Hydrogen Peroxide Induced Cell Death: The Major Defences Relative Roles and Consequences in E. coli

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

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

Metallo-Glycodendrimeric Materials against Enterotoxigenic Escherichia coli

Conjugation of carbohydrates to nanomaterials has been extensively studied and recognized as an alternative in the biomedical field. Dendrimers synthesized with mannose at the end group and with entrapped zero-valent copper/silver could be a potential candidate against bacterial proliferation. This study is aimed at investigating the bactericidal activity of metal-glycodendrimers. The Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction was used to synthesize a new mannosylated dendrimer containing 12 mannopyranoside residues in the periphery. The enterotoxigenic Escherichia coli fimbriae 4 (ETEC:F4) viability, measured at 600 nm, showed the half-inhibitory concentration (IC50) of metal-free glycodendrimers (D), copper-loaded glycodendrimers (D:Cu) and silver-loaded glycodendrimers (D:Ag) closed to 4.5 × 101, 3.5 × 101 and to 1.0 × 10-2 µg/mL, respectively, and minimum inhibitory concentration (MIC) of D, D:Cu and D:Ag of 2.0, 1.5 and 1.0 × 10-4 µg/mL, respectively. The release of bacteria contents onto broth and the inhibition of ETEC:F4 biofilm formation increased with the number of metallo-glycodendrimer materials, with a special interest in silver-containing nanomaterial, which had the highest activity, suggesting that glycodendrimer-based materials interfered with bacteria-bacteria or bacteria-polystyrene interactions, with bacteria metabolism and can disrupt bacteria cell walls. Our findings identify metal-mannose-dendrimers as potent bactericidal agents and emphasize the effect of entrapped zero-valent metal against ETEC:F4.

Chaos in a bacterial stress response

Cellular responses to environmental changes are often highly heterogeneous and exhibit seemingly random dynamics. The astonishing insight of chaos theory is that such unpredictable patterns can, in principle, arise without the need for any random processes, i.e., purely deterministically without noise. However, while chaos is well understood in mathematics and physics, its role in cell biology remains unclear because the complexity and noisiness of biological systems make testing difficult. Here, we show that chaos explains the heterogeneous response of Escherichia coli cells to oxidative stress. We developed a theoretical model of the gene expression dynamics and demonstrate that chaotic behavior arises from rapid molecular feedbacks that are coupled with cell growth dynamics and cell-cell interactions. Based on theoretical predictions, we then designed single-cell experiments to show we can shift gene expression from periodic oscillations to chaos on demand. Our work suggests that chaotic gene regulation can be employed by cell populations to generate strong and variable responses to changing environments.

Physiological analysis of the improved ε-polylysine production induced by reactive oxygen species

INTRODUCTION

Epsilon-poly-L-lysine (ε-PL) is produced by Streptomyces species in acidic and aerobic conditions, which inevitably induces rapid generation of reactive oxygen species (ROS). The devastating effects of ROS on biomolecules and cell vitality have been well-studied, while the positive effects of ROS are rarely reported.

RESULTS

In this study, we found that a proper dose of intracellular ROS (about 3.3 μmol H₂O₂ /g DCW) could induce a physiological modification to promote the ε-PL production (from 1.2 to 1.5 g/L). It resulted in larger sizes of colony and mycelial pellets as well as vibrant, aggregated, and more robust mycelia, which were of high capability of ROS detoxication. Physiological studies showed that appropriate doses of ROS activated the metabolism of the pentose phosphate pathway at both transcriptional and enzymatic levels, which was beneficial for biomass accumulation. The biosynthesis of lysine was also promoted in terms of transcriptional regulatory overexpression, increased transcription and enzymatic activity of key genes, larger pools of metabolites in the TCA cycle, replenishment pathway, and diaminoheptanedioic acid pathway. In addition, energy provision was ensured by activated metabolism of the TCA cycle, a larger pool of NADH, and higher activity of the electron transport system. Increased transcription of HrdD and pls further accelerated the ε-PL biosynthesis.

SIGNIFICANCE

These results indicated that ROS at proper intracellular dose could act as an inducing signal to activate the ε-PL biosynthesis, which laid a foundation for further process regulation to maintain optimal ROS dose in industrial ε-PL production and was of theoretical and practical significance.

KEY POINTS

• A proper dose of intracellular ROS positively influences the ε-PL production. • Proper dose of ROS enhanced the mycelial activity and antioxidative capability. • ROS increased lysine synthesis metabolism, energy provision and pls expression.

Does light-based tertiary treatment prevent the spread of antibiotic resistance genes? Performance, regrowth and future direction

The common occurrence of antibiotic-resistance genes (ARGs) originating from pathogenic and facultative pathogenic bacteria pose a high risk to aquatic environments. Low removal of ARGs in conventional wastewater treatment processes and horizontal dissemination of resistance genes between environmental bacteria and human pathogens have made antibiotic resistance evolution a complex global health issue. The phenomenon of regrowth of bacteria after disinfection raised some concerns regarding the long-lasting safety of treated waters. Despite the inactivation of living antibiotic-resistant bacteria (ARB), the possibility of transferring intact and liberated DNA containing ARGs remains. A step in this direction would be to apply new types of disinfection methods addressing this issue in detail, such as light-based advanced oxidation, that potentially enhance the effect of direct light interaction with DNA. This study is devoted to comprehensively and critically review the current state-of-art for light-driven disinfection. The main focus of the article is to provide an insight into the different photochemical disinfection methods currently being studied worldwide with respect to ARGs removal as an alternative to conventional methods. The systematic comparison of UV/chlorination, UV/H₂O₂, sulfate radical based-AOPs, photocatalytic processes and photoFenton considering their mode of action on molecular level, operational parameters of the processes, and overall efficiency of removal of ARGs is presented. An in-depth discussion of different light-dependent inactivation pathways, influence of DBP and DOM on ARG removal and the potential bacterial regrowth after treatment is presented. Based on presented revision the risk of ARG transfer from reactivated bacteria has been evaluated, leading to a future direction for research addressing the challenges of light-based disinfection technologies.

dinF Elicits Nitric Oxide Signaling Induced by Periplanetasin-4 from American Cockroach in Escherichia coli

Modern antibiotics have been developed with the aim of destroying cellular function; however, the risk of antibiotic-resistance is increasing continuously. As a result, antimicrobial peptide (AMP) is considered a novel strategy to substitute traditional drugs. This study focused on revealing the antibacterial mechanism(s) of periplanetasn-4, an AMP identified from Cockroach. To elucidate whether periplanetasin-4 generates reactive oxygen species (ROS), a crucial stress factor for cell death, intracellular ROS was measured in Escherichia coli. The degree of membrane and DNA damage was determined using the properties that ROS causes oxidative stress to cell components. Unlike normal cell death, membrane depolarization was observed but DNA fragmentation did not occur. In addition, accumulation of nitric oxide (NO), a free radical with high toxicity, was measured and the byproduct of NO also induced severe intracellular damage. Periplanetasin-4-induced NO also impacted on cytosol calcium levels and triggered lipid peroxidation and DNA oxidation. These features were weakened when NO synthesis was interrupted, and this data suggested that perplanetasin-4-induced NO participates in E. coli cell damage. Moreover, this AMP-induced NO stimulates expression of SOS repair proteins and activation of RecA, a bacterial caspase-like protein. Features of nitrosative damage did not occur especially without dinF gene which is associated with oxidative stress. Therefore, it was indicated that when there is a NO signal, dinF promotes cell death. In conclusion, the combined investigations demonstrated that the antibacterial mechanism(s) of periplanetasin-4 was a NO-induced cell death, and dinF gene is closely related to cell death pathway.

Use of a model to understand the synergies underlying the antibacterial mechanism of H2O2-producing honeys

Honey has been valued as a powerful antimicrobial since ancient times. However, the understanding of the underlying antibacterial mechanism is incomplete. The complexity and variability of honey composition represent a challenge to this scope. In this study, a simple model system was used to investigate the antibacterial effect of, and possible synergies between, the three main stressors present in honey: sugars, gluconic acid, and hydrogen peroxide (H₂O₂), which result from the enzymatic conversion of glucose on honey dilution. Our results demonstrated that the synergy of H₂O₂ and gluconic acid is essential for the antibacterial activity of honey. This synergy caused membrane depolarization, destruction of the cell wall, and eventually growth inhibition of E. coli K-12. The presence of H₂O₂ stimulated the generation of other long-lived ROS in a dose-dependent manner. Sugars caused osmosis-related morphological changes, however, decreased the toxicity of the H₂O₂/gluconic acid. The susceptibility of catalase and general stress response sigma factor mutants confirmed the synergy of the three stressors, which is enhanced at higher H₂O₂ concentrations. By monitoring cellular phenotypic changes caused by model honey, we explained how this can be bactericidal even though the antimicrobial compounds which it contains are at non-inhibitory concentrations.

Employing bacterial mutations for the elucidation of photo-Fenton disinfection: Focus on the intracellular and extracellular inactivation mechanisms induced by UVA and H2O2

The bacterial inactivation mechanisms by solar light and the photo-Fenton process is still a matter of debate. In this study, we bring evidence towards the elucidation of the mechanisms that govern photo-Fenton disinfection at near-neutral pH. With the use of porin-deficient and catalase over-producing E. coli strains, in conjunction with measurements of cell wall oxidation and permeability, we are able to i) highlight the role of the aforementioned components in bacterial inactivation and ii) localize the damages in the intracellular domain, despite the addition of the Fenton reagents in the bulk. We report that H₂O₂ oxidizes cell walls but under light the process is of low significance; UVA initiated an intracellular oxidation process based on excess accumulated H₂O₂, while the UVA+H₂O₂ and UVA+H₂O₂+Fe²⁺ processes have the same effect with light, albeit enhanced, as shown by malondialdehyde (MDA) production and ONPG hydrolysis rates. Finally, compared to the UVA-assisted photo-Fenton process, its solar counterpart is enhanced by the direct UVB effects on bacterial DNA. In conclusion, we have sufficient evidence to postulate that the photo-Fenton process is intracellular and propose the pathways that form the integrated bacterial inactivation mechanism by photo-Fenton.

A Method for Deciphering Major Drivers of Bacterial Iron Stress Response in the Presence of Oxidative Stressors

This paper describes a method for deciphering major drivers of bacterial stress response using an empirically informed computational approach. We develop a working model of iron flux regulation and concomitant oxidative stress response in Escherichia coli. The integrated model is used to investigate the temporal effects of iron and hydrogen peroxide stress on bacterial growth and metabolism. We employ a sensitivity analysis platform and, using various measures, probe for major mechanistic drivers of the bacterial response to iron stress.

Visible light plays a significant role during bacterial inactivation by the photo-fenton process, even at sub-critical light intensities

The aim of this research is to clarify the contribution of sunlight wavelengths, irradiance and Fe²⁺/H₂O₂ during bacterial disinfection by the photo-Fenton process in clear surface waters. We considered different solar spectrum distributions (visible, UVA-Visible), sub-critical irradiances (0-400 W/m²), focusing on the action modes of E. coli inactivation by the constituents involved in the composite process, at low μM reactants concentration (Fe²⁺/H₂O₂) in in ultrapure (MQ) water. We report that solar disinfection improved with Fenton reagents (photo-Fenton process) is a reality from very low light irradiance values (200 W/m²), and made possible even without the presence of UVA radiation, even when using low quantities of the Fenton reagents (0.5 mg/L Fe²⁺, 5 mg/L H₂O₂). Under light exposure, H₂O₂ was found to augment the intracellular Fenton process and Fe²⁺ to initiate further, distinct oxidative actions. Finally, validation was performed in Lake Geneva water over a wider irradiance range, where the photo-Fenton process was found to be reagent-dependent in low irradiance, shifting to light-driven in the higher values.

Engineering microbial pathways for production of bio-based chemicals from lignocellulosic sugars: current status and perspectives

Lignocellulose is the most abundant biomass on earth with an annual production of about 2 × 10¹¹ tons. It is an inedible renewable carbonaceous resource that is very rich in pentose and hexose sugars. The ability of microorganisms to use lignocellulosic sugars can be exploited for the production of biofuels and chemicals, and their concurrent biotechnological processes could advantageously replace petrochemicals' processes in a medium to long term, sustaining the emerging of a new economy based on bio-based products from renewable carbon sources. One of the major issues to reach this objective is to rewire the microbial metabolism to optimally configure conversion of these lignocellulosic-derived sugars into bio-based products in a sustainable and competitive manner. Systems' metabolic engineering encompassing synthetic biology and evolutionary engineering appears to be the most promising scientific and technological approaches to meet this challenge. In this review, we examine the most recent advances and strategies to redesign natural and to implement non-natural pathways in microbial metabolic framework for the assimilation and conversion of pentose and hexose sugars derived from lignocellulosic material into industrial relevant chemical compounds leading to maximal yield, titer and productivity. These include glycolic, glutaric, mesaconic and 3,4-dihydroxybutyric acid as organic acids, monoethylene glycol, 1,4-butanediol and 1,2,4-butanetriol, as alcohols. We also discuss the big challenges that still remain to enable microbial processes to become industrially attractive and economically profitable.

Solar photo-Fenton disinfection of 11 antibiotic-resistant bacteria (ARB) and elimination of representative AR genes. Evidence that antibiotic resistance does not imply resistance to oxidative treatment

The emergence of antibiotic resistance represents a major threat to human health. In this work we investigated the elimination of antibiotic resistant bacteria (ARB) by solar light and solar photo-Fenton processes. As such, we have designed an experimental plan in which several bacterial strains (Staphylococcus aureus, Escherichia coli and Klebsiella pneumoniae) possessing different drug-susceptible and -resistant patterns and structures (Gram-positive and Gram-negative) were subjected to solar light and the photo-Fenton oxidative treatment in water. We showed that both solar light and solar photo-Fenton processes were effective in the elimination of ARB in water and that the time necessary for solar light disinfection and solar photo-Fenton disinfection were similar for antibiotic-susceptible and antibiotic-resistant strains (mostly 180-240 and 90-120 min, respectively). Moreover, the bacterial structure did not significantly affect the effectiveness of the treatment. Similar regrowth pattern was observed (compared to the susceptible strain) and no development of bacteria with higher drug-resistance values was found in waters after any treatment. Finally, both processes were effective to reduce AR genes (ARGs), although solar photo-Fenton was more rapid than solar light. In conclusion, the solar photo-Fenton process ensured effective disinfection of ARB and elimination of ARGs in water (or wastewater) and is a potential mean to ensure limitation of ARB and ARG spread in nature.

Analogies and differences among bacterial and viral disinfection by the photo-Fenton process at neutral pH: a mini review

Over the last years, the photo-Fenton process has been established as an effective, green alternative to chemical disinfection of waters and wastewaters. Microorganisms' inactivation is the latest success story in the application of this process at near-neutral pH, albeit without clearly elucidated inactivation mechanisms. In this review, the main pathways of the combined photo-Fenton process against the most frequent pathogen models (Escherichia coli for bacteria and MS2 bacteriophage for viruses) are analyzed. Firstly, the action of solar light is described and the specific inactivation mechanisms in bacteria (internal photo-Fenton) and viruses (genome damage) are presented. The contribution of the external pathways due to the potential presence of organic matter in generating reactive oxygen species (ROS) and their effects on microorganism inactivation are discussed. Afterwards, the effects of the gradual addition of Fe and H₂O₂ are assessed and the differences among bacterial and viral inactivation are highlighted. As a final step, the simultaneous addition of both reagents induces the photo-Fenton in the bulk, focusing on the differences induced by the homogeneous or heterogeneous fraction of the process and the variation among the two respective targets. This work exploits the accumulated evidence on the mechanisms of bacterial inactivation and the scarce ones towards viral targets, aiming to bridge this knowledge gap and make possible the further application of the photo-Fenton process in the field of water/wastewater treatment.

Microbial cells can cooperate to resist high-level chronic ionizing radiation

Understanding chronic ionizing radiation (CIR) effects is of utmost importance to protecting human health and the environment. Diverse bacteria and fungi inhabiting extremely radioactive waste and disaster sites (e.g. Hanford, Chernobyl, Fukushima) represent new targets of CIR research. We show that many microorganisms can grow under intense gamma-CIR dose rates of 13–126 Gy/h, with fungi identified as a particularly CIR-resistant group of eukaryotes: among 145 phylogenetically diverse strains tested, 78 grew under 36 Gy/h. Importantly, we demonstrate that CIR resistance can depend on cell concentration and that certain resistant microbial cells protect their neighbors (not only conspecifics, but even radiosensitive species from a different phylum), from high-level CIR. We apply a mechanistically-motivated mathematical model of CIR effects, based on accumulation/removal kinetics of reactive oxygen species (ROS) and antioxidants, in bacteria (3 Escherichia coli strains and Deinococcus radiodurans) and in fungi (Candida parapsilosis, Kazachstania exigua, Pichia kudriavzevii, Rhodotorula lysinophila, Saccharomyces cerevisiae, and Trichosporon mucoides). We also show that correlations between responses to CIR and acute ionizing radiation (AIR) among studied microorganisms are weak. For example, in D. radiodurans, the best molecular correlate for CIR resistance is the antioxidant enzyme catalase, which is dispensable for AIR resistance; and numerous CIR-resistant fungi are not AIR-resistant. Our experimental findings and quantitative modeling thus demonstrate the importance of investigating CIR responses directly, rather than extrapolating from AIR. Protection of radiosensitive cell-types by radioresistant ones under high-level CIR is a potentially important new tool for bioremediation of radioactive sites and development of CIR-resistant microbiota as radioprotectors.