Oxidative Stress in Bacteria and the Central Dogma of Molecular Biology

Molecular insights into cobalt homeostasis in estuarine microphytobenthos: A meta-transcriptomics and biogeochemical approach

Meta-transcriptomics data supported by biofilm physico-chemical parameters unravelled the molecular and biochemical processes utilized by multicomponent intertidal biofilms to endure cobalt toxicity. Findings indicated activation of influx (BtuB, ABC-type transporters) and efflux pumps (RND, CZC) to maintain metal ion homeostasis. Enhanced specific activity of antioxidant enzymes namely catalases and peroxidases (KatG, SodA) mitigated oxidative damage. Heightened synthesis of capsular polysaccharide components, specifically uronic acid and carbohydrate via PEP-CTERM sorting system, wzy pathway and glycosyltransferases protected biofilms against cobalt exposure. Despite chlorophyll biosynthesis genes being upregulated, metal toxicity impeded chlorophyll replenishment. Principal pathways associated with iron acquisition (AfuA), energy metabolism (AtpG), general metabolic activities (FruK, NifD, coABC) and central dogma regulation (DPS, AsrR, RRM) were activated to combat cobalt toxicity. This investigation offered novel insights into the regulatory network employed by intertidal microphytobenthic communities for maintaining cobalt homeostasis and underlined the basis for their application as biomarkers for estuarine cobalt pollution.

Host immunity and intracellular bacteria evasion mechanisms: Enhancing host-directed therapies with drug delivery systems

Host-directed therapies (HDTs) have been investigated as a potential solution to combat intracellular and drug-resistant bacteria. HDTs stem from extensive research on the intricate interactions between the host and intracellular bacteria, leading to a treatment approach that relies on immunoregulation. To improve the bioavailability and safety of HDTs, researchers have utilized diverse drug delivery systems (DDS) to encapsulate and transport therapeutic agents to target cells. In this review, we first introduce the three mechanisms of bactericidal action and intracellular bacterial evasion: autophagy, reactive oxygen species (ROS), and inflammatory cytokines, with a particular focus on autophagy. Special attention is given to the detailed mechanism of xenophagy in clearing intracellular bacteria, a crucial selective autophagy process that specifically targets and degrades intracellular pathogens. Following this, we present the application of DDS to modulate these regulatory methods for intracellular bacteria elimination. By integrating insights from immunology and nanomedicine, this review highlights the emerging role of DDS in advancing HDTs for intracellular bacterial infections and paving the way for innovative therapeutic interventions.

New insights on antibacterial mode of action of blue-light photoactivated berberine and curcumin-antibiotic combinations against Staphylococcus aureus

Antimicrobial photodynamic inactivation (aPDI), using photosensitisers in combination with antibiotics, is a promising multi-target strategy to address antibiotic resistance, particularly in wound infections. This study aimed to elucidate the antibacterial mode of action of combinations of berberine (Ber) or curcumin (Cur) with selected antibiotics (Ber-Ab or Cur-Ab) under blue light irradiation (420 nm) against Staphylococcus aureus, including methicillin-resistant (MRSA) and methicillin-susceptible (MSSA) strains. Multiple physiological parameters were assessed using complementary assays (fluorometry, epifluorescence microscopy, flame emission and atomic absorption spectroscopy, zeta potential, flow cytometry, and the plate agar method) to examine the effect on ROS production, membrane integrity, DNA damage, motility and virulence factors of S. aureus. Results indicated that blue light photoactivated Ber-Ab and Cur-Ab combinations led to substantial ROS generation, even at low concentrations, causing oxidative stress that severely impacted bacterial membrane integrity (approximately 90 % in MRSA and 40 % in MSSA). Membrane destabilization was further confirmed by elevated intercellular potassium release (≈ 2.00 and 2.40 µg/mL in MRSA and MSSA, respectively). Furthermore, significant DNA damage was observed in both strains (≈ 50 %). aPDI treatment with blue light also reduced S. aureus pathogenicity by impairing motility and inhibiting key virulence factors such as proteases, lipases, and gelatinases, all of which play key roles in the infectious process. Overall, Ber-Ab combinations demonstrated the highest efficacy across all parameters tested, highlighting for the first time the multi-target therapeutic potential of this phytochemical-based aPDI strategy to combat antibiotic-resistant S. aureus infections and improve wound infection treatment outcomes.

Lessons from RatA: Why the Basics in Molecular Biology Are Still Crucial!

Since the first bacterial genomes were sequenced and annotated over 25 years ago, sequencing technologies have rapidly advanced in both speed and cost efficiency. To date, over two million annotated bacterial genomes have been deposited in the National Center for Biotechnology Information (NCBI) database. Yet, there are many genes with unknown functions and, furthermore, conflicting results have been published for many investigated genes. One example is the ratA (or pasT) gene from Escherichia coli (E. coli) K-12 strains. Initially identified as a ribosome-targeting toxin, later studies described RatA as the bacterial homolog of the mitochondrial Coq10 protein and, therefore, beneficial for E. coli cells during aerobic growth. This study shows that these conflicting results originated from a mis-annotation of the start codon in the genomic sequence. Overexpression of the ratA gene as currently annotated leads to the synthesis of two RatA protein variants, a toxic and a non-toxic one. This study further identifies the endogenous ratA promoter and shows that only the shorter, non-toxic variant of RatA is synthesized during different growth phases specifically under aerobic conditions. Our findings thereby not only solidify the role of RatA in E. coli, but also demonstrate the importance of first validating the basics of molecular biology when investigating a previously poorly described gene, even in times of advanced high-throughput techniques.

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.

Proteomic profiling and pre-clinical efficacy of antimicrobial lithium complex and colistin combination against multi-drug resistant Acinetobacter baumannii

Multi-drug resistant (MDR) Acinetobacter baumannii accounts for high mortality rates in hospital-acquired infections. Colistin is the last resort treatment despite nephrotoxic effects and the emergence of colistin resistant A. baumannii is an emerging issue. To tackle this dilemma, metal complexes can be used to potentiate colistin as combination therapy. However, mechanistic and in vivo studies are lacking to present them as compelling therapeutic options. In this study, a lithium complex ([Li(phen)2sal]) based on salicylic acid and 1,10-phenanthroline was used in synergy with colistin to test its antimicrobial and anti-biofilm potential against MDR A. baumannii. Furthermore, proteomics via mass spectrometry, flow cytometry and scanning electron microscopy was performed to study the cellular targets of the treatment. Combination therapy was also tested against pneumonia model in mice to observe pre-clinical efficacy. The lithium complex showed synergistic and additive interaction with colistin and inhibited >85 % of bacterial cells and biofilm formation in A. baumannii strains. Proteomic analysis revealed that combination therapy downregulated significantly more membrane proteins as compared to the individual doses. Flow cytometry indicated that combination therapy caused hyperpolarization in bacteria which led to the cellular damage as observed in scanning electron microscopy. Combination therapy was non-toxic in mice and reduced the clinical score to 0 with bacterial load lessened to 5.56 ± 0.90 log10 CFU in 48 h. Therefore, parenchymal sections had lesser inflammatory regions with intact alveoli. Consequently, combination therapy can be an alternative therapeutic approach with antimicrobial, anti-biofilm, and pre-clinical efficacy against MDR A. baumannii infection.

The RNA chaperone Hfq is a novel regulator of catalase expression and hydrogen peroxide-induced oxidative stress response in Listeria monocytogenes EGD-e

The RNA chaperone Hfq plays a pivotal role in many bacteria, acting as a regulator of gene expression and promoting interaction between mRNA-sRNA pairs in Gram-negative bacteria. However, in Gram-positive bacteria this protein is expendable for riboregulation, and the main function of Hfq remains elusive. This work unveils a novel function for Hfq in the oxidative stress response of the human pathogen Listeria monocytogenes, a Gram-positive bacterium responsible for the infectious disease listeriosis. Disruption of hfq gene (Δhfq) results in a hypersensitive phenotype towards hydrogen peroxide (H2O2), in which sub-inhibitory concentrations of this reactive oxygen species (ROS) severely impair growth and viability of L. monocytogenes EGD-e. A Δhfq-complemented strain does not show this phenotype. This Hfq-dependent regulation of oxidative stress seems specific for H2O2, as exposure to superoxides caused no differences. We demonstrate that Hfq has a dual regulatory role in the expression of catalase (kat), the key enzyme involved in H2O2 detoxification. Hfq influences kat transcription under non-stress conditions by modulating the levels of the transcriptional repressor PerR, and also acts post-transcriptionally by stabilizing kat mRNA under H2O2-induced stress. Indeed, enzymatic assays revealed reduced catalase activity in Δhfq cell extracts, a result unrelated to differences in cellular iron content. Bacterial infection triggers immune cells to produce massive amounts of ROS, like H2O2. We show that inactivation of Hfq increases susceptibility to macrophage killing, connecting Hfq with the stress resistance and virulence of L. monocytogenes EGD-e. Overall, these findings advance the understanding of Hfq function within Gram-positive bacteria, revealing for the first time that Hfq is a novel regulator of catalase expression. This paves the way for the study of yet unknown oxidative stress response pathways regulated by Hfq in other pathogens.

First whole genome report of Mangrovibacter phragmitis PSU-3885-11 isolated from a patient in Thailand

Mangrovibacter phragmitis is a Gram-negative bacterium typically found in plant roots that supports nitrogen fixation in nutrient-poor environments such as mangrove ecosystems. Although primarily found in environmental niches, an unusual case in Thailand of M. phragmitis strain PSU-3885-11 isolated from the sputum of a 29-year-old female patient with spinal tuberculosis. This isolate was initially misidentified as part of the Enterobacter cloacae complex (ECC) by MALDI-TOF. However, WGS subsequently confirmed its correct identity as M. phragmitis. The genome contains 4,651 coding sequences, along with 72 tRNA genes and 1 tmRNA. Moreover, comparative genomic analysis showed 99.32 % average nucleotide identity (ANI) similar to M. phragmitis MP23, and several antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) were identified in the PSU-3885-11 genome which may contribute to its ability to survive in diverse environments, including human hosts. The PSU-3885-11 displayed resistance to beta-lactam antibiotics such as ampicillin and cefotaxime, while remaining sensitive to a wide range of other antibiotics. Key virulence genes including ompA, hcp/tssD, and rpoS, were identified which may play a role in its persistence in human hosts as an opportunistic pathogen. The presence of ribosomally synthesized and post-translationally modified peptides (RiPPs) and bacteriocins indicates the antimicrobial properties that may provide a competitive advantage in both environmental and clinical settings of this strain. Therefore, this study provides valuable insights into the genomic features, antibiotic resistance, and potential pathogenicity of M. phragmitis PSU-3885-11. The findings also emphasize the importance of continued surveillance and genomic analysis of environmental bacteria that may emerge as opportunistic pathogens in human infections.

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.

Production, Isolation, and Characterization of Stable Isotope-Labeled Standards for Mass Spectrometric Measurements of Oxidatively-Damaged Nucleosides in RNA

RNA undergoes oxidatively induced damage in living organisms analogous to DNA. RNA is even more vulnerable to damage than DNA due to its greater abundance, single-strandedness, lack of repair and chromatin proteins shield, and instability, among other effects. RNA damage can adversely affect gene expression, leading to protein synthesis alterations, cell death, and other detrimental biological consequences. Growing indications suggest the involvement of oxidatively induced RNA damage in the pathogenesis of various human diseases, aging, and age-related diseases. Oxidatively induced damage can cause modifications to all four heterocyclic bases in RNA. Precise measurement of such modifications in RNA is essential for understanding the biological effects of oxidatively induced RNA damage. In the past, mass spectrometry has been used for this purpose. In mass spectrometric measurements, the use of stable isotope-labeled analogues of analytes as internal standards is essential for accurate quantifications. Past work utilized a stable isotope-labeled analogue of 8-hydroxyguanosine only as an internal standard. Thus, far, no stable isotope-labeled analogues of other oxidatively modified RNA nucleosides were available. In the present work, we report on the preparation, isolation, and characterization of the 13C- and 15N-labeled analogues of a variety of modified pyrimidine- and purine-derived RNA nucleosides. We also show the application of these internal standards for the measurement of oxidatively induced RNA damage in several commercially available RNA samples and in DNA along with DNA damage.

Bacillus cabrialesii subsp. cabrialesii Strain TE5: A Promising Biological Control Bacterium Against the Causal Agent of Spot Blotch in Wheat

Strain TE5 was isolated from a wheat (Triticum turgidum L. subsp. durum) rhizosphere grown in a commercial field of wheat in the Yaqui Valley in Mexico. In this work, we present strain TE5 as a promising biological control agent against Bipolaris sorokiniana. First, after its genome sequencing through Illumina NovaSeq, this strain showed a genome size of 4,262,927 bp, with a 43.74% G + C content, an N50 value of 397,059 bp, an L50 value of 4 bp, and 41 contigs (>500 bp). Taxonomical affiliation was carried out by using overall genome relatedness indexes (OGRIs) and the construction of a phylogenomic tree based on the whole genome. The results indicated that strain TE5 identifies with Bacillus cabrialesii subsp. cabrialesii. Genomic annotation using Rapid Annotation Using Subsystems Technology (RAST) and Rapid Prokaryotic Genome Annotation (Prokka) indicated the presence of 4615 coding DNA sequences (CDSs) distributed across 330 subsystems, which included gene families associated with biocontrol, stress response, and iron competition. Furthermore, when the antiSMASH 7.1 platform was used for genome mining, the results indicated the presence of seven putative biosynthetic gene clusters related to the production of biocontrol metabolites, namely subtilosin A, bacillibactin, fengycin, bacillaene, bacilysin, surfactin, and rhizocticin A. Moreover, the antifungal activity of strain TE5 and its cell-free extract (CFE) was evaluated against Bipolaris sorokiniana, an emergent wheat pathogen. The results of in vitro dual confrontation showed fungal growth inhibition of 67% by strain TE5. Additionally, its CFE almost completely inhibited (93%) the growth of the studied phytopathogenic fungus on liquid media. Further observations of the impact of these bacterial metabolites on fungal spore germination exhibited inhibition of fungal spores through degrading the germinative hypha, avoiding mycelium development. Finally, the protective effect of strain TE5 against Bipolaris sorokiniana was evaluated for wheat seedlings. The results showed a significant decrease (83%) in disease severity in comparison with the plant infection without inoculation of the biological control agent. Thus, this work proposes Bacillus cabrialesii subsp. cabrialesii strain TE5 as a promising biological control agent against the wheat pathogen Bipolaris sorokiniana while suggesting lipopeptides as the potential mode of action, together with plant growth and defense stimulation.

Deciphering the Molecular Mechanism of Peracetic Acid Response in Listeria monocytogenes

Peracetic acid (PAA), a strong oxidizing agent, has been widely used as a disinfectant in food processing settings as it does not produce harmful chlorinated by-products. In the present study, the transcriptional response of Listeria monocytogenes to a sub-lethal concentration of PAA (2.5 ppm) was assessed using RNA-sequencing (RNA-seq). Our analysis revealed 12 differentially expressed protein-coding genes, of which nine were upregulated (ohrR, ohrA, rpsN, lmo0637, lmo1973, fur, lmo2492, zurM, and lmo1007), and three were down-regulated (argG, lmo0604 and lmo2156) in PAA-treated samples compared to the control samples. A non-coding small RNA gene (rli32) was also found to be down-regulated. In detail, the organic peroxide toxicity protection (OhrA-OhrR) system, the metal homeostasis genes fur and zurM, the SbrE-regulated lmo0636-lmo0637 operon and a carbohydrate phosphotransferase system (PTS) operon component were induced under exposure of L. monocytogenes to PAA. Hence, this study identified key elements involved in the primary response of L. monocytogenes to oxidative stress caused by PAA, including the expression of the peroxide detoxification system and fine-tuning the levels of redox-active metals in the cell. The investigation of the molecular mechanism of PAA response in L. monocytogenes is of utmost importance for the food industry, as residual PAA can lead to stress tolerance in pathogens.

Detection of Viable but Nonculturable E. coli Induced by Low-Level Antimicrobials Using AI-Enabled Hyperspectral Microscopy

Rapid detection of bacterial pathogens is essential for food safety and public health, yet bacteria can evade detection by entering a viable but nonculturable (VBNC) state under sublethal stress, such as antimicrobial residues. These bacteria remain active but undetectable by standard culture-based methods without extensive enrichment, necessitating advanced detection methods. This study developed an AI-enabled hyperspectral microscope imaging (HMI) framework for rapid VBNC detection under low-level antimicrobials. The objectives were to (i) induce the VBNC state in Escherichia coli K-12 by exposure to selected antimicrobial stressors, (ii) obtain HMI data capturing physiological changes in VBNC cells, and (iii) automate the classification of normal and VBNC cells using deep learning image classification. The VBNC state was induced by low-level oxidative (0.01% hydrogen peroxide) and acidic (0.001% peracetic acid) stressors for 3 days, confirmed by live-dead staining and plate counting. HMI provided spatial and spectral data, extracted into pseudo-RGB images using three characteristic spectral wavelengths. An EfficientNetV2-based convolutional neural network architecture was trained on these pseudo-RGB images, achieving 97.1% accuracy of VBNC classification (n = 200), outperforming the model trained on RGB images at 83.3%. The results highlight the potential for rapid, automated VBNC detection using AI-enabled hyperspectral microscopy, contributing to timely intervention to prevent foodborne illnesses and outbreaks.

Gene Variant Related Neurological and Molecular Biomarkers Predict Psychosis Progression, with Potential for Monitoring and Prevention

The (MTHFR) C677T gene polymorphism is associated with neurological disorders and schizophrenia. Patients diagnosed with schizophrenia and schizoaffective disorder and controls (n 134) had data collected for risk factors, molecular and neuro-sensory variables, symptoms, and functional outcomes. Promising gene variant-related predictive biomarkers were identified for diagnosis by Receiver Operating Characteristics and for illness duration by linear regression. These were then analyzed using Spearman's correlation in relation to the duration of illness. Significant correlations were ranked by strength and plotted on graphs for each MTHFR C677T variant. Homozygous MTHFR 677 TT carriers displayed a mid-illness switch to depression, with suicidality and a late-phase shift from lower to higher methylation, with activated psychosis symptoms. MTHFR 677 CC variant carriers displayed significant premorbid correlates for family history, developmental disorder, learning disorder, and head injury. These findings align with those of low methylation, oxidative stress, multiple neuro-sensory processing deficits, and disability outcomes. Heterozygous MTHFR 677 CT carriers displayed multiple shifts in mood and methylation with multiple adverse outcomes. The graphically presented ranked biomarker correlates for illness duration allow a perspective of psychosis development across gene variants, with the potential for phase of illness monitoring and new therapeutic insights to prevent or delay psychosis and its adverse outcomes.

Selective 8-oxo-rG stalling occurs in the catalytic core of polynucleotide phosphorylase (PNPase) during degradation

RNA oxidation, predominantly through the accumulation of 8-oxo-7,8-dihydroguanosine (8-oxo-rG), represents an important biomarker for cellular oxidative stress. Polynucleotide phosphorylase (PNPase) is a 3'-5' exoribonuclease that has been shown to preferentially recognize 8-oxo-rG-containing RNA and protect Escherichia coli cells from oxidative stress. However, the impact of 8-oxo-rG on PNPase-mediated RNA degradation has not been studied. Here, we show that the presence of 8-oxo-rG in RNA leads to catalytic stalling of E. coli PNPase through in vitro RNA degradation experiments and electrophoretic analysis. We also link this stalling to the active site of the enzyme through resolution of single-particle cryo-EM structures for PNPase in complex with singly or doubly oxidized RNA oligonucleotides. Following identification of Arg399 as a key residue in recognition of both single and sequential 8-oxo-rG nucleotides, we perform follow-up in vitro analysis to confirm the importance of this residue in 8-oxo-rG-specific PNPase stalling. Finally, we investigate the effects of mutations to active site residues implicated in 8-oxo-rG binding through E. coli cell growth experiments under H2O2-induced oxidative stress. Specifically, Arg399 mutations show significant effects on cell growth under oxidative stress. Overall, we demonstrate that 8-oxo-rG-specific stalling of PNPase is relevant to bacterial survival under oxidative stress and speculate that this enzyme might associate with other cellular factors to mediate this stress.

Exploring mechanisms of skin aging: insights for clinical treatment

The skin is the largest organ in the human body and is made up of various cells and structures. Over time, the skin will age, which is not only influenced by internal factors, but also by external environmental factors, especially ultraviolet radiation. Aging causes immune system weakening in the elderly, which makes them more susceptible to dermatosis, such as type 2 inflammatory mediated pruritus. The immune response in this condition is marked by senescent cells consistently releasing low amounts of pro-inflammatory cytokines through a senescence-associated secretory phenotype (SASP). This continuous inflammation may accelerate immune system aging and establish a connection between immune aging and type 2 inflammatory skin diseases. In addition, two chronic pigmentation disorders, vitiligo and chloasma, are also associated with skin aging. Aged cells escape the immune system and accumulate in tissues, forming a microenvironment that promotes cancer. At the same time, "photoaging" caused by excessive exposure to ultraviolet radiation is also an important cause of skin cancer. This manuscript describes the possible links between skin aging and type 2 inflammation, chronic pigmentation disorders, and skin cancer and suggests some treatment options.

Multi-targets of antimicrobial photodynamic therapy mediated by erythrosine against Staphylococcus aureus identified by proteomic approach

Staphylococcus aureus is a global challenge to the clinical field and food industry. Therefore, the development of antimicrobial photodynamic therapy (aPDT) has become one of the valuable methods to control this pathogen. The antibacterial activity of photoinactivation by erythrosine (Ery) against S. aureus has been reported, but its modes of action are unclear. This study aimed to employ a proteomic approach to analyze modes of action of Ery-aPDT against S. aureus. We determined the antibacterial effect by Ery-aPDT assays, quantified reactive oxygen species (ROS) and injury to the cell membrane, and determined protein expression using a proteomic approach combined with bioinformatic tools. Ery-aPDT was effective in reducing S. aureus to undetectable levels. In addition, the increment of ROS accompanied the increase in the reduction of cell viability, and damage to cellular membranes was shown by sublethal injury. In proteomic analysis, we found 17 differentially expressed proteins. These proteins revealed changes mainly associated with defense to oxidative stress, energy metabolism, translation, and protein biosynthesis. Thus, these results suggest that the effectiveness of Ery-aPDT is due to multi-targets in the bacterial cell that cause the death of S. aureus.

Non-antibiotic compounds associated with humans and the environment can promote horizontal transfer of antimicrobial resistance genes

Horizontal gene transfer plays a key role in the global dissemination of antimicrobial resistance (AMR). AMR genes are often carried on self-transmissible plasmids, which are shared amongst bacteria primarily by conjugation. Antibiotic use has been a well-established driver of the emergence and spread of AMR. However, the impact of commonly used non-antibiotic compounds and environmental pollutants on AMR spread has been largely overlooked. Recent studies found common prescription and over-the-counter drugs, artificial sweeteners, food preservatives, and environmental pollutants, can increase the conjugative transfer of AMR plasmids. The potential mechanisms by which these compounds promote plasmid transmission include increased membrane permeability, upregulation of plasmid transfer genes, formation of reactive oxygen species, and SOS response gene induction. Many questions remain around the impact of most non-antibiotic compounds on AMR plasmid conjugation in clinical isolates and the long-term impact on AMR dissemination. By elucidating the role of routinely used pharmaceuticals, food additives, and pollutants in the dissemination of AMR, action can be taken to mitigate their impact by closely monitoring use and disposal. This review will discuss recent progress on understanding the influence of non-antibiotic compounds on plasmid transmission, the mechanisms by which they promote transfer, and the level of risk they pose.

Diagnosis of extraintestinal pathogenic Escherichia coli pathogenesis in urinary tract infection

Extra-intestinal pathogenic Escherichia coli (ExPEC) is a virulent pathogen found in humans that causes the majority of urinary tract infections, and other infections such as meningitis and sepsis. ExPEC can enter the urinary tract through two modes: ascending from the bladder or descending from the kidneys. Human anatomical structures generally prevent the transmission of pathogens between the extra-intestinal area, kidneys, bladder, and urinary tract. However, adhesins, a virulence protein of ExPEC, promote the initial bacterial attachment and invasion of host cells. In addition to adhesion proteins, ExPEC contains iron acquisition systems and toxins to evade the host immune system, acquire essential nutrients, and gain antibiotic resistance. The presence of antibiotic-resistant genes makes treating ExPEC in urinary tract infections (UTIs) more complicated. Therefore, screening for the presence of ExPEC among other uropathogens in UTI patients is essential, as it can potentially aid in the effective treatment and mitigation of ExPEC pathogens. Several diagnostic techniques are available for detecting ExPEC, including urine culture, polymerase chain reaction, serological testing, loop-mediated isothermal amplification, and biochemical tests. This review addresses strain-specific diagnostic techniques for screening ExPEC in UTI patients.

Proteomic profiling of antibiotic-resistant Escherichia coli GW-AmxH19 isolated from hospital wastewater treated with physical plasma

Microorganisms which are resistant to antibiotics are a global threat to the health of humans and animals. Wastewater treatment plants are known hotspots for the dissemination of antibiotic resistances. Therefore, novel methods for the inactivation of pathogens, and in particular antibiotic-resistant microorganisms (ARM), are of increasing interest. An especially promising method could be a water treatment by physical plasma which provides charged particles, electric fields, UV-radiation, and reactive species. The latter are foremost responsible for the antimicrobial properties of plasma. Thus, with plasma it might be possible to reduce the amount of ARM and to establish this technology as additional treatment stage for wastewater remediation. However, the impact of plasma on microorganisms beyond a mere inactivation was analyzed in more detail by a proteomic approach. Therefore, Escherichia coli GW-AmxH19, isolated from hospital wastewater in Germany, was used. The bacterial solution was treated by a plasma discharge ignited between each of four pins and the liquid surface. The growth of E. coli and the pH-value decreased during plasma treatment in comparison with the untreated control. Proteome and antibiotic resistance profile were analyzed. Concentrations of nitrite and nitrate were determined as long-lived indicative products of a transient chemistry associated with reactive nitrogen species (RNS). Conversely, hydrogen peroxide served as indicator for reactive oxygen species (ROS). Proteome analyses revealed an oxidative stress response as a result of plasma-generated RNS and ROS as well as a pH-balancing reaction as key responses to plasma treatment. Both, the generation of reactive species and a decreased pH-value is characteristic for plasma-treated solutions. The plasma-mediated changes of the proteome are discussed also in comparison with the Gram-positive bacterium Bacillus subtilis. Furthermore, no effect of the plasma treatment, on the antibiotic resistance of E. coli, was determined under the chosen conditions. The knowledge about the physiological changes of ARM in response to plasma is of fundamental interest to understand the molecular basis for the inactivation. This will be important for the further development and implementation of plasma in wastewater remediation.

Enhanced photocatalytic performance of colored Ti2O3-Ti3O5-TiO2 heterostructure for the degradation of antibiotic ofloxacin and bactericidal effect

Removing emergent contaminants, such as pharmaceuticals, and inhibiting bacteria by photocatalysis represents an interesting alternative for water remediation. We report the effective preparation of colored powders containing Ti2O3, Ti3O5, and TiO2, by a simple thermal oxidation reaction of a Ti2O3 precursor from 400 °C to 800 °C. The material obtained at 500 °C (P500 sample) exhibited the highest photocatalytic performance under simulated solar light, reaching 54% degradation of antibiotic ofloxacin and a bacteria inactivation of 51% and 62% for Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus), respectively. The superoxide anion radical was the main specie contributing to the photodegradation of ofloxacin, while the hydroxyl radical showed negligible effect. A synergy between the physicochemical properties of the phases in the P500 sample contributes to the electrons transfer, visible light absorption capability and generation of reactive oxygen species, resulting in its remarkable photoactivity. The comparison in terms of surface-specific activity revealed that the P500 sample is more efficient than commercially available TiO2 P25. This fact opens the option of using commercially available Ti2O3 and TiO2 P25 to obtain composites for promoting photoinduced reactions using natural solar light.

BD Vacutainer™ Urine Culture & Sensitivity Preservative PLUS Plastic Tubes Minimize the Harmful Impact of Stressors Dependent on Temperature and Time Storage in Uropathogenic Bacteria

Background: Urinary tract infection is a worldwide health problem. According to the Clinical Laboratory Improvement Amendments and the European Urinalysis Guideline, urine samples should be tested within 2 h of collection. Thus, using chemical preservatives that guarantee the pre-analytical conditions is a practical tool. However, the effects of temperature and storage time as uropathogenic bacteria stressors are unclear. Methods: Gram-negative and -positive ATTC strains, E. coli, P. mirabilis, E. faecalis, and S. aureus, were used in this study. Strains in liquid media were stored at 4, 25, and 37 °C for 0, 2, 12, 24, and 48 h in tubes with and without preservatives. Then, reactive oxygen species (ROS) levels, viable but non-culturable bacteria (VBNC), and bacteria growth were analyzed. Results: A high ROS level was associated with the presence of VBNC and dead bacteria with low CFU counts, but a low ROS level increased the CFU number, depending on temperature and storage time in tubes without preservatives (boric acid, sodium borate, and formate). The BD Vacutainer™ Urine Culture & Sensitivity Preservative PLUS Plastic Tubes (C&S-PP) prevent this ROS increase, maintaining the CFU number for longer. Conclusions: C&S-PP tubes minimize the stressor effects (temperature and time storage) on uropathogenic bacteria when stored, improving the pre-analytical conditions of cultures realized by the clinical laboratory.

Dual role of phage terminase in Salmonella enterica oxidative stress response

The adaptive survival mechanisms of bacterial pathogens under host-induced stress are crucial for understanding pathogenesis. Recently, Uppalapati et al. revealed a unique dual function of the Gifsy-1 prophage terminase in Salmonella enterica: it acts as a transfer ribonuclease (tRNase) under oxidative stress. The Gifsy-1 prophage terminase targets and fragments tRNALeu to halt translation and temporarily impairs bacterial growth when exposed to high levels of ROS generated by the host immune cells. This response not only preserves genomic integrity by facilitating DNA repair but also inhibits prophage mobilization, thereby aiding in bacterial survival within vertebrate hosts. This study highlights a novel intersection between phage biology and bacterial adaptive strategies.

Repeated glucose oscillations in high cell-density cultures influence stress-related functions of Escherichia coli

Engineering microbial cells for the commercial production of biomolecules and biochemicals requires understanding how cells respond to dynamically changing substrate (feast-famine) conditions in industrial-scale bioreactors. Scale-down methods that oscillate substrate are commonly applied to predict the industrial-scale behavior of microbes. We followed a compartment modeling approach to design a scale-down method based on the simulation of an industrial-scale bioreactor. This study uses high cell-density scale-down experiments to investigate Escherichia coli knockout strains of five major glucose-sensitive transcription factors (Cra, Crp, FliA, PrpR, and RpoS) to study their regulatory role during glucose oscillations. RNA-sequencing analysis revealed that the glucose oscillations caused the down-regulation of several stress-related functions in E. coli. An in-depth analysis of strain physiology and transcriptome revealed a distinct phenotype of the strains tested under glucose oscillations. Specifically, the knockout strains of Cra, Crp, and RpoS resulted in a more sensitive transcriptional response than the control strain, while the knockouts of FliA and PrpR responded less severely. These findings imply that the regulation orchestrated by Cra, Crp, and RpoS may be essential for robust E. coli production strains. In contrast, the regulation by FliA and PrpR may be undesirable for temporal oscillations in glucose availability.

A chemically engineered water-soluble block copolymer for redox responsive SO2 release in antibacterial therapy

Sulfur dioxide (SO2) has emerged as a promising gasotransmitter for various therapeutic applications, including antibacterial activities. However, the potential of polymeric SO2 donors for antimicrobial activities remains largely unexplored. Herein, we report a water-soluble, redox-responsive, SO2-releasing amphiphilic block copolymer poly(polyethylene glycol methyl ether methacrylate) (PPEGMA)-b-poly(2-((2,4-dinitrophenyl)sulfonamido)ethyl methacrylate (PM)) (BCPx) to investigate their antibacterial properties. BCPx contains hydrophilic polyethylene glycol (PEG) pendants and a hydrophobic SO2-releasing PM block, facilitating the formation of self-assembled nanoparticles (BCPxNp) in an aqueous medium, studied by critical aggregation concentration (CAC) measurements, dynamic light scattering (DLS), field emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM). BCPxNp exhibits sustained SO2 release up to 12 h in the presence of glutathione (GSH), with a yield of 30-80% of theoretical SO2 release. In vitro antibacterial studies unveil the outstanding antibacterial activity of BCP3Np against Gram-positive bacteria Bacillus subtilis, as evidenced by FESEM and live/dead cell fluorescence assay. We further elucidate the antibacterial mechanism through reactive oxygen species (ROS) generation studies. Overall, the polymer exhibits excellent biocompatibility at effective antimicrobial concentrations and provides insights into the design of a new class of SO2-releasing polymeric antibacterial agents.

Antimicrobial Activity of Gallium(III) Compounds: Pathogen-Dependent Targeting of Multiple Iron/Heme-Dependent Biological Processes

Metals play vital roles in biological systems, with iron/heme being essential for cellular and metabolic functions necessary for survival and/or virulence in many bacterial pathogens. Given the rise of bacterial resistance to current antibiotics, there is an urgent need for the development of non-toxic and novel antibiotics that do not contribute to resistance to other antibiotics. Gallium, which mimics iron, has emerged as a promising antimicrobial agent, offering a novel approach to combat bacterial infections. Gallium does not have any known functions in biological systems. Gallium exerts its effects primarily by replacing iron in redox enzymes, effectively inhibiting bacterial growth by targeting multiple iron/heme-dependent biological processes and suppressing the development of drug resistance. The aim of this review is to highlight recent findings on the mechanisms of action of gallium and provide further insights into the development of gallium-based compounds. Understanding the mechanisms underlying gallium's biological activities is crucial for designing drugs that enhance their therapeutic therapies while minimizing side effects, offering promising avenues for the treatment of infectious diseases.

CemR atypical response regulator impacts energy conversion in Campylobacteria

Campylobacter jejuni and Arcobacter butzleri are microaerobic food-borne human gastrointestinal pathogens that mainly cause diarrheal disease. These related species of the Campylobacteria class face variable atmospheric environments during infection and transmission, ranging from nearly anaerobic to aerobic conditions. Consequently, their lifestyles require that both pathogens need to adjust their metabolism and respiration to the changing oxygen concentrations of the colonization sites. Our transcriptomic and proteomic studies revealed that C. jejuni and A. butzleri, lacking a Campylobacteria-specific regulatory protein, C. jejuni Cj1608, or a homolog, A. butzleri Abu0127, are unable to reprogram tricarboxylic acid cycle or respiration pathways, respectively, to produce ATP efficiently and, in consequence, adjust growth to changing oxygen supply. We propose that these Campylobacteria energy and metabolism regulators (CemRs) are long-sought transcription factors controlling the metabolic shift related to oxygen availability, essential for these bacteria's survival and adaptation to the niches they inhabit. Besides their significant universal role in Campylobacteria, CemRs, as pleiotropic regulators, control the transcription of many genes, often specific to the species, under microaerophilic conditions and in response to oxidative stress.

IMPORTANCE

C. jejuni and A. butzleri are closely related pathogens that infect the human gastrointestinal tract. In order to infect humans successfully, they need to change their metabolism as nutrient and respiratory conditions change. A regulator called CemR has been identified, which helps them adapt their metabolism to changing conditions, particularly oxygen availability in the gastrointestinal tract so that they can produce enough energy for survival and spread. Without CemR, these bacteria, as well as a related species, Helicobacter pylori, produce less energy, grow more slowly, or, in the case of C. jejuni, do not grow at all. Furthermore, CemR is a global regulator that controls the synthesis of many genes in each species, potentially allowing them to adapt to their ecological niches as well as establish infection. Therefore, the identification of CemR opens new possibilities for studying the pathogenicity of C. jejuni and A. butzleri.

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

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

Untangling the adaptive strategies of thermophilic bacterium Anoxybacillus rupiensis TPH1 under low temperature

The present study investigates the low temperature tolerance strategies of thermophilic bacterium Anoxybacillus rupiensis TPH1, which grows optimally at 55 °C , by subjecting it to a temperature down-shift of 10 °C (45 °C) for 4 and 6 h followed by studying its growth, morphophysiological, molecular and proteomic responses. Results suggested that although TPH1 experienced increased growth inhibition, ROS production, protein oxidation and membrane disruption after 4 h of incubation at 45 °C yet maintained its DNA integrity and cellular structure through the increased expression of DNA damage repair and cell envelop synthesizing proteins and also progressively alleviated growth inhibition by 20% within two hours i.e., 6 h, by inducing the expression of antioxidative enzymes, production of unsaturated fatty acids, capsular and released exopolysaccharides and forming biofilm along with chemotaxis proteins. Conclusively, the adaptation of Anoxybacillus rupiensis TPH1 to lower temperature is mainly mediated by the synthesis of large numbers of defense proteins and exopolysaccharide rich biofilm formation.

The emerging role of oxidative stress in inflammatory bowel disease

Inflammatory bowel disease (IBD) is a chronic immune-mediated condition that affects the digestive system and includes Crohn's disease (CD) and ulcerative colitis (UC). Although the exact etiology of IBD remains uncertain, dysfunctional immunoregulation of the gut is believed to be the main culprit. Amongst the immunoregulatory factors, reactive oxygen species (ROS) and reactive nitrogen species (RNS), components of the oxidative stress event, are produced at abnormally high levels in IBD. Their destructive effects may contribute to the disease's initiation and propagation, as they damage the gut lining and activate inflammatory signaling pathways, further exacerbating the inflammation. Oxidative stress markers, such as malondialdehyde (MDA), 8-hydroxy-2'-deoxyguanosine (8-OHdG), and serum-free thiols (R-SH), can be measured in the blood and stool of patients with IBD. These markers are elevated in patients with IBD, and their levels correlate with the severity of the disease. Thus, oxidative stress markers can be used not only in IBD diagnosis but also in monitoring the response to treatment. It can also be targeted in IBD treatment through the use of antioxidants, including vitamin C, vitamin E, glutathione, and N-acetylcysteine. In this review, we summarize the role of oxidative stress in the pathophysiology of IBD, its diagnostic targets, and the potential application of antioxidant therapies to manage and treat IBD.

Transcriptional landscape of a hypoxia response identifies cell-specific pathways for adaptation

How the HIF-1 (Hypoxia-Inducible) transcription factor drives and coordinates distinct responses to low oxygen across diverse cell types is poorly understood. We present a multi-tissue single-cell gene-expression atlas of the hypoxia response of the nematode Caenorhabditis elegans . This atlas highlights how cell-type-specific HIF-1 responses overlap and diverge among and within neuronal, intestinal, and muscle tissues. Using the atlas to guide functional analyses of candidate muscle-specific HIF-1 effectors, we discovered that HIF-1 activation drives downregulation of the tspo-1 ( TSPO, Translocator Protein) gene in vulval muscle cells to modulate a hypoxia-driven change in locomotion caused by contraction of body-wall muscle cells. We further showed that in human cardiomyocytes HIF-1 activation decreases levels of TSPO and thereby alters intracellular cholesterol transport and the mitochondrial network. We suggest that TSPO-1 is an evolutionarily conserved mediator of HIF-1-dependent modulation of muscle and conclude that our gene-expression atlas can help reveal how HIF-1 drives cell-specific adaptations to hypoxia.

A rapid prototyped atmospheric non-thermal plasma-activated aerosol device and anti-bacterial characterisation

Non-plasma technologies are being extensively investigated for their potential to mitigate microbial growth through the production of various reactive species. Predominantly, studies utilise atmospheric non-thermal plasma to produce plasma-activated liquids. The advancement of plasma-liquid applications has led to the investigation of plasma-activated aerosols (PAAs). This study aimed to produce a rapid-prototyped plasma-activated aerosol setup and perform chemical and anti-bacterial characterisation on the resultant activated aerosols. The setup was produced using stereolithography 3D printing, and air was used as the carrier gas. The novel design of the device allowed for the direct production of PAAs without the prior generation of plasma-activated water and subsequent aerosolisation. The generated PAAs were assessed for nitrite, hydrogen peroxide and ozone content using colourimetric assays. Anti-bacterial efficacy was tested against three human pathogenic strains: Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Salmonella enterica. It was observed that nitrite and ozone contact concentration increased with exposure time, yet no hydrogen peroxide was detected. The generated PAAs showed significant zones of no growth for all bacterial strains. These devices, therefore, show potential to be used as anti-bacterial disinfection technologies.

Oxidative stress responses in biofilms

Oxidizing agents are low-molecular-weight molecules that oxidize other substances by accepting electrons from them. They include reactive oxygen species (ROS), such as superoxide anions (O2-), hydrogen peroxide (H2O2), and hydroxyl radicals (HO-), and reactive chlorine species (RCS) including sodium hypochlorite (NaOCl) and its active ingredient hypochlorous acid (HOCl), and chloramines. Bacteria encounter oxidizing agents in many different environments and from diverse sources. Among them, they can be produced endogenously by aerobic respiration or exogenously by the use of disinfectants and cleaning agents, as well as by the mammalian immune system. Furthermore, human activities like industrial effluent pollution, agricultural runoff, and environmental activities like volcanic eruptions and photosynthesis are also sources of oxidants. Despite their antimicrobial effects, bacteria have developed many mechanisms to resist the damage caused by these toxic molecules. Previous research has demonstrated that growing as a biofilm particularly enhances bacterial survival against oxidizing agents. This review aims to summarize the current knowledge on the resistance mechanisms employed by bacterial biofilms against ROS and RCS, focussing on the most important mechanisms, including the formation of biofilms in response to oxidative stressors, the biofilm matrix as a protective barrier, the importance of detoxifying enzymes, and increased protection within multi-species biofilm communities. Understanding the complexity of bacterial responses against oxidative stress will provide valuable insights for potential therapeutic interventions and biofilm control strategies in diverse bacterial species.

Ultrastructural and morphological studies on variables affecting Escherichia coli with selected commercial antibiotics

Background

Many studies reported the effects of antibiotic exposure on E. coli bacterial growth and cell modification. However, scarce descriptive information on ultrastructural effects upon exposure of commercial antibiotics.

Methods

This study described the morphological and ultrastructural alterations caused by selected antibiotics (amoxicillin-clavulanate, ceftriaxone, polymyxin B, colistin, gentamicin, and amikacin) that targeted cell wall, plasma membrane, and cytoplasmic density, and also proteins synthesis. We determined extracellular morphological changes of exposure through scanning electron microscopy (FESEM) and intracellular activities through transmission electron microscopy (TEM) investigation.

Results

FESEM and TEM micrograph of E. coli exposed with selected antibiotics shows ultrastructural changes in beta-lactam class (amoxicillin-clavulanate, ceftriaxone) elongated the cells as the cell wall was altered as it inhibits bacterial cell wall synthesis, polymyxin class (polymyxin B, colistin) had plasmid and curli-fimbriae as it breaking down the plasma/cytoplasmic membrane, and aminoglycoside class (gentamicin, and amikacin) reduced ribosome concentration as it inhibits bacterial protein synthesis by binding to 30 s ribosomes.

Conclusion

Morphological and ultrastructural alterations of E. coli's mechanism of actions were translated and depicted. This study could be reference for characterization studies for morphological and ultrastructural of E. coli upon exposure to antimicrobial agents.

Caffeic acid phenethyl ester attenuates Enterococcus faecalis infection in vivo: antioxidants and NF-κB have a protective role against stomach damage

The mammalian gastrointestinal tract hosts a significant microbial symbiont community, an intriguing feature of this complex organ system. This study aimed to investigate the anti-inflammatory, antioxidant, and protective effects of caffeic acid phenethyl ester (CAPE) against Enterococcus faecalis infection in the stomach at a dose of 106 CFU in Swiss mice. A total of 30 mice were randomly assigned to three groups of ten mice each. Group I was the negative control, Group II was infected orally with E. faecalis for 18 days, and Group III was infected with E. faecalis and treated with CAPE orally at a daily dose of 4 mg/kg for 18 days. We assessed the antioxidant activities of stomach homogenate and the immunohistochemical expressions of the transcription factor nuclear factor kappa B (NF-κB) and proliferating cell nuclear antigen (PCNA). Histopathological examination was performed on the stomachs of all mice. Group II had decreased levels of antioxidant activity and positive expressions of NF-κB and PCNA. Histological observations revealed an increase in mucosal and glandular thickness compared with Group I. Group III, treated with CAPE, showed a significant increase in antioxidant activities and a significant decrease in NF-κB and PCNA immunoreactivities compared with Group II. In addition, Group III showed restoration of the normal thickness of the non-glandular and glandular parts of the stomach. Our results revealed that E. faecalis infection has damaging effects on the stomach and proved that CAPE has promising protective, anti-inflammatory, and antioxidant effects against E. faecalis. Further studies may investigate the potential therapeutic effects of CAPE against E. faecalis infection.

Enhanced antimicrobial efficacy and energy efficiency of low irradiance 405-nm light for bacterial decontamination

Due to its increased safety over ultraviolet light, there is interest in the development of antimicrobial violet-blue light technologies for infection control applications. To ensure compatibility with exposed materials and tissue, the light irradiances and dose regimes used must be suitable for the target application. This study investigates the antimicrobial dose responses and germicidal efficiency of 405 nm violet-blue light when applied at a range of irradiance levels, for inactivation of surface-seeded and suspended bacteria. Bacteria were seeded onto agar surfaces (101-108 CFUplate-1) or suspended in PBS (103-109 CFUmL-1) and exposed to increasing doses of 405-nm light (≤ 288 Jcm-2) using various irradiances (0.5-150 mWcm-2), with susceptibility at equivalent light doses compared. Bacterial reductions ≥ 96% were demonstrated in all cases for lower irradiance (≤ 5 mWcm-2) exposures. Comparisons indicated, on a per unit dose basis, that significantly lower doses were required for significant reductions of all species when exposed at lower irradiances: 3-30 Jcm-2/0.5 mWcm-2 compared to 9-75 Jcm-2/50 mWcm-2 for low cell density (102 CFUplate-1) surface exposures and 22.5 Jcm-2/5 mWcm-2 compared to 67.5 Jcm-2/150 mWcm-2 for low density (103 CFUmL-1) liquid exposures (P ≤ 0.05). Similar patterns were observed at higher densities, excluding S. aureus exposed at 109 CFUmL-1, suggesting bacterial density at predictable levels has minimal influence on decontamination efficacy. This study provides fundamental evidence of the greater energy efficacy of 405-nm light for inactivation of clinically-significant pathogens when lower irradiances are employed, further supporting its relevance for practical decontamination applications.

Radiotolerance of N-cycle bacteria and their transcriptomic response to low-dose space-analogue ionizing irradiation

The advancement of regenerative life support systems (RLSS) is crucial to allow long-distance space travel. Within the Micro-Ecological Life Support System Alternative (MELiSSA), efficient nitrogen recovery from urine and other waste streams is vital to produce liquid fertilizer to feed food and oxygen production in subsequent photoautotrophic processes. This study explores the effects of ionizing radiation on nitrogen cycle bacteria that transform urea to nitrate. In particular, we assess the radiotolerance of Comamonas testosteroni, Nitrosomonas europaea, and Nitrobacter winogradskyi after exposure to acute γ-irradiation. Moreover, a comprehensive whole transcriptome analysis elucidates the effects of spaceflight-analogue low-dose ionizing radiation on the individual axenic strains and on their synthetic community o. This research sheds light on how the spaceflight environment could affect ureolysis and nitrification processes from a transcriptomic perspective.

In Vitro Antimicrobial Photodynamic Therapy for Pseudomonas aeruginosa (P. aeruginosa) and methicillin-resistant Staphylococcus aureus (MRSA) Inhibition Using a Green Light Source

Photodynamic therapy (PDT) has been based on using photosensitizers (PS) and applying light of a specific wavelength. When this technique is used for treating infections, it is known as antimicrobial photodynamic therapy (aPDT). Currently, the use of lighting sources for in vitro studies using aPDT is generally applied in multiwell cell culture plates; however, depending on the lighting arrangement, there are usually errors in the application of the technique because the light from a well can affect the neighboring wells or it may be that not all the wells are used in the same experiment. In addition, one must be awarded high irradiance values, which can cause unwanted photothermal problems in the studies. Thus, this manuscript presents an in vitro antimicrobial photodynamic therapy for a Pseudomonas aeruginosa (P. aeruginosa) and methicillin-resistant Staphylococcus aureus (MRSA) inhibition study using an arrangement of thermally isolated and independently illuminated green light source systems for eight tubes in vitro aPDT, determining the effect of the following factors: (i) irradiance level, (ii) exposure time, and (iii) Rose Bengal (RB) concentration (used as a PS), registering the Pseudomonas aeruginosa (P. aeruginosa) and methicillin-resistant Staphylococcus aureus (MRSA) inhibition rates. The results show that in the dark, RB had a poor antimicrobial rate for P. aeruginosa, finding the maximum inhibition (2.7%) at 30 min with an RB concentration of 3 µg/mL. However, by applying light in a correct dosage (time × irradiance) and the adequate RB concentration, the inhibition rate increased by over 37%. In the case of MRSA, there was no significant inhibition with RB in complete darkness and, in contrast, the rate was 100% for those experiments that were irradiated.

Prophage terminase with tRNase activity sensitizes Salmonella enterica to oxidative stress

Phage viruses shape the evolution and virulence of their bacterial hosts. The Salmonella enterica genome encodes several stress-inducible prophages. The Gifsy-1 prophage terminase protein, whose canonical function is to process phage DNA for packaging in the virus head, unexpectedly acts as a transfer ribonuclease (tRNase) under oxidative stress, cleaving the anticodon loop of tRNALeu. The ensuing RNA fragmentation compromises bacterial translation, intracellular survival, and recovery from oxidative stress in the vertebrate host. S. enterica adapts to this transfer RNA (tRNA) fragmentation by transcribing the RNA repair Rtc system. The counterintuitive translational arrest provided by tRNA cleavage may subvert prophage mobilization and give the host an opportunity for repair as a way of maintaining bacterial genome integrity and ultimately survival in animals.

Metallic nanoparticle actions on the outer layer structure and properties of Bacillus cereus and Staphylococcus epidermidis

Although the antimicrobial activity of nanoparticles (NPs) penetrating inside the cell is widely recognised, the toxicity of large NPs (>10 nm) that cannot be translocated across bacterial membranes remains unclear. Therefore, this study was performed to elucidate the direct effects of Ag-NPs, Cu-NPs, ZnO-NPs and TiO2-NPs on relative membrane potential, permeability, hydrophobicity, structural changes within chemical compounds at the molecular level and the distribution of NPs on the surfaces of the bacteria Bacillus cereus and Staphylococcus epidermidis. Overall analysis of the results indicated the different impacts of individual NPs on the measured parameters in both strains depending on their type and concentration. B. cereus proved to be more resistant to the action of NPs than S. epidermidis. Generally, Cu-NPs showed the most substantial toxic effect on both strains; however, Ag-NPs exhibited negligible toxicity. All NPs had a strong affinity for cell surfaces and showed strain-dependent characteristic dispersion. ATR-FTIR analysis explained the distinctive interactions of NPs with bacterial functional groups, leading to macromolecular structural modifications. The results presented provide new and solid evidence for the current understanding of the interactions of metallic NPs with bacterial membranes.

Piperine, a phytochemical prevents the biofilm city of methicillin-resistant Staphylococcus aureus: A biochemical approach to understand the underlying mechanism

Methicillin-resistant Staphylococcus aureus (MRSA), a drug-resistant human pathogen causes several nosocomial as well as community-acquired infections involving biofilm machinery. Hence, it has gained a wide interest within the scientific community to impede biofilm-induced MRSA-associated health complications. The current study focuses on the utilization of a natural bioactive compound called piperine to control the biofilm development of MRSA. Quantitative assessments like crystal violet, total protein recovery, and fluorescein-di-acetate (FDA) hydrolysis assays, demonstrated that piperine (8 and 16 μg/mL) could effectively compromise the biofilm formation of MRSA. Light and scanning electron microscopic image analysis confirmed the same. Further investigation revealed that piperine could reduce extracellular polysaccharide production by down-regulating the expression of icaA gene. Besides, piperine could reduce the cell-surface hydrophobicity of MRSA, a crucial factor of biofilm formation. Moreover, the introduction of piperine could interfere with microbial motility indicating the interaction of piperine with the quorum-sensing components. A molecular dynamics study showed a stable binding between piperine and AgrA protein (regulator of quorum sensing) suggesting the possible meddling of piperine in quorum-sensing of MRSA. Additionally, the exposure to piperine led to the accumulation of intracellular reactive oxygen species (ROS) and potentially heightened cell membrane permeability in inhibiting microbial biofilm formation. Besides, piperine could reduce the secretion of diverse virulence factors from MRSA. Further exploration revealed that piperine interacted with extracellular DNA (e-DNA), causing disintegration by weakening the biofilm architecture. Conclusively, this study suggests that piperine could be a potential antibiofilm molecule against MRSA-associated biofilm infections.

Active pH regulation facilitates Bacillus subtilis biofilm development in a minimally buffered environment

Biofilms provide individual bacteria with many advantages, yet dense cellular proliferation can also create intrinsic metabolic challenges including excessive acidification. Because such pH stress can be masked in buffered laboratory media-such as MSgg commonly used to study Bacillus subtilis biofilms-it is not always clear how such biofilms cope with minimally buffered natural environments. Here, we report how B. subtilis biofilms overcome this intrinsic metabolic challenge through an active pH regulation mechanism. Specifically, we find that these biofilms can modulate their extracellular pH to the preferred neutrophile range, even when starting from acidic and alkaline initial conditions, while planktonic cells cannot. We associate this behavior with dynamic interplay between acetate and acetoin biosynthesis and show that this mechanism is required to buffer against biofilm acidification. Furthermore, we find that buffering-deficient biofilms exhibit dysregulated biofilm development when grown in minimally buffered conditions. Our findings reveal an active pH regulation mechanism in B. subtilis biofilms that could lead to new targets to control unwanted biofilm growth.IMPORTANCEpH is known to influence microbial growth and community dynamics in multiple bacterial species and environmental contexts. Furthermore, in many bacterial species, rapid cellular proliferation demands the use of overflow metabolism, which can often result in excessive acidification. However, in the case of bacterial communities known as biofilms, these acidification challenges can be masked when buffered laboratory media are employed to stabilize the pH environment for optimal growth. Our study reveals that B. subtilis biofilms use an active pH regulation mechanism to mitigate both growth-associated acidification and external pH challenges. This discovery provides new opportunities for understanding microbial communities and could lead to new methods for controlling biofilm growth outside of buffered laboratory conditions.

8-OxoG-Dependent Regulation of Global Protein Responses Leads to Mutagenesis and Stress Survival in Bacillus subtilis

The guanine oxidized (GO) system of Bacillus subtilis, composed of the YtkD (MutT), MutM and MutY proteins, counteracts the cytotoxic and genotoxic effects of the oxidized nucleobase 8-OxoG. Here, we report that in growing B. subtilis cells, the genetic inactivation of GO system potentiated mutagenesis (HPM), and subsequent hyperresistance, contributes to the damaging effects of hydrogen peroxide (H2O2) (HPHR). The mechanism(s) that connect the accumulation of the mutagenic lesion 8-OxoG with the ability of B. subtilis to evolve and survive the noxious effects of oxidative stress were dissected. Genetic and biochemical evidence indicated that the synthesis of KatA was exacerbated, in a PerR-independent manner, and the transcriptional coupling repair factor, Mfd, contributed to HPHR and HPM of the ΔGO strain. Moreover, these phenotypes are associated with wider pleiotropic effects, as revealed by a global proteome analysis. The inactivation of the GO system results in the upregulated production of KatA, and it reprograms the synthesis of the proteins involved in distinct types of cellular stress; this has a direct impact on (i) cysteine catabolism, (ii) the synthesis of iron-sulfur clusters, (iii) the reorganization of cell wall architecture, (iv) the activation of AhpC/AhpF-independent organic peroxide resistance, and (v) increased resistance to transcription-acting antibiotics. Therefore, to contend with the cytotoxic and genotoxic effects derived from the accumulation of 8-OxoG, B. subtilis activates the synthesis of proteins belonging to transcriptional regulons that respond to a wide, diverse range of cell stressors.

Strategies to enhance stress tolerance in lactic acid bacteria across diverse stress conditions

Lactic acid bacteria (LAB) hold significant importance in diverse fields, including food technology, industrial biotechnology, and medicine. As basic components of starter cultures, probiotics, immunomodulators, and live vaccines, LAB cells resist a variety of stressors, including temperature fluctuations, osmotic and pH shocks, exposure to oxidants and ultraviolet radiation, substrate deprivation, mechanical damage, and more. To stay alive in these adversities, LAB employ a wide range of stress response strategies supported by various mechanisms, for example rearrangement of metabolism, expression of specialized biomolecules (e.g., chaperones and antioxidants), exopolysaccharide synthesis, and complex repair and regulatory systems. LAB can coordinate responses to various stressors using global regulators. In this review, we summarize current knowledge about stress response strategies used by LAB and consider mechanisms of response to specific stressful factors, supported by illustrative examples. In addition, we discuss technical approaches to increase the stress resistance of LAB, including pre-adaptation, genetic modification of strains, and adjustment of cultivation conditions. A critical analysis of the recent findings in this field augments comprehension of stress tolerance mechanisms in LAB, paving the way for prospective research directions with implications in fundamental and practical areas.

Deterministic effect of oxygen level variation on shaping antibiotic resistome

An increase in acquisition of antibiotic resistance genes (ARGs) by pathogens under antibiotic selective pressure poses public health threats. Sub-inhibitory antibiotics induce bacteria to generate reactive oxygen species (ROS) dependent on dissolved oxygen (DO) levels, while molecular connection between ROS-mediated ARG emergence through DNA damage and metabolic changes remains elusive. Thus, the study investigates antibiotic resistome dynamics, microbiome shift, and pathogen distribution in hyperoxic (5-7 mg L-1), normoxic (2-4 mg L-1), and hypoxic (0.5-1 mg L-1) conditions using lab-scale bioreactor. Composite inoculums in the reactor were designed to represent comprehensive microbial community and AR profile from selected activated sludge. RT-qPCR and metagenomic analysis showed an increase in ARG count (100.98 ppm) with enrichment of multidrug efflux pumps (acrAB, mexAB) in hyperoxic condition. Conversely, total ARGs decreased (0.11 ppm) under hypoxic condition marked by a major decline in int1 abundance. Prevalence of global priority pathogens increased in hyperoxic (22.5%), compared to hypoxic (0.9%) wherein major decrease were observed in Pseudomonas, Shigella, and Borrelia. The study observed an increase in superoxide dismutase (sodA, sodB), DNA repair genes (nfo, polA, recA, recB), and ROS (10.4 µmol L-1) in adapted biomass with spiked antibiotics. This suggests oxidative damage that facilitates stress-induced mutagenesis providing evidence for observed hyperoxic enrichment of ARGs. Moreover, predominance of catalase (katE, katG) likely limit oxidative damage that deplete ARG breeding in hypoxic condition. The study proposes a link between oxygen levels and AR development that offers insights into mitigation and intervention of AR by controlling oxygen-related stress and strategic selection of bacterial communities.

Mechanisms of oxidative response during biodegradation of malathion by S. oneidensis MR-1

Malathion, an extensively used organophosphorus pesticide, poses a high potential risk of toxicity to humans and the environment. Shewanella (S.) oneidensis MR-1 has been proposed as a strain with excellent bioremediation capabilities, capable of efficiently removing a wide range of hard-to-degrade pollutants. However, the physiological and biochemical response of S. oneidensis MR-1 to malathion is unknown. Therefore, this study aimed to examine how S. oneidensis MR-1 responds physiologically and biochemically to malathion while also investigating the biodegradation properties of the pesticide. The results showed that the 7-day degradation rates of S. oneidensis MR-1 were 84.1, 91.6, and 94.0% at malathion concentrations of 10, 20, and 30 mg/L, respectively. As the concentration of malathion increased, superoxide dismutase and catalase activities were inhibited, leading to a significant rise in malondialdehyde content. This outcome can be attributed to the excessive production of reactive oxygen species (ROS) triggered by malathion stress. In addition, ROS production stimulates the secretion of soluble polysaccharides, which alleviates oxidative stress caused by malathion. Malathion-induced oxidative damage further exacerbated the changes in the cellular properties of S. oneidensis MR-1. During the initial stages of degradation, the cell density and total intracellular protein increased significantly with increasing malathion exposure. This can be attributed to the remarkable resistance of S. oneidensis MR-1 to malathion. Based on scanning electron microscopy observations, continuous exposure to contaminants led to a reduction in biomass and protein content, resulting in reduced cell activity and ultimately leading to cell rupture. In addition, this was accompanied by a decrease in Na+/K+- ATPase and Ca2+/Mg2+-ATPase levels, suggesting that malathion-mediated oxidative stress interfered with energy metabolism in S. oneidensis MR-1. The findings of this study provide new insights into the environmental risks associated with organophosphorus pesticides, specifically malathion, and their potential for bioremediation.

RNA-binding proteins that preferentially interact with 8-oxoG-modified RNAs: our current understanding

Cells encounter a variety of stresses throughout their lifetimes. Oxidative stress can occur via a myriad of factors, including exposure to chemical toxins or UV light. Importantly, these stressors induce chemical changes (e.g. chemical modifications) to biomolecules, such as RNA. Commonly, guanine is oxidized to form 8-oxo-7,8-hydroxyguanine (8-oxoG) and this modification can disrupt a plethora of cellular processes including messenger RNA translation and stability. Polynucleotide phosphorylase (PNPase), heterogeneous nuclear ribonucleoprotein D (HNRPD/Auf1), poly(C)-binding protein (PCBP1/HNRNP E1), and Y-box binding protein 1 (YB-1) have been identified as four RNA-binding proteins that preferentially bind 8-oxoG-modified RNA over unmodified RNA. All four proteins are native to humans and PNPase is additionally found in bacteria. Additionally, under oxidative stress, cell survival declines in mutants that lack PNPase, Auf1, or PCBP1, suggesting they are critical to the oxidative stress response. This mini-review captures the current understanding of the PNPase, HNRPD/Auf1, PCBP1, and YB-1 proteins and the mechanism that has been outlined so far by which they recognize and interact with 8-oxoG-modified RNAs.

Dendrobium Nobile Alcohol Extract Extends the Lifespan of Caenorhabditis elegans via hsf-1 and daf-16

Dendrobium nobile is a traditional Chinese herb with anti-inflammatory, antioxidant, and neuroprotective properties. However, its antiaging effects are unclear. Herein, we studied the aging-related functions and the mechanism of action of the alcohol extract of Dendrobium nobile (DnAE) in the model organism Caenorhabditis elegans. The results indicated that 1 mg/mL DnAE slowed lipofuscin accumulation, decreased the levels of reactive oxygen species, elevated superoxide dismutase activity, enhanced oxidative and heat stress resistance, extended the lifespan of nematodes, protected their dopamine neurons from 6-hydroxydopamine-induced neurodegeneration, and reduced Aβ-induced neurotoxicity. DnAE upregulated the mRNA expression of the transcription factors DAF-16 and HSF-1, promoted the nuclear localization of DAF-16, and enhanced the fluorescence intensity of HSP-16.2. However, it had no effect on the lifespan of DAF-16 mutants. Thus, DnAE can significantly extend lifespan, enhance heat stress tolerance, and delay age-related diseases through a DAF-16-dependent pathway.

The multiplicity of thioredoxin systems meets the specific lifestyles of Clostridia

Cells are unceasingly confronted by oxidative stresses that oxidize proteins on their cysteines. The thioredoxin (Trx) system, which is a ubiquitous system for thiol and protein repair, is composed of a thioredoxin (TrxA) and a thioredoxin reductase (TrxB). TrxAs reduce disulfide bonds of oxidized proteins and are then usually recycled by a single pleiotropic NAD(P)H-dependent TrxB (NTR). In this work, we first analyzed the composition of Trx systems across Bacteria. Most bacteria have only one NTR, but organisms in some Phyla have several TrxBs. In Firmicutes, multiple TrxBs are observed only in Clostridia, with another peculiarity being the existence of ferredoxin-dependent TrxBs. We used Clostridioides difficile, a pathogenic sporulating anaerobic Firmicutes, as a model to investigate the biological relevance of TrxB multiplicity. Three TrxAs and three TrxBs are present in the 630Δerm strain. We showed that two systems are involved in the response to infection-related stresses, allowing the survival of vegetative cells exposed to oxygen, inflammation-related molecules and bile salts. A fourth TrxB copy present in some strains also contributes to the stress-response arsenal. One of the conserved stress-response Trx system was found to be present both in vegetative cells and in the spores and is under a dual transcriptional control by vegetative cell and sporulation sigma factors. This Trx system contributes to spore survival to hypochlorite and ensure proper germination in the presence of oxygen. Finally, we found that the third Trx system contributes to sporulation through the recycling of the glycine-reductase, a Stickland pathway enzyme that allows the consumption of glycine and contributes to sporulation. Altogether, we showed that Trx systems are produced under the control of various regulatory signals and respond to different regulatory networks. The multiplicity of Trx systems and the diversity of TrxBs most likely meet specific needs of Clostridia in adaptation to strong stress exposure, sporulation and Stickland pathways.