Cellular defenses against superoxide and hydrogen peroxide

Hypermutability of Mycolicibacterium smegmatis due to ribonucleotide reductase-mediated oxidative homeostasis and imbalanced dNTP pools

Ribonucleotide reductase (RNR) catalyzes the synthesis of four deoxyribonucleoside triphosphates (dNTPs), which are essential for DNA replication. Although dNTP imbalances reduce replication fidelity and elevate mutation rates, the impact of RNR dysfunction on Mycobacterium tuberculosis (Mtb) physiology and drug resistance remains unknown. Here, we constructed inducible knockdown strains for the RNR R1 subunit NrdE in Mtb and Mycolicibacterium smegmatis (Msm). NrdE knockdown significantly impaired growth and metabolic imbalances, indirectly disrupting oxidative homeostasis and mycolic acid synthesis, while increasing levels of intracellular ROS accumulation and enhancing cell wall permeability. Additionally, we developed genomic mutant strains, Msm-Y252A and Msm-Q255A, featuring targeted point mutations in the substrate-specific site (S-site) of the RNR loop domain, which determines NDP reduction specificity. The Msm-Y252A displayed a 1.9-fold decrease in dATP and increases in dGTP (1.6-fold), dTTP (9.0-fold), and dCTP (1.3-fold). In contrast, Msm-Q255A exhibited elevated intracellular levels of dGTP (1.6-fold), dTTP (6.1-fold), and dATP (1.5-fold), while dCTP levels remained unchanged. Neither the NrdE knockdown strain nor the S-site mutants exhibited direct resistance development; however, they both showed genomic instability, enhancing the emergence of rifampicin-resistant mutants, even with a 70-fold and a 25-fold increase in mutation frequency for Msm-Y252A and Msm-Q255A, respectively. This study demonstrates that NrdE is integral to Mycobacterium survival and genomic stability and that its RNR dysfunction creates a mutagenic environment under selective pressure, indirectly contributes to the development of drug resistance, positioning NrdE as an effective target for therapeutic strategies and a valuable molecular marker for early detection of drug-resistant Mtb.

aPDT activity of new water soluble phenalenone derivatives with shifted UV-Vis absorption

Antibacterial therapy is one of the most important medical developments of the 20th century, but several decades of antibiotic misuse and abuse have created a health emergency. Antibiotics resistance and ineffectiveness have spread through the community, threatening the enormous gains made by the availability of therapies. The emergence of drug-resistant infections has encouraged research community to develop new mechanisms against bacterial infections, mainly focused on multi-target strategies like "Antibacterial Photodynamic Therapy (aPDT)", where singlet oxygen (an excited state of oxygen) is able to oxidize a wide range of biomolecules including proteins, lipids and nucleic acids, leading to bacterial death. Singlet oxygen oxidative damage in aqueous media is restricted by its short diffusion range, around 150 nm. It is crucial to increase photosensitizer solubility in aqueous media keeping the capability of partition in apolar media (like membranes). We have previously demonstrated that an alkoxy substitution in position 6 of phenalenone scaffold (6-alkoxy-PNF) promotes a bathochromic shift of UV-Vis absorption when compared to clean phenalenone, (with maximum absorption wavelength centered at around 430-450 nm depending on the solvent). Their quantum yields of singlet oxygen generation remained high, in most media. To take advantage of the photo-physical properties of 6-alkoxy-PNF framework, increase solubility in water and promote attractive electrostatic interaction on the bacterial surface, a trimethylammonium group was introduced in the molecule. Moreover, depending on the length of methylene chain included, hydrophilic lipophilic balance of molecules can be tuned. This substitution through a methylene linker would maintain distance from the 6-alkoxy-PNF, keeps almost unchanged their visible absorption bands (displaced to the red) and their singlet oxygen generation capacity. Their ability to generate singlet oxygen and hence inactivate bacteria was tested. Our results show that the behavior of this family of compounds is dependent on the length of the alkyl chain, particularly in micro-heterogeneous systems. Synergic effect can be attributed to 12C surfactant associated with antimicrobial surfactant ability and singlet oxygen generation.

ROS-induced stress promotes enrichment and emergence of antibiotic resistance in conventional activated sludge processes

Since the Great Oxidation Event 2.4 billion years ago, microorganisms have evolved sophisticated responses to oxidative stress. These ancient adaptations remain relevant in modern engineered systems, particularly in conventional activated sludge (CAS) processes, which serve as significant reservoirs of antibiotic resistance genes (ARGs). While ROS-induced stress responses are known to promote ARG enrichment/emergence in pure cultures, their impact on ARG dynamics in wastewater treatment processes remains unexplored. Shotgun-metagenomics analysis of two hospital wastewater treatment plants showed that only 35-53 % of hospital effluent resistome was retained in final effluent. Despite this reduction, approximately 29-36 % of ARGs in CAS showed higher abundance than upstream stages, of which 20-22 % emerged de novo. Beta-lactamases and efflux pumps constituted nearly 47-53 % of these enriched ARGs. These ARGs exhibited significant correlations (p < 0.05) with ROS stress response genes (oxyR, soxR, sodAB, katG and ahpCF). The CAS resistome determined 58-75 % of the effluent ARG profiles, indicating treatment processes outweigh influent composition in shaping final resistome. Proof-of-concept batch reactor experiments confirmed increased ROS and ARG levels under high dissolved oxygen (8 mg/L) compared to low oxygen (2 mg/L) concentrations. Untargeted metaproteomics revealed higher expression of resistant proteins (e.g., OXA-184, OXA-576, PME-1, RpoB2, Tet(W/32/O)) under elevated ROS levels. Our findings demonstrate that CAS processes actively shape effluent resistome through ROS-mediated selection, indicating that treatment processes, rather than initial wastewater composition, determine final ARG profiles. This study indicates that the emergence of ARGs needs to be considered as an integral aspect of wastewater treatment design and operation to prevent antibiotic resistance dissemination.

Genome-wide characterization of hypothiocyanite stress response in Escherichia coli

Oxidative stress is one of the major methods of microbial population control and pathogen clearing by the mammalian immune system. The methods by which bacteria are able to escape damage by host-derived oxidants such as hydrogen peroxide (H2O2) and hypochlorous acid (HOCl) have been relatively well described, while other oxidants' effects on bacteria and their genetic responses are not as well understood. Hypothiocyanite/hypothiocyanous acid (OSCN-/HOSCN) is one such oxidative stress agent. In this study, we used RNA-sequencing to characterize the global transcriptional response of Escherichia coli to treatment with HOSCN and the impact of deletions of the HOSCN resistance proteins RclA (HOSCN reductase), RclB, and RclC on that response. The HOSCN response of E. coli was different from the previously characterized responses of E. coli to other oxidants such as H2O2, superoxide, or HOCl and distinct from the reported responses of other bacteria such as Streptococcus pneumoniae and Pseudomonas aeruginosa to HOSCN. Strikingly, deletion of any one of the Rcl proteins had very similar effects on the transcriptional response to HOSCN, indicating that any disruption of HOSCN defense in E. coli results in similar impacts, despite the fact that we do not currently understand the mechanism(s) by which RclB and RclC contribute to that defense.

IMPORTANCE

Understanding how bacteria sense and respond to oxidative stress provides insights into how our bodies interact with the microbial population within us. In this study, we have characterized the genetic response of E. coli to the important immune oxidant hypothiocyanite and investigated the role of rclABC genes in that response.

Redox Homeostasis within the Drug-Resistant Malarial Parasite Digestive Vacuole

We have developed a cost-effective strategy for the complete synthesis of azetidinyl coumarin fluorophore derivatives that report changes in physiologic levels of glutathione (GSH), which includes a more cost- effective synthesis of the probe precursor hydroxyl derivative and its subsequent derivatization to promote subcellular localization. We functionalize coumarin derivatives with a cyano side chain similar to a previous strategy (Jiang X. et al., Nature Communications 2017, 8; 16087) and validate the 7-azetidinyl conformation as an explanation for enhanced GSH-dependent coumarin fluorescence. We couple the azetidinyl probe to different mass dextrans using either no linker or a 6C linker and also synthesize a morpholino derivative. We titrate the fluorescence of the different functionalized probes vs [GSH] in vitro. We load one dextran-conjugated probe within the digestive vacuole (DV) of live intraerythrocytic P. falciparum malarial parasites and also measure cytosolic localization of the morpholino probe. Using significantly improved single-cell photometry (SCP) methods, we show that the morpholino probe faithfully reports [GSH] from the live parasite cytosol, while the 70 kDa dextran-conjugated probe reports DV redox homeostasis for control chloroquine-sensitive (CQS) and artemisinin-sensitive (ARTS) transfectant parasites vs their genetically matched chloroquine-resistant (CQR)/artemisinin-sensitive (CQR/ARTS) and CQR artemisinin-resistant (CQR/ARTR) strains, respectively. We quantify rapid changes in DV redox homeostasis for these parasites ± drug pulses under live-cell perfusion conditions. The results are important for understanding the pharmacology of antimalarial drugs and the molecular mechanisms underlying CQR and ARTR phenomena.

Metal-polyphenol nanocomposite hybrid hydrogel: A multifunctional platform for treating diabetic foot ulcers through metabolic microenvironment reprogramming

Diabetic foot ulcer (DFU) is a prevalent and challenging clinical condition characterized by impaired microcirculation, chronic wound infections, and a hyperglycemic, high-reactive oxygen species (ROS) environment. These factors make treatment particularly complex, often requiring a multidisciplinary approach that yields suboptimal results. In this study, a novel therapeutic strategy was developed using metal-polyphenol nanoparticles synthesized from (-)-Epigallocatechin-3-gallate (EGCG) and ferric ions (Fe3+). These nanoparticles were further loaded with salvianolic acid B (SAB) and glucose oxidase (GOx) to enhance their multifunctional biological properties. Complementing these nanoparticles, a polysaccharide hydrogel was engineered using quaternized chitosan (QCS) and oxidized fucoidan (OFu), forming a robust and stable network through Schiff base linkages. This innovative platform demonstrated strong antibacterial activity against DFU-associated pathogens. Within the ulcer's hostile microenvironment, the hydrogel degraded via dynamic bond cleavage, releasing nanoparticles that boosted mitochondrial metabolism, induced M2 macrophage polarization, promoted angiogenesis and reduced ROS levels. These combined effects accelerated tissue regeneration and wound healing. The results suggest that this advanced hydrogel system holds significant promise as a therapeutic option for improving DFU management and addressing its multifaceted challenges.

Ferroptosis-Like Death Induction in Saccharomyces cerevisiae by Gold Nanoparticles

Ferroptosis, a novel form of regulated cell death (RCD), has emerged as a promising therapeutic strategy for cancer treatment. While gold nanoparticles (AuNPs) are known to induce cell death and ferroptosis in combination with certain antibiotics, the mechanisms underlying ferroptosis in microorganisms remain poorly understood. This study aimed to investigate whether AuNPs induce ferroptosis-like cell death in the eukaryotic microbe Saccharomyces cerevisiae. Our findings revealed that AuNPs significantly reduced cell viability in S. cerevisiae, suggesting their ability to trigger cell death. Ferroptosis-related precursors, including intracellular iron overload and depletion of glutathione (GSH), were observed, leading to the inactivation of glutathione peroxidase (GPx). These changes were associated with the accumulation of reactive oxygen species (ROS) and lipid peroxidation, which amplified oxidative stress within the cells. Elevated ROS levels and lipid peroxidation further resulted in membrane rupture and the formation of 8-hydroxydeoxyguanosine, indicating DNA damage. Mitochondrial dysfunction, a hallmark of ferroptosis, was also evident. AuNP treatment caused mitochondrial membrane potential hyperpolarization and a reduction in mitochondrial membrane density. Unlike previously characterized forms of RCD, ferroptosis-like death in S. cerevisiae did not involve chromatin condensation, DNA fragmentation, or metacaspase activation. Finally, ferroptosis-like characteristics were confirmed using Liperfluo, a lipid ROS-specific probe. In conclusion, this study demonstrated that AuNPs can induce ferroptosis-like cell death in S. cerevisiae. These findings highlight the potential of AuNPs as antifungal agents and contribute to the broader understanding of ferroptosis in eukaryotic microbes.

The small GTPase Rap1A expedites the NOX2 oxidative burst by facilitating Rac and NOX2 autoactivations

Rac and Rap1A are small GTPases with the redox-sensitive GX4GK(S/T)C/ECS and NKCD motif. Of the known NADPH oxidase (NOX) isoforms, NOX1 and NOX2 function with the redox-sensitive Rac. Both exhibit an oxidative burst in which superoxide production is initially lagged but then accelerated. This burst is a reflection of NOX1 and NOX2 autoactivations occurring alongside the redox-dependent Rac autoactivation. NOX2 also contains the redox-sensitive Rap1A. However, its role in NOX2 function was unknown. In this study, we show that Rap1A is also autoactivated by its redox response, which is coupled to Rac and NOX2 autoactivations. This coupling is found to be mediated through the Rap1A-dependent recruitment of the Rac GEF P-REX1 to the NOX2 system. We further show that the initiation threshold and propagation rate of Rap1A autoactivation are lower and slower, respectively, than those of Rac and NOX2. The low-threshold Rap1A autoactivation recruits P-REX1 to the NOX2 system, resulting in the production of active Rac, thereby aiding the high-threshold initiation and propagation of Rac and NOX2 autoactivations. This results in the rapid completion of the NOX2 oxidative burst, which is specific to NOX2 because NOX1 lacks Rap1A. The redox response differences between the Rap1A NKCD motif and the Rac GX4GK(S/T)C/ECS motif appear to be the basis for the feature differences between Rap1A autoactivation and those of Rac and NOX2 autoactivations. The GX4GK(S/T)C/ECS and NKCD motifs are found in many redox-sensitive Rho/Rab and Ras family GTPases, respectively. Findings here shed light on previously unknown redox-dependent functional distinctions between these small GTPases.

Defense arsenal of the strict anaerobe Clostridioides difficile against reactive oxygen species encountered during its infection cycle

Clostridioides difficile, a strict anaerobe, is the major cause of antibiotic-associated diarrhea. This enteropathogen must adapt to oxidative stress mediated by reactive oxygen species (ROS), notably those released by the neutrophils and macrophages recruited to the site of infection or those endogenously produced upon high oxygen (O2) exposure. C. difficile uses a superoxide reductase, Sor, and several peroxidases to detoxify ROS. We showed that Sor has a superoxide reductase activity in vitro and protects the bacterium from exposure to menadione, a superoxide donor. After confirming the peroxidase activity of the rubrerythrin, Rbr, we showed that this enzyme together with the peroxiredoxin, Bcp, plays a central role in the detoxification of H2O2 and promotes the survival of C. difficile in the presence of not only H2O2 but also air or 4% O2. Under high O2 concentrations encountered in the gastrointestinal tract, the bacterium generated endogenous H2O2. The two O2 reductases, RevRbr2 and FdpF, have also a peroxidase activity and participate in H2O2 resistance. The CD0828 gene, which also contributes to H2O2 protection, forms an operon with rbr, sor, and perR encoding a H2O2-sensing repressor. The expression of the genes encoding the ROS reductases and the CD0828 protein was induced upon exposure to either H2O2 or air. We showed that the induction of the rbr operon is mediated not only by PerR but also by OseR, a recently identified O2-responsive regulator of C. difficile, and indirectly by σB, the sigma factor of the stress response, whereas the expression of bcp is only controlled by σB.

IMPORTANCE

ROS plays a fundamental role in intestinal homeostasis, limiting the proliferation of pathogenic bacteria. Clostridioides difficile is an important enteropathogen that induces an intense immune response, characterized by the massive recruitment of immune cells responsible for secreting ROS, mainly H2O2 and superoxide. We showed in this work that ROS exposure leads to the production of an armada of enzymes involved in ROS detoxification. This includes a superoxide reductase and four peroxidases, Rbr, Bcp, revRbr2, and FdpF. These enzymes likely contribute to the survival of vegetative cells of C. difficile in the colon during the host immune response. Distinct regulations are also observed for the genes encoding the ROS detoxification enzymes allowing a fine tuning of the adaptive response to ROS exposure. Understanding the mechanisms of ROS protection during infection could shed light on how C. difficile survives under conditions of an exacerbated inflammatory response.

Two routes for tyrosol production by metabolic engineering of Corynebacterium glutamicum

BACKGROUND

The phenolic compound tyrosol is widely used in the pharmaceutical industry, owing to its beneficial effects on human health and its use as a precursor for key pharmaceuticals, including β1-receptor blockers. Tyrosol can be found in olive oil, but despite its natural biosynthesis in plants, low extraction efficiencies render microbial production a more viable alternative.

RESULTS

Here, we engineered the L-tyrosine overproducing Corynebacterium glutamicum strain AROM3 for the de novo production of tyrosol. Two routes were established and compared: one via 4-OH-phenylpyruvate as intermediate and the other via tyramine. We initially expected the first route to require heterologous expression of a prephenate dehydrogenase gene, given that C. glutamicum lacks this enzymatic function. However, heterologous expression of ARO10 from Saccharomyces cerevisiae (ARO10Sc), which encodes a phenylpyruvate decarboxylase, was sufficient to establish tyrosol production in strain AROM3. We identified that 4-OH-phenylpyruvate is synthesized from L-tyrosine by native aminotransferases, which is subsequently decarboxylated by Aro10Sc, and reduced to tyrosol by native alcohol dehydrogenases, leading to a titer of 9.4 ± 1.1 mM (1.30 ± 0.15 g/L). We identified the furfural dehydrogenase FudC as major enzyme involved in this pathway, as its gene deletion reduced tyrosol production by 75%. Given the instability of 4-OH-phenylpyruvate, the synthesis of tyrosol via the stable intermediate tyramine was pursued via the second route. Decarboxylation of L-tyrosine followed by oxidative deamination was accomplished by overexpression of the L-tyrosine decarboxylase gene tdc from Levilactobacillus brevis (tdcLb) and the tyramine oxidase gene tyo from Kocuria rhizophila (tyoKr). Using this route, tyrosol production was increased by 44% compared to the route via 4-OH-phenylpyruvate. With a division of labor approach by co-cultivating L-tyrosine producing strains that either express tdcLb or tyoKr, the highest titer of 14.1 ± 0.3 mM (1.95 ± 0.04 g/L) was achieved.

CONCLUSIONS

This study demonstrates the potential of endotoxin-free C. glutamicum as production host for the L-tyrosine-derived product tyrosol. Due to its L-arogenate pathway for L-tyrosine synthesis, the unstable 4-OH-phenylpyruvate could be excluded as intermediate in the Tdc-Tyo pathway, outcompeting the most often utilized production route via phenylpyruvate decarboxylases.

Alternative NADH dehydrogenase: A complex I backup, a drug target, and a tool for mitochondrial gene therapy

Alternative NADH dehydrogenase, also known as type II NADH dehydrogenase (NDH-2), catalyzes the same redox reaction as mitochondrial respiratory chain complex I. Specifically, it oxidizes reduced nicotinamide adenine dinucleotide (NADH) while simultaneously reducing ubiquinone to ubiquinol. However, unlike complex I, this enzyme is non-proton pumping, comprises of a single subunit, and is resistant to rotenone. Initially identified in bacteria, fungi and plants, NDH-2 was subsequently discovered in protists and certain animal taxa including sea squirts. The gene coding for NDH-2 is also present in the genomes of some annelids, tardigrades, and crustaceans. For over two decades, NDH-2 has been investigated as a potential substitute for defective complex I. In model organisms, NDH-2 has been shown to ameliorate a broad spectrum of conditions associated with complex I malfunction, including symptoms of Parkinson's disease. Recently, lifespan extension has been observed in animals expressing NDH-2 in a heterologous manner. A variety of mechanisms have been put forward by which NDH-2 may extend lifespan. Such mechanisms include the activation of pro-longevity pathways through modulation of the NAD+/NADH ratio, decreasing production of reactive oxygen species (ROS) in mitochondria, or then through moderate increases in ROS production followed by activation of defense pathways (mitohormesis). This review gives an overview of the latest research on NDH-2, including the structural peculiarities of NDH-2, its inhibitors, its role in the pathogenicity of mycobacteria and apicomplexan parasites, and its function in bacteria, fungi, and animals.

Erectile Dysfunction and Oxidative Stress: A Narrative Review

Erectile dysfunction (ED) is a prevalent condition affecting male sexual health, characterized by the inability to achieve or maintain satisfactory erections. ED has a multifactorial pathogenesis in which psychological, hormonal, neurologic, cardiovascular, and lifestyle factors all contribute to a progressive decline of erectile function. A critical underlying mechanism involves oxidative stress (OS), an imbalance between reactive oxygen species (ROS) production and antioxidant defenses, which disrupts endothelial function, reduces nitric oxide (NO) bioavailability, and contributes to vascular dysfunction. This narrative review explores the interplay between OS and ED, focusing on the roles of ROS sources such as NADPH oxidase, xanthine oxidase, uncoupled nitric oxide synthase, and mitochondrial dysfunction. It examines the impact of OS on chronic conditions like hypertension, diabetes mellitus, hyperlipidemia, hypogonadism, and lifestyle factors like smoking and obesity, which exacerbate ED through endothelial and systemic effects. Emerging research underscores the potential of antioxidant therapies and lifestyle interventions to restore redox balance, improve endothelial function, and mitigate ED's progression. This review also highlights gaps in understanding the molecular pathways linking ROS to ED, emphasizing the need for further research to develop targeted therapeutic strategies.

Characterizing Common Factors Affecting Replication Initiation During H2O2 Exposure and Genetic Mutation-Induced Oxidative Stress in Escherichia coli

Oxidative stress is prevalent in organisms, and excessive oxidative damage can trigger cell death. Bacteria have evolved multiple pathways to cope with adverse stress, including the regulation of the cell cycle. Previous studies show that non-lethal exposure to H2O2 and mutations in antioxidant enzymes suppress replication initiation in Escherichia coli. The existence of common regulatory factors governing replication initiation across diverse causes-induced oxidative stress remains unclear. In this study, we utilized flow cytometry to determine the replication pattern of E. coli, and found that oxidative stress also participated in the inhibition of replication initiation by a defective iron regulation (fur-bfr-dps deletion). Adding a certain level of ATP promoted replication initiation in various antioxidant enzyme-deficient mutants and the ΔfurΔbfrΔdps mutant, suggesting that low ATP levels could be a common factor in the inhibition of replication initiation by different causes-induced oxidative stress. More potential common factors were screened using proteomics, followed by genetic validation with H2O2 stress. We found that oxidative stress might mediate the inhibition of replication initiation by interfering with the metabolism of glycine, glutamate, ornithine, and aspartate. Blocking CcmA-dependent cytochrome c biosynthesis, deleting the efflux pump proteins MdtABCD and TolC, or the arabinose transporter AraFHG eliminated the replication initiation inhibition by H2O2. In conclusion, this study uncovers a common multifactorial pathway of different causes-induced oxidative stress inhibiting replication initiation. Dormant and persistent bacteria exhibit an arrested or slow cell cycle, and non-lethal oxidative stress promotes their formation. Our findings contribute to exploring strategies to limit dormant and persistent bacterial formation by maintaining faster DNA replication initiation (cell cycle progression).

Dynamic PRDX S-acylation modulates ROS stress and signaling

Peroxiredoxins (PRDXs) are a highly conserved family of peroxidases that serve as the primary scavengers of peroxides. Post-translational modifications play crucial roles modulating PRDX activities, tuning the balance between reactive oxygen species (ROS) signaling and stress. We previously reported that S-acylation occurs at the "peroxidatic" cysteine (Cp) site of PRDX5 and that it inhibits PRDX5 activity. Here, we show that the PRDX family more broadly is subject to S-acylation at the Cp site of all PRDXs and that PRDX S-acylation dynamically responds to cellular ROS levels. Using activity-based fluorescent imaging with DPP-Red, a red-shifted fluorescent indicator for acyl-protein thioesterase (APT) activity, we also discover that the instigation of ROS-stress via exogenous H2O2 activates both the cytosolic and mitochondrial APTs, whereas epidermal growth factor (EGF)-stimulated endogenous H2O2 deactivates the cytosolic APTs. These results indicate that APTs help tune H2O2 signal transduction and ROS protection through PRDX S-deacylation.

Two redox-responsive LysR-type transcription factors control the oxidative stress response of Agrobacterium tumefaciens

Pathogenic bacteria often encounter fluctuating reactive oxygen species (ROS) levels, particularly during host infection, necessitating robust redox-sensing mechanisms for survival. The LysR-type transcriptional regulator (LTTR) OxyR is a widely conserved bacterial thiol-based redox sensor. However, members of the Rhizobiales also encode LsrB, a second LTTR with potential redox-sensing function. This study explores the roles of OxyR and LsrB in the plant-pathogen Agrobacterium tumefaciens. Through single and combined deletions, we observed increased H2O2 sensitivity, underscoring their function in oxidative defense. Genome-wide transcriptome profiling under H2O2 exposure revealed that OxyR and LsrB co-regulate key antioxidant genes, including katG, encoding a bifunctional catalase/peroxidase. Agrobacterium tumefaciens LsrB possesses four cysteine residues potentially involved in redox sensing. To elucidate the structural basis for redox-sensing, we applied single-particle cryo-EM (cryogenic electron microscopy) to experimentally confirm an AlphaFold model of LsrB, identifying two proximal cysteine pairs. In vitro thiol-trapping coupled with mass spectrometry confirmed reversible thiol modifications of all four residues, suggesting a functional role in redox regulation. Collectively, these findings reveal that A. tumefaciens employs two cysteine-based redox sensing transcription factors, OxyR and LsrB, to withstand oxidative stress encountered in host and soil environments.

Shear flow patterns antimicrobial gradients across bacterial populations

Bacterial populations experience chemical gradients in nature. However, most experimental systems either ignore gradients or fail to capture gradients in mechanically relevant contexts. Here, we use microfluidic experiments and biophysical simulations to explore how host-relevant shear flow affects antimicrobial gradients across communities of the highly resistant pathogen Pseudomonas aeruginosa. We discover that flow patterns gradients of three chemically distinct antimicrobials: hydrogen peroxide, gentamicin, and carbenicillin. Without flow, resistant P. aeruginosa cells generate local gradients by neutralizing all three antimicrobials through degradation or chemical modification. As flow increases, delivery overwhelms neutralization, allowing antimicrobials to penetrate deeper into bacterial populations. By imaging single cells across long microfluidic channels, we observe that upstream cells protect downstream cells, and protection is abolished in higher flow regimes. Together, our results reveal that physical flow can promote antimicrobial effectiveness, which could inspire the incorporation of flow into the discovery, development, and implementation of antimicrobials.

AlphaFold2-Guided Functional Screens Reveal a Conserved Antioxidant Protein at ER Membranes

Oxidative protein folding in the endoplasmic reticulum (ER) is essential for all eukaryotic cells yet generates hydrogen peroxide (H2O2), a reactive oxygen species (ROS). The ER-transmembrane protein that provides reducing equivalents to ER and guards the cytosol for antioxidant defense remains unidentified. Here we combine AlphaFold2-based and functional reporter screens in C. elegans to discover a previously uncharacterized and evolutionarily conserved protein ERGU-1 that fulfills these roles. Deleting C. elegans ERGU-1 causes excessive H2O2 and transcriptional gene up-regulation through SKN-1, homolog of mammalian antioxidant master regulator NRF2. ERGU-1 deficiency also impairs organismal reproduction and behavioral responses to H2O2. Both C. elegans and human ERGU-1 proteins localize to ER membranes and form network reticulum structures. Human and Drosophila homologs of ERGU-1 can rescue C. elegans mutant phenotypes, demonstrating evolutionarily ancient and conserved functions. In addition, purified ERGU-1 and human homolog TMEM161B exhibit redox-modulated oligomeric states. Together, our results reveal an ER-membrane-specific protein machinery for peroxide detoxification and suggest a previously unknown and conserved mechanisms for antioxidant defense in animal cells.

Molecular Principles of Proton-Coupled Quinone Reduction in the Membrane-Bound Superoxide Oxidase

Reactive oxygen species (ROS) are physiologically harmful radical species generated as byproducts of aerobic respiration. To detoxify ROS, most cells employ superoxide scavenging enzymes that disproportionate superoxide (O2·-) to oxygen (O2) and hydrogen peroxide (H2O2). In contrast, the membrane-bound superoxide oxidase (SOO) is a minimal 4-helical bundle protein that catalyzes the direct oxidation of O2·- to O2 and drives quinone reduction by mechanistic principles that remain unknown. Here, we combine multiscale hybrid quantum/classical (QM/MM) free energy calculations and microsecond molecular dynamics simulations with functional assays and site-directed mutagenesis experiments to probe the mechanistic principles underlying the charge transfer reactions of the superoxide-driven quinone reduction. We characterize a cluster of charged residues at the periplasmic side of the membrane that functions as a O2·- collecting antenna, initiating electron transfer via two b hemes to the active site for quinone reduction at the cytoplasmic side. Based on multidimensional QM/MM string simulations, we find that a proton-coupled electron transfer (PCET) reaction from the active site heme b and nearby histidine residues (H87, H158) results in quinol (QH2) formation, followed by proton uptake from the cytoplasmic side of the membrane. The functional relevance of the identified residues is supported by site-directed mutagenesis and activity assays, with mutations leading to inhibition of the O2·--driven quinone reduction activity. We suggest that the charge transfer reactions could build up a proton motive force that supports the bacterial energy transduction machinery, while the PCET machinery provides unique design principles of a minimal oxidoreductase.

A colorimetric fluorescent probe for reversible detection of HSO3-/H2O2 and effective discrimination of HSO3-/ClO- and its application in food and bioimaging

In view of the significant role of reactive sulfur species (RSS) and reactive oxygen species (ROS) in maintaining the redox homeostasis of organisms, we proposed a colorimetric fluorescent probe (HTN) for reversible detection of HSO3-/H2O2 and effective discrimination of HSO3-/ClO-. C = C is the active site for the Michael addition of HSO3- and the oxidation of ClO-. When HTN interacts with HSO3- and ClO-, it exhibits fluorescence quenching. The addition of oxidizing H2O2 to the system can restore the conjugate structure of the addition product of HSO3- (HTN-HSO3-) and the fluorescence recovery, but it cannot restore the structure of the oxidation product of ClO- (HTN-ClO-). By studying the change of the reversibility/non-reversibility of the probe structure with the addition of H2O2, the purpose of reversible detection of HSO3-/H2O2 and distinguishing HSO3-/ClO- is achieved. In addition, HTN can not only be used as a fluorescent ink to detect HSO3- on the test paper, but also has excellent detection effect on HSO3- and ClO- in real food samples and water samples. Meantime, HTN has good biocompatibility and can target mitochondria to achieve reversible detection of HSO3-/H2O2 and effective discrimination of HSO3-/ClO- in living cells. Therefore, HTN has great potential as a molecular tool for studying redox homeostasis in the interaction network of complex living systems.

High temperatures promote antibiotic resistance genes conjugative transfer under residual chlorine: Mechanisms and risks

The impact of residual chlorine on the dissemination of antibiotic resistance during the distribution and storage of water has become a critical concern. However, the influence of rising temperatures attributed to global warming on this process remains ambiguous, warranting further investigation. This study investigated the effects of different temperatures (17, 27, 37, and 42°C) on the conjugative transfer of antibiotic resistance genes (ARGs) under residual chlorine (0, 0.1, 0.3, and 0.5 mg/L). The results indicated that high temperatures significantly increased the conjugative transfer frequency of ARGs in intra-species under residual chlorine. Compared to 17°C, the transfer frequencies at 27°C, 37°C, and 42°C increased by 1.07-2.43, 1.20-4.80, and 1.24-2.82 times, respectively. The promoting effect of high temperatures was mainly due to the generation of reactive oxygen species, the triggered SOS response, and the formation of pilus channels. Transcriptomic analysis demonstrated that higher temperature stimulates the electron transport chain, thereby enhancing ATP production and facilitating the processes of conjugative, as confirmed by inhibitor validation. Additionally, rising temperatures similarly promoted the frequency of conjugative transfer in inter-species and communities under residual chlorine. These further highlighted the risk of antibiotic resistance spread in extreme and prolonged high-temperature events. The increased risk of antibiotic resistance in the process of drinking water transmission under the background of climate warming is emphasized.

Manipulating Intracellular Oxidative Conditions to Enhance Porphyrin Production in Escherichia coli

Being essential intermediates for the biosynthesis of heme, chlorophyll, and several other biologically critical compounds, porphyrins have wide practical applications. However, up till now, their bio-based production remains challenging. In this study, we identified potential metabolic factors limiting the biosynthesis of type-III stereoisomeric porphyrins in Escherichia coli. To alleviate this limitation, we developed bioprocessing strategies by redirecting more dissimilated carbon flux toward the HemD-enzymatic pathway to enhance the production of type-III uroporphyrin (UP-III), which is a key precursor for heme biosynthesis. Our approaches included the use of antioxidant reagents and strain engineering. Supplementation with ascorbic acid (up to 1 g/L) increased the UP-III/UP-I ratio from 0.62 to 2.57. On the other hand, overexpression of ROS-scavenging genes such as sod- and kat-genes significantly enhanced UP production in E. coli. Notably, overexpression of sodA alone led to a 72.9% increase in total porphyrin production (1.56 g/L) while improving the UP-III/UP-I ratio to 1.94. Our findings highlight the potential of both antioxidant supplementation and strain engineering to mitigate ROS-induced oxidative stress and redirect more dissimilated carbon flux toward the biosynthesis of type-III porphyrins in E. coli. This work offers an effective platform to enhance the bio-based production of porphyrins.

Uncovering the effects of non-lethal oxidative stress on replication initiation in Escherichia coli

Cell cycle adaptability assists bacteria in response to adverse stress. The effect of oxidative stress on replication initiation in Escherichia coli remains unclear. This work examined the impact of exogenous oxidant and genetic mutation-mediated oxidative stress on replication initiation. We found that 0-0.5 mM H2O2 suppresses E. coli replication initiation in a concentration-dependent manner but does not lead to cell death. Deletion of antioxidant enzymes SodA-SodB, KatE, or AhpC results in delayed replication initiation. The antioxidant N-acetylcysteine (NAC) promotes replication initiation in ΔkatE and ΔsodAΔsodB mutants. We then explored the factors that mediate the inhibition of replication initiation by oxidative stress. MutY, a base excision repair DNA glycosylase, resists inhibition of replication initiation by H2O2. Lon protease deficiency eliminates inhibition of replication initiation mediated by exogenous H2O2 exposure but not by katE or sodA-sodB deletion. The absence of clpP and hslV further delays replication initiation in the ΔktaE mutant, whereas hflK deletion promotes replication initiation in the ΔkatE and ΔsodAΔsodB mutants. In conclusion, non-lethal oxidative stress inhibits replication initiation, and AAA+ proteases are involved and show flexible regulation in E. coli.

Mimicking the Effects of Antimicrobial Blue Light: Exploring Single Stressors and Their Impact on Microbial Growth

Antimicrobial blue light (aBL) has become a promising non-invasive method that uses visible light, typically within the 405-470 nm wavelength range, to efficiently inactivate a wide variety of pathogens. However, the mechanism of antimicrobial blue light (aBL) has not been fully understood. In this study, our research group investigated the sensitivity of Escherichia coli BW25113 single-gene deletion mutants to individual stressors generated by aBL. Sixty-four aBL-sensitive mutants were tested under conditions mimicking the stress generated by irradiation with aBL, with their growth defects compared to the wild-type strain. Results revealed no positive correlation between aBL and single stressors, indicating that aBL's effectiveness is due to the simultaneous generation of multiple stressors. This multifactorial effect suggests that aBL targets microbial cells more precisely than single stressors such as hydrogen peroxide. No single gene knockout conferred specific resistance, highlighting aBL's potential as an antimicrobial strategy.

Ribose-induced advanced glycation end products reduce the lifespan in Drosophila melanogaster by changing the redox state and down-regulating the Sirtuin genes

Advanced Glycation End (AGE) products are one such factor that accumulates during aging and age-related diseases. However, how exogenous AGE compounds cause aging is an area that needs to be explored. Specifically, how an organ undergoes aging and aging-related phenomena that need further investigation. The intestine is the most exposed area to food substances. How AGEs affect the intestine in terms of aging need to be explored. Drosophila melanogaster, a well-known model organism, is used to decode aging and age-associated phenomena. In this study, we fed Ribose induced Advanced Glycation End products (Rib-AGE) to D. melanogaster to study the aging mechanism. The Rib-AGE-induced aging was checked in Drosophila. We found a series of changes in Rib-AGE-fed flies. Reactive oxygen species (ROS) and nitric oxide species (NOs) were higher in the Rib-AGE-fed flies, and the antioxidant level was lower. The intestinal permeability was altered. The microorganism load was higher inside the gut. The structural arrangement of the gut's microfilament was found to be damaged, and the nuclear shape was found to be irregular. Cell death within the gut was elevated in comparison to control. The food intake was found to be reduced. The relative mRNA expression of the Sirtuin 2 and Sirtuin 6 gene of D. melanogaster was downregulated in Rib-AGE-fed flies compared to the control. All these findings strongly suggest that Rib-AGE accelerates aging and age-related disorders in D. melanogaster.

Antibiotic tolerance due to restriction of cAMP-Crp regulation by mannitol, a non-glucose-family PTS carbon source

Enzyme-IIA (EIIAGlc, Crr) of the phosphotransferase system (PTS) connects the uptake of glucose-family sugars to the cAMP-Crp regulatory cascade; phosphorylated EIIAGlc enhances cAMP-Crp activity, which then contributes to the antibiotic-mediated accumulation of reactive oxygen species (ROS) and cell death. Defects in PTS cause antibiotic and disinfectant tolerance. We report that mannitol, a carbon source whose uptake does not use EIIAGlc, reduces antibiotic-mediated killing of Escherichia coli without affecting antibiotic minimal inhibitory concentration. Thus, mannitol promotes antibiotic tolerance. The tolerance pathway was defined by the loss of ciprofloxacin lethality from the deletion of ptsI (first gene in PTS), mtlA (mannitol-specific Enzyme-II), cyaA (cAMP synthase), and crp (cAMP receptor protein) but not crr (EIIAGlc). A crp* mutant, which encodes a constitutively active Crp that bypasses the need for cAMP activation, also decreased mannitol-mediated antibiotic tolerance, as did exogenous cAMP. Thus, inhibition of antibiotic lethality by mannitol involves both PTS-mediated mannitol uptake and suppression of cAMP-Crp action, independent of EIIAGlc. Mannitol suppressed the downstream antibiotic-mediated transcription of genes involved in NADH production and cellular respiration, expression of a superoxide reporter gene (soxS), and accumulation of antibiotic-mediated ROS. Similar phenomena were observed with mannose and sorbitol, demonstrating that non-glucose PTS carbon sources can cause antibiotic tolerance by a novel path that reduces the ROS-promoting activity of cAMP-Crp. The work emphasizes that antibiotic tolerance, which contributes to disease relapse and the need for prolonged antibiotic treatment, can result from commonly consumed carbohydrates. This finding, plus mutations that interfere specifically with antibiotic lethality, makes tolerance a high probability event.IMPORTANCEBacterial tolerance constitutes a significant threat to anti-infective therapy and potentially to the use of disinfectants. Deficiency mutations that reduce glucose uptake, central carbon metabolism, and cellular respiration confer antibiotic/disinfectant tolerance by reducing the accumulation of reactive metabolites, such as reactive oxygen species. We identified novel environmental generators of tolerance by showing that non-glucose carbohydrates, such as mannitol, mannose, and sorbitol, generate tolerance to multiple antibiotic classes. Finding that these sugars inhibit a universal, stress-mediated death pathway emphasizes the potential danger of compounds that block the lethal response to severe stress. Immediate practical importance derives from mannitol being a popular food sweetener, a treatment for glaucoma, and a dehydrating agent for treating cerebral edema, including cases caused by bacterial infection: antibiotic tolerance could contra-indicate the use of mannitol and related carbohydrates during antibiotic treatment. Overall, the work shows that the presence of sugars must be considered during antimicrobial and perhaps disinfectant use.

"Ca. Nitrosocosmicus" members are the dominant archaea associated with plant rhizospheres

Archaea catalyzing the first step of nitrification in the rhizosphere possibly have an influence on plant growth and development. In this study, we found a distinct archaeal community, dominated by ammonia-oxidizing archaea (AOA), associated with the root system of pepper (Capsicum anuum L.) and ginseng plants (Panax ginseng C.A. Mey.) compared to bulk soil not penetrated by roots. While the abundance of total AOA decreased in the rhizosphere soils, AOA related to "Candidatus Nitrosocosmicus," which harbor gene encoding manganese catalase (MnKat) in contrast to most other AOA, dominated the AOA community in the rhizosphere soils. For both plant species, the ratio of copy numbers of the AOA MnKat gene to the amoA gene (encoding the ammonia monooxygenase subunit A) was significantly higher in the rhizospheres than in bulk soils. In contrast to MnKat-negative strains from other AOA clades, the catalase activity of a representative isolate of "Ca. Nitrosocosmicus" was demonstrated. Members of this clade were enriched in H2O2-amended bulk soils, and constitutive expression of their MnKat gene was observed in both bulk and rhizosphere soils. Due to their abundance, "Ca. Nitrosocosmicus" members can be considered important players mediating the nitrification process in rhizospheres. The dominance of this MnKat-containing AOA in rhizospheres of agriculturally important plants hints at a previously overlooked AOA-plant interaction.

IMPORTANCE

Ammonia-oxidizing archaea (AOA) are widespread in terrestrial environments and outnumber other ammonia oxidizers in the rhizosphere, possibly exerting an influence on plant growth and development. However, little is known about the selection forces that shape their composition, functions, survival, and proliferation strategies in the rhizosphere. Here, we observed a distinct AOA community on root systems of two different plant species compared to bulk soil. Our results show that the "Ca. Nitrosocosmicus" clade, which possesses functional MnKat genes unlike most other AOA, dominated the rhizosphere soils. Moreover, members of this clade were enriched in H2O2-amended bulk soil, which mimics the ROS stress in root systems. While research on AOA-plant interactions in the rhizosphere is still in its infancy, these findings suggest that "Ca. Nitrosocosmicus" may be an important clade of AOA with potential AOA-plant interaction.

Combining multiple stressors blocks bacterial migration and growth

In nature, organisms experience combinations of stressors. However, laboratory studies use batch cultures, which simplify reality and focus on population-level responses to individual stressors.1,2,3,4,5 In recent years, bacterial stress responses have been examined with single-cell resolution using microfluidics.6,7,8,9,10,11,12 Here, we use a microfluidic approach to simultaneously provide a physical stressor (shear flow) and a chemical stressor (H2O2) to the human pathogen Pseudomonas aeruginosa. By treating cells with levels of flow and H2O2 that commonly co-occur in human host tissues,13,14,15,16,17,18 we discover that previous reports significantly overestimate the H2O2 levels required to block bacterial growth. Specifically, we establish that flow increases H2O2 effectiveness 50-fold, explaining why previous studies lacking flow required much higher concentrations. Using natural H2O2 levels, we identify the core H2O2 regulon, characterize OxyR-mediated dynamic regulation, and demonstrate that multiple H2O2 scavenging systems have redundant roles. By examining single-cell behavior, we serendipitously discover that the combined effects of H2O2 and flow block pilus-driven surface migration. Thus, our results counter previous studies and reveal that natural levels of H2O2 and flow synergize to restrict bacterial motility and survival. By studying two stressors at once, our research highlights the limitations of oversimplifying nature and demonstrates that physical and chemical stress can combine to yield unpredictable effects.

Ribosome-inactivation by a class of widely distributed C-tail anchored membrane proteins

Ribosome hibernation is a commonly used strategy that protects ribosomes under unfavorable conditions and regulates developmental processes. Multiple ribosome-hibernation factors have been identified in all domains of life, but due to their structural diversity and the lack of a common inactivation mechanism, it is currently unknown how many different hibernation factors exist. Here, we show that the YqjD/ElaB/YgaM paralogs, initially discovered as membrane-bound ribosome binding proteins in E. coli, constitute an abundant class of ribosome-hibernating proteins, which are conserved across all proteobacteria and some other bacterial phyla. Our data demonstrate that they inhibit in vitro protein synthesis by interacting with the 50S ribosomal subunit. In vivo cross-linking combined with mass spectrometry revealed their specific interactions with proteins surrounding the ribosomal tunnel exit and even their penetration into the ribosomal tunnel. Thus, YqjD/ElaB/YgaM inhibit translation by blocking the ribosomal tunnel and thus mimic the activity of antimicrobial peptides and macrolide antibiotics.

Pleiotropic cellular responses underlying antibiotic tolerance in Campylobacter jejuni

Antibiotic tolerance enables antibiotic-susceptible bacteria to withstand prolonged exposure to high concentrations of antibiotics. Although antibiotic tolerance presents a major challenge for public health, its underlying molecular mechanisms remain unclear. Previously, we have demonstrated that Campylobacter jejuni develops tolerance to clinically important antibiotics, including ciprofloxacin and tetracycline. To identify cellular responses associated with antibiotic tolerance, RNA-sequencing was conducted on C. jejuni after inducing antibiotic tolerance through exposure to ciprofloxacin or tetracycline. Additionally, knockout mutants were constructed for genes exhibiting significant changes in expression levels during antibiotic tolerance. The genes involved in protein chaperones, bacterial motility, DNA repair system, drug efflux pump, and iron homeostasis were significantly upregulated during antibiotic tolerance. These mutants displayed markedly reduced viability compared to the wild-type strain, indicating the critical role of these cellular responses in sustaining antibiotic tolerance. Notably, the protein chaperone mutants exhibited increased protein aggregation under antibiotic treatment, suggesting that protein chaperones play a critical role in managing protein disaggregation and facilitating survival during antibiotic tolerance. Our findings demonstrate that various cellular defense mechanisms collectively contribute to sustaining antibiotic tolerance in C. jejuni, providing novel insights into the molecular mechanisms underlying antibiotic tolerance.

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.

Streptomyces sp. from desert soil as a biofactory for antioxidants with radical scavenging and iron chelating potential

Iron homeostasis is vital for normal physiology, but in the majority of circumstances, like iron overload, this equilibrium is upset leading to free iron in the plasma. This condition with excess iron is known as hemochromatosis, which has been linked to many side effects, including cancer and liver cirrhosis. The current research aimed to investigate active molecules from Streptomyces sp. isolated from the extreme environment of Bahawalpur deserts. The strain was characterized using 16 S rRNA sequencing. Chemical analysis of the ethyl acetate cure extract revealed the presence of phenols, flavonoids, alkaloids, and tannins. Multiple ultraviolet (UV) active metabolites that were essential for the stated pharmacological activities were also demonstrated by thin layer chromatography (TLC) and high-performance liquid chromatography (HPLC). Additionally, Gas chromatography/mass spectrometry (GC-MS) analysis revealed the primary constituents of the extract to compose of phenol and ester compounds. The 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay was used to assess the extract's antioxidant capacity, and the results showed a good half-maximal inhibitory concentration (IC50) value of 0.034 µg/mL in comparison to the positive control ascorbic acid's 0.12 µg/mL. In addition, iron chelation activity of extract showed significant chelation potential at 250 and 125 µg/mL, while 62.5 µg/mL showed only mild chelation of the ferrous ion using ethylene diamine tetra acetic acid (EDTA) as a positive control. Likewise, the extract's cytotoxicity was analyzed through 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay using varying concentrations of the extract and showed 51% cytotoxicity at 350 µg/mL and 65% inhibition of cell growth at 700 µg/mL, respectively. The bioactive compounds from Streptomyces sp. demonstrated strong antioxidant and iron chelating potentials and can prolong the cell survival in extreme environment.

Fundamentals and Exceptions of the LysR-type Transcriptional Regulators

LysR-type transcriptional regulators (LTTRs) are emerging as a promising group of macromolecules for the field of biosensors. As the largest family of bacterial transcription factors, the LTTRs represent a vast and mostly untapped repertoire of sensor proteins. To fully harness these regulators for transcription factor-based biosensor development, it is crucial to understand their underlying mechanisms and functionalities. In the first part, this Review discusses the established model and features of LTTRs. As dual-function regulators, these inducible transcription factors exude precise control over their regulatory targets. In the second part of this Review, an overview is given of the exceptions to the "classic" LTTR model. While a general regulatory mechanism has helped elucidate the intricate regulation performed by LTTRs, it is essential to recognize the variations within the family. By combining this knowledge, characterization of new regulators can be done more efficiently and accurately, accelerating the expansion of transcriptional sensors for biosensor development. Unlocking the pool of LTTRs would significantly expand the currently limited range of detectable molecules and regulatory functions available for the implementation of novel synthetic genetic circuitry.

ATH434, a promising iron-targeting compound for treating iron regulation disorders

Cytotoxic accumulation of loosely bound mitochondrial Fe2+ is a hallmark of Friedreich's Ataxia (FA), a rare and fatal neuromuscular disorder with limited therapeutic options. There are no clinically approved medications targeting excess Fe2+ associated with FA or the neurological disorders Parkinson's disease and Multiple System Atrophy. Traditional iron-chelating drugs clinically approved for systemic iron overload that target ferritin-stored Fe3+ for urinary excretion demonstrated limited efficacy in FA and exacerbated ataxia. Poor treatment outcomes reflect inadequate binding to excess toxic Fe2+ or exceptionally high affinities (i.e. ≤10-31) for non-pathologic Fe3+ that disrupts intrinsic iron homeostasis. To understand previous treatment failures and identify beneficial factors for Fe2+-targeted therapeutics, we compared traditional Fe3+ chelators deferiprone (DFP) and deferasirox (DFX) with additional iron-binding compounds including ATH434, DMOG, and IOX3. ATH434 and DFX had moderate Fe2+ binding affinities (Kd's of 1-4  µM), similar to endogenous iron chaperones, while the remaining had weaker divalent metal interactions. These compounds had low/moderate affinities for Fe3+(0.46-9.59 µM) relative to DFX and DFP. While all compounds coordinated iron using molecular oxygen and/or nitrogen ligands, thermodynamic analyses suggest ATH434 completes Fe2+ coordination using H2O. ATH434 significantly stabilized bound Fe2+ from ligand-induced autooxidation, reducing reactive oxygen species (ROS) production, whereas DFP and DFX promoted production. The comparable affinity of ATH434 for Fe2+ and Fe3+ position it to sequester excess Fe2+ and facilitate drug-to-protein iron metal exchange, mimicking natural endogenous iron binding proteins, at a reduced risk of autooxidation-induced ROS generation or perturbation of cellular iron stores.

A sbiT-sbiRS-gloIo regulatory circuit is involved in oxidative stress tolerance of Stenotrophomonas maltophilia

The sbiT-sbiR-sbiS operon of Stenotrophomonas maltophilia encodes an inner-membrane protein SbiT and a SbiS-SbiR two-component regulatory system. A sbiT mutant displayed a growth defect in LB agar. Mechanism studies revealed that sbiT deletion resulted in SbiSR activation and gloIo upregulation, which increased intracellular ROS level and caused growth defect.

Antioxidant and Pro-Oxidant Properties of Selected Clinically Applied Antibiotics: Therapeutic Insights

BACKGROUND

The balance between antioxidants and pro-oxidants plays a significant role in the context of oxidative stress, influenced by both physiological and non-physiological factors.

OBJECTIVES

In this study, 18 prescribed antibiotics (including doxycycline hydrochloride, tigecycline, rifampicin, tebipenem, cefuroxime, cefixime, potassium clavulanate, colistin, ampicillin, amoxicillin, amikacin, nalidixic acid, azithromycin, pipemidic acid trihydrate, pivmecillinam, aztreonam, fosfomycin sodium, and ciprofloxacin) were subjected to simultaneous determination of antioxidant and pro-oxidant potential to assess if pro-oxidant activity is a dominant co-mechanism of antibacterial activity or if any antibiotic exhibits a balanced effect.

METHODS

This study presents a recently developed approach for the simultaneous assessment of antioxidant and pro-oxidant potential on a single microplate in situ, applied to prescribed antibiotics.

RESULTS

Ten antibiotics from eighteen showed lower antioxidant or pro-oxidant potential, while five exhibited only mild potential with DPPH50 values over 0.5 mM. The pro-oxidant antioxidant balance index (PABI) was also calculated to determine whether antioxidant or pro-oxidant activity was dominant for each antibiotic. Surprisingly, three antibiotics-doxycycline hydrochloride, tigecycline, and rifampicin-showed significant measures of both antioxidant and pro-oxidant activities. Especially notable was tebipenem, a broad-spectrum, orally administered carbapenem, showed a positive PABI index ratio, indicating a dominant antioxidant over pro-oxidant effect.

CONCLUSIONS

These findings could be significant for both therapy, where the antibacterial effect is enhanced by radical scavenging activity, and biotechnology, where substantial pro-oxidant activity might limit microbial viability in cultures and consequently affect yield.

The impact of heat treatment on E. coli cell physiology in rich and minimal media considering oxidative secondary stress

AIMS

This study investigates the cell physiology of thermally injured bacterial cells, with a specific focus on oxidative stress and the repair mechanisms associated with oxidative secondary stress.

METHODS AND RESULTS

We explored the effect of heat treatment on the activity of two protective enzymes, levels of intracellular reactive oxygen species, and redox potential. The findings reveal that enzyme activity slightly increased after heat treatment, gradually returning to baseline levels during subculture. The response of Escherichia coli cells to heat treatment, as assessed by the level of superoxide radicals generated and redox potential, varied based on growth conditions, namely minimal and rich media. Notably, the viability of injured cells improved when antioxidants were added to agar media, even in the presence of metabolic inhibitors.

CONCLUSIONS

These results suggest a complex system involved in repairing damage in heat-treated cells, particularly in rich media. While repairing membrane damage is crucial for cell regrowth and the electron transport system plays a critical role in the recovery process of injured cells under both tested conditions.

The complexity of extracellular vesicles: Bridging the gap between cellular communication and neuropathology

Brain-derived extracellular vesicles (EVs) serve a prominent role in maintaining homeostasis and contributing to pathology in health and disease. This review establishes a crucial link between physiological processes leading to EV biogenesis and their impacts on disease. EVs are involved in the clearance and transport of proteins and nucleic acids, responding to changes in cellular processes associated with neurodegeneration, including autophagic disruption, organellar dysfunction, aging, and other cell stresses. In neurodegenerative disorders (e.g., Alzheimer's disease, Parkinson's disease, etc.), EVs contribute to the spread of pathological proteins like amyloid β, tau, ɑ-synuclein, prions, and TDP-43, exacerbating neurodegeneration and accelerating disease progression. Despite evidence for both neuropathological and neuroprotective effects of EVs, the mechanistic switch between their physiological and pathological functions remains elusive, warranting further research into their involvement in neurodegenerative disease. Moreover, owing to their innate ability to traverse the blood-brain barrier and their ubiquitous nature, EVs emerge as promising candidates for novel diagnostic and therapeutic strategies. The review uniquely positions itself at the intersection of EV cell biology, neurophysiology, and neuropathology, offering insights into the diverse biological roles of EVs in health and disease.

Rufibacter psychrotolerans sp. nov., a Cold-Tolerating Novel Species Isolated from Desert Soil

Strain SYSU D00308T, a short-rod-shaped bacterium, was isolated from a sandy soil collected from the Gurbantunggut Desert, Xinjiang, PR China. Strain SYSU D00308T was Gram-stain-negative, aerobic, pink-pigmented, non-motile, catalase- and oxidase-positive. The strain grew at 4-37 ℃, pH 5.0-8.0 and 0-1.5% (w/v) NaCl. 16S rRNA gene sequencing analyses demonstrated that strain SYSU D00308T belonged to the genus Rufibacter and exhibited the highest sequence similarity (97.4%) to Rufibacter glacialis MDT1-10-3T. Summed features 3, 4, and iso-C15:0 were the major fatty acids, and menaquinone 7 (MK-7) was the sole respiratory menaquinone. The polar lipid profiles comprised phosphatidylethanolamine, an unidentified glycolipid, an unidentified phospholipid, two unidentified aminophospholipids, and two unidentified lipids. The genome size and DNA G + C content of strain SYSU D00308T were 5,176,683 bp and 54.8%, respectively. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between SYSU D00308T and members of the genus Rufibacter were 77.7-81.8% and 20.4-23.4% respectively, which were less than the corresponding thresholds (ANI: 95-96%; dDDH: 70%) for prokaryotic species definition. According to the genotypic, phenotypic and phylogenetic characteristics, strain SYSU D00308T represents a novel species of the genus Rufibacter. We propose the name, Rufibacter psychrotolerans sp. nov., with SYSU D00308T (= CGMCC 1.18621T = KCTC 82275T = MCCC 1K04970T) as the type strain.

Membrane depolarization kills dormant Bacillus subtilis cells by generating a lethal dose of ROS

The bactericidal activity of several antibiotics partially relies on the production of reactive oxygen species (ROS), which is generally linked to enhanced respiration and requires the Fenton reaction. Bacterial persister cells, an important cause of recurring infections, are tolerant to these antibiotics because they are in a dormant state. Here, we use Bacillus subtilis cells in stationary phase, as a model system of dormant cells, to show that pharmacological induction of membrane depolarization enhances the antibiotics' bactericidal activity and also leads to ROS production. However, in contrast to previous studies, this results primarily in production of superoxide radicals and does not require the Fenton reaction. Genetic analyzes indicate that Rieske factor QcrA, the iron-sulfur subunit of respiratory complex III, seems to be a primary source of superoxide radicals. Interestingly, the membrane distribution of QcrA changes upon membrane depolarization, suggesting a dissociation of complex III. Thus, our data reveal an alternative mechanism by which antibiotics can cause lethal ROS levels, and may partially explain why membrane-targeting antibiotics are effective in eliminating persisters.

Resistance or tolerance? Highlighting the need for precise terminology in the field of disinfection

The terms 'resistance' and 'tolerance' are well defined in the context of antibiotic research. However, in the field of disinfection, these terms are often used synonymously, which creates ambiguity and can lead to misunderstandings and misconceptions. In addition, this inconsistency in terminology makes it difficult to assess the risk of a disinfectant resistance. This general review aims to discuss existing definitions of the terms 'adaptation', 'susceptibility', 'tolerance', 'persistence' and 'resistance' in the light of disinfectants. The most ambiguity is found between tolerance and resistance. Whereas the former describes the not necessarily heritable survival of transient exposure to usually lethal concentrations, resistance is the strictly heritable ability to survive otherwise lethal concentrations of an antimicrobial agent, regardless of exposure time. A simple transfer of experience from antibiotic research is not recommended when assessing the risk of resistance to disinfectants, as there are important differences between antibiotics and disinfectants, although both are antimicrobials: (i) disinfectants are usually applied at concentrations that exceed the minimum inhibitory concentration by orders of magnitude, (ii) the exposure times of disinfectants are in the range of seconds, minutes, or a few hours, (iii) the mode of action of disinfectants is less specific, and (iv) disinfectants often contain more than one active agent with additive or synergistic effects. It is important to recognize that disinfectants, like other antimicrobial agents such as antibiotics, have a dualistic nature and should be used correctly and with caution.

Ten "Cheat Codes" for Measuring Oxidative Stress in Humans

Formidable and often seemingly insurmountable conceptual, technical, and methodological challenges hamper the measurement of oxidative stress in humans. For instance, fraught and flawed methods, such as the thiobarbituric acid reactive substances assay kits for lipid peroxidation, rate-limit progress. To advance translational redox research, we present ten comprehensive "cheat codes" for measuring oxidative stress in humans. The cheat codes include analytical approaches to assess reactive oxygen species, antioxidants, oxidative damage, and redox regulation. They provide essential conceptual, technical, and methodological information inclusive of curated "do" and "don't" guidelines. Given the biochemical complexity of oxidative stress, we present a research question-grounded decision tree guide for selecting the most appropriate cheat code(s) to implement in a prospective human experiment. Worked examples demonstrate the benefits of the decision tree-based cheat code selection tool. The ten cheat codes define an invaluable resource for measuring oxidative stress in humans.

High Levels of Erucic Acid Cause Lipid Deposition, Decreased Antioxidant and Immune Abilities via Inhibiting Lipid Catabolism and Increasing Lipogenesis in Black Carp (Mylopharyngodon piceus)

This study investigated the effects of dietary erucic acid (EA) on growth, lipid accumulation, antioxidant and immune abilities, and lipid metabolism in black carp fed six diets containing varying levels of EA (0.00%, 0.44%, 0.81%, 1.83%, 2.74%, and 3.49%), for 8 weeks. Results showed that fish fed the 3.49% EA diet exhibited lower weight gain, compared to those fed the 0.81% EA diet. In a dose-dependent manner, the serum triglycerides and total cholesterol were significantly elevated in the EA groups. The 1.83%, 2.74%, and 3.49% levels of EA increased alanine aminotransferase and aspartate aminotransferase activities, as well as decreased acid phosphatase and alkaline phosphatase values compared to the EA-deficient group. The hepatic catalase activity and transcriptional level were notably reduced, accompanied by increased hydrogen peroxide contents in the EA groups. Furthermore, dietary EA primarily increased the C22:1n-9 and C20:1n-9 levels, while decreasing the C18:0 and C18:1n-9 contents. In the EA groups, expressions of genes, including hsl, cpt1a, cpt1b, and ppara were downregulated, whereas the fas and gpat expressions were enhanced. Additionally, dietary EA elevated the mRNA level of il-1β and reduced the expression of il-10. Collectively, high levels of EA (2.74% and 3.49%) induced lipid accumulation, reduced antioxidative and immune abilities in black carp by inhibiting lipid catabolism and increasing lipogenesis. These findings provide valuable insights for optimizing the use of rapeseed oil rich in EA for black carp and other carnivorous fish species.

Collective peroxide detoxification determines microbial mutation rate plasticity in E. coli

Mutagenesis is responsive to many environmental factors. Evolution therefore depends on the environment not only for selection but also in determining the variation available in a population. One such environmental dependency is the inverse relationship between mutation rates and population density in many microbial species. Here, we determine the mechanism responsible for this mutation rate plasticity. Using dynamical computational modelling and in culture mutation rate estimation, we show that the negative relationship between mutation rate and population density arises from the collective ability of microbial populations to control concentrations of hydrogen peroxide. We demonstrate a loss of this density-associated mutation rate plasticity (DAMP) when Escherichia coli populations are deficient in the degradation of hydrogen peroxide. We further show that the reduction in mutation rate in denser populations is restored in peroxide degradation-deficient cells by the presence of wild-type cells in a mixed population. Together, these model-guided experiments provide a mechanistic explanation for DAMP, applicable across all domains of life, and frames mutation rate as a dynamic trait shaped by microbial community composition.

Microbiological interpretation of weak ultrasound enhanced biological wastewater treatment - using Escherichia coli degrading glucose as model system

The Escherichia coli (E.coli) degrading glucose irradiated by ultrasound irradiation (20 W, 14 min) was investigated as the model system, the glucose degradation increased by 13 % while the E.coli proliferation decreased by 10 % after culture for 18 h. It indicated a tradeoff effect between substrate degradation and cell proliferation, which drove the enhanced contaminants removal and excess sludge reduction in a weak ultrasound enhanced biological wastewater treatment. The enzymatic activities (catalase, superoxide dismutase, adenosine triphosphatases, lactic dehydrogenase, membrane permeability, intracellular reactive oxygen species and calcium ion of E. coli increased immediately by 12 %, 63 %, 124 %, 19 %, 15 %, 4-fold and 38-fold, respectively by ultrasound irradiation power of 20 W for 14 min. Furthermore, the membrane permeability of irradiated E. coli increased by 26 % even though the ultrasound stopped for 10 h. Additionally, pathways associated with glucose degradation and cell proliferation were continuously up-regulated and down-regulated, respectively.

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.

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.

Dietary Erucic Acid Induces Fat Accumulation, Hepatic Oxidative Damage, and Abnormal Lipid Metabolism in Nile Tilapia (Oreochromis niloticus)

Erucic acid (EA) in rapeseed oil has adverse effects on terrestrial animal and fish health. However, its antinutritional role in fish remains unclear due to the limited information on EA. Therefore, this study was conducted to assess the impact of EA on growth performance, antioxidative capacity, fatty acid profile, and lipid metabolism in tilapia. Six diets containing different amounts of EA (0, 3, 6, 12, 20, and 27 g/kg diet) were fed to tilapia (initial weight: 3.01 ± 0.01 g) for 8 weeks. The results exhibited that dietary EA did not affect growth performance but remarkedly increased the crude lipid contents (in the whole body, liver, and muscle). It also markedly increased the levels of low-density lipoprotein cholesterol, total cholesterol, nonesterified fatty acids, and triglyceride in the liver and serum in a dose-dependent manner. The EA groups had lower values of total superoxide dismutase, total antioxidant capacity, catalase, and higher activities of aspartate aminotransferase and alanine aminotransferase, as dietary EA levels increased. Feeding fish with diets containing EA (20 and 27 g/kg diet) significantly increased the malondialdehyde content. Moreover, dietary EA greatly altered the fatty acid profile in the liver and muscle. It especially elevated the percentages of C18 : 2n-6, C20 : 1n-9, and C22 : 1n-9 while decreasing the C18 : 0 and C16 : 0 levels. When the levels of EA in diets were 12, 20, and 27 g/kg, genes correlated with lipophagy, lipolysis, and β-oxidation were significantly reduced. Meanwhile, genes concerned in triglyceride synthesis were largely increased in the liver and muscle. In summary, high-dose EA (20 g/kg diet) in the diets significantly induced fat accumulation, hepatic oxidative damage, and abnormal lipid metabolism in tilapia. The current findings expand our understanding on the antinutritional role of EA in lipid homeostasis and fish health.

Chemomixoautotrophy and stress adaptation of anammox bacteria: A review

Anaerobic ammonium oxidizing (anammox) bacteria, which were first discovered nearly three decades ago, are crucial for treating ammonium-containing wastewater. Studies have reported on the biochemical nitrogen conversion process and the physiological, phylogenic, and ecological features of anammox bacteria. For a long time, anammox bacteria were assumed to have a lithoautotrophic lifestyle. However, recent studies have suggested the functional versatility of anammox bacteria. Genome-based analysis and experiments with enrichment cultures have demonstrated the association of the metabolic activities of anammox bacteria with different stress conditions, revealing the importance of utilizing specific organic substances, including organoautotrophy, for growth and adaptation to stress conditions. Our understanding regarding the utilization and metabolism of organic substances and their associations with anammox reactions in anammox bacteria is growing but still incomplete. In this review, we summarize the effect of the utilization of organic substances by anammox bacteria under environmental stress conditions, emphasizing their potential organoautotrophic activity and metabolic flexibility. Although most anammox bacteria may utilize specific organic substances, Ca. Brocadia exhibited the highest level of mixoautotrophic activity. The environmental factors that substantially affect the organoautotrophic activities of anammox bacteria were also examined. This review provides a new perspective on the organoautotrophic capacity of anammox bacteria.

The Cd resistant mechanism of Proteus mirabilis Ch8 through immobilizing and detoxifying

Cadmium (Cd) pollution is a serious global environmental problem, which requires a global concern and practical solutions. Microbial remediation has received widespread attention owing to advantages, such as environmental friendliness and soil amelioration. However, Cd toxicity also severely deteriorates the remediation performance of functional microorganisms. Analyzing the mechanism of bacterial resistance to Cd stress will be beneficial for the application of Cd remediation. In this study, the bacteria strain, up to 1400 mg/L Cd resistance, was employed and identified as Proteus mirabilis Ch8 (Ch8) through whole genome sequence analyses. The results indicated that the multiple pathways of immobilizing and detoxifying Cd maintained the growth of Ch8 under Cd stress, which also possessed high Cd extracellular adsorption. Firstly, the changes in surface morphology and functional groups of Ch8 cells were observed under different Cd conditions through SEM-EDS and FTIR analyses. Under 100 mg/L Cd, Ch8 cells exhibited aggregation and less flagella; the Cd biosorption of Ch8 was predominately by secreting exopolysaccharides (EPS) and no significant change of functional groups. Under 500 mg/L Cd, Ch8 were present irregular polymers on the cell surface, some cells with wrapping around; the Cd biosorption capacity exhibited outstanding effects (38.80 mg/g), which was mainly immobilizing Cd by secreting and interacting with EPS. Then, Ch8 also significantly enhanced the antioxidant enzyme activity and the antioxidant substance content under different Cd conditions. The activities of SOD and CAT, GSH content of Ch8 under 500 mg/L Cd were significantly increased by 245.47%, 179.52%, and 241.81%, compared to normal condition. Additionally, Ch8 significantly induced the expression of Acr A and Tol C (the resistance-nodulation-division (RND) efflux pump), and some antioxidant genes (SodB, SodC, and Tpx) to reduce Cd damage. In particular, the markedly higher expression levels of SodB under Cd stress. The mechanism of Ch8 lays a foundation for its application in solving soil remediation.

Combining multiple stressors unexpectedly blocks bacterial migration and growth

In nature, organisms experience combinations of stressors. However, laboratory studies typically simplify reality and focus on the effects of an individual stressor. Here, we use a microfluidic approach to simultaneously provide a physical stressor (shear flow) and a chemical stressor (H 2 O 2 ) to the human pathogen Pseudomonas aeruginosa . By treating cells with levels of flow and H 2 O 2 that commonly co-occur in nature, we discover that previous reports significantly overestimate the H 2 O 2 levels required to block bacterial growth. Specifically, we establish that flow increases H 2 O 2 effectiveness 50-fold, explaining why previous studies lacking flow required much higher concentrations. Using natural H 2 O 2 levels, we identify the core H 2 O 2 regulon, characterize OxyR-mediated dynamic regulation, and dissect the redundant roles of multiple H 2 O 2 scavenging systems. By examining single-cell behavior, we serendipitously discover that the combined effects of H 2 O 2 and flow block pilus-driven surface migration. Thus, our results counter previous studies and reveal that natural levels of H 2 O 2 and flow synergize to restrict bacterial colonization and survival. By studying two stressors at once, our research highlights the limitations of oversimplifying nature and demonstrates that physical and chemical stress can combine to yield unpredictable effects.