases and auxiliary activities were important CAZymes families of lignocellulose degradation, and their abundance was higher in the ZVI group. Redundancy analysis showed that the increased H₂O₂ and •OH content was a critical factor in improving lignocellulose degradation. Overall, H₂O₂ as a co-substrate enhanced the enzymatic efficiency, •OH unspecifically attacked lignocellulose, and the increase in functional microbial abundance was the main reason for promoting lignocellulose degradation in composting.

Machine learning-based inverse design for electrochemically controlled microscopic gradients of O2 and H2O2

In microbiology, extracellular oxygen (O₂) and reactive oxygen species (ROS) are spatiotemporally heterogenous, ubiquitously, at macroscopic level. Such spatiotemporal heterogeneities are critical to microorganisms, yet a well-defined method of studying such heterogenous microenvironments is lacking. This work develops a machine learning–based inverse design strategy that builds an electrochemical platform for achieving spatiotemporal control of O₂ and ROS microenvironments relevant to microbiology. The inverse design strategy not only demonstrates the power of machine learning to design concentration profiles in electrochemistry but also accelerates the development of custom microenvironments for specific microbial systems and allows researchers to better study how microenvironments affect microorganisms in myriads of environmental, biomedical, and sustainability-related applications.

A fundamental understanding of extracellular microenvironments of O₂ and reactive oxygen species (ROS) such as H₂O₂, ubiquitous in microbiology, demands high-throughput methods of mimicking, controlling, and perturbing gradients of O₂ and H₂O₂ at microscopic scale with high spatiotemporal precision. However, there is a paucity of high-throughput strategies of microenvironment design, and it remains challenging to achieve O₂ and H₂O₂ heterogeneities with microbiologically desirable spatiotemporal resolutions. Here, we report the inverse design, based on machine learning (ML), of electrochemically generated microscopic O₂ and H₂O₂ profiles relevant for microbiology. Microwire arrays with suitably designed electrochemical catalysts enable the independent control of O₂ and H₂O₂ profiles with spatial resolution of ∼10¹ μm and temporal resolution of ∼10° s. Neural networks aided by data augmentation inversely design the experimental conditions needed for targeted O₂ and H₂O₂ microenvironments while being two orders of magnitude faster than experimental explorations. Interfacing ML-based inverse design with electrochemically controlled concentration heterogeneity creates a viable fast-response platform toward better understanding the extracellular space with desirable spatiotemporal control.

Identifying the mediators of intracellular E. coli inactivation under UVA light: The (photo) Fenton process and singlet oxygen

Solar disinfection (SODIS) was probed for its underlying mechanism. When Escherichia coli was exposed to UVA irradiation, the dominant solar fraction acting in SODIS process, cells exhibited a shoulder before death ensued. This profile resembles cell killing by hydrogen peroxide (H2O2). Indeed, the use of specialized strains revealed that UVA exposure triggers intracellular H2O2 formation. The resultant H2O2 stress was especially impactful because UVA also inactivated the processes that degrade H2O2-peroxidases through the suppression of metabolism, and catalases through direct enzyme damage. Cell killing was enhanced when water was replaced with D2O, suggesting that singlet oxygen plays a role, possibly as a precursor to H2O2 and/or as the mediator of catalase damage. UVA was especially toxic to mutants lacking miniferritin (dps) or recombinational DNA repair (recA) enzymes, indicating that reactions between ferrous iron and UVA-generated H2O2 lead to lethal DNA damage. Importantly, experiments showed that the intracellular accumulation of H2O2 alone is insufficient to kill cells; therefore, UVA must do something more to enable death. A possibility is that UVA stimulates the reduction of intracellular ferric iron to its ferrous form, either by stimulating O2•- formation or by generating photoexcited electron donors. These observations and methods open the door to follow-up experiments that can probe the mechanisms of H2O2 formation, catalase inactivation, and iron reduction. Of immediate utility, the data highlight the intracellular pathways formed under UVA light during SODIS, and that the presence of micromolar iron accelerates the rate at which radiation disinfects water.

Adaptive Response of Thermophiles to Redox Stress and Their Role in the Process of dye Degradation From Textile Industry Wastewater

Release of dye-containing textile wastewater into the environment causes severe pollution with serious consequences on aquatic life. Bioremediation of dyes using thermophilic microorganisms has recently attracted attention over conventional treatment techniques. Thermophiles have the natural ability to survive under extreme environmental conditions, including high dye concentration, because they possess stress response adaptation and regulation mechanisms. Therefore, dye detoxification by thermophiles could offer enormous opportunities for bioremediation at elevated temperatures. In addition, the processes of degradation generate reactive oxygen species (ROS) and subject cells to oxidative stress. However, thermophiles exhibit better adaptation to resist the effects of oxidative stress. Some of the major adaptation mechanisms of thermophiles include macromolecule repair system; enzymes such as superoxide dismutase, catalase, and glutathione peroxidase; and non-enzymatic antioxidants like extracellular polymeric substance (EPSs), polyhydroxyalkanoates (PHAs), etc. In addition, different bacteria also possess enzymes that are directly involved in dye degradation such as azoreductase, laccase, and peroxidase. Therefore, through these processes, dyes are first degraded into smaller intermediate products finally releasing products that are non-toxic or of low toxicity. In this review, we discuss the sources of oxidative stress in thermophiles, the adaptive response of thermophiles to redox stress and their roles in dye removal, and the regulation and crosstalk between responses to oxidative stress.

Improved Hydrogen Peroxide Stress Resistance of Zymomonas mobilis NADH Dehydrogenase (ndh) and Alcohol Dehydrogenase (adhB) Mutants

Unintended shifts in stress resistance of microbial strains with engineered central metabolism may impact their growth and production performance under oxidative, lignocellulosic, solvent, and other stress conditions, and as such, must be taken into account in bioprocess design. In the present work, we studied oxidative stress resistance in mutant strains of the facultatively anaerobic, ethanologenic bacterium Zymomonas mobilis with modified respiratory (inactivated NADH dehydrogenase Ndh, by disruption of ndh) and ethanologenic (inactivated iron-containing alcohol dehydrogenase isoenzyme ADH II, by disruption of adhB) catabolism, using exogenously added H2O2 in the concentration range of 2–6 mM as the oxidative stressor. Both mutations improved H2O2 resistance and enhanced catalase activity by a factor of 2–5, while the overexpression of Ndh had an opposite effect. Strains with a catalase-negative background were unable to grow already at 1 mM hydrogen peroxide, and their H2O2 resistance did not depend on AdhB or Ndh expression levels. Hence, the improved resistance of the ndh and adhB mutants to H2O2 resulted from their elevated catalase activity. The interrelation between these mutations, the catabolic redox balance, catalase activity, and oxidative stress defense in Z. mobilis is discussed.

Structural and mechanistic basis for redox sensing by the cyanobacterial transcription regulator RexT

Organisms have a myriad of strategies for sensing, responding to, and combating reactive oxygen species, which are unavoidable consequences of aerobic life. In the heterocystous cyanobacterium Nostoc sp. PCC 7120, one such strategy is the use of an ArsR-SmtB transcriptional regulator RexT that senses H₂O₂ and upregulates expression of thioredoxin to maintain cellular redox homeostasis. Different from many other members of the ArsR-SmtB family which bind metal ions, RexT has been proposed to use disulfide bond formation as a trigger to bind and release DNA. Here, we present high-resolution crystal structures of RexT in the reduced and H₂O₂-treated states. These structures reveal that RexT showcases the ArsR-SmtB winged-helix-turn-helix fold and forms a vicinal disulfide bond to orchestrate a response to H₂O₂. The importance of the disulfide-forming Cys residues was corroborated using site-directed mutagenesis, mass spectrometry, and H₂O₂-consumption assays. Furthermore, an entrance channel for H₂O₂ was identified and key residues implicated in H₂O₂ activation were pinpointed. Finally, bioinformatics analysis of the ArsR-SmtB family indicates that the vicinal disulfide “redox switch” is a unique feature of cyanobacteria in the Nostocales order, presenting an interesting case where an ArsR-SmtB protein scaffold has been evolved to showcase peroxidatic activity and facilitate redox-based regulation.

The DNA binding and H₂O₂ sensing mechanisms are revealed for RexT, a transcriptional regulator found in cyanobacteria of the Nostocales order.

Elemental Sulfur Inhibits Yeast Growth via Producing Toxic Sulfide and Causing Disulfide Stress

Elemental sulfur is a common fungicide, but its inhibition mechanism is unclear. Here, we investigated the effects of elemental sulfur on the single-celled fungus Saccharomyces cerevisiae and showed that the inhibition was due to its function as a strong oxidant. It rapidly entered S. cerevisiae. Inside the cytoplasm, it reacted with glutathione to generate glutathione persulfide that then reacted with another glutathione to produce H₂S and glutathione disulfide. H₂S reversibly inhibited the oxygen consumption by the mitochondrial electron transport chain, and the accumulation of glutathione disulfide caused disulfide stress and increased reactive oxygen species in S. cerevisiae. Elemental sulfur inhibited the growth of S. cerevisiae; however, it did not kill the yeast for up to 2 h exposure. The combined action of elemental sulfur and hosts’ immune responses may lead to the demise of fungal pathogens.

A Fluorescent Probe to Detect Quick Disulfide Reductase Activity in Bacteria

The Trx and Grx systems, two disulfide reductase systems, play critical roles in various cell activities. There are great differences between the thiol redox systems in prokaryotes and mammals. Though fluorescent probes have been widely used to detect these systems in mammalian cells. Very few methods are available to detect rapid changes in the redox systems of prokaryotes. Here we investigated whether Fast-TRFS, a disulfide-containing fluorescent probe utilized in analysis of mammalian thioredoxin reductase, could be used to detect cellular disulfide reducibility in bacteria. Fast-TRFS exhibited good substrate qualities for both bacterial thioredoxin and GSH-glutaredoxin systems in vitro, with Trx system having higher reaction rate. Moreover, the Fast-TRFS was used to detect the disulfide reductase activity in various bacteria and redox-related gene null E. coli. Some glutaredoxin-deficient bacteria had stronger fast disulfide reducibility. The Trx system was shown to be the predominant disulfide reductase for fast disulfide reduction rather than the Grx system. These results demonstrated that Fast-TRFS is a viable probe to detect thiol-dependent disulfide reductases in bacteria. It also indicated that cellular disulfide reduction could be classified into fast and slow reaction, which are predominantly catalyzed by E. coli Trx and Grx system, respectively.

Unique functional insights into the antioxidant response of the cyanobacterial Mn-catalase (KatB)

KatB, a hexameric Mn-catalase, plays a vital role in overcoming oxidative and salinity stress in the ecologically important, N₂-fixing cyanobacterium, Anabaena. The 5 N-terminal residues of KatB, which show a high degree of conservation in cyanobacteria, form an antiparallel β-strand at the subunit interface of the KatB hexamer. In this study, the contribution of these N-terminal non-active site residues, towards the maintenance of the structure, biochemical properties, and redox balance was evaluated. Each N-terminal amino acid residue from the 2nd to the 7th position of KatB was individually mutated to Ala (to express KatBF2A/KatBF3A/KatBH4A/KatBK5E/KatBK6A/KatBE7A) or this entire 6 amino acid stretch was deleted (to yield KatBTrunc). All the above-mentioned KatB variants, along with the wild-type KatB protein (KatBWT), were overproduced in E. coli and purified. In comparison to KatBWT, the KatBF2A/KatBH4A/KatBTrunc proteins were less compact, more prone to chemical/thermal denaturation, and were unexpectedly inactive. KatBF3A/KatBK5E/KatBK6A showed biophysical/biochemical properties that were in between that of KatBWT and KatBF2A/KatBH4A/KatBTrunc. Surprisingly, KatBE7A was more thermostable with higher activity than KatBWT. On exposure to H₂O₂, E. coli expressing KatBWT/KatBE7A showed considerably reduced formation of ROS and increased survival than the other KatB variants. Utilizing the KatB structure, the molecular basis responsible for the altered stability/activity of the KatB mutants was delineated. This study demonstrates the physiological importance of the N-terminal β-strand of Mn-catalases in combating H₂O₂ stress and shows that the non-active site residues can be used for rational protein engineering to develop Mn-catalases with improved characteristics.

Bacterial Response to Oxidative Stress and RNA Oxidation

Bacteria have to cope with oxidative stress caused by distinct Reactive Oxygen Species (ROS), derived not only from normal aerobic metabolism but also from oxidants present in their environments. The major ROS include superoxide O₂⁻, hydrogen peroxide H₂O₂ and radical hydroxide HO^•. To protect cells under oxidative stress, bacteria induce the expression of several genes, namely the SoxRS, OxyR and PerR regulons. Cells are able to tolerate a certain number of free radicals, but high levels of ROS result in the oxidation of several biomolecules. Strikingly, RNA is particularly susceptible to this common chemical damage. Oxidation of RNA causes the formation of strand breaks, elimination of bases or insertion of mutagenic lesions in the nucleobases. The most common modification is 8-hydroxyguanosine (8-oxo-G), an oxidized form of guanosine. The structure and function of virtually all RNA species (mRNA, rRNA, tRNA, sRNA) can be affected by RNA oxidation, leading to translational defects with harmful consequences for cell survival. However, bacteria have evolved RNA quality control pathways to eliminate oxidized RNA, involving RNA-binding proteins like the members of the MutT/Nudix family and the ribonuclease PNPase. Here we summarize the current knowledge on the bacterial stress response to RNA oxidation, namely we present the different ROS responsible for this chemical damage and describe the main strategies employed by bacteria to fight oxidative stress and control RNA damage.

The H2O2 Concentration-Dependent Kinetics of Gene Expression: Linking the Intensity of Oxidative Stress and Mycobacterial Physiological Adaptation

Defence against oxidative stress is crucial for Mycobacterium tuberculosis to survive and replicate within macrophages. Mycobacteria have evolved multilayer antioxidant systems, including scavenging enzymes, iron homeostasis, repair pathways, and metabolic adaptation, for coping with oxidative stress. How these systems are coordinated to enable the physiological adaptation to different intensities of oxidative stress, however, remains unclear. To address this, we investigated the expression kinetics of the well-characterized antioxidant genes at bacteriostatic H₂O₂ concentrations ranging from 1 mM to 10 mM employing Mycolicibacterium smegmatis as a model. Our results showed that most of the selected genes were expressed in a H₂O₂ concentration-dependent manner, whereas a subset exhibited sustained induction or repression without dose–effect, reflecting H₂O₂ concentration-dependent physiological adaptations. Through analyzing the dynamics of the coordinated gene expression, we demonstrated that the expressions of the H₂O₂ scavenging enzymes, DNA damage response, and Fe–S cluster repair function were strikingly correlated to the intensity of oxidative stress. The sustained induction of mbtB, irtA, and dnaE2 indicated that mycobacteria might deploy increased iron acquisition and error-prone lesion bypass function as fundamental strategies to counteract oxidative damages, which are distinct from the defence tactics of Escherichia coli characterized by shrinking the iron pool and delaying the DNA repair. Moreover, the distinct gene expression kinetics among the tricarboxylic acid cycle, glyoxylate shunt, and methylcitrate cycle suggested that mycobacteria could dynamically redirect its metabolic fluxes according to the intensity of oxidative stress. This work defines the H₂O₂ concentration-dependent gene expression kinetics and provides unique insights into mycobacterial antioxidant defence strategies.

Corrosion Inhibition and Disinfection of Heating and Cooling Water Systems Using In Situ Generated Hydrogen Peroxide

Aqueous solutions of MnCl2·4H2O and Tiron (disodium 4,5-dihydroxy-1,3-benzenedisulfonate) rapidly remove dioxygen (O2) from aqueous solution at a rate of ~20 mg∙ L -1 min-1 with turnover frequencies (TOFs) of up...

Escherichia coli induces DNA repair enzymes to protect itself from low-grade hydrogen peroxide stress

E. coli responds to hydrogen peroxide (H₂ O₂ ) by inducing defenses that protect H₂ O₂ -sensitive enzymes. DNA is believed to be another important target of oxidation, and E. coli contains enzymes that can repair oxidative lesions in vitro. However, those enzymes are not known to be induced by H₂ O₂ , and experiments have indicated that they are not necessary for the cell to withstand natural (low-micromolar) concentrations. In this study we used H₂ O₂ -scavenging mutants to impose controlled doses of H₂ O₂ for extended time. Transcriptomic analysis revealed that in the presence of 1 µM cytoplasmic H₂ O₂ , the OxyR transcription factor induced xthA, encoding exonuclease III. The xthA mutants survived a conventional 15-minute exposure to even 100 times this level of H₂ O₂ . However, when these mutants were exposed to 1 µM H₂ O₂ for hours, they accumulated DNA lesions, failed to propagate, and eventually died. Although endonuclease III (nth) was not induced, nth mutants struggled to grow. Low-grade H₂ O₂ stress also activated the SOS regulon, and when this induction was blocked, cell replication stopped. Collectively, these data indicate that physiological levels of H₂ O₂ are a real threat to DNA, and the engagement of the base-excision-repair and SOS systems is necessary to enable propagation during protracted stress.

Pervasive RNA Regulation of Metabolism Enhances the Root Colonization Ability of Nitrogen-Fixing Symbiotic α-Rhizobia

The rhizosphere and rhizoplane are nutrient-rich but selective environments for the root microbiome. Here, we deciphered a posttranscriptional network regulated by the homologous trans-small RNAs (sRNAs) AbcR1 and AbcR2, which rewire the metabolism of the nitrogen-fixing α-rhizobium Sinorhizobium meliloti during preinfection stages of symbiosis with its legume host alfalfa. The LysR-type regulator LsrB, which transduces the cell redox state, is indispensable for AbcR1 expression in actively dividing bacteria, whereas the stress-induced transcription of AbcR2 depends on the alternative σ factor RpoH1. MS2 affinity purification coupled with RNA sequencing unveiled exceptionally large and overlapping AbcR1/2 mRNA interactomes, jointly representing ⁓6% of the S. meliloti protein-coding genes. Most mRNAs encode transport/metabolic proteins whose translation is silenced by base pairing to two distinct anti-Shine Dalgarno motifs that function independently in both sRNAs. A metabolic model-aided analysis of the targetomes predicted changes in AbcR1/2 expression driven by shifts in carbon/nitrogen sources, which were confirmed experimentally. Low AbcR1/2 levels in some defined media anticipated overexpression growth phenotypes linked to the silencing of specific mRNAs. As a proof of principle, we confirmed AbcR1/2-mediated downregulation of the l-amino acid AapQ permease. AbcR1/2 interactomes are well represented in rhizosphere-related S. meliloti transcriptomic signatures. Remarkably, a lack of AbcR1 specifically compromised the ability of S. meliloti to colonize the root rhizoplane. The AbcR1 regulon likely ranks the utilization of available substrates to optimize metabolism, thus conferring on S. meliloti an advantage for efficient rhizosphere/rhizoplane colonization. AbcR1 regulation is predicted to be conserved in related α-rhizobia, which opens unprecedented possibilities for engineering highly competitive biofertilizers. IMPORTANCE Nitrogen-fixing root nodule symbioses between rhizobia and legume plants provide more than half of the combined nitrogen incorporated annually into terrestrial ecosystems, rendering plant growth independent of environmentally unfriendly chemical fertilizers. The success of symbiosis depends primarily on the capacity of rhizobia to establish competitive populations in soil and rhizosphere environments. Here, we provide insights into the regulation and architecture of an extensive RNA posttranscriptional network that fine-tunes the metabolism of the alfalfa symbiont S. meliloti, thereby enhancing the ability of this beneficial bacterium to colonize nutrient-rich but extremely selective niches, such as the rhizosphere of its host plant. This pervasive RNA regulation of metabolism is a major adaptive mechanism, predicted to operate in diverse rhizobial species. Because RNA regulation relies on modifiable base-pairing interactions, our findings open unexplored avenues for engineering the legumes rhizobiome within sustainable agricultural practices.