Phylogenetic distribution of catalase-peroxidases: are there patches of order in chaos?

Shifts in phytoplankton and zooplankton communities in three cyanobacteria-dominated lakes after treatment with hydrogen peroxide

Cyanobacteria can reach high densities in eutrophic lakes, which may cause problems due to their potential toxin production. Several methods are in use to prevent, control or mitigate harmful cyanobacterial blooms. Treatment of blooms with low concentrations of hydrogen peroxide (H2O2) is a promising emergency method. However, effects of H2O2 on cyanobacteria, eukaryotic phytoplankton and zooplankton have mainly been studied in controlled cultures and mesocosm experiments, while much less is known about the effectiveness and potential side effects of H2O2 treatments on entire lake ecosystems. In this study, we report on three different lakes in the Netherlands that were treated with average H2O2 concentrations ranging from 2 to 5 mg L-1 to suppress cyanobacterial blooms. Effects on phytoplankton and zooplankton communities, on cyanotoxin concentrations, and on nutrient availability in the lakes were assessed. After every H2O2 treatment, cyanobacteria drastically declined, sometimes by more than 99%, although blooms of Dolichospermum sp., Aphanizomenon sp., and Planktothrix rubescens were more strongly suppressed than a Planktothrix agardhii bloom. Eukaryotic phytoplankton were not significantly affected by the H2O2 additions and had an initial advantage over cyanobacteria after the treatment, when ample nutrients and light were available. In all three lakes, a new cyanobacterial bloom developed within several weeks after the first H2O2 treatment, and in two lakes a second H2O2 treatment was therefore applied to again suppress the cyanobacterial population. Rotifers strongly declined after most H2O2 treatments except when the H2O2 concentration was ≤ 2 mg L-1, whereas cladocerans were only mildly affected and copepods were least impacted by the added H2O2. In response to the treatments, the cyanotoxins microcystins and anabaenopeptins were released from the cells into the water column, but disappeared after a few days. We conclude that lake treatments with low concentrations of H2O2 can be a successful tool to suppress harmful cyanobacterial blooms, but may negatively affect some of the zooplankton taxa in lakes. We advise pre-tests prior to the treatment of lakes to define optimal treatment concentrations that kill the majority of the cyanobacteria and to minimize potential side effects on non-target organisms. In some cases, the pre-tests may discourage treatment of the lake.

Key candidate genes for male sterility in peppers unveiled via transcriptomic and proteomic analyses

This study aimed to enhance the use of male sterility in pepper to select superior hybrid generations. Transcriptomic and proteomic analyses of fertile line 1933A and nucleic male sterility line 1933B of Capsicum annuum L. were performed to identify male sterility-related proteins and genes. The phylogenetic tree, physical and chemical characteristics, gene structure characteristics, collinearity and expression characteristics of candidate genes were analyzed. The study identified 2,357 differentially expressed genes, of which 1,145 and 229 were enriched in the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases, respectively. A total of 7,628 quantifiable proteins were identified and 29 important proteins and genes were identified. It is worth noting that the existence of CaPRX genes has been found in both proteomics and transcriptomics, and 3 CaPRX genes have been identified through association analysis. A total of 66 CaPRX genes have been identified at the genome level, which are divided into 13 subfamilies, all containing typical CaPRX gene conformal domains. It is unevenly distributed across 12 chromosomes (including the virtual chromosome Chr00). Salt stress and co-expression analysis show that male sterility genes are expressed to varying degrees, and multiple transcription factors are co-expressed with CaPRXs, suggesting that they are involved in the induction of pepper salt stress. The study findings provide a theoretical foundation for genetic breeding by identifying genes, metabolic pathways, and molecular mechanisms involved in male sterility in pepper.

The Structural Biology of Catalase Evolution

Catalases are essential enzymes for removal of hydrogen peroxide, enabling aerobic and anaerobic metabolism in an oxygenated atmosphere. Monofunctional heme catalases, catalase-peroxidases, and manganese catalases, evolved independently more than two billion years ago, constituting a classic example of convergent evolution. Herein, the diversity of catalase sequences is analyzed through sequence similarity networks, providing the context for sequence distribution of major catalase families, and showing that many divergent catalase families remain to be experimentally studied.

Catalase from the Antarctic Fungus Aspergillus fumigatus I-9-Biosynthesis and Gene Characterization

Extremely cold habitats are a serious challenge for the existing there organisms. Inhabitants of these conditions are mostly microorganisms and lower mycetae. The mechanisms of microbial adaptation to extreme conditions are still unclear. Low temperatures cause significant physiological and biochemical changes in cells. Recently, there has been increasing interest in the relationship between low-temperature exposure and oxidative stress events, as well as the importance of antioxidant enzymes for survival in such conditions. The catalase is involved in the first line of the cells' antioxidant defense. Published information supports the concept of a key role for catalase in antioxidant defense against cold stress in a wide range of organisms isolated from the Antarctic. Data on representatives of microscopic fungi, however, are rarely found. There is scarce information on the characterization of catalase synthesized by adapted to cold stress organisms. Overall, this study aimed to observe the role of catalase in the survival strategy of filamentous fungi in extremely cold habitats and to identify the gene encoded catalase enzyme. Our results clearly showed that catalase is the main part of antioxidant enzyme defense in fungal cells against oxidative stress caused by low temperature exposure.

Broad spectrum and species specificity of plant allelochemicals 1,2-benzenediol and 3-indoleacrylic acid against marine and freshwater harmful algae

Allelochemicals derived from plants have shown great potential in mitigating harmful algal blooms (HABs), although different algal species can respond differently to these chemicals. Therefore, we first investigated the allelopathic effects of two newly identified plant-derived allelochemicals, 1,2-benzenediol (1,2-BD) and 3-indoleacrylic acid (3-IDC), on six algal species. Then we further evaluated the allelopathic responses of two bloom-forming species, Microcystis aeruginosa FACHB-905 and Heterosigma akashiwo to 1,2-BD. Results showed that 1,2-BD had a broader antialgal spectrum than 3-IDC. Allelopathic response analysis indicated that 1,2-BD consistently and stably inhibit the growth of M. aeruginosa FACHB-905, with inhibitory mechanism being disruption of photosynthetic activity, overwhelming of the antioxidant system and activation of programmed cell death (PCD). H. akashiwo displayed resistance to 1,2-BD during exposure, and the growth inhibition was mainly attributed to PCD. Therefore, the species-specific allelopathic responses provide new insights for controlling HABs using 1,2-BD and 3-IDC.

The harmful cyanobacterium Microcystis aeruginosa PCC7806 is more resistant to hydrogen peroxide at elevated CO2

Rising atmospheric CO2 can intensify harmful cyanobacterial blooms in eutrophic lakes. Worldwide, these blooms are an increasing environmental concern. Low concentrations of hydrogen peroxide (H2O2) have been proposed as a short-term but eco-friendly approach to selectively mitigate cyanobacterial blooms. However, sensitivity of cyanobacteria to H2O2 can vary depending on the available resources. To find out how cyanobacteria respond to H2O2 under elevated CO2, Microcystis aeruginosa PCC 7806 was cultured in chemostats with nutrient-replete medium under C-limiting and C-replete conditions (150 ppm and 1500 ppm CO2, respectively). Microcystis chemostats exposed to high CO2 showed higher cell densities, biovolumes, and microcystin contents, but a lower photosynthetic efficiency and pH compared to the cultures grown under low CO2. Subsamples of the chemostats were treated with different concentrations of H2O2 (0-10 mg·L-1 H2O2) in batch cultures under two different light intensities (15 and 100 μmol photons m-2·s-1) and the response in photosynthetic vitality was monitored during 24 h. Results showed that Microcystis was more resistant to H2O2 at elevated CO2 than under carbon-limited conditions. Both low and high CO2-adapted cells were more sensitive to H2O2 at high light than at low light. Microcystins (MCs) leaked out of the cells of cultures exposed to 2-10 mg·L-1 H2O2, while the sum of intra- and extracellular MCs decreased. Although both H2O2 and CO2 concentrations in lakes vary in response to many factors, these results imply that it may become more difficult to suppress cyanobacterial blooms in eutrophic lakes when atmospheric CO2 concentrations continue to rise.

Comparison of Fungal Thermophilic and Mesophilic Catalase-Peroxidases for Their Antioxidative Properties

Catalase-peroxidases (KatGs) are unique bifunctional oxidoreductases that contain heme in their active centers allowing both the peroxidatic and catalatic reaction modes. These originally bacterial enzymes are broadly distributed among various fungi allowing them to cope with reactive oxygen species present in the environment or inside the cells. We used various biophysical, biochemical, and bioinformatics methods to investigate differences between catalase-peroxidases originating in thermophilic and mesophilic fungi from different habitats. Our results indicate that the architecture of the active center with a specific post-translational modification is highly similar in mesophilic and thermophilic KatG and also the peroxidatic acitivity with ABTS, guaiacol, and L-DOPA. However, only the thermophilic variant CthedisKatG reveals increased manganese peroxidase activity at elevated temperatures. The catalatic activity releasing molecular oxygen is comparable between CthedisKatG and mesophilic MagKatG1 over a broad temperature range. Two constructed point mutations in the active center were performed selectively blocking the formation of described post-translational modification in the active center. They exhibited a total loss of catalatic activity and changes in the peroxidatic activity. Our results indicate the capacity of bifunctional heme enzymes in the variable reactivity for potential biotech applications.

Comparative assessment of algaecide performance on freshwater phytoplankton: Understanding differential sensitivities to frame cyanobacteria management

Cyanobacterial bloom represent a growing threat to global water security. With fast proliferation, they raise great concern due to potential health and socioeconomic concerns. Algaecides are commonly employed as a mitigative measure to suppress and manage cyanobacteria. However, recent research on algaecides has a limited phycological focus, concentrated predominately on cyanobacteria and chlorophytes. Without considering phycological diversity, generalizations crafted from these algaecide comparisons present a biased perpective. To limit the collateral impacts of algaecide interventions on phytoplankton communities it is critical to understand differential phycological sensitivities for establishing optimal dosage and tolerance thresholds. This research attempts to fill this knowledge gap and provide effective guidelines to frame cyanobacterial management. We investigate the effect of two common algaecides, copper sulfate (CuSO₄) and hydrogen peroxide (H₂O₂), on four major phycological divisions (chlorophytes, cyanobacteria, diatoms, and mixotrophs). All phycological divisions exhibited greater sensitivity to copper sulfate, except chlorophytes. Mixotrophs and cyanobacteria displayed the highest sensitivity to both algaecides with the highest to lowest sensitivity being observed as follows: mixotrophs, cyanobacteria, diatoms, and chlorophytes. Our results suggest that H₂O₂ represents a comparable alternative to CuSO₄ for cyanobacterial control. However, some eukaryotic divisions such as mixotrophs and diatoms mirrored cyanobacteria sensitivity, challenging the assumption that H₂O₂ is a selective cyanocide. Our findings suggest that optimizing algaecide treatments to suppress cyanobacteria while minimizing potential adverse effects on other phycological members is unattainable. An apparent trade-off between effective cyanobacterial management and conserving non-targeted phycological divisions is expected and should be a prime consideration of lake management.

Repeated hydrogen peroxide dosing briefly reduces cyanobacterial blooms and microcystin while increasing fecal bacteria indicators in a eutrophic pond

This study explored the effects of H₂O₂ on Cyanobacteria and non-target microbes using fluorometry, microscopy, flow cytometry, and high throughput DNA sequencing of the 16S rRNA gene during a series of mesocosm and whole-ecosystem experiments in a eutrophic pond in NY, USA. The addition of H₂O₂ (8 mg/L) significantly reduced Cyanobacteria concentrations during a majority of experiments (66%; 6 of 9) and significantly increased eukaryotic green and unicellular brown algae in 78% and 45% of experiments, respectively. While heterotrophic bacteria declined significantly following H₂O₂ addition in all experiments, bacteria indicative of potential fecal contamination (Escherichia coli, Enterococcus, fecal coliform bacteria) consistently and significantly increased in response to H₂O₂, evidencing a form of 'pollution swapping'. H₂O₂ more effectively reduced Cyanobacteria in enclosed mesocosms compared to whole-ecosystem applications. Ten whole-pond H₂O₂ applications over a two-year period temporarily reduced cyanobacterial levels but never reduced concentrations below bloom thresholds and populations always rebounded in two weeks or less. The bacterial phyla of Cyanobacteria, Actinobacteria, and Planctomycetes were the most negatively impacted by H₂O₂. Microcystis was always reduced by H₂O₂, as was the toxin microcystin, but Microcystis remained dominant even after repeated H₂O₂ treatments. Although H₂O₂ favored the growth of eukaryotic algae over potentially harmful Cyanobacteria, the inability of H₂O₂ to end cyanobacterial blooms in this eutrophic waterbody suggests it is a non-ideal mitigation approach in high biomass ecosystems and should be used judiciously due to potential negative impacts on non-target organisms and promotion of bacteria indicative of fecal contamination.

Catalases in the pathogenesis of Sporothrix schenckii research

Pathogenic fungal infection success depends on the ability to escape the immune response. Most strategies for fungal infection control are focused on the inhibition of virulence factors and increasing the effectiveness of antifungal drugs. Nevertheless, little attention has been focused on their physiological resistance to the host immune system. Hints may be found in pathogenic fungi that also inhabit the soil. In nature, the saprophyte lifestyle of fungi is also associated with predators that can induce oxidative stress upon cell damage. The natural sources of nutrients for fungi are linked to cellulose degradation, which in turn generates reactive oxygen species (ROS). Overall, the antioxidant arsenal needed to thrive both in free-living and pathogenic lifestyles in fungi is fundamental for success. In this review, we present recent findings regarding catalases and oxidative stress in fungi and how these can be in close relationship with pathogenesis. Additionally, special focus is placed on catalases of Sporothrix schenckii as a pathogenic model with a dual lifestyle. It is assumed that catalase expression is activated upon exposure to H₂O₂, but there are reports where this is not always the case. Additionally, it may be relevant to consider the role of catalases in S. schenckii survival in the saprophytic lifestyle and why their study can assess their involvement in the survival and therefore, in the virulence phenotype of different species of Sporothrix and when each of the three catalases are required. Also, studying antioxidant mechanisms in other isolates of pathogenic and free-living fungi may be linked to the virulence phenotype and be potential therapeutic and diagnostic targets. Thus, the rationale for this review to place focus on fungal catalases and their role in pathogenesis in addition to counteracting the effect of immune system reactive oxygen species. Fungi that thrive in soil and have mammal hosts could shed light on the importance of these enzymes in the two types of lifestyles. We look forward to encouraging more research in a myriad of areas on catalase biology with a focus on basic and applied objectives and placing these enzymes as virulence determinants.

Impact of melatonin on the hydrogen peroxide treatment efficacy in Microcystis aeruginosa: Cell growth, oxidative stress response, and gene transcription

A study was conducted to determine how melatonin (MLT), a growth regulator, affects Microcystis aeruginosa cell behaviour and how MLT exposed cells respond to hydrogen peroxide (H₂O₂) treatment. MLT promotes the growth, chl-a content, Fv/Fm values, and microcystins (MCs) production of M. aeruginosa at low concentrations of 1-2.5 μmol/L but suppresses the growth at high concentrations (5-10 μmol/L). The cellular and genetic responses of MLT pre-treated cells to H₂O₂ treatment were examined further. Further research found that the cells pre-treated with MLT were susceptible to a range of growth-promoting, inhibiting and lethal effects when exposed to higher levels of H₂O₂. A dose-dependent pattern was observed under conditions of 0.05-0.2 mmol/L H₂O₂ with 0.5-2.5 μmol/L MLT concentrations to different degrees. High doses of H₂O₂ (0.2 and 0.3 mmol/L) typically lead to cell lysis and release of MCs in 5.0 and 10 μmol/L MLT pre-treated cells. A decrease in SOD/CAT activities and an increase in MDA levels validated the growth reduction. Furthermore, higher cell lysis and release of intracellular MCs were observed when H₂O₂ was increased for 5-10 μmol/L MLT pre-treated cells. This led to a higher accumulation of extracellular MCs. The results provide insight into how MLT influences H₂O₂ damage and assist in identifying situations where H₂O₂ treatment of cyanobacterial blooms is most appropriate.

Suppressing cyanobacterial dominance by UV-LED TiO2-photocatalysis in a drinking water reservoir: A mesocosm study

Cyanobacteria and their toxic secondary metabolites present challenges for water treatment globally. In this study we have assessed TiO₂ immobilized onto recycled foamed glass beads by a facile calcination method, combined in treatment units with 365 nm UV-LEDs. The treatment system was deployed in mesocosms within a eutrophic Brazilian drinking water reservoir. The treatment units were deployed for 7 days and suppressed cyanobacterial abundance by 85% while at the same time enhancing other water quality parameters; turbidity and transparency improved by 40 and 81% respectively. Genomic analysis of the microbiota in the treated mesocosms revealed that the composition of the cyanobacterial community was affected and the abundance of Bacteroidetes and Proteobacteria increased during cyanobacterial suppression. The effect of the treatment on zooplankton and other eukaryotes was also monitored. The abundance of zooplankton decreased while Chrysophyte and Alveolata loadings increased. The results of this proof-of-concept study demonstrate the potential for full-scale, in-reservoir application of advanced oxidation processes as complementary water treatment processes.

Neuronal temperature perception induces specific defenses that enable C. elegans to cope with the enhanced reactivity of hydrogen peroxide at high temperature

Hydrogen peroxide is the most common reactive chemical that organisms face on the microbial battlefield. The rate with which hydrogen peroxide damages biomolecules required for life increases with temperature, yet little is known about how organisms cope with this temperature-dependent threat. Here, we show that Caenorhabditis elegans nematodes use temperature information perceived by sensory neurons to cope with the temperature-dependent threat of hydrogen peroxide produced by the pathogenic bacterium Enterococcus faecium. These nematodes preemptively induce the expression of specific hydrogen peroxide defenses in response to perception of high temperature by a pair of sensory neurons. These neurons communicate temperature information to target tissues expressing those defenses via an insulin/IGF1 hormone. This is the first example of a multicellular organism inducing their defenses to a chemical when they sense an inherent enhancer of the reactivity of that chemical.

A Large-Scale Multiple Genome Comparison of Acidophilic Archaea (pH ≤ 5.0) Extends Our Understanding of Oxidative Stress Responses in Polyextreme Environments

Acidophilic archaea thrive in anaerobic and aerobic low pH environments (pH < 5) rich in dissolved heavy metals that exacerbate stress caused by the production of reactive oxygen species (ROS) such as hydrogen peroxide (H2O2), hydroxyl radical (OH) and superoxide (O2−). ROS react with lipids, proteins and nucleic acids causing oxidative stress and damage that can lead to cell death. Herein, genes and mechanisms potentially involved in ROS mitigation are predicted in over 200 genomes of acidophilic archaea with sequenced genomes. These organisms are often be subjected to simultaneous multiple stresses such as high temperature, high salinity, low pH and high heavy metal loads. Some of the topics addressed include: (1) the phylogenomic distribution of these genes and what this can tell us about the evolution of these mechanisms in acidophilic archaea; (2) key differences in genes and mechanisms used by acidophilic versus non-acidophilic archaea and between acidophilic archaea and acidophilic bacteria and (3) how comparative genomic analysis predicts novel genes or pathways involved in oxidative stress responses in archaea and likely horizontal gene transfer (HGT) events.

Differential Effect of Hydroxen Peroxide οn Toxic Cyanobacteria of Hypertrophic Mediterranean Waterbodies

Cyanobacterial blooms have been known since ancient times; however, they are currently increasing globally. Human and ecological health risks posed by harmful cyanobacterial blooms have been recorded around the world. These risks are mainly associated with their ability to affect the ecosystem chain by different mechanisms like the production of cyanotoxins, especially microcystins. Their expansion and their harmful effects have led many researchers to seek techniques and strategies to control them. Among them, hydrogen peroxide could be a promising tool against cyanobacteria and cyanotoxins and it is well-established as an environmentally friendly oxidizing agent because of its rapid decomposition into oxygen and water. The aim of the present study was to evaluate the effect of hydrogen peroxide on phytoplankton from two hypertrophic waterbodies in Greece. The effect of hydrogen peroxide on concentration of microcystins found in the waterbodies was also studied. Treatment with 4 mg/L hydrogen peroxide was applied to water samples originated from the waterbodies and Cyanobacterial composition and biomass, phycocyanin, chlorophyll-a, and intra-cellular and total microcystin concentrations were studied. Cyanobacterial biomass and phycocyanin was reduced significantly after the application of 4 mg/L hydrogen peroxide in water treatment experiments while chlorophytes and extra-cellular microcystin concentrations were increased. Raphidiopsis (Cylindrospermopsis) raciborskii was the most affected cyanobacterial species after treatment of the water of the Karla Reservoir in comparison to Aphanizomenon favaloroi, Planktolyngbya limnetica, and Chroococcus sp. Furthermore, Microcystis aeruginosa was more resistant to the treatment of Pamvotis lake water in comparison with Microcystis wesenbergii and Microcystis panniformis. Our study showed that hydrogen peroxide differentially impacts the members of the phytoplankton community, affecting, thus, its overall efficacy. Different effects of hydrogen peroxide treatment were observed among cyanobacerial genera as well as among cyanobacterial species of the same genus. Different effects could be the result of the different resistance mechanisms of each genus or species to hydrogen peroxide. Hydrogen peroxide could be used as a treatment for the mitigation of cyanobacterial blooms in a waterbody; however, the biotic and abiotic characteristics of the waterbody should be considered.

Modulation of sensory perception by hydrogen peroxide enables Caenorhabditis elegans to find a niche that provides both food and protection from hydrogen peroxide

Hydrogen peroxide (H2O2) is the most common chemical threat that organisms face. Here, we show that H2O2 alters the bacterial food preference of Caenorhabditis elegans, enabling the nematodes to find a safe environment with food. H2O2 induces the nematodes to leave food patches of laboratory and microbiome bacteria when those bacterial communities have insufficient H2O2-degrading capacity. The nematode's behavior is directed by H2O2-sensing neurons that promote escape from H2O2 and by bacteria-sensing neurons that promote attraction to bacteria. However, the input for H2O2-sensing neurons is removed by bacterial H2O2-degrading enzymes and the bacteria-sensing neurons' perception of bacteria is prevented by H2O2. The resulting cross-attenuation provides a general mechanism that ensures the nematode's behavior is faithful to the lethal threat of hydrogen peroxide, increasing the nematode's chances of finding a niche that provides both food and protection from hydrogen peroxide.

A critical review on operation and performance of source water control strategies for cyanobacterial blooms: Part I-chemical control methods

Cyanobacterial blooms produce nuisance metabolites (e.g., cyanotoxins and T&O compounds) thereby posing water quality management issues for aquatic sources used for potable water production, aquaculture, and recreation. A variety of in-lake/reservoir control measures are implemented to reduce the abundance of nuisance cyanobacteria biomass or decrease the amount of available phosphorous (P). This paper critically reviews the chemical control strategies implemented for in-lake/reservoir management of cyanobacterial blooms, i.e., algaecides and nutrient sequestering coagulants/flocculants, by highlighting (i) their mode of action, (ii) cases of successful and unsuccessful treatment, (iii) and factors influencing performance (e.g., water quality, process control techniques, source water characteristics, etc.). Algaecides generally result in immediate improvements in water quality and offer selective cyanobacterial control when peroxide-based alagecides are used. However, they have a range of limitations: causing cell lysis and release of cyanotoxins, posing negative impacts on aquatic plants and animals, leaving behind environmentally relevant treatment residuals (e.g., Cu in water and sediments), and offering only short-term bloom control characterized by cyanobacterial rebound. Coagulants/flocculants (alum, iron, calcium, and lanthanum bentonite) offer long-term internal nutrient control when external nutrient loading is controlled. Treatment performance is often influenced by background water quality conditions, and source water characteristics (e.g., surface area, depth, mixing regimes, and residence time). The reviewed case studies highlight that external nutrient load reduction is the most fundamental aspect of cyanobacterial control. None of the reviewed control strategies provide a comprehensive solution to cyanobacterial blooms.

Divergence of reactions to arsenic (As) toxicity in tobacco (Nicotiana benthamiana) plants: A lesson from peroxidase involvement

To evaluate the multiplicity of reactions to toxic metalloid arsenic (As) with specific emphasis on the role of plant peroxidases, a model plant Nicotiana benthamiana was cultivated in in vitro conditions at various doses of As (applied as As5+ up to 80 μM). After 28-day cultivation, several physiological characteristics such as plant growth, photosynthetic pigment concentration, As concentration, peroxidase (POX) expression levels, and POX activity were evaluated. A newly sequenced gene for POX has been identified, that belongs to the Class III plant extracellular peroxidases, and its relationship to the genus Solanum as the most relative species has been confirmed. In the control and selected As treatments (20As, 50As, and 80As), newly identified POX expression and POX activity were continuously detected during the whole cultivation period. The plant reactions to As stress were distinguished into three groups: low As, moderate As, and high As. A tight relationship was found between the photosynthetic pigments and POX expression. Accumulation of As in roots and shoots showed correlations with POX activities. The results showed that the diversity of reactions depends on As dose and time exposure and indicate an interface of peroxidase functional role with other physiological processes in plants suffering from As toxicity.

Effect of hydrogen peroxide on natural phytoplankton and bacterioplankton in a drinking water reservoir: Mesocosm-scale study

Cyanobacterial blooms are increasingly reported worldwide, presenting a challenge to water treatment plants and concerning risks to human health and aquatic ecosystems. Advanced oxidative processes comprise efficient and safe methods for water treatment. Hydrogen peroxide (H₂O₂) has been proposed as a sustainable solution to mitigate bloom-forming cyanobacteria since this group presents a higher sensitivity compared to other phytoplankton, with no major risks to the environment at low concentrations. Here, we evaluated the effects of a single H₂O₂ addition (10 mg L^-1) over 120 h in mesocosms introduced in a reservoir located in a semi-arid region presenting a Planktothrix-dominated cyanobacterial bloom. We followed changes in physical and chemical parameters and in the bacterioplankton composition. H₂O₂ efficiently suppressed cyanobacteria, green algae, and diatoms over 72 h, leading to an increase in transparency and dissolved organic carbon, and a decrease in dissolved oxygen and pH, while nutrient concentrations were not affected. After 120 h, cyanobacterial abundance remained low and green algae became dominant. 16S rRNA sequencing revealed that the original cyanobacterial bloom was composed by Planktothrix, Cyanobium and Microcystis. Only Cyanobium increased in relative abundance at 120 h, suggesting regrowth. A prominent change in the composition of heterotrophic bacteria was observed with Exiguobacterium, Paracoccus and Deinococcus becoming the most abundant genera after the H₂O₂ treatment. Our results indicate that this approach is efficient in suppressing cyanobacterial blooms and improving water quality in tropical environments. Monitoring changes in abiotic parameters and the relative abundance of specific bacterial taxa could be used to anticipate the regrowth of cyanobacteria after H₂O₂ degradation and to indicate where in the reservoir H₂O₂ should be applied so the effects are still felt in the water treatment plant intake.

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 Efficacy of Hydrogen Peroxide in Mitigating Cyanobacterial Blooms and Altering Microbial Communities across Four Lakes in NY, USA

Hydrogen peroxide (H₂O₂) has been proposed as an agent to mitigate toxic cyanobacterial blooms due to the heightened sensitivity of cyanobacteria to reactive oxygen species relative to eukaryotic organisms. Here, experiments were conducted using water from four diverse, eutrophic lake ecosystems to study the effects of H₂O₂ on cyanobacteria and non-target members of the microbial community. H₂O₂ was administered at 4 µg L^-1 and a combination of fluorometry, microscopy, flow cytometry, and high throughput DNA sequencing were used to quantify the effects on eukaryotic and prokaryotic plankton communities. The addition of H₂O₂ resulted in a significant reduction in cyanobacteria levels in nearly all experiments (10 of 11), reducing their relative abundance from, on average, 85% to 29% of the total phytoplankton community with Planktothrix being highly sensitive, Microcystis being moderately sensitive, and Cylindrospermopsis being most resistant. Concurrently, eukaryotic algal levels increased in 75% of experiments. The bacterial phyla Actinobacteria, cyanobacteria, Planctomycetes, and Verrucomicrobia were most negatively impacted by H₂O₂, with Actinobacteria being the most sensitive. The ability of H₂O₂ to reduce, but not fully eliminate, cyanobacteria from the eutrophic water bodies studied here suggests it may not be an ideal mitigation approach in high biomass ecosystems.

Global analysis of non-animal peroxidases provides insights into the evolution of this gene family in the green lineage

The non-animal peroxidases belong to a superfamily of oxidoreductases that reduce hydrogen peroxide and oxidize numerous substrates. Since their initial characterization in 1992, a number of studies have provided an understanding of the origin and evolution of this protein family. Here, we report a comprehensive evolutionary analysis of non-animal peroxidases using integrated in silico and biochemical approaches. Thanks to the availability of numerous genomic sequences from more than 2500 species belonging to 14 kingdoms together with expert and comprehensive annotation of peroxidase sequences that have been centralized in a dedicated database, we have been able to use phylogenetic reconstructions to increase our understanding of the evolutionary processes underlying the diversification of non-animal peroxidases. We analysed the distribution of all non-animal peroxidases in more than 200 eukaryotic organisms in silico. First, we show that the presence or absence of non-animal peroxidases correlates with the presence or absence of certain organelles or with specific biological processes. Examination of almost 2000 organisms determined that ascorbate peroxidases (APxs) and cytochrome c peroxidases (CcPs) are present in those containing chloroplasts and mitochondria, respectively. Plants, which contain both organelles, are an exception and contain only APxs without CcP. Class II peroxidases (CII Prxs) are only found in fungi with wood-decay and plant-degradation abilities. Class III peroxidases (CIII Prxs) are only found in streptophyte algae and land plants, and have been subjected to large family expansion. Biochemical activities of APx, CcP, and CIII Prx assessed using protein extracts from 30 different eukaryotic organisms support the distribution of the sequences resulting from our in silico analysis. The biochemical results confirmed both the presence and classification of the non-animal peroxidase encoding sequences.

Caenorhabditis elegans processes sensory information to choose between freeloading and self-defense strategies

Hydrogen peroxide is the preeminent chemical weapon that organisms use for combat. Individual cells rely on conserved defenses to prevent and repair peroxide-induced damage, but whether similar defenses might be coordinated across cells in animals remains poorly understood. Here, we identify a neuronal circuit in the nematode Caenorhabditis elegans that processes information perceived by two sensory neurons to control the induction of hydrogen peroxide defenses in the organism. We found that catalases produced by Escherichia coli, the nematode's food source, can deplete hydrogen peroxide from the local environment and thereby protect the nematodes. In the presence of E. coli, the nematode's neurons signal via TGFβ-insulin/IGF1 relay to target tissues to repress expression of catalases and other hydrogen peroxide defenses. This adaptive strategy is the first example of a multicellular organism modulating its defenses when it expects to freeload from the protection provided by molecularly orthologous defenses from another species.

Proteomic mechanisms for the stimulatory effects of antibiotics on Microcystis aeruginosa during hydrogen peroxide treatment

Application of low dosage of H₂O₂ at early stage of cyanobacterial life cycle is a promising route for cyanobacterial bloom mitigation, which could minimize adverse effects on non-target organisms. Besides, influence of co-existing contaminants on cyanobacterial bloom mitigation under combined pollution conditions remains unclear. This study assessed the influence of a mixture of four frequently detected antibiotics (tetracycline, sulfamethoxazole, ciprofloxacin and amoxicillin) during H₂O₂ treatment of Microcystis aeruginosa at early growth stage. H₂O₂ significantly (p < 0.05) inhibited growth rate, chlorophyll a content, F_v/F_m and rETR_max in a dose-dependent manner at low doses of 0.25-1 mg L^-1, through downregulating proteins involved in cell division, cellular component organization, gene expression and photosynthesis. Although H₂O₂ increased microcystin content in each cyanobacterial cell through the upregulation of microcystin synthetases (mcyC and mcyF), total microcystin concentration in H₂O₂ treated groups was significantly (p < 0.05) reduced due to the decrease of cell density. Existence of 80 and 200 ng L^-1 mixed antibiotics during H₂O₂ treatment facilitated the scavenging of ROS by antioxidant enzymes and significantly (p < 0.05) stimulated growth, photosynthesis, microcystin synthesis and microcystin release in H₂O₂ treated cells, through the upregulation of proteins involved in photosynthesis, oxidation-reduction process, biosynthesis, gene expression and transport. Mixed antibiotics increased the hazard of M. aeruginosa during H₂O₂ treatment, through the stimulation of microcystin synthesis and release at the proteomic level. Each target antibiotic should be controlled below 5 ng L^-1 before the application of H₂O₂ for eliminating the interference of antibiotics on cyanobacterial bloom mitigation.

Studies on peroxidase production and detection of Sporotrichum thermophile-like catalase-peroxidase gene in a B acillus species isolated from Hogsback forest reserve, South Africa

This study sought to determine the process conditions for optimum peroxidase production by a Bacillus species (Bacillus sp. FALADE-1-KX640922) isolated from Hogsback forest reserve in South Africa and characterize the peroxidase gene in the bacteria. We optimized peroxidase production by manipulating the environmental and nutritional parameters under submerged fermentation. Subsequently, the gene encoding heme-peroxidase was determined through nested polymerase chain reaction and Sanger DNA sequencing. The studied bacteria had maximum peroxidase production at pH 8, 30 °C and 150 rpm. The addition of guaiacol to lignin fermentation medium enhanced peroxidase production by over 100 % in the studied bacteria. However, the other lignin monomers (veratryl alcohol, vanillin, vanillic acid and ferulic acid) repressed the enzyme activity. Modification of the fermentation medium with ammonium sulphate gave the maximum peroxidase yield (8.87 U mL⁻¹). Under the predetermined culture conditions, Bacillus sp. FALADE-1 expressed maximum specific peroxidase activity at 48 h (8.32 U mg⁻¹). Interestingly, a search of the sequenced gene in PeroxiBase showed 100% similarity to Sporotrichum thermophile catalase-peroxidase gene (katG), as well, the deduced protein sequence clustered with bacterial catalase-peroxidases and had a molecular weight of about 11.45 kDa with 7.01 as the estimated isoelectric point. Subsequently, the nucleotide sequence was deposited in the National Center for Biotechnology Information (NCBI) repository with the accession number MF407314. In conclusion, Bacillus sp. FALADE-1 is a promising candidate for improved peroxidase production.

Suppressing Cyanobacteria with Hydrogen Peroxide Is More Effective at High Light Intensities

Hydrogen peroxide (H₂O₂) can be used as an emergency method to selectively suppress cyanobacterial blooms in lakes and drinking water reservoirs. However, it is largely unknown how environmental parameters alter the effectiveness of H₂O₂ treatments. In this study, the toxic cyanobacterial strain Microcystis aeruginosa PCC 7806 was treated with a range of H₂O₂ concentrations (0 to 10 mg/L), while being exposed to different light intensities and light colors. H₂O₂ treatments caused a stronger decline of the photosynthetic yield in high light than in low light or in the dark, and also a stronger decline in orange than in blue light. Our results are consistent with the hypothesis that H₂O₂ causes major damage at photosystem II (PSII) and interferes with PSII repair, which makes cells more sensitive to photoinhibition. Furthermore, H₂O₂ treatments caused a decrease in cell size and an increase in extracellular microcystin concentrations, indicative of leakage from disrupted cells. Our findings imply that even low H₂O₂ concentrations of 1–2 mg/L can be highly effective, if cyanobacteria are exposed to high light intensities. We therefore recommend performing lake treatments during sunny days, when a low H₂O₂ dosage is sufficient to suppress cyanobacteria, and may help to minimize impacts on non-target organisms.

In silico definition of new ligninolytic peroxidase sub-classes in fungi and putative relation to fungal life style

Ligninolytic peroxidases are microbial enzymes involved in depolymerisation of lignin, a plant cell wall polymer found in land plants. Among fungi, only Dikarya were found to degrade lignin. The increase of available fungal genomes allows performing an expert annotation of lignin-degrading peroxidase encoding sequences with a particular focus on Class II peroxidases (CII Prx). In addition to the previously described LiP, MnP and VP classes, based on sequence similarity, six new sub-classes have been defined: three found in plant pathogen ascomycetes and three in basidiomycetes. The presence of CII Prxs could be related to fungal life style. Typically, necrotrophic or hemibiotrophic fungi, either ascomycetes or basidiomycetes, possess CII Prxs while symbiotic, endophytic or biotrophic fungi do not. CII Prxs from ascomycetes are rarely subjected to duplications unlike those from basidiomycetes, which can form large recent duplicated families. Even if these CII Prxs classes form two well distinct clusters with divergent gene structures (intron numbers and positions), they share the same key catalytic residues suggesting that they evolved independently from similar ancestral sequences with few or no introns. The lack of CII Prxs encoding sequences in early diverging fungi, together with the absence of duplicated class I peroxidase (CcP) in fungi containing CII Prxs, suggests the potential emergence of an ancestral CII Prx sequence from the duplicated CcP after the separation between ascomycetes and basidiomycetes. As some ascomycetes and basidiomycetes did not possess CII Prx, late gene loss could have occurred.

Metalloproteins in the Biology of Heterocysts

Cyanobacteria are photoautotrophic microorganisms present in almost all ecologically niches on Earth. They exist as single-cell or filamentous forms and the latter often contain specialized cells for N₂ fixation known as heterocysts. Heterocysts arise from photosynthetic active vegetative cells by multiple morphological and physiological rearrangements including the absence of O₂ evolution and CO₂ fixation. The key function of this cell type is carried out by the metalloprotein complex known as nitrogenase. Additionally, many other important processes in heterocysts also depend on metalloproteins. This leads to a high metal demand exceeding the one of other bacteria in content and concentration during heterocyst development and in mature heterocysts. This review provides an overview on the current knowledge of the transition metals and metalloproteins required by heterocysts in heterocyst-forming cyanobacteria. It discusses the molecular, physiological, and physicochemical properties of metalloproteins involved in N₂ fixation, H₂ metabolism, electron transport chains, oxidative stress management, storage, energy metabolism, and metabolic networks in the diazotrophic filament. This provides a detailed and comprehensive picture on the heterocyst demands for Fe, Cu, Mo, Ni, Mn, V, and Zn as cofactors for metalloproteins and highlights the importance of such metalloproteins for the biology of cyanobacterial heterocysts.

An environmentally friendly approach for mitigating cyanobacterial bloom and their toxins in hypereutrophic ponds: Potentiality of a newly developed granular hydrogen peroxide-based compound

Cyanobacterial blooms and their associated toxins are growing issues for many aquatic resources, and pose a major threat to human health and ecological welfare. To control cyanobacterial blooms and their toxins, the efficacy of a newly developed granular compound (sodium carbonate peroxyhydrate 'SCP', trade name 'PAK® 27' algaecide) containing hydrogen peroxide (H₂O₂) as the active ingredient was investigated. First, the dose efficacy of the SCP that corresponded to 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 5.0 and 8.0 mg/L H₂O₂ was tested for 10 days in small-scale tanks installed in 0.1-acre experimental hypereutrophic ponds dominated by blooms of the toxic cyanobacterium Planktothrix sp. SCP ranging from 2.5-4.0 mg/L H₂O₂ selectively killed Planktothrix sp. without major impacts on either eukaryotic phytoplankton (e.g., diatom Synedra sp., green algae Spirogyra sp. and Cladophora sp.) or zooplankton (e.g., rotifers Brachionus sp. and cladocerans Daphnia sp.). Based on these results, SCP at 2.5 mg/L and 4.0 mg/L H₂O₂ were homogeneously introduced into entire water volume of the experimental ponds in parallel with untreated control ponds. The dynamics of cyanobacterium Planktothrix sp., microcystins (commonly occurring cyanotoxins), eukaryotic phytoplankton, zooplankton, and water quality parameters were measured daily for 10 days and followed by a weekly sampling for 6 weeks. Temporal analysis indicated that Planktothrix sp. blooms collapsed remarkably in both 2.5 mg/L and 4.0 mg/L H₂O₂ treatments. Both treatments also were accompanied by an overall reduction in the total microcystin concentration. At 2.5 mg/L H₂O₂, the growth of eukaryotic phytoplankton (Synedra and Cladophora sp.) increased, but these populations along with zooplankton (Brachionus and Daphnia sp.) were suppressed at 4.0 mg/L H₂O₂. The longevity of 2.5 and 4.0 mg/L H₂O₂ treatment effects were up to 5 weeks. In addition, the added granular algaecide degraded within a few days, thereby leaving no long-term traces of H₂O₂ in the environment.

Structure, kinetics, molecular and redox properties of a cytosolic and developmentally regulated fungal catalase-peroxidase

CAT-2, a cytosolic catalase-peroxidase (CP) from Neurospora crassa, which is induced during asexual spore formation, was heterologously expressed and characterized. CAT-2 had the Met-Tyr-Trp (M-Y-W) adduct required for catalase activity. Its K_M for H₂O₂ was micromolar for peroxidase and millimolar for catalase activity. A E_m = -158 mV reduction potential value was obtained and the Soret band shift suggested a mixture of low and high spin ferric iron. CAT-2 EPR spectrum at 10 K indicated an axial and a rhombic component. With peroxyacetic acid (PAA), formation of Compound I* was observed with EPR. CAT-2 homodimer crystallographic structure contained two K⁺ ions; Glu107 residues were displaced to bind them. CAT-2 showed the essential amino acid residues for activity in similar positions to other CPs. CAT-2 Arg426 is oriented towards the M-Y-W adduct, interacting with the deprotonated Tyr238 hydroxyl group. A perhydroxy modification of the indole nitrogen of Trp90 was oriented toward the catalytic His91. In contrast to cytochrome c peroxidase and ascorbate peroxidase, the catalase-peroxidase heme propionates are not exposed to the solvent. Together with other N. crassa enzymes that utilize H₂O₂ as a substrate, CAT-2 has many tryptophan and proline residues at its surface, probably related to H₂O₂ selection in water.

Separation of peroxidases from Miscanthus x giganteus, their partial characterisation and application for degradation of dyes

Due to wide applicative potential of peroxidases (POXs), the search for novel sources and forms, possibly with better characteristics and performances, is justified. In this study, POXs from Miscanthus x giganteus rhizomes grown in chernozem-like soil and mine tailings were examined. Higher activity of POXs in samples originating from the metal-contaminated soil was found. The quantity of acidic isoforms was much greater than basic. The rates of reactions catalysed by acidic POX isoforms decreased slightly at 50 °C, whereas stability of basic isoforms was affected at 40 °C. Concentrations of Zn, Mn and Fe were higher in rhizomes grown in mine tailings, and negatively correlated with the concentration of proteins. Basic POX isoforms effectively degraded CBB R250, while Amidoblack 10b was predominantly degraded by acidic isoforms. Thus, Miscanthus x giganteus can be used as a source of POXs which can be applied for dye decomposition and, possibly, waste water management.

Mutual synergy between catalase and peroxidase activities of the bifunctional enzyme KatG is facilitated by electron hole-hopping within the enzyme

KatG is a bifunctional, heme-dependent enzyme in the front-line defense of numerous bacterial and fungal pathogens against H₂O₂-induced oxidative damage from host immune responses. Contrary to the expectation that catalase and peroxidase activities should be mutually antagonistic, peroxidatic electron donors (PxEDs) enhance KatG catalase activity. Here, we establish the mechanism of synergistic cooperation between these activities. We show that at low pH values KatG can fully convert H₂O₂ to O₂ and H₂O only if a PxED is present in the reaction mixture. Stopped-flow spectroscopy results indicated rapid initial rates of H₂O₂ disproportionation slowing concomitantly with the accumulation of ferryl-like heme states. These states very slowly returned to resting (i.e. ferric) enzyme, indicating that they represented catalase-inactive intermediates. We also show that an active-site tryptophan, Trp-321, participates in off-pathway electron transfer. A W321F variant in which the proximal tryptophan was replaced with a non-oxidizable phenylalanine exhibited higher catalase activity and less accumulation of off-pathway heme intermediates. Finally, rapid freeze-quench EPR experiments indicated that both WT and W321F KatG produce the same methionine-tyrosine-tryptophan (MYW) cofactor radical intermediate at the earliest reaction time points and that Trp-321 is the preferred site of off-catalase protein oxidation in the native enzyme. Of note, PxEDs did not affect the formation of the MYW cofactor radical but could reduce non-productive protein-based radical species that accumulate during reaction with H₂O₂ Our results suggest that catalase-inactive intermediates accumulate because of off-mechanism oxidation, primarily of Trp-321, and PxEDs stimulate KatG catalase activity by preventing the accumulation of inactive intermediates.

Using H2O2 treatments for the degradation of cyanobacteria and microcystins in a shallow hypertrophic reservoir

Toxins produced by cyanobacteria in freshwater ecosystems constitute a serious health risk worldwide for humans that may use the affected water bodies for recreation, drinking water, and/or irrigation. Cyanotoxins have also been deemed responsible for loss of animal life in many places around the world. This paper explores the effect of H₂O₂ treatments on cyanobacteria and microcystins in natural samples from a hypertrophic reservoir in microcosm experiments. According to the results, cyanobacteria were more easily affected by H₂O₂ than by other phytoplanktonic groups. This was shown by the increase in the fractions of chlorophyll-a (a proxy for phytoplankton) and chlorophyll-b (a proxy for green algae) over total phytoplankton pigments and the decrease in the fraction of phycocyanin (a proxy for cyanobacteria) over total phytoplankton pigments. Thus, while an overall increase in phytoplankton occurred, a preferential decrease in cyanobacteria was observed with H₂O₂ treatments over a few hours. Moreover, significant degradation of total microcystins was observed under H₂O₂ treatments, while more microcystins were degraded when UV radiation was used in combination with H₂O₂. The combination of H₂O₂ and ultraviolet (UV) treatment in natural samples resulted in total microcystin concentrations that were below the World Health Organization limit for safe consumption of drinking water of 1 μg/L. Although further investigation into the effects of H₂O₂ addition on ecosystem function must be performed, our results show that the application of H₂O₂ could be a promising method for the degradation of microcystins in reservoirs and the reduction of public health risks related to the occurrence of harmful algal blooms.

Enzymatic Antioxidant Systems in Early Anaerobes: Theoretical Considerations

It is widely accepted that cyanobacteria-dependent oxygen that was released into Earth's atmosphere ca. 2.5 billion years ago sparked the evolution of the aerobic metabolism and the antioxidant system. In modern aerobes, enzymes such as superoxide dismutases (SODs), peroxiredoxins (PXs), and catalases (CATs) constitute the core of the enzymatic antioxidant system (EAS) directed against reactive oxygen species (ROS). In many anaerobic prokaryotes, the superoxide reductases (SORs) have been identified as the main force in counteracting ROS toxicity. We found that 93% of the analyzed strict anaerobes possess at least one antioxidant enzyme, and 50% have a functional EAS, that is, consisting of at least two antioxidant enzymes: one for superoxide anion radical detoxification and another for hydrogen peroxide decomposition. The results presented here suggest that the last universal common ancestor (LUCA) was not a strict anaerobe. O2 could have been available for the first microorganisms before oxygenic photosynthesis evolved, however, from the intrinsic activity of EAS, not solely from abiotic sources.

KEY WORDS

Archaea-Atmospheric gases-Evolution-H2O2 resistance-Oxygenic photosynthesis. Astrobiology 16, 348-358.

Comparative Genomics of the Genus Porphyromonas Identifies Adaptations for Heme Synthesis within the Prevalent Canine Oral Species Porphyromonas cangingivalis

Porphyromonads play an important role in human periodontal disease and recently have been shown to be highly prevalent in canine mouths. Porphyromonas cangingivalis is the most prevalent canine oral bacterial species in both plaque from healthy gingiva and plaque from dogs with early periodontitis. The ability of P. cangingivalis to flourish in the different environmental conditions characterized by these two states suggests a degree of metabolic flexibility. To characterize the genes responsible for this, the genomes of 32 isolates (including 18 newly sequenced and assembled) from 18 Porphyromonad species from dogs, humans, and other mammals were compared. Phylogenetic trees inferred using core genes largely matched previous findings; however, comparative genomic analysis identified several genes and pathways relating to heme synthesis that were present in P. cangingivalis but not in other Porphyromonads. Porphyromonas cangingivalis has a complete protoporphyrin IX synthesis pathway potentially allowing it to synthesize its own heme unlike pathogenic Porphyromonads such as Porphyromonas gingivalis that acquire heme predominantly from blood. Other pathway differences such as the ability to synthesize siroheme and vitamin B12 point to enhanced metabolic flexibility for P. cangingivalis, which may underlie its prevalence in the canine oral cavity.

Combatting cyanobacteria with hydrogen peroxide: a laboratory study on the consequences for phytoplankton community and diversity

Experiments with different phytoplankton densities in lake samples showed that a high biomass increases the rate of hydrogen peroxide (HP) degradation and decreases the effectiveness of HP in the selective suppression of dominant cyanobacteria. However, selective application of HP requires usage of low doses only, accordingly this defines the limits for use in lake mitigation. To acquire insight into the impact of HP on other phytoplankton species, we have followed the succession of three phytoplankton groups in lake samples that were treated with different concentrations of HP using a taxa-specific fluorescence emission test. This fast assay reports relatively well on coarse changes in the phytoplankton community; the measured data and the counts from microscopical analysis of the phytoplankton matched quite well. The test was used to pursue HP application in a Planktothrix agardhii-dominated lake sample and displayed a promising shift in the phytoplankton community in only a few weeks. From a low-diversity community, a change to a status with a significantly higher diversity and increased abundance of eukaryotic phytoplankton species was established. Experiments in which treated samples were re-inoculated with original P. agardhii-rich lake water demonstrated prolonged suppression of cyanobacteria, and displayed a remarkable stability of the newly developed post-HP treatment state of the phytoplankton community.

fPoxDB: fungal peroxidase database for comparative genomics

BACKGROUND

Peroxidases are a group of oxidoreductases which mediate electron transfer from hydrogen peroxide (H2O2) and organic peroxide to various electron acceptors. They possess a broad spectrum of impact on industry and fungal biology. There are numerous industrial applications using peroxidases, such as to catalyse highly reactive pollutants and to breakdown lignin for recycling of carbon sources. Moreover, genes encoding peroxidases play important roles in fungal pathogenicity in both humans and plants. For better understanding of fungal peroxidases at the genome-level, a novel genomics platform is required. To this end, Fungal Peroxidase Database (fPoxDB; http://peroxidase.riceblast.snu.ac.kr/) has been developed to provide such a genomics platform for this important gene family.

DESCRIPTION

In order to identify and classify fungal peroxidases, 24 sequence profiles were built and applied on 331 genomes including 216 from fungi and Oomycetes. In addition, NoxR, which is known to regulate NADPH oxidases (NoxA and NoxB) in fungi, was also added to the pipeline. Collectively, 6,113 genes were predicted to encode 25 gene families, presenting well-separated distribution along the taxonomy. For instance, the genes encoding lignin peroxidase, manganese peroxidase, and versatile peroxidase were concentrated in the rot-causing basidiomycetes, reflecting their ligninolytic capability. As a genomics platform, fPoxDB provides diverse analysis resources, such as gene family predictions based on fungal sequence profiles, pre-computed results of eight bioinformatics programs, similarity search tools, a multiple sequence alignment tool, domain analysis functions, and taxonomic distribution summary, some of which are not available in the previously developed peroxidase resource. In addition, fPoxDB is interconnected with other family web systems, providing extended analysis opportunities.

CONCLUSIONS

fPoxDB is a fungi-oriented genomics platform for peroxidases. The sequence-based prediction and diverse analysis toolkits with easy-to-follow web interface offer a useful workbench to study comparative and evolutionary genomics of peroxidases in fungi.

Phylogenetic analysis of ligninolytic peroxidases: preliminary insights into the alternation of white-rot and brown-rot fungi in their lineage

White-rot and brown-rot fungi employ different mechanisms to degrade lignocellulose. These fungi are not monophyletic and even alternate in their common lineage. To explore the reason for this, seventy-six ligninolytic peroxidases (LPs), including 14 sequences newly identified from available basidiomycetous whole-genome and EST databases in this study, were utilized for phylogenetic and selective pressure analyses. We demonstrate that LPs were subjected to the mixed process of concerted and birth-and-death evolution. After the duplication events of original LPs, various LP types may originate from mutation events of several key residues driven by positive selection, which may change LP types and even rot types in a small fraction of wood-decaying fungi. Our findings provide preliminary insights into the cause for the alternation of the two fungal rot types within the same lineage.

Expression of a bacterial catalase in a strictly anaerobic methanogen significantly increases tolerance to hydrogen peroxide but not oxygen

Haem-dependent catalase is an antioxidant enzyme that degrades H2O2, producing H2O and O2, and is common in aerobes. Catalase is present in some strictly anaerobic methane-producing archaea (methanogens), but the importance of catalase to the antioxidant system of methanogens is poorly understood. We report here that a survey of the sequenced genomes of methanogens revealed that the majority of species lack genes encoding catalase. Moreover, Methanosarcina acetivorans is a methanogen capable of synthesizing haem and encodes haem-dependent catalase in its genome; yet, Methanosarcina acetivorans cells lack detectable catalase activity. However, inducible expression of the haem-dependent catalase from Escherichia coli (EcKatG) in the chromosome of Methanosarcina acetivorans resulted in a 100-fold increase in the endogenous catalase activity compared with uninduced cells. The increased catalase activity conferred a 10-fold increase in the resistance of EcKatG-induced cells to H2O2 compared with uninduced cells. The EcKatG-induced cells were also able to grow when exposed to levels of H2O2 that inhibited or killed uninduced cells. However, despite the significant increase in catalase activity, growth studies revealed that EcKatG-induced cells did not exhibit increased tolerance to O2 compared with uninduced cells. These results support the lack of catalase in the majority of methanogens, since methanogens are more likely to encounter O2 rather than high concentrations of H2O2 in the natural environment. Catalase appears to be a minor component of the antioxidant system in methanogens, even those that are aerotolerant, including Methanosarcina acetivorans. Importantly, the experimental approach used here demonstrated the feasibility of engineering beneficial traits, such as H2O2 tolerance, in methanogens.

Characterization of a novel catalase-peroxidase (KATG) gene from the dinoflagellate Prorocentrum minimum

Dinoflagellates are a group of eukaryotic microalgae that have many unusual cytological and genomic characteristics. Here, we report the detection of a novel catalase-peroxidase (KatG) gene from the dinoflagellate Prorocentrum minimum, and its transcript levels under copper sulfate (CuSO4 ) treatment. cDNA analysis yielded a 1,293 bp complete open reading frame (ORF) encoding a 431-amino acid (aa) polypeptide (46.6 kDa). The conserved dinoflagellate splice leader (DinoSL) indicates that this gene is nucleus encoded, and a signal sequence at the N-terminus of the deduced protein indicates that the KatG protein may pass across the endoplasmic reticulum or cytoplasmic membrane, but its precise subcellular location is not known. Unlike the typical KatG proteins, P. minimum KatG (PmKatG) only has one conserved domain (N-domain). Gene expression of PmKatG dramatically increased with increasing concentrations of CuSO4 , suggesting that it functions in the defense mechanisms associated with oxidative stress.

Molecular evolution of hydrogen peroxide degrading enzymes

For efficient removal of intra- and/or extracellular hydrogen peroxide by dismutation to harmless dioxygen and water (2H(2)O(2) → O(2) + 2H(2)O), nature designed three metalloenzyme families that differ in oligomeric organization, monomer architecture as well as active site geometry and catalytic residues. Here we report on the updated reconstruction of the molecular phylogeny of these three gene families. Ubiquitous typical (monofunctional) heme catalases are found in all domains of life showing a high structural conservation. Their evolution was directed from large subunit towards small subunit proteins and further to fused proteins where the catalase fold was retained but lost its original functionality. Bifunctional catalase-peroxidases were at the origin of one of the two main heme peroxidase superfamilies (i.e. peroxidase-catalase superfamily) and constitute a protein family predominantly present among eubacteria and archaea, but two evolutionary branches are also found in the eukaryotic world. Non-heme manganese catalases are a relatively small protein family with very old roots only present among bacteria and archaea. Phylogenetic analyses of the three protein families reveal features typical (i) for the evolution of whole genomes as well as (ii) for specific evolutionary events including horizontal gene transfer, paralog formation and gene fusion. As catalases have reached a striking diversity among prokaryotic and eukaryotic pathogens, understanding their phylogenetic and molecular relationship and function will contribute to drug design for prevention of diseases of humans, animals and plants.

High conformational stability of secreted eukaryotic catalase-peroxidases: answers from first crystal structure and unfolding studies

Catalase-peroxidases (KatGs) are bifunctional heme enzymes widely spread in archaea, bacteria, and lower eukaryotes. Here we present the first crystal structure (1.55 Å resolution) of an eukaryotic KatG, the extracellular or secreted enzyme from the phytopathogenic fungus Magnaporthe grisea. The heme cavity of the homodimeric enzyme is similar to prokaryotic KatGs including the unique distal (+)Met-Tyr-Trp adduct (where the Trp is further modified by peroxidation) and its associated mobile arginine. The structure also revealed several conspicuous peculiarities that are fully conserved in all secreted eukaryotic KatGs. Peculiarities include the wrapping at the dimer interface of the N-terminal elongations from the two subunits and cysteine residues that cross-link the two subunits. Differential scanning calorimetry and temperature- and urea-mediated unfolding followed by UV-visible, circular dichroism, and fluorescence spectroscopy combined with site-directed mutagenesis demonstrated that secreted eukaryotic KatGs have a significantly higher conformational stability as well as a different unfolding pattern when compared with intracellular eukaryotic and prokaryotic catalase-peroxidases. We discuss these properties with respect to the structure as well as the postulated roles of this metalloenzyme in host-pathogen interactions.

Oxygen and hydrogen peroxide in the early evolution of life on earth: in silico comparative analysis of biochemical pathways

In the Universe, oxygen is the third most widespread element, while on Earth it is the most abundant one. Moreover, oxygen is a major constituent of all biopolymers fundamental to living organisms. Besides O(2), reactive oxygen species (ROS), among them hydrogen peroxide (H(2)O(2)), are also important reactants in the present aerobic metabolism. According to a widely accepted hypothesis, aerobic metabolism and many other reactions/pathways involving O(2) appeared after the evolution of oxygenic photosynthesis. In this study, the hypothesis was formulated that the Last Universal Common Ancestor (LUCA) was at least able to tolerate O(2) and detoxify ROS in a primordial environment. A comparative analysis was carried out of a number of the O(2)-and H(2)O(2)-involving metabolic reactions that occur in strict anaerobes, facultative anaerobes, and aerobes. The results indicate that the most likely LUCA possessed O(2)-and H(2)O(2)-involving pathways, mainly reactions to remove ROS, and had, at least in part, the components of aerobic respiration. Based on this, the presence of a low, but significant, quantity of H(2)O(2) and O(2) should be taken into account in theoretical models of the early Archean atmosphere and oceans and the evolution of life. It is suggested that the early metabolism involving O(2)/H(2)O(2) was a key adaptation of LUCA to already existing weakly oxic zones in Earth's primordial environment.

The Black Queen Hypothesis: evolution of dependencies through adaptive gene loss

Reductive genomic evolution, driven by genetic drift, is common in endosymbiotic bacteria. Genome reduction is less common in free-living organisms, but it has occurred in the numerically dominant open-ocean bacterioplankton Prochlorococcus and "Candidatus Pelagibacter," and in these cases the reduction appears to be driven by natural selection rather than drift. Gene loss in free-living organisms may leave them dependent on cooccurring microbes for lost metabolic functions. We present the Black Queen Hypothesis (BQH), a novel theory of reductive evolution that explains how selection leads to such dependencies; its name refers to the queen of spades in the game Hearts, where the usual strategy is to avoid taking this card. Gene loss can provide a selective advantage by conserving an organism's limiting resources, provided the gene's function is dispensable. Many vital genetic functions are leaky, thereby unavoidably producing public goods that are available to the entire community. Such leaky functions are thus dispensable for individuals, provided they are not lost entirely from the community. The BQH predicts that the loss of a costly, leaky function is selectively favored at the individual level and will proceed until the production of public goods is just sufficient to support the equilibrium community; at that point, the benefit of any further loss would be offset by the cost. Evolution in accordance with the BQH thus generates "beneficiaries" of reduced genomic content that are dependent on leaky "helpers," and it may explain the observed nonuniversality of prototrophy, stress resistance, and other cellular functions in the microbial world.

Wood utilization is dependent on catalase activities in the filamentous fungus Podospora anserina

Catalases are enzymes that play critical roles in protecting cells against the toxic effects of hydrogen peroxide. They are implicated in various physiological and pathological conditions but some of their functions remain unclear. In order to decipher the role(s) of catalases during the life cycle of Podospora anserina, we analyzed the role of the four monofunctional catalases and one bifunctional catalase-peroxidase genes present in its genome. The five genes were deleted and the phenotypes of each single and all multiple mutants were investigated. Intriguingly, although the genes are differently expressed during the life cycle, catalase activity is dispensable during both vegetative growth and sexual reproduction in laboratory conditions. Catalases are also not essential for cellulose or fatty acid assimilation. In contrast, they are strictly required for efficient utilization of more complex biomass like wood shavings by allowing growth in the presence of lignin. The secreted CATB and cytosolic CAT2 are the major catalases implicated in peroxide resistance, while CAT2 is the major player during complex biomass assimilation. Our results suggest that P. anserina produces external H₂O₂ to assimilate complex biomass and that catalases are necessary to protect the cells during this process. In addition, the phenotypes of strains lacking only one catalase gene suggest that a decrease of catalase activity improves the capacity of the fungus to degrade complex biomass.

Selective suppression of harmful cyanobacteria in an entire lake with hydrogen peroxide

Although harmful cyanobacteria form a major threat to water quality, few methods exist for the rapid suppression of cyanobacterial blooms. Since laboratory studies indicated that cyanobacteria are more sensitive to hydrogen peroxide (H(2)O(2)) than eukaryotic phytoplankton, we tested the application of H(2)O(2) in natural waters. First, we exposed water samples from a recreational lake dominated by the toxic cyanobacterium Planktothrix agardhii to dilute H(2)O(2). This reduced the photosynthetic vitality by more than 70% within a few hours. Next, we installed experimental enclosures in the lake, which revealed that H(2)O(2) selectively killed the cyanobacteria without major impacts on eukaryotic phytoplankton, zooplankton, or macrofauna. Based on these tests, we introduced 2 mg L(-1) (60 μM) of H(2)O(2) homogeneously into the entire water volume of the lake with a special dispersal device, called the water harrow. The cyanobacterial population as well as the microcystin concentration collapsed by 99% within a few days. Eukaryotic phytoplankton (including green algae, cryptophytes, chrysophytes and diatoms), zooplankton and macrofauna remained largely unaffected. Following the treatment, cyanobacterial abundances remained low for 7 weeks. Based on these results, we propose the use of dilute H(2)O(2) for the selective elimination of harmful cyanobacteria from recreational lakes and drinking water reservoirs, especially when immediate action is urgent and/or cyanobacterial control by reduction of eutrophication is currently not feasible. A key advantage of this method is that the added H(2)O(2) degrades to water and oxygen within a few days, and thus leaves no long-term chemical traces in the environment.

Eukaryotic extracellular catalase-peroxidase from Magnaporthe grisea - Biophysical/chemical characterization of the first representative from a novel phytopathogenic KatG group

All phytopathogenic fungi have two catalase-peroxidase paralogues located either intracellularly (KatG1) or extracellularly (KatG2). Here, for the first time a secreted bifunctional, homodimeric catalase-peroxidase (KatG2 from the rice blast fungus Magnaporthe grisea) has been produced heterologously with almost 100% heme occupancy and comprehensively investigated by using a broad set of methods including UV-Vis, ECD and resonance Raman spectroscopy (RR), thin-layer spectroelectrochemistry, mass spectrometry, steady-state & presteady-state spectroscopy. RR spectroscopy reveals that MagKatG2 shows a unique mixed-spin state, non-planar heme b, and a proximal histidine with pronounced imidazolate character. At pH 7.0 and 25 °C, the standard reduction potential E°' of the Fe(III)/Fe(II) couple for the high-spin native protein was found to fall in the range typical for the KatG family. Binding of cyanide was relatively slow at pH 7.0 and 25 °C and with a K(d) value significantly higher than for the intracellular counterpart. Demonstrated by mass spectrometry MagKatG2 has the typical Trp118-Tyr251-Met277 adduct that is essential for its predominantly catalase activity at the unique acidic pH optimum. In addition, MagKatG2 acts as a versatile peroxidase using both one- and two-electron donors. Based on these data, structure-function relationships of extracellular eukaryotic KatGs are discussed with respect to intracellular KatGs and possible role(s) in host-pathogen interaction.