Enzymatic Antioxidant Systems in Early Anaerobes: Theoretical Considerations

Inorganic Fe-O and Fe-S oxidoreductases: paradigms for prebiotic chemistry and the evolution of enzymatic activity in biology

Oxidoreductases play crucial roles in electron transfer during biological redox reactions. These reactions are not exclusive to protein-based biocatalysts; nano-size (<100 nm), fine-grained inorganic colloids, such as iron oxides and sulfides, also participate. These nanocolloids exhibit intrinsic redox activity and possess direct electron transfer capacities comparable to their biological counterparts. The unique metal ion architecture of these nanocolloids, including electron configurations, coordination environment, electron conductivity, and the ability to promote spontaneous electron hopping, contributes to their transfer capabilities. Nano-size inorganic colloids are believed to be among the earliest 'oxidoreductases' to have 'evolved' on early Earth, playing critical roles in biological systems. Representing a distinct type of biocatalysts alongside metalloproteins, these nanoparticles offer an early alternative to protein-based oxidoreductase activity. While the roles of inorganic nano-sized catalysts in current Earth ecosystems are intuitively significant, they remain poorly understood and underestimated. Their contribution to chemical reactions and biogeochemical cycles likely helped shape and maintain the balance of our planet's ecosystems. However, their potential applications in biomedical, agricultural, and environmental protection sectors have not been fully explored or exploited. This review examines the structure, properties, and mechanisms of such catalysts from a material's evolutionary standpoint, aiming to raise awareness of their potential to provide innovative solutions to some of Earth's sustainability challenges.

Optimization and Enhancement of the Peroxidase-like Activity of Hemin in Aqueous Solutions of Sodium Dodecylsulfate

Iron porphyrins play several important roles in present-day living systems and probably already existed in very early life forms. Hemin (= ferric protoporphyrin IX = ferric heme b), for example, is the prosthetic group at the active site of heme peroxidases, catalyzing the oxidation of a number of different types of reducing substrates after hemin is first oxidized by hydrogen peroxide as the oxidizing substrate of the enzyme. The active site of heme peroxidases consists of a hydrophobic pocket in which hemin is embedded noncovalently and kept in place through coordination of the iron atom to a proximal histidine side chain of the protein. It is this partially hydrophobic local environment of the enzyme which determines the efficiency with which the sequential reactions of the oxidizing and reducing substrates proceed at the active site. Free hemin, which has been separated from the protein moiety of heme peroxidases, is known to aggregate in an aqueous solution and exhibits low catalytic activity. Based on previous reports on the use of surfactant micelles to solubilize free hemin in a nonaggregated state, the peroxidase-like activity of hemin in the presence of sodium dodecyl sulfate (SDS) at concentrations below and above the critical concentration for SDS micelle formation (critical micellization concentration (cmc)) was systematically investigated. In most experiments, 3,3',5,5'-tetramethylbenzidine (TMB) was applied as a reducing substrate at pH = 7.2. The presence of SDS clearly had a positive effect on the reaction in terms of initial reaction rate and reaction yield, even at concentrations below the cmc. The highest activity correlated with the cmc value, as demonstrated for reactions at three different HEPES concentrations. The 4-(2-hydroxyethyl)-1-piperazineethanesulfonate salt (HEPES) served as a pH buffer substance and also had an accelerating effect on the reaction. At the cmc, the addition of l-histidine (l-His) resulted in a further concentration-dependent increase in the peroxidase-like activity of hemin until a maximal effect was reached at an optimal l-His concentration, probably corresponding to an ideal mono-l-His ligation to hemin. Some of the results obtained can be understood on the basis of molecular dynamics simulations, which indicated the existence of intermolecular interactions between hemin and HEPES and between hemin and SDS. Preliminary experiments with SDS/dodecanol vesicles at pH = 7.2 showed that in the presence of the vesicles, hemin exhibited similar peroxidase-like activity as in the case of SDS micelles. This supports the hypothesis that micelle- or vesicle-associated ferric or ferrous iron porphyrins may have played a role as primitive catalysts in membranous prebiotic compartment systems before cellular life emerged.

Toxic reactive oxygen species stresses for reconfiguring central carbon metabolic fluxes in foodborne bacteria: Sources, mechanisms and pathways

The toxic reactive oxygen species (toxROS) is the reactive oxygen species (ROS) beyond the normal concentration of cells, which has inactivation and disinfection effects on foodborne bacteria. However, foodborne bacteria can adapt and survive by physicochemical regulation of antioxidant systems, especially through central carbon metabolism (CCM), which is a significant concern for food safety. It is thus necessary to study the antioxidant regulation mechanisms of CCM in foodborne bacteria under toxROS stresses. Therefore, the purpose of this review is to provide an update and comprehensive overview of the reconfiguration of CCM fluxes in foodborne bacteria that respond to different toxROS stresses. In this review, two key types of toxROS including exogenous toxROS (exo-toxROS) and endogenous toxROS (endo-toxROS) are introduced. Exo-toxROS are produced by disinfectants, such as H₂O₂ and HOCl, or during food non-thermal processing such as ultraviolet (UV/UVA), cold plasma (CP), ozone (O₃), electrolyzed water (EW), pulsed electric field (PEF), pulsed light (PL), and electron beam (EB) processing. Endo-toxROS are generated by bioreagents such as antibiotics (aminoglycosides, quinolones, and β-lactams). Three main pathways for CCM in foodborne bacteria under the toxROS stress are also highlighted, which are glycolysis (EMP), pentose phosphate pathway (PPP), and tricarboxylic acid cycle (TCA). In addition, energy metabolisms throughout these pathways are discussed. Finally, challenges and future work in this area are suggested. It is hoped that this review should be beneficial in providing insights for future research on bacterial antioxidant CCM defence under both exo-toxROS stresses and endo-toxROS stresses.

Functionalized Prussian Blue Nanozyme as Dual-Responsive Drug Therapeutic Nanoplatform Against Maxillofacial Infection via Macrophage Polarization

Purpose

Maxillofacial infection is a common disease in stomatology and is difficult to treat owing to its high potential to spread to vital anatomical structures. Excessive levels of reactive oxygen species (ROS) in infected tissues lead to cellular damage and impede tissue regeneration. However, uncontrollable strategies to remove ROS have limited therapeutic efficacy. Nanoparticle systems for scavenging ROS and remodeling the inflammatory microenvironment offer much promise in the treatment of maxillofacial inflammation.

Methods

Here, a novel microenvironment-stimuli-responsive drug delivery nanoplatform (HMPB@Cur@PDA) based on a polydopamine (PDA)-functionalized hollow mesoporous Prussian blue (HMPB) nanozyme was developed for the delivery of curcumin (Cur) in the treatment of maxillofacial infection. Low pH and excess ROS in the inflammatory microenvironment cause degradation of the outer PDA layer of the nanocomplex, exposing the HMPB nanozyme and loaded Cur, which synergistically act as a ROS scavenger and anti-inflammatory agent, respectively, and induce macrophage polarization from the pro-inflammatory M1 to the anti-inflammatory M2 phenotype.

Results

Experiments in vitro provided strong evidence for the application of novel nanocomplexes in scavenging multiple ROS and inhibiting lipopolysaccharide-induced inflammation. In addition, in vivo results obtained using a mouse maxillofacial infection model demonstrated that HMPB@Cur@PDA had excellent biocompatibility, significantly attenuated the inflammatory response in periodontal tissue, and improved the repair of damaged tissue.

Conclusion

Our results indicate that HMPB@Cur@PDA nanocomposites have great potential for ROS regulation as well as having anti-inflammatory effects, providing new insights for the development of dual-response maxillofacial infection treatments.

Application of Spectroscopic Methods for the Identification of Superoxide Dismutases in Cyanobacteria

Superoxide dismutases (SODs) belong to the group of metalloenzymes that remove superoxide anion radicals and they have been identified in three domains of life: Bacteria, Archaea and Eucarya. SODs in Synechocystis sp. PCC 6803, Gloeobacter violaceus CCALA 979, and Geitlerinema sp. ZHR1A were investigated. We hypothesized that iron (FeSOD) and/or manganese (MnSOD) dominate as active forms in these cyanobacteria. Activity staining and three different spectroscopic methods of SOD activity bands excised from the gels were used to identify a suitable metal in the separated samples. FeSODs or enzymes belonging to the Fe-MnSOD superfamily were detected. The spectroscopic analyses showed that only Fe is present in the SOD activity bands. We found FeSOD in Synechocystis sp. PCC 6803 while two forms in G. violaceus and Geitlerinema sp. ZHR1A: FeSOD1 and FeSOD2 were present. However, no active Cu/ZnSODs were identified in G. violaceus and Geitlerinema sp. ZHR1A. We have shown that selected spectroscopic techniques can be complementary to the commonly used method of staining for SOD activity in a gel. Furthermore, the occurrence of active SODs in the cyanobacteria studied is also discussed in the context of SOD evolution in oxyphotrophs.

Characterization of ancestral Fe/Mn superoxide dismutases indicates their cambialistic origin

Superoxide dismutases (SODs) are critical metalloenzymes mitigating the damages of the modern oxygenated world. However, the emergence of one family of SODs, the Fe/Mn SOD, has been recurrently proposed to predate the great oxygenation event (GOE). This ancient family lacks metal binding selectivity, but displays strong catalytic selectivity. Therefore, some homologues would only be active when bound to Fe or Mn, although others, dubbed cambialistic, would function when loaded with either ion. This posed the longstanding question about the identity of the cognate metal ion of the first SODs to emerge. In this work, we utilize ancestral sequence reconstruction techniques to infer the earliest SODs. We show that the "ancestors" are active in vivo and in vitro. Further, we test their metal specificity and demonstrate that they are cambialistic in nature. Our findings shed light on how the predicted Last Common Universal Ancestor was capable of dealing with decomposition of the superoxide anion, and the early relationship between life, oxygen, and metal ion availability.

Oxidative stress and antioxidant mechanisms of obligate anaerobes involved in biological waste treatment processes: A review

In-depth understanding of the molecular mechanisms and physiological consequences of oxidative stress is still limited for anaerobes. Anaerobic biotechnology has become widely accepted by the wastewater/sludge industry as a better alternative to more conventional but costly aerobic processes. However, the functional anaerobic microorganisms used in anaerobic biotechnology are frequently hampered by reactive oxygen/nitrogen species (ROS/RNS)-mediated oxidative stress caused by exposure to stressful factors (e.g., oxygen and heavy metals), which negatively impact treatment performance. Thus, identifying stressful factors and understanding antioxidative defense mechanisms of functional obligate anaerobes are crucial for the optimization of anaerobic bioprocesses. Herein, we present a comprehensive overview of oxidative stress and antioxidant mechanisms of obligate anaerobes involved in anaerobic bioprocesses; as examples, we focus on anaerobic ammonium oxidation bacteria and methanogenic archaea. We summarize the primary stress factors in anaerobic bioprocesses and the cellular antioxidant defense systems of functional anaerobes, a consortia of enzymatic and nonenzymatic mechanisms. The dual role of ROS/RNS in cellular processes is elaborated; at low concentrations, they have vital cell signaling functions, but at high concentrations, they cause oxidative damage. Finally, we highlight gaps in knowledge and future work to uncover antioxidant and damage repair mechanisms in obligate anaerobes. This review provides in-depth insights and guidance for future research on oxidative stress of obligate anaerobes to boost the accurate regulation of anaerobic bioprocesses in challenging and changing operating conditions.

From Foods to Chemotherapeutics: The Antioxidant Potential of Dietary Phytochemicals

Food plants have been recognized for their medicinal properties for millennia, a concept supported by epidemiological studies indicating long-term health benefits for people consuming greater amounts of fruits and vegetables. As our technology and instrumentation advance, researchers have the ability to identify promising phytochemicals, and examine their potential benefits, or detriments, to human health. While results from trials investigating single chemical supplementation have sometimes produced negative health results, studies investigating the synergistic action of phytochemicals—either within our diet or as an adjuvant to radiation or chemotherapy—appear promising. Utilizing phytochemicals as synergistic agents may lower the chemotherapeutic doses needed to incur physiological results, while also using chemicals with fewer toxic effects. This review investigates a variety of plant-produced chemicals humans typically ingest, their impacts on overall health patterns, molecular mechanisms associated with their health impacts, and the potential of their synergistic use for therapeutic purposes.

Thriving in Oxygen While Preventing ROS Overproduction: No Two Systems Are Created Equal

From 2.5 to 2.0 billion years ago, atmospheric oxygen concentration [O₂] rose thousands of times, leading to the first mass extinction. Reactive Oxygen Species (ROS) produced by the non-catalyzed partial reduction of O₂ were highly toxic eliminating many species. Survivors developed different strategies to cope with ROS toxicity. At the same time, using O₂ as the final acceptor in respiratory chains increased ATP production manifold. Thus, both O₂ and ROS were strong drivers of evolution, as species optimized aerobic metabolism while developing ROS-neutralizing mechanisms. The first line of defense is preventing ROS overproduction and two mechanisms were developed in parallel: 1) Physiological uncoupling systems (PUS), which increase the rate of electron fluxes in respiratory systems. 2) Avoidance of excess [O₂]. However, it seems that as avoidance efficiency improved, PUSs became less efficient. PUS includes branched respiratory chains and proton sinks, which may be proton specific, the mitochondrial uncoupling proteins (UCPs) or unspecific, the mitochondrial permeability transition pore (PTP). High [O₂] avoidance also involved different strategies: 1) Cell association, as in biofilms or in multi-cellularity allowed gas-permeable organisms (oxyconformers) from bacterial to arthropods to exclude O_2. 2) Motility, to migrate from hypoxic niches. 3) Oxyregulator organisms: as early as in fish, and O₂-impermeable epithelium excluded all gases and only exact amounts entered through specialized respiratory systems. Here we follow the parallel evolution of PUS and O₂-avoidance, PUS became less critical and lost efficiency. In regard, to proton sinks, there is fewer evidence on their evolution, although UCPs have indeed drifted in function while in some species it is not clear whether PTPs exist.

What are the inorganic nanozymes? Artificial or inorganic enzymes!

The research on inorganic nanozymes remains very active since the first paper on the “intrinsic peroxidase-like properties of ferromagnetic nanoparticles” was published in Nature Nanotechnology in 2007. However, there is...

Prussian Blue Nanozymes Prevent Anthracycline-Induced Liver Injury by Attenuating Oxidative Stress and Regulating Inflammation

Anthracycline-induced liver injury (AILI) is becoming an increasingly serious and potential clinical complication and is linked to reactive oxygen species (ROS) production and subsequent inflammatory response. Herein, we demonstrated that artificial Prussian blue nanozymes (PBZs) prevented daunorubicin-induced liver injury, a prototype of AILI, by attenuating ROS production and regulating inflammation. PBZs exhibited multienzyme activity and could scavenge ROS and free radicals. At the cellular level, PBZs could effectively eliminate ROS, suppress hepatocyte apoptosis, reduce deoxyribonucleic acid damage, and decrease the levels of inflammatory cytokines and chemokines. According to the results of the in vivo study, pretreatment with PBZs also resulted in a desirable protective effect against AILI, as indicated by both a decrease in biochemical indicator levels and hepatocyte necrosis. PBZs upregulated antioxidative genes by activating the Nrf2 pathway to reduce oxidative stress. Meanwhile, PBZs counteracted the inflammatory response based on the decreased expression levels of myeloperoxidase and F4/80 in the liver. Collectively, our findings indicate that PBZ-based nanotherapy is a novel strategy for protecting against AILI.

Self-cascade MoS2 nanozymes for efficient intracellular antioxidation and hepatic fibrosis therapy

Cascade biocatalytic reactions involving multiple antioxidative enzymes are necessary in living cells to regulate cellular metabolism and redox homeostasis. Substantial efforts have been made to construct cascade reactions through engineered enzyme mimics to improve intracellular metabolic flux, especially under pathophysiological conditions. Here, we show that MoS₂ nanozymes exhibit activities of four major cellular cascade antioxidant enzymes, including superoxide dismutase, catalase, peroxidase, and glutathione peroxidase. Meanwhile, MoS₂ nanozymes attenuate electron transfer in cytochrome c/H₂O₂ to ameliorate the inherent antioxidant defense system under stress conditions. Thus, MoS₂ nanozymes function as a self-cascade platform to inhibit intracellular reactive oxygen species (ROS) production by modulating mitochondrial function and scavenging abundant ROS through their intrinsic antioxidant capacity. Density functional theory calculations reveal the underlying mechanisms of the intracellular environment-dependent catalase-like activity of MoS₂ nanozymes. Furthermore, we find that the MoS₂ nanozymes play a cytoprotective role in cells and significantly improve the treatment outcomes in a hepatic fibrosis mouse model. These results demonstrate the ROS-scavenging capacity of a single-component MoS₂ nanozyme-based cascade reaction system and reveal the in-depth mechanism, which may advance the development of nanozyme-based antioxidative agents.

Multiple toxicity endpoints induced by carbon nanofibers in Amazon turtle juveniles: Outspreading warns about toxicological risks to reptiles

The toxicity of carbon-based nanomaterials (CNs) has been observed in different organisms; however, little is known about the impact of water polluted with carbon nanofibers (CNFs) on reptiles. Thus, the aim of the current study was to assess the chronic effects (7.5 months) of 1 and 10 mg/L of CNF on Podocnemis expansa (Amazon turtle) juveniles (4 months old) based on different biomarkers. Increased total organic carbon (TOC) concentrations observed in the liver and brain (which suggests CNF uptake) were closely correlated to changes in REDOX systems of turtles exposed to CNFs, mainly to higher nitrite, hydrogen peroxide and lipid peroxidation levels. Increased levels of antioxidants such as total glutathione, catalase and superoxide dismutase in the exposed animals were also observed. The uptake of CNFs and the observed biochemical changes were associated with higher frequency of erythrocyte nuclear abnormalities (assessed through micronucleus assays), as well as with both damage in erythrocyte DNA (assessed through comet assays) and higher apoptosis and necrosis rates in erythrocytes of exposed turtles. Cerebral and hepatic acetylcholinesterase (AChE) increased in turtles exposed to CNFs, and this finding suggested the neurotoxic effect of these nanomaterials. Data in the current study reinforced the toxic potential of CNFs and evidenced the biochemical, mutagenic, genotoxic, cytotoxic, and neurotoxic effects of CNFs on P. expansa.

Platinum-Copper Bimetallic Colloid Nanoparticle Cluster Nanozymes with Multiple Enzyme-like Activities for Scavenging Reactive Oxygen Species

Fabrication of high-performance artificial antioxidant enzyme (AAE) systems based on a single nanozyme possessing multi-enzymatic activities is fascinating but challenging. Here, polyvinylpyrrolidone (PVP)-platinum-copper nanoparticle clusters (PVP-PtCuNCs) are prepared by a facile one-pot chemical coreduction method. PVP-PtCuNCs possess efficient superoxide dismutase (SOD)-like, peroxidase (POD)-like, and catalase (CAT)-like activities, and the multi-enzymatic activities depend on the bimetal component and cluster structure. Compared with individual platinum nanoparticle clusters (PVP-PtNCs), PVP-PtCuNCs can effectively eliminate reactive oxygen species (ROS) including superoxide anions, hydrogen peroxide, and hydroxyl radicals. The doping of copper not only reduces the usage of Pt content but also improves the catalytic efficiency and versatility effectively through the synergistic effect of bimetal components and the nanocluster structure. The results not only demonstrate that a single bimetallic nanozyme has the potential as an efficient AAE system in the biomedical application but also demonstrate that traditional concepts of structure-activity relationships can be used to fabricate nanozymes with the desired multi-enzymatic activities.

Elemental iron modifies the redox environment of the gastrointestinal tract: A novel therapeutic target and test for metabolic syndrome

Metabolic syndrome (MetS, i.e., type 2 diabetes and obesity) is often associated with dysbiosis, inflammation, and leaky gut syndrome, which increase the content of oxygen and reactive oxygen species (ROS) in the gastrointestinal (GI) tract. Using near-infrared fluorescent, in situ imaging of ROS, we evaluated the effects of oral administration of elemental iron powder (Fe⁰) on luminal ROS in the GI tract and related these changes to glucose metabolism and the gut microbiome. C57Bl/6J mice fed low-fat or high-fat diets and gavaged with Fe⁰ (2.5 g per kg), in both single- and repeat-doses, demonstrated decreased levels of luminal ROS. Fourteen days of repeated Fe⁰ administration reduced hyperglycemia and improved glucose tolerance in the obese and hyperglycemic animals compared to the untreated obese controls and reduced the relative amount of iron oxides in the feces, which indicated an increased redox environment of the GI tract. We determined that Fe⁰ administration can also be used as a diagnostic assay to assess the GI microenvironment. Improved metabolic outcomes and decreased gastrointestinal ROS in Fe⁰-treated, high-fat diet-fed animals correlated with the increase in a co-abundance group of beneficial bacteria, including Lactobacillus, and the suppression of detrimental populations, including Oscillibacter, Peptococcus, and Intestinimonas. Daily Fe⁰ treatment also increased the relative abundance of amplicon sequence variants that lacked functional enzymatic antioxidant systems, which is consistent with the ability of Fe⁰ to scavenge ROS and oxygen in the GI, thus favoring the growth of oxygen-sensitive bacteria. These findings delineate a functional role for antioxidants in modification of the GI microenvironment and subsequent reversal of metabolic dysfunction.

Methionine Sulfoxide Reductases Contribute to Anaerobic Fermentative Metabolism in Bacillus cereus

Reversible oxidation of methionine to methionine sulfoxide (Met(O)) is a common posttranslational modification occurring on proteins in all organisms under oxic conditions. Protein-bound Met(O) is reduced by methionine sulfoxide reductases, which thus play a significant antioxidant role. The facultative anaerobe Bacillus cereus produces two methionine sulfoxide reductases: MsrA and MsrAB. MsrAB has been shown to play a crucial physiological role under oxic conditions, but little is known about the role of MsrA. Here, we examined the antioxidant role of both MsrAB and MrsA under fermentative anoxic conditions, which are generally reported to elicit little endogenous oxidant stress. We created single- and double-mutant Δmsr strains. Compared to the wild-type and ΔmsrAB mutant, single- (ΔmsrA) and double- (ΔmsrAΔmsrAB) mutants accumulated higher levels of Met(O) proteins, and their cellular and extracellular Met(O) proteomes were altered. The growth capacity and motility of mutant strains was limited, and their energy metabolism was altered. MsrA therefore appears to play a major physiological role compared to MsrAB, placing methionine sulfoxides at the center of the B. cereus antioxidant system under anoxic fermentative conditions.

How Microbes Evolved to Tolerate Oxygen

Ancient microbes invented biochemical mechanisms and assembled core metabolic pathways on an anoxic Earth. Molecular oxygen appeared far later, forcing microbes to devise layers of defensive tactics that fend off the destructive actions of both reactive oxygen species (ROS) and oxygen itself. Recent work has pinpointed the enzymes that ROS attack, plus an array of clever protective strategies that abet the well known scavenging systems. Oxygen also directly damages the low-potential metal centers and radical-based mechanisms that optimize anaerobic metabolism; therefore, committed anaerobes have evolved customized tactics that defend these various enzymes from occasional oxygen exposure. Thus a more comprehensive, detailed, and surprising view of oxygen toxicity is coming into view.

The evolution of oxygen-utilizing enzymes suggests early biosphere oxygenation

Production of molecular oxygen was a turning point in the Earth's history. The geological record indicates the Great Oxidation Event, which marked a permanent transition to an oxidizing atmosphere around 2.4 Ga. However, the degree to which oxygen was available to life before oxygenation of the atmosphere remains unknown. Here, phylogenetic analysis of all known oxygen-utilizing and -producing enzymes (O₂-enzymes) indicates that oxygen became widely available to living organisms well before the Great Oxidation Event. About 60% of the O₂-enzyme families whose birth can be dated appear to have emerged at the separation of terrestrial and marine bacteria (22 families, compared to two families assigned to the last universal common ancestor). This node, dubbed the last universal oxygen ancestor, coincides with a burst of emergence of both oxygenases and other oxidoreductases, thus suggesting a wider availability of oxygen around 3.1 Ga.

Physiological and metabolic responses to hypersalinity reveal interpopulation tolerance in the green macroalga Ulva compressa with different pollution histories

There is scarce investigation addressing interpopulation tolerance responses to address the influence of a history of chronic stress exposure, as that occurring in polluted environments, in photoautotrophs. We evaluated ecophysiological (photosynthetic activity) and metabolic (oxidative stress and damage) responses of two populations of green macroalga Ulva compressa from polluted (Ventanas) and non-polluted (Cachagua) localions of central Chile, and exposed to controlled hypersalinity conditions of 32 (control), 42, 62 and 82 psu (practical salinity units) for 6 h, 48 h and 6 d. Both primary production (ETR_max) and photosynthetic efficiency (α_ETR) were generally higher in the population from Cachagua compared to Ventanas at all times and salinities. Moreover, at most experimental times and salinities the population from Ventanas had greater levels of H₂O₂ and lipid peroxidation that individuals from Cachagua. Total ascorbate was higher in the population of Cachagua than Ventanas at 42 and 82 psu after 6 and 48 h, respectively, while at 6 d concentrations were similar between both populations at all salinities. Total glutathione was greater in both populations after 6 h at all salinities, but at 48 h its concentrations were higher only in the population from Cachagua, a trend that was maintained at 6 d under 82 psu only. Reduced and oxidized ascorbate (ASC and DHA, respectively) and glutathione (GSH and GSSG, respectively) demonstrated similar patterns between U. compressa populations, with an increase oxidation with greater salinities but efficient recycling to maintain sufficient batch of ASC and GSH. When assessing the expression of antioxidant enzymes catalase (CAT), superoxide dismutase (SOD) and dehydroascorbate reductase (DHAR), while the population of Ventanas displayed a general trend of upregulation with increasing salinities along the experiments, U. compressa from Cachagua revealed patterns of downregulation. Results demonstrated that although both populations were still viable after the applied hypersalinities during all experimental times, biological performance was usually more affected in the population from the Ventanas than Cachagua, likely due to a depressed baseline metabolism after a long history of exposition to environmental pollution.

Sulfur Chemistry May Have Paved the Way for Evolution of Antioxidants

The first organisms on the young Earth, just 1-1.5 billion years old, were likely chemolithoautotrophic anaerobes, thriving in an anoxic world rich in water, CO₂, and N₂. It is generally assumed that, until the accumulation of O₂ in the atmosphere, life was exempted from the oxidative stress that reactive oxygen species (ROS) impose on hydrocarbon-based life. Therefore, it is perplexing to note that life on the early Earth already carried antioxidants such as superoxide dismutase enzymes, catalase, and peroxiredoxins, the function of which is to counteract all forms of ROS, including H₂O₂. Phylogenetic investigations suggest that the presence of these enzymes in the last universal common ancestor, far predating the great oxygenation event (GOE) sometime between 2.3 and 2.7 billion years ago, is thought to be due to the appearance of oxygen-producing microorganisms and the subsequent need to respond to the appearance of ROS. Since the metabolic enzymes that counteract ROS have been found in all domains of life, they are considered of primitive origin. Two questions arise: (1) Could there be a nonbiological source of ROS that predates the oxygenic microbial activity? (2) Could sulfur, the homologue of oxygen, have played that role? Reactive sulfur species (RSS) may have triggered the evolution of antioxidants such that the ROS antioxidants started out as "antisulfur" enzymes developed to cope with, and take advantage of, various forms of RSS that were abundantly present on the early Earth.

How to define obligatory anaerobiosis? An evolutionary view on the antioxidant response system and the early stages of the evolution of life on Earth

One of the former definitions of "obligate anaerobiosis" was based on three main criteria: 1) it occurs in organisms, so-called obligate anaerobes, which live in environments without oxygen (O₂), 2) O₂-dependent (aerobic) respiration, and 3) antioxidant enzymes are absent in obligate anaerobes. In contrast, aerobes need O₂ in order to grow and develop properly. Obligate (or strict) anaerobes belong to prokaryotic microorganisms from two domains, Bacteria and Archaea. A closer look at anaerobiosis covers a wide range of microorganisms that permanently or in a time-dependent manner tolerate different concentrations of O₂ in their habitats. On this basis they can be classified as obligate/facultative anaerobes, microaerophiles and nanaerobes. Paradoxically, O₂ tolerance in strict anaerobes is usually, as in aerobes, associated with the activity of the antioxidant response system, which involves different antioxidant enzymes responsible for removing excess reactive oxygen species (ROS). In our opinion, the traditional definition of "obligate anaerobiosis" loses its original sense. Strict anaerobiosis should only be restricted to the occurrence of O₂-independent pathways involved in energy generation. For that reason, a term better than "obligate anaerobes" would be O₂/ROS tolerant anaerobes, where the role of the O₂/ROS detoxification system is separated from O₂-independent metabolic pathways that supply energy. Ubiquitous key antioxidant enzymes like superoxide dismutase (SOD) and superoxide reductase (SOR) in contemporary obligate anaerobes might suggest that their origin is ancient, maybe even the beginning of the evolution of life on Earth. It cannot be ruled out that c. 3.5 Gyr ago, local microquantities of O₂/ROS played a role in the evolution of the last universal common ancestor (LUCA) of all modern organisms. On the basis of data in the literature, the hypothesis that LUCA could be an O₂/ROS tolerant anaerobe is discussed together with the question of the abiotic sources of O₂/ROS and/or the early evolution of cyanobacteria that perform oxygenic photosynthesis.

On the origin of microbial magnetoreception

A broad range of organisms, from prokaryotes to higher animals, have the ability to sense and utilize Earth's geomagnetic field—a behavior known as magnetoreception. Although our knowledge of the physiological mechanisms of magnetoreception has increased substantially over recent decades, the origin of this behavior remains a fundamental question in evolutionary biology. Despite this, there is growing evidence that magnetic iron mineral biosynthesis by prokaryotes may represent the earliest form of biogenic magnetic sensors on Earth. Here, we integrate new data from microbiology, geology and nanotechnology, and propose that initial biomineralization of intracellular iron nanoparticles in early life evolved as a mechanism for mitigating the toxicity of reactive oxygen species (ROS), as ultraviolet radiation and free-iron-generated ROS would have been a major environmental challenge for life on early Earth. This iron-based system could have later been co-opted as a magnetic sensor for magnetoreception in microorganisms, suggesting an origin of microbial magnetoreception as the result of the evolutionary process of exaptation.

Fullerene-like MoS2 Nanoparticles as Cascade Catalysts Improving Lubricant and Antioxidant Abilities of Artificial Synovial Fluid

Intraarticular injection of hyaluronic acid (HA) for viscosupplementation is a nonsurgical therapy for osteoarthritis (OA). However, HA fails to lubricate under a significant load and tends to be depolymerized by the overproduction of reactive oxygen species (ROS) in inflammation. Here, we for the first time reported that fullerene-like MoS₂ (F-MoS₂) nanoparticles are efficient lubricants and antioxidants for artificial synovial fluid. A model of arthrosis was built, to evaluate the tribological behavior of F-MoS₂ nanoparticles. The tests showed that they significantly improve the antiwear and friction-reducing abilities of the artificial synovial fluid. More importantly, the F-MoS₂ nanoparticles possess intrinsic dual-enzyme-like activity, mimicking superoxide dismutases (SOD) and catalases (CAT) under physiological conditions (pH 7.4, 25 °C). By coupling of these unique properties, a self-organized cascade catalytic system was constructed, which includes the disproportionation of superoxide radicals (O₂^•-) to hydrogen peroxide (H₂O₂) and subsequently the disproportionation of H₂O₂ into oxygen (O₂). The effectiveness of the detox system was evaluated by human umbilical vein endothelial cells (HUVEC) models exposed to oxidative stress. After that, F-MoS₂ nanoparticles were used to regulate the ROS level in artificial synovial fluid containing HA. Relative viscosity measurements showed the excellent protective effect of F-MoS₂ nanoparticles against HA oxidative damage offered by O₂^•-. These results indicate that F-MoS₂ nanoparticles are promising candidates for treatment of OA and other diseases caused by lubrication deficiency or oxidative stress.

The Power Without the Glory: Multiple Roles of Hydrogen Peroxide in Mediating the Origin of Life

The hydrogen peroxide (HP) crucible hypothesis proposed here holds that life began in a localized environment on Earth that was perfused with a flow of hydrogen peroxide from a sustained external source, which powered and mediated molecular evolution and the protocellular RNA world. In this article, we consolidate and review recent evidence, both circumstantial and tested in simulation in our work and in the laboratory in others' work, for its multiple roles in the evolution of the first living systems: (1) it provides a periodic power source as the thiosulfate-hydrogen peroxide (THP) redox oscillator, (2) it may act as an agent of molecular change and evolution and mediator of homochirality, and (3) the THP oscillator, subject to Brownian input perturbations, produces a weighted distribution of output thermal fluctuations that favor polymerization and chemical diversification over chemical degradation and simplification. The hypothesis can help to clarify the hero and villain roles of hydrogen peroxide in cell function, and on the singularity of life: of necessity, life evolved early an armory of catalases, the continuing, and all-pervasive presence of which prevents hydrogen peroxide from accumulating anywhere in sufficient quantities to host a second origin. The HP crucible hypothesis is radical, but based on well-known chemistry and physics, it is eminently testable in the laboratory, and many of our simulations provide recipes for such experiments.

Redox biology of regulated cell death in cancer: A focus on necroptosis and ferroptosis

Redox changes and generation of reactive oxygen species (ROS) are part of normal cell metabolism. While low ROS levels are implicated in cellular signaling pathways necessary for survival, higher levels play major roles in cancer development as well as cell death signaling and execution. A role for redox changes in apoptosis has been long established; however, several new modalities of regulated cell death have been brought to light, for which the importance of ROS production as well as ROS source and targets are being actively investigated. In this review, we summarize recent findings on the role of ROS and redox changes in the activation and execution of two major forms of regulated cell death, necroptosis and ferroptosis. We also discuss the potential of using modulators of these two forms of cell death to exacerbate ROS as a promising anticancer therapy.

Aerobic prokaryotes do not have higher GC contents than anaerobic prokaryotes, but obligate aerobic prokaryotes have

Background

Among the four bases, guanine is the most susceptible to damage from oxidative stress. Replication of DNA containing damaged guanines results in G to T mutations. Therefore, the mutations resulting from oxidative DNA damage are generally expected to predominantly consist of G to T (and C to A when the damaged guanine is not in the reference strand) and result in decreased GC content. However, the opposite pattern was reported 16 years ago in a study of prokaryotic genomes. Although that result has been widely cited and confirmed by nine later studies with similar methods, the omission of the effect of shared ancestry requires a re-examination of the reliability of the results.

Results

When aerobic and obligate aerobic prokaryotes were mixed together and anaerobic and obligate anaerobic prokaryotes were mixed together, phylogenetic controlled analyses did not detect significant difference in GC content between aerobic and anaerobic prokaryotes. This result is consistent with two generally neglected studied that had accounted for the phylogenetic relationship. However, when obligate aerobic prokaryotes were compared with aerobic prokaryotes, anaerobic prokaryotes, and obligate anaerobic prokaryotes separately using phylogenetic regression analysis, a significant positive association was observed between aerobiosis and GC content, no matter it was calculated from whole genome sequences or the 4-fold degenerate sites of protein-coding genes. Obligate aerobes have significantly higher GC content than aerobes, anaerobes, and obligate anaerobes.

Conclusions

The positive association between aerobiosis and GC content could be attributed to a mutational force resulting from incorporation of damaged deoxyguanosine during DNA replication rather than oxidation of the guanine nucleotides within DNA sequences. Our results indicate a grade in the aerobiosis-associated mutational force, strong in obligate aerobes, moderate in aerobes, weak in anaerobes and obligate anaerobes.

Electronic supplementary material

The online version of this article (10.1186/s12862-019-1365-8) contains supplementary material, which is available to authorized users.

RETRACTED ARTICLE: The quantum physiology of oxygen; from electrons to the evolution of redox signaling in the human brain

Rising atmospheric oxygen (O₂) levels provided a selective pressure for the evolution of O₂-dependent micro-organisms that began with the autotrophic eukaryotes. Since these primordial times, the respiring mammalian cell has become entirely dependent on the constancy of electron flow with molecular O₂ serving as the terminal electron acceptor in mitochondrial oxidative phosphorylation. Indeed, the ability to “sense” O₂ and maintain homeostasis is considered one of the most important roles of the central nervous system (CNS) and likely represented a major driving force in the evolution of the human brain. Today, modern humans have evolved with an oversized brain committed to a continually active state and as a consequence, paradoxically vulnerable to failure if the O₂ supply is interrupted. However, our pre-occupation with O₂, the elixir of life, obscures the fact that it is a gas with a Janus Face, capable of sustaining life in physiologically controlled amounts yet paradoxically deadly to the CNS when in excess. A closer look at its quantum structure reveals precisely why; the triplet ground state diatomic O₂ molecule is paramagnetic and exists in air as a free radical, constrained from reacting aggressively with the brain’s organic molecules due to its “spin restriction”, a thermodynamic quirk of evolutionary fate. By further exploring O₂’s free radical “quantum quirkiness” including emergent quantum physiological phenomena, our understanding of precisely how the human brain senses O₂ deprivation (hypoxia) and the elaborate redox-signaling defense mechanisms that defend O₂ homeostasis has the potential to offer unique insights into the pathophysiology and treatment of human brain disease.

A Tale of Two Concepts: Harmonizing the Free Radical and Antagonistic Pleiotropy Theories of Aging

SIGNIFICANCE

The two foremost concepts of aging are the mechanistic free radical theory (FRT) of how we age and the evolutionary antagonistic pleiotropy theory (APT) of why we age. Both date from the late 1950s. The FRT holds that reactive oxygen species (ROS) are the principal contributors to the lifelong cumulative damage suffered by cells, whereas the APT is generally understood as positing that genes that are good for young organisms can take over a population even if they are bad for the old organisms. Recent Advances: Here, we provide a common ground for the two theories by showing how aging can result from the inherent chemical reactivity of many biomolecules, not just ROS, which imposes a fundamental constraint on biological evolution. Chemically reactive metabolites spontaneously modify slowly renewable macromolecules in a continuous way over time; the resulting buildup of damage wrought by the genes coding for enzymes that generate such small molecules eventually masquerades as late-acting pleiotropic effects. In aerobic organisms, ROS are major agents of this damage but they are far from alone.

CRITICAL ISSUES

Being related to two sides of the same phenomenon, these theories should be compatible. However, the interface between them is obscured by the FRT mistaking a subset of damaging processes for the whole, and the APT mistaking a cumulative quantitative process for a qualitative switch.

FUTURE DIRECTIONS

The manifestations of ROS-mediated cumulative chemical damage at the population level may include the often-observed negative correlation between fitness and the rate of its decline with increasing age, further linking FRT and APT. Antioxid. Redox Signal. 29, 1003-1017.

Methionine Sulfoxide Reductases of Archaea

Methionine sulfoxide reductases are found in all domains of life and are important in reversing the oxidative damage of the free and protein forms of methionine, a sulfur containing amino acid particularly sensitive to reactive oxygen species (ROS). Archaea are microbes of a domain of life distinct from bacteria and eukaryotes. Archaea are well known for their ability to withstand harsh environmental conditions that range from habitats of high ROS, such as hypersaline lakes of intense ultraviolet (UV) radiation and desiccation, to hydrothermal vents of low concentrations of dissolved oxygen at high temperature. Recent evidence reveals the methionine sulfoxide reductases of archaea function not only in the reduction of methionine sulfoxide but also in the ubiquitin-like modification of protein targets during oxidative stress, an association that appears evolutionarily conserved in eukaryotes. Here is reviewed methionine sulfoxide reductases and their distribution and function in archaea.

Nanozymatic Antioxidant System Based on MoS2 Nanosheets

The enzymatic antioxidant system (EAS) protects aerobic cells from oxidative stress. However, it is brittle and susceptible of inactivation of reactive oxygen species (ROS) immoderate production. Here, we demonstrated that MoS₂ nanosheets (few-layer MoS₂), as a multifunctional nanozyme, possess intrinsic activity of mimicking enzymes of superoxide dismutases (SODs), catalases (CATs), and peroxidases (PODs) under physiological conditions (pH 7.4, 25 °C). Further, MoS₂ nanosheets showed POD-like activity by transferring electrons instead of generating ROS. Similar to EAS, a defense termed nanozymatic antioxidant system (NAS) was developed by MoS₂ nanosheets, for regulation of oxidative stress. Surprisingly, this NAS can effectively scavenge other free radicals including hydroxyl radicals (^•OH), nitrogen-centered free radicals (^•DPPH), and nitric oxide (^•NO). To evaluate these unique properties of MoS₂-based NAS in vivo, Escherichia coli ( E. coli), Staphylococcus aureus ( S. aureus), and A549 cell models were established, respectively. These results showed MoS₂ nanosheets superiorly protect bacteria and cells against oxidative injury caused by H₂O₂. This work makes MoS₂ nanosheets promising antioxidants in the pathological processes and expands their application in biocatalysis and nano-biomedicine.

RubisCO Early Oxygenase Activity: A Kinetic and Evolutionary Perspective

RubisCO (D-ribulose 1,5-bisphosphate carboxylase/oxygenase) is Earth's main enzyme responsible for CO₂ fixation via carboxylation of ribulose-1,5-bisphosphate (RuBP) into organic matter. Besides the carboxylation reaction, RubisCO also catalyzes the oxygenation of RuBP by O₂ , which is probably as old as its carboxylation properties. Based on molecular phylogeny, the occurrence of the reactive oxygen species (ROS)-removing system and kinetic properties of different RubisCO forms, we postulated that RubisCO oxygenase activity appeared in local microoxic areas, yet before the appearance of oxygenic photosynthesis. Here, in reviewing the literature, we present a novel hypothesis: the RubisCO early oxygenase activity hypothesis. This hypothesis may be compared with the exaptation hypothesis, according to which latent RubisCO oxygenase properties emerged later during the oxygenation of the Earth's atmosphere. The reconstruction of ancestral RubisCO forms using ancestral sequence reconstruction (ASR) techniques, as a promising way for testing of RubisCO early oxygenase activity hypothesis, is presented.

The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels

Ancient oxygenic photosynthetic prokaryotes produced oxygen as a waste product, but existed for a long time under an oxygen-free (anoxic) atmosphere, before an oxic atmosphere emerged. The change in oxygen levels in the atmosphere influenced the chemistry and structure of many enzymes that contained prosthetic groups that were inactivated by oxygen. In the genome of Acaryochloris marina, multiple gene copies exist for proteins that are normally encoded by a single gene copy in other cyanobacteria. Using high throughput RNA sequencing to profile transcriptome responses from cells grown under microoxic and hyperoxic conditions, we detected 8446 transcripts out of the 8462 annotated genes in the Cyanobase database. Two-thirds of the 50 most abundant transcripts are key proteins in photosynthesis. Microoxic conditions negatively affected the levels of expression of genes encoding photosynthetic complexes, with the exception of some subunits. In addition to the known regulation of the multiple copies of psbA, we detected a similar transcriptional pattern for psbJ and psbU, which might play a key role in the altered components of photosystem II. Furthermore, regulation of genes encoding proteins important for reactive oxygen species-scavenging is discussed at genome level, including, for the first time, specific small RNAs having possible regulatory roles under varying oxygen levels.