Transcriptomic Analysis of E. coli after Exposure to a Sublethal Concentration of Hydrogen Peroxide Revealed a Coordinated Up-Regulation of the Cysteine Biosynthesis Pathway

From the Gut to the Brain: Transcriptomic Insights into Neonatal Meningitis Escherichia coli Across Diverse Host Niches

Neonatal Meningitis-causing Escherichia coli (NMEC) is the leading cause of neonatal meningitis and exhibits remarkable adaptability to diverse host environments. Understanding its transcriptional responses across different host niches is crucial for deciphering pathogenesis and identifying potential therapeutic targets. We performed a comparative transcriptomic analysis of NMEC RS218, the prototype strain of NMEC, under four distinct host-mimicking conditions: colonic fluid (CF), serum (S), human brain endothelial cells (HBECs), and cerebrospinal fluid (CSF). Differential gene expression analysis was conducted to assess metabolic shifts, virulence factor regulation, and niche-specific adaptation strategies, in which RS218 demonstrated niche-specific transcriptional reprogramming. In CF, genes associated with biofilm formation, motility, efflux pumps, and cell division regulation were upregulated, aiding gut colonization. The serum environment triggered the expression of siderophore-mediated iron acquisition, enterobactin biosynthesis, and heme utilization genes, facilitating immune evasion and bacterial persistence. In HBECs, NMEC upregulated genes linked to nucleoside metabolism, membrane remodeling, pilus organization, and blood-brain barrier (BBB) traversal. In CSF, genes related to oxidative stress resistance, chemotaxis, DNA repair, biofilm formation, and amino acid biosynthesis were enriched, reflecting NMEC's adaptive mechanisms for survival under nutrient-depleted conditions. Energy-intensive pathways were consistently downregulated across all niches, highlighting the need for an energy conservation strategy. This study provides novel insights into NMEC's adaptive strategies across different host environments, emphasizing its metabolic flexibility, virulence regulation, and immune evasion mechanisms, offering potential targets for therapeutic intervention.

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.

The Role of Heat Shock Protein (Hsp) Chaperones in Environmental Stress Adaptation and Virulence of Plant Pathogenic Bacteria

Plant pathogenic bacteria are responsible for a substantial number of plant diseases worldwide, resulting in significant economic losses. Bacteria are exposed to numerous stress factors during their epiphytic life and within the host. Their ability to survive in the host and cause symptomatic infections depends on their capacity to overcome stressors. Bacteria have evolved a range of defensive and adaptive mechanisms to thrive under varying environmental conditions. One such mechanism involves the induction of chaperone proteins that belong to the heat shock protein (Hsp) family. Together with proteases, these proteins are integral components of the protein quality control system (PQCS), which is essential for maintaining cellular proteostasis. However, knowledge of their action is considerably less extensive than that of human and animal pathogens. This study discusses the modulation of Hsp levels by phytopathogenic bacteria in response to stress conditions, including elevated temperature, oxidative stress, changes in pH or osmolarity of the environment, and variable host conditions during infection. All these factors influence bacterial virulence. Finally, the secretion of GroEL and DnaK proteins outside the bacterial cell is considered a potentially important virulence trait.

Escherichia coli growing under antimicrobial gallium nitrate stress reveals new processes of tolerance and toxicity

Metals have been used throughout history to manage disease. With the rising incidence of antibiotic-resistant bacterial strains, metal-based antimicrobials (MBAs) have re-emerged as an alternative to combat infections. Gallium nitrate has shown promising efficacy against several pathogens. Although its main toxicity mechanisms have focused on oxidative stress and its "trojan horse" iron mimetic strategy, there are still many knowledge gaps in the full-systems response elicited to counteract its toxic effects, especially in non-acute toxicity models that evaluate longer exposure times. In this study, we explore the transcriptomic response profile of Escherichia coli K12 BW25113 when challenged to grow planktonically for 10 h in the presence of a sublethal inhibitory concentration of gallium nitrate. 581 genes were significantly up-regulated, and 791 down-regulated. Some of the affected biological systems identified in our analysis include iron homeostasis, sulfate metabolism, oxidative and nitrosative stress response, cysteine biosynthesis, anaerobic respiration, toxin-antitoxin interactions, and DNA repair. Altogether, this work provides a valuable snapshot of how E. coli acclimates to this MBA and expands the current knowledge of mechanisms of sensitivity and tolerance. This is a significant step in understanding how bacteria can adjust their physiology to coexist with sublethal concentrations of toxic metals.

Persistent Photoinduced Antibacterial Activity of MoS2 Nanosheets Immobilized in Porous Polymer Beads

Reactive oxygen species (ROS) photogenerated by two-dimensional (2D) nanomaterials provide a means of delivering persistent antibacterial activity in fluid media. Semiconducting molybdenum disulfide (MoS2) nanosheets are an attractive option for exploiting such activity by using visible light. However, the tendency of MoS2 nanosheets in suspension to restack or otherwise aggregate remains a critical obstacle, as it results in the loss of the desired photoactivity. We report here the development of persistent antibacterial activity by successfully immobilizing MoS2 nanosheets within porous cross-linked polymer beads. The nanosheet-loaded beads demonstrate continuous antibacterial activity against model species under visible-light exposure. The bactericidal activity is associated with ROS-mediated oxidative organismal stress, as assessed through chemical methods using fluorescent probes and gene-level biological studies. The porous beads demonstrate an effective antifouling capability and were physically stable with sustained bactericidal activity at an average of 99% over 5 cycles. The ability to confer reusable, continuous antibacterial activity under visible-light illumination is attractive in the context of the development of sustainable solutions for photoinduced antibacterial materials.

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.

Why is HSO5- so effective against bacteria? Insights into the mechanisms of Escherichia coli disinfection by unactivated peroxymonosulfate

This study examined the antimicrobial efficacy of peroxymonosulfate (PMS) against bacteria, using Escherichia coli (E. coli) as a model organism. Our investigation delineates the complex mechanisms exerted by unactivated PMS. Thus, an initial redox reaction between PMS and the target biomolecules of bacteria generates SO4•- as the pivotal reactive species for bacterial inactivation; to a lesser extent, •OH, 1O2, or O2•- may also participate. Damage generated during oxidation was identified using an array of biochemical techniques. Specifically, redox processes are promoted by PMS and SO4•- targets and disrupt various components of bacterial cells, predominantly causing extracellular damage as well as intracellular lesions. Among these, external events are the key to cell death. Finally, by employing gene knockout mutants, we uncovered the role of specific gene responses in the intracellular damage induced by radical pathways. The findings of this study not only expand the understanding of PMS-mediated bacterial inactivation but also explain the ten-fold higher effectiveness of PMS than that reported for H2O2. Hence, we provide clear evidence that unactivated PMS solutions generate SO4•- in the presence of bacteria, and consequently, should be considered an effective disinfection method.

Temporal dynamics of stress response in Halomonas elongata to NaCl shock: physiological, metabolomic, and transcriptomic insights

BACKGROUND

The halophilic bacterium Halomonas elongata is an industrially important strain for ectoine production, with high value and intense research focus. While existing studies primarily delve into the adaptive mechanisms of this bacterium under fixed salt concentrations, there is a notable dearth of attention regarding its response to fluctuating saline environments. Consequently, the stress response of H. elongata to salt shock remains inadequately understood.

RESULTS

This study investigated the stress response mechanism of H. elongata when exposed to NaCl shock at short- and long-time scales. Results showed that NaCl shock induced two major stresses, namely osmotic stress and oxidative stress. In response to the former, within the cell's tolerable range (1-8% NaCl shock), H. elongata urgently balanced the surging osmotic pressure by uptaking sodium and potassium ions and augmenting intracellular amino acid pools, particularly glutamate and glutamine. However, ectoine content started to increase until 20 min post-shock, rapidly becoming the dominant osmoprotectant, and reaching the maximum productivity (1450 ± 99 mg/L/h). Transcriptomic data also confirmed the delayed response in ectoine biosynthesis, and we speculate that this might be attributed to an intracellular energy crisis caused by NaCl shock. In response to oxidative stress, transcription factor cysB was significantly upregulated, positively regulating the sulfur metabolism and cysteine biosynthesis. Furthermore, the upregulation of the crucial peroxidase gene (HELO_RS18165) and the simultaneous enhancement of peroxidase (POD) and catalase (CAT) activities collectively constitute the antioxidant defense in H. elongata following shock. When exceeding the tolerance threshold of H. elongata (1-13% NaCl shock), the sustained compromised energy status, resulting from the pronounced inhibition of the respiratory chain and ATP synthase, may be a crucial factor leading to the stagnation of both cell growth and ectoine biosynthesis.

CONCLUSIONS

This study conducted a comprehensive analysis of H. elongata's stress response to NaCl shock at multiple scales. It extends the understanding of stress response of halophilic bacteria to NaCl shock and provides promising theoretical insights to guide future improvements in optimizing industrial ectoine production.

Disinfectants and antiseptics: mechanisms of action and resistance

Chemical biocides are used for the prevention and control of infection in health care, targeted home hygiene or controlling microbial contamination for various industrial processes including but not limited to food, water and petroleum. However, their use has substantially increased since the implementation of programmes to control outbreaks of methicillin-resistant Staphylococcus aureus, Clostridioides difficile and severe acute respiratory syndrome coronavirus 2. Biocides interact with multiple targets on the bacterial cells. The number of targets affected and the severity of damage will result in an irreversible bactericidal effect or a reversible bacteriostatic one. Most biocides primarily target the cytoplasmic membrane and enzymes, although the specific bactericidal mechanisms vary among different biocide chemistries. Inappropriate usage or low concentrations of a biocide may act as a stressor while not killing bacterial pathogens, potentially leading to antimicrobial resistance. Biocides can also promote the transfer of antimicrobial resistance genes. In this Review, we explore our current understanding of the mechanisms of action of biocides, the bacterial resistance mechanisms encompassing both intrinsic and acquired resistance and the influence of bacterial biofilms on resistance. We also consider the impact of bacteria that survive biocide exposure in environmental and clinical contexts.

Cysteine and resistance to oxidative stress: implications for virulence and antibiotic resistance

Reactive oxygen species (ROS), including the superoxide radical anion (O2•-), hydrogen peroxide (H2O2), and the hydroxyl radical (•HO), are inherent components of bacterial metabolism in an aerobic environment. Bacteria also encounter exogenous ROS, such as those produced by the host cells during the respiratory burst. As ROS have the capacity to damage bacterial DNA, proteins, and lipids, detoxification of ROS is critical for bacterial survival. It has been recently recognised that low-molecular-weight (LMW) thiols play a central role in this process. Here, we review the emerging role of cysteine in bacterial resistance to ROS with a link to broader elements of bacterial lifestyle closely associated with cysteine-mediated oxidative stress response, including virulence and antibiotic resistance.

Molecular Signatures of the Eagle Effect Induced by the Artificial Siderophore Conjugate LP-600 in E. coli

Achieving cellular uptake is a central challenge for novel antibiotics targeting Gram-negative bacterial pathogens. One strategy is to hijack the bacterial iron transport system by siderophore-antibiotic conjugates that are actively imported into the cell. This was realized with the MECAM-ampicillin conjugate LP-600 we recently reported that was highly active against E. coli. In the present study, we investigate a paradoxical regrowth of E. coli upon treatment of LP-600 at concentrations 16-32 times above the minimum inhibitory concentration (MIC). The phenomenon, coined "Eagle-effect" in other systems, was not due to resistance formation, and it occurred for the siderophore conjugate but not for free ampicillin. To investigate the molecular imprint of the Eagle effect, a combined transcriptome and untargeted metabolome analysis was conducted. LP-600 induced the expression of genes involved in iron acquisition, SOS response, and the e14 prophage upon regrowth conditions. The Eagle effect was diminished in the presence of sulbactam, which we ascribe to a putative synergistic antibiotic action but not to β-lactamase inhibition. The study highlights the relevance of the Eagle effect for siderophore conjugates. Through the first systematic -omics investigations, it also demonstrates that the Eagle effect manifests not only in a paradoxical growth but also in unique gene expression and metabolite profiles.

Hydrogen Peroxide Signaling in Physiology and Pathology

Reactive oxygen species (ROS) were originally described as toxic by-products of aerobic cellular energy metabolism associated with the development of several diseases, such as cancer, neurodegenerative diseases, and diabetes [...]

Genes Vary Greatly in Their Propensity for Collateral Fitness Effects of Mutations

Mutations can have deleterious fitness effects when they decrease protein specific activity or decrease active protein abundance. Mutations will also be deleterious when they cause misfolding or misinteractions that are toxic to the cell (i.e., independent of whether the mutations affect specific activity and abundance). The extent to which protein evolution is shaped by these and other collateral fitness effects is unclear in part because little is known of their frequency and magnitude. Using deep mutational scanning (DMS), we previously found at least 42% of missense mutations in the TEM-1 β-lactamase antibiotic resistance gene cause deleterious collateral fitness effects. Here, we used DMS to comprehensively determine the collateral fitness effects of missense mutations in three genes encoding the antibiotic resistance proteins New Delhi metallo-β-lactamase (NDM-1), chloramphenicol acetyltransferase I (CAT-I), and 2″-aminoglycoside nucleotidyltransferase (AadB). AadB (20%), CAT-I (0.9%), and NDM-1 (0.2%) were less susceptible to deleterious collateral fitness effects than TEM-1 (42%) indicating that genes have different propensities for these effects. As was observed with TEM-1, all the studied deleterious aadB mutants increased aggregation. However, aggregation did not correlate with collateral fitness effects for many of the deleterious mutants of CAT-I and NDM-1. Select deleterious mutants caused unexpected phenotypes to emerge. The introduction of internal start codons in CAT-1 caused loss of the episome and a mutation in aadB made its cognate antibiotic essential for growth. Our study illustrates how the complexity of the cell provides a rich environment for collateral fitness effects and new phenotypes to emerge.

Quantitative Proteomics Reveal the Inherent Antibiotic Resistance Mechanism against Norfloxacin Resistance in Aeromonas hydrophila

Recently, the prevalence of Aeromonas hydrophila antibiotic-resistant strains has been reported in aquaculture, but its intrinsic antibiotic resistance mechanisms are largely unknown. In the present study, a label-free proteomics technology was used to compare the differential protein abundances in response to norfloxacin (NOR) stress in A. hydrophila. The results showed that there were 186 proteins decreasing and 220 proteins increasing abundances in response to NOR stress. Bioinformatics analysis showed that the differentially expressed proteins were enriched in several biological processes, such as sulfur metabolism and homologous recombination. Furthermore, the antibiotic sensitivity assays showed that the deletion of AHA_0904, cirA, and cysI significantly decreased the resistance against NOR, whereas ΔAHA_1239, ΔcysA, ΔcysD, and ΔcysN significantly increased the resistance against NOR. Our results provide insights into NOR resistance mechanisms and indicate that AHA_0904, cirA, AHA_1239, and sulfur metabolism may play important roles in NOR resistance in A. hydrophila.

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

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