Evolution of catalases from bacteria to humans

LSU family members and NBR1 are novel factors that contribute to homeostasis of catalases and peroxisomes in Arabidopsis thaliana

The short coiled-coil LSU (RESPONSE TO LOW SULFUR) proteins are linked to sulfur metabolism and have numerous protein partners. However, most of these partners lack direct links to sulfur metabolism, and the role of such interactions remains elusive. Here, we confirmed LSU binding to Arabidopsis catalase (CAT) and revealed that NBR1, a selective autophagy receptor, strongly interacts with LSU1 but not with CAT. Consequently, we observed the involvement of autophagy but not NBR1 in CAT removal. The lsu and nbr1 mutants differed from the wild-type plants in size and the number of yellow fluorescent protein (YFP)-CAT condensates, the number of peroxisomes, and photosynthetic pigments levels in the presence and absence of stress. We conclude that LSU family members and NBR1 contribute directly or indirectly to CAT and peroxisome homeostasis, and the overall fitness of plants. Our structural models of CAT-LSU complexes show at least two regions of interaction in CAT, one of which is at the N-terminus. Indeed, the N-terminally truncated variants of CAT2 and CAT3 interact more weakly with LSU1 than their full-length variants, but the extent of reduction is higher for CAT2, suggesting differences in recognition of CAT2 and CAT3 by LSU1.

The significance of the apelinergic system in doxorubicin-induced cardiotoxicity

Cancer is the leading cause of death worldwide, and the number of cancer-related deaths is expected to increase. Common types of cancer include skin, breast, lung, prostate, and colorectal cancers. While clinical research has improved cancer therapies, these treatments often come with significant side effects such as chronic fatigue, hair loss, and nausea. In addition, cancer treatments can cause long-term cardiovascular complications. Doxorubicin (DOX) therapy is one example, which can lead to decreased left ventricle (LV) echocardiography (ECHO) parameters, increased oxidative stress in cellular level, and even cardiac fibrosis. The apelinergic system, specifically apelin and its receptor, together, has shown properties that could potentially protect the heart and mitigate the damages caused by DOX anti-cancer treatment. Studies have suggested that stimulating the apelinergic system may have therapeutic benefits for heart damage induced by DOX. Further research in chronic preclinical models is needed to confirm this hypothesis and understand the mechanism of action for the apelinergic system. This review aims to collect and present data on the effects of the apelinergic system on doxorubicin-induced cardiotoxicity.

Catalase immobilization: Current knowledge, key insights, applications, and future prospects - A review

Catalase (CAT), a ubiquitous enzyme in all oxygen-exposed organisms, effectively decomposes hydrogen peroxide (H2O2), a harmful by-product, into water and oxygen, mitigating oxidative stress and cellular damage, safeguarding cellular organelles and tissues. Therefore, CAT plays a crucial role in maintaining cellular homeostasis and function. Owing to its pivotal role, CAT has garnered considerable interest. However, many challenges arise when used, especially in multiple practical processes. "Immobilization", a widely-used technique, can help improve enzyme properties. CAT immobilization offers numerous advantages, including enhanced stability, reusability, and facilitated downstream processing. This review presents a comprehensive overview of CAT immobilization. It starts with discussing various immobilization mechanisms, support materials, advantages, drawbacks, and factors influencing the performance of immobilized CAT. Moreover, the review explores the application of the immobilized CAT in various industries and its prospects, highlighting its essential role in diverse fields and stimulating further research and investigation. Furthermore, the review highlights some of the world's leading companies in the field of the CAT industry and their substantial potential for economic contribution. This review aims to serve as a discerning, source of information for researchers seeking a comprehensive cutting-edge overview of this rapidly evolving field and have been overwhelmed by the size of publications.

Pepper catalase: a broad analysis of its modulation during fruit ripening and by nitric oxide

Catalase is a major antioxidant enzyme located in plant peroxisomes that catalyzes the decomposition of H2O2. Based on our previous transcriptomic (RNA-Seq) and proteomic (iTRAQ) data at different stages of pepper (Capsicum annuum L.) fruit ripening and after exposure to nitric oxide (NO) enriched atmosphere, a broad analysis has allowed us to characterize the functioning of this enzyme. Three genes were identified, and their expression was differentially modulated during ripening and by NO gas treatment. A dissimilar behavior was observed in the protein expression of the encoded protein catalases (CaCat1-CaCat3). Total catalase activity was down-regulated by 50% in ripe (red) fruits concerning immature green fruits. This was corroborated by non-denaturing polyacrylamide gel electrophoresis, where only a single catalase isozyme was identified. In vitro analyses of the recombinant CaCat3 protein exposed to peroxynitrite (ONOO-) confirmed, by immunoblot assay, that catalase underwent a nitration process. Mass spectrometric analysis identified that Tyr348 and Tyr360 were nitrated by ONOO-, occurring near the active center of catalase. The data indicate the complex regulation at gene and protein levels of catalase during the ripening of pepper fruits, with activity significantly down-regulated in ripe fruits. Nitration seems to play a key role in this down-regulation, favoring an increase in H2O2 content during ripening. This pattern can be reversed by the exogenous NO application. While plant catalases are generally reported to be tetrameric, the analysis of the protein structure supports that pepper catalase has a favored quaternary homodimer nature. Taken together, data show that pepper catalase is down-regulated during fruit ripening, becoming a target of tyrosine nitration, which provokes its inhibition.

Intricate balance of dually-localized catalase modulates infectivity of Leptomonas seymouri (Kinetoplastea: Trypanosomatidae)

Nearly all aerobic organisms are equipped with catalases, powerful enzymes scavenging hydrogen peroxide and facilitating defense against harmful reactive oxygen species. In trypanosomatids, this enzyme was not present in the common ancestor, yet it had been independently acquired by different lineages of monoxenous trypanosomatids from different bacteria at least three times. This observation posited an obvious question: why was catalase so "sought after" if many trypanosomatid groups do just fine without it? In this work, we analyzed subcellular localization and function of catalase in Leptomonas seymouri. We demonstrated that this enzyme is present in the cytoplasm and a subset of glycosomes, and that its cytoplasmic retention is H2O2-dependent. The ablation of catalase in this parasite is not detrimental in vivo, while its overexpression resulted in a substantially higher parasite load in the experimental infection of Dysdercus peruvianus. We propose that the capacity of studied flagellates to modulate the catalase activity in the midgut of its insect host facilitates their development and protects them from oxidative damage at elevated temperatures.

Potential role of molecular hydrogen therapy on oxidative stress and redox signaling in chronic kidney disease

Oxidative stress plays a key role in chronic kidney disease (CKD) development and progression, inducing kidney cell damage, inflammation, and fibrosis. However, effective therapeutic interventions to slow down CKD advancement are currently lacking. The multifaceted pharmacological effects of molecular hydrogen (H2) have made it a promising therapeutic avenue. H2 is capable of capturing harmful •OH and ONOO- while maintaining the crucial reactive oxygen species (ROS) involved in cellular signaling. The NRF2-KEAP1 system, which manages cell redox balance, could be used to treat CKD. H2 activates this pathway, fortifying antioxidant defenses and scavenging ROS to counteract oxidative stress. H2 can improve NRF2 signaling by using the Wnt/β-catenin pathway and indirectly activate NRF2-KEAP1 in mitochondria. Additionally, H2 modulates NF-κB activity by regulating cellular redox status, inhibiting MAPK pathways, and maintaining Trx levels. Treatment with H2 also attenuates HIF signaling by neutralizing ROS while indirectly bolstering HIF-1α function. Furthermore, H2 affects FOXO factors and enhances the activity of antioxidant enzymes. Despite the encouraging results of bench studies, clinical trials are still limited and require further investigation. The focus of this review is on hydrogen's role in treating renal diseases, with a specific focus on oxidative stress and redox signaling regulation, and it discusses its potential clinical applications.

Analysis of the adhesive secreting cells of Arion subfuscus: insights into the role of microgels in a tough, fast-setting hydrogel glue

The slug Arion subfuscus produces a tough, highly adhesive defensive secretion. This secretion is a flexible hydrogel that is toughened by a double network mechanism. While synthetic double network gels typically require extensive time to prepare, this slug creates a tough gel in seconds. To gain insight into how the glue forms a double-network hydrogel so rapidly, the secretory apparatus of this slug was analyzed. The goal was to determine how the major components of the glue were distributed and mixed. Most of the glue comes from two types of large unicellular glands; one secretes polyanionic polysaccharides in small, membrane-bound packets, the other secretes proteins that appear to form a cross-linked network. The latter gland shows distinct regions where cross-linking appears to be occurring. These regions are darker, more homogeneous and appear more solid than the rest of the secretory material. The enzyme catalase is highly abundant in these regions, as are basic proteins. These results suggest that a rapid oxidation event occurs in this protein-containing gland, triggering cross-linking before the glue is released. The cross-linked microgels would then join together after secretion to form a granular hydrogel. The polysaccharide-filled packets would be mixed and interspersed among these microgels and may contribute to joining them together. This is an unexpected and highly effective way to form a tough gel rapidly.

Unraveling radiation resistance strategies in two bacterial strains from the high background radiation area of Chavara-Neendakara: A comprehensive whole genome analysis

This paper reports the results of gamma irradiation experiments and whole genome sequencing (WGS) performed on vegetative cells of two radiation resistant bacterial strains, Metabacillus halosaccharovorans (VITHBRA001) and Bacillus paralicheniformis (VITHBRA024) (D10 values 2.32 kGy and 1.42 kGy, respectively), inhabiting the top-ranking high background radiation area (HBRA) of Chavara-Neendakara placer deposit (Kerala, India). The present investigation has been carried out in the context that information on strategies of bacteria having mid-range resistance for gamma radiation is inadequate. WGS, annotation, COG and KEGG analyses and manual curation of genes helped us address the possible pathways involved in the major domains of radiation resistance, involving recombination repair, base excision repair, nucleotide excision repair and mismatch repair, and the antioxidant genes, which the candidate could activate to survive under ionizing radiation. Additionally, with the help of these data, we could compare the candidate strains with that of the extremely radiation resistant model bacterium Deinococccus radiodurans, so as to find the commonalities existing in their strategies of resistance on the one hand, and also the rationale behind the difference in D10, on the other. Genomic analysis of VITHBRA001 and VITHBRA024 has further helped us ascertain the difference in capability of radiation resistance between the two strains. Significantly, the genes such as uvsE (NER), frnE (protein protection), ppk1 and ppx (non-enzymatic metabolite production) and those for carotenoid biosynthesis, are endogenous to VITHBRA001, but absent in VITHBRA024, which could explain the former's better radiation resistance. Further, this is the first-time study performed on any bacterial population inhabiting an HBRA. This study also brings forward the two species whose radiation resistance has not been reported thus far, and add to the knowledge on radiation resistant capabilities of the phylum Firmicutes which are abundantly observed in extreme environment.

Antioxidant Systems of Plant Pathogenic Fungi: Functions in Oxidative Stress Response and Their Regulatory Mechanisms

During the infection process, plant pathogenic fungi encounter plant-derived oxidative stress, and an appropriate response to this stress is crucial to their survival and establishment of the disease. Plant pathogenic fungi have evolved several mechanisms to eliminate oxidants from the external environment and maintain cellular redox homeostasis. When oxidative stress is perceived, various signaling transduction pathways are triggered and activate the downstream genes responsible for the oxidative stress response. Despite extensive research on antioxidant systems and their regulatory mechanisms in plant pathogenic fungi, the specific functions of individual antioxidants and their impacts on pathogenicity have not recently been systematically summarized. Therefore, our objective is to consolidate previous research on the antioxidant systems of plant pathogenic fungi. In this review, we explore the plant immune responses during fungal infection, with a focus on the generation and function of reactive oxygen species. Furthermore, we delve into the three antioxidant systems, summarizing their functions and regulatory mechanisms involved in oxidative stress response. This comprehensive review provides an integrated overview of the antioxidant mechanisms within plant pathogenic fungi, revealing how the oxidative stress response contributes to their pathogenicity.

Synergistic effects of combined probiotics Bacillus pumilis D5 and Leuconostoc mesenteroide B4 on immune enhancement and disease resistance in Litopenaeus vannamei

This study investigated the effects of two distinct probiotics, Leuconostoc mesenteroides B4 (B4) and Bacillus pumilus D5 (D5), along with their combination, on the diet of white shrimp (Litopenaeus vannamei) during an eight-week feeding trial. The diets tested included B4 + dextran at 107 CFU/g feed (the B4 group), D5 alone at 107 CFU/g feed (the D5 group), and a combination of B4 + dextran and D5 at 5 × 106 CFU/g feed each (the B4+dextran + D5 group). Relative to the control group, those administered probiotics exhibited moderate enhancements in growth. By the eighth week, the weight gain for the B4, D5, and B4+D5 groups was 696.50 ± 78.15%, 718.53 ± 130.73%, and 693.05 ± 93.79%, respectively, outperforming the control group's 691.66 ± 31.10% gain. The feed conversion ratio was most efficient in the B4 group (2.16 ± 0.06), closely followed by B4+D5 (2.21 ± 0.03) and D5 (2.22 ± 0.06), with the control group having the highest ratio (2.27 ± 0.03). While phenoloxidase activity was somewhat elevated in the B4 and D5 groups, no significant differences were noted in respiratory burst activity or total hemocyte count across all groups. Challenge tests at weeks 4 and 8 showed that the B4 + D5 combination offered superior protection against AHPND-causing Vibrio parahaemolyticus. The 4-week cumulative survival rate was highest in shrimp treated with B4 + dextran + D5 (56.25%), followed by B4 + dextran (31.25%), control (18.75%), and lowest in D5 (12.5%). By week 8, the B4 + dextran + D5 (43.75%) and B4 + dextran (37.5%) groups significantly outperformed the control group (6.25%, p < 0.05), with no significant difference observed between the D5 group (37.5%) and the control group at day 56. Analysis of the shrimp's foregut microbiota revealed an increase in unique OTUs in the B4 and B4 + D5 groups. Compared to the control, Proteobacteria abundance was reduced in all probiotic groups. Potential pathogens like Vibrio, Bacteroides, Neisseria, Botrytis, Clostridioides, and Deltaentomopoxvirus were detected in the control but were reduced or absent in probiotic groups. Beneficial microbes such as Methanobrevibacter and Dictyostelium in the B4+D5 group, and Sugiyamaella in the B4 group, showed significant increases. Probiotics also led to higher transcript levels of nitric oxide synthase in the hemocytes, and lysozyme and transglutaminase in the midgut, along with lysozyme and α2-macroglobulin in the foregut. Notably, the combined B4 + D5 probiotics synergistically enhanced the expression of superoxide dismutase and prophenoloxidase in the foregut, indicating an improved immune response. In summary, this study demonstrates that the probiotics evaluated, especially when used in combination, significantly boost the expression of specific immune-related genes, enhance the bacterial diversity and richness of the intestine, and thus prevent the colonization and proliferation of Vibrio spp. in L. vannamei.

Inorganic catalase-powered nanomotors with hyaluronic acid coating for pneumonia therapy

Clinical therapy for widespread infections caused by Streptococcus pneumoniae (S. pneumoniae), such as community-acquired pneumonia, is highly challenging. As an important bacterial toxin, hydrogen peroxide (H2O2) secreted by S. pneumoniae can suppress the host's immune system and cause more severe disease. To address this problem, a hyaluronic acid (HA)-coated inorganic catalase-driven Janus nanomotor was developed, which can cleverly utilize and decompose H2O2 to reduce the burden of bacterial infection, and have excellent drug loading capacity. HA coating prevents rapid leakage of loaded antibiotics and improves the biocompatibility of the nanomaterials. The Janus nanomotor converted H2O2 into oxygen (O2), gave itself the capacity to move actively, and encouraged widespread dispersion in the lesion site. Encouragingly, animal experiments demonstrated that the capability of the nanomotors to degrade H2O2 contributes to diminishing the proliferation of S. pneumoniae and lung tissue damage. This self-propelled drug delivery platform provides a new therapeutic strategy for infections with toxin-secreting bacteria.

Biological activity and molecular mechanism of inactivation of Microcystis aeruginosa by ultrasound irradiation

Harmful algal blooms (HABs) significantly impact on water quality and ecological balance. Ultrasound irradiation has proven to be an effective method for algal control. Nevertheless, the molecular mechanisms underlying the inactivation of M. aeruginosa by ultrasound are still unknown. In this study, the physiological activity and molecular mechanism of algal cells exposed to different frequencies of ultrasound were studied. The results indicated a pronounced inhibition of algal cell growth by high-frequency, high-dose ultrasound. Moreover, with increasing ultrasound dosage, there was a higher percentage of algal cell membrane ruptures. SEM and TEM observed obvious disruptions in membrane structure and internal matrix. Hydroxyl radicals generated by high-frequency ultrasound inflicted substantial cell membrane damage, while increased antioxidant enzyme activities fortified cells against oxidative stress. Following 2 min of ultrasound irradiation at 740 kHz, significant differential gene expression occurred in various aspects, including energy metabolism, carbohydrate metabolism, and environmental information processing pathways. Moreover, ultrasound irradiation influenced DNA repair and cellular apoptosis, suggesting that the algal cells underwent biological stress to counteract the damage caused by ultrasound. These findings reveal that ultrasound irradiation inactivates algae by destroying their cell structures and metabolic pathways, thereby achieving the purpose of algal suppression.

Methionine oxidation of carbohydrate-active enzymes during white-rot wood decay

White-rot fungi employ secreted carbohydrate-active enzymes (CAZymes) along with reactive oxygen species (ROS), like hydrogen peroxide (H2O2), to degrade lignocellulose in wood. H2O2 serves as a co-substrate for key oxidoreductases during the initial decay phase. While the degradation of lignocellulose by CAZymes is well documented, the impact of ROS on the oxidation of the secreted proteins remains unclear, and the identity of the oxidized proteins is unknown. Methionine (Met) can be oxidized to Met sulfoxide (MetO) or Met sulfone (MetO2) with potential deleterious, antioxidant, or regulatory effects. Other residues, like proline (Pro), can undergo carbonylation. Using the white-rot Pycnoporus cinnabarinus grown on aspen wood, we analyzed the Met content of the secreted proteins and their susceptibility to oxidation combining H218O2 with deep shotgun proteomics. Strikingly, their overall Met content was significantly lower (1.4%) compared to intracellular proteins (2.1%), a feature conserved in fungi but not in metazoans or plants. We evidenced that a catalase, widespread in white-rot fungi, protects the secreted proteins from oxidation. Our redox proteomics approach allowed the identification of 49 oxidizable Met and 40 oxidizable Pro residues within few secreted proteins, mostly CAZymes. Interestingly, many of them had several oxidized residues localized in hotspots. Some Met, including those in GH7 cellobiohydrolases, were oxidized up to 47%, with a substantial percentage of sulfone (13%). These Met are conserved in fungal homologs, suggesting important functional roles. Our findings reveal that white-rot fungi safeguard their secreted proteins by minimizing their Met content and by scavenging ROS and pinpoint redox-active residues in CAZymes.IMPORTANCEThe study of lignocellulose degradation by fungi is critical for understanding the ecological and industrial implications of wood decay. While carbohydrate-active enzymes (CAZymes) play a well-established role in lignocellulose degradation, the impact of hydrogen peroxide (H2O2) on secreted proteins remains unclear. This study aims at evaluating the effect of H2O2 on secreted proteins, focusing on the oxidation of methionine (Met). Using the model white-rot fungi Pycnoporus cinnabarinus grown on aspen wood, we showed that fungi protect their secreted proteins from oxidation by reducing their Met content and utilizing a secreted catalase to scavenge exogenous H2O2. The research identified key oxidizable Met within secreted CAZymes. Importantly, some Met, like those of GH7 cellobiohydrolases, undergone substantial oxidation levels suggesting important roles in lignocellulose degradation. These findings highlight the adaptive mechanisms employed by white-rot fungi to safeguard their secreted proteins during wood decay and emphasize the importance of these processes in lignocellulose breakdown.

How do biomarkers dance? Specific moves of defense and damage biomarkers for biological interpretation of dose-response model trends

Omics studies are currently increasingly used in ecotoxicology to highlight the induction of known or novel biomarkers when organisms are exposed to contaminants. Although it is virtually impossible to identify all biomarkers from all organisms, biomarkers can be grouped as defense or damage biomarkers, exhibiting a limited number of response trends. Our working hypothesis is that defense and damage biomarkers follow different dose-response patterns. A meta-analysis of 156 articles and 2595 observations of dose-response curves of defense and damage biomarkers was carried out in order to characterize the response trends of these biological parameters in a large panel of living organisms (18 phyla) exposed to inorganic or organic contaminants (176 in total). Using multinomial logistic regression models, defense biomarkers were found to describe biphasic responses (bell- and U-shaped) to a greater extent (2.5 times) than damage biomarkers. In contrast, damage biomarkers varied mainly monotonically (decreasing or increasing), representing 85% of the observations. Neither the nature of the contaminant nor the type of organisms belonging to 4 kingdoms, influence these specific responses. This result suggests that cellular defense and damage mechanisms are not specific to stressors and are conserved throughout life. Trend analysis of dose-response models as a biological interpretation of biomarkers could thus be a valuable way to exploit large omics datasets.

Co-Delivery of Bioengineered Exosomes and Oxygen for Treating Critical Limb Ischemia in Diabetic Mice

Diabetic patients with critical limb ischemia face a high rate of limb amputation. Regeneration of the vasculature and skeletal muscles can salvage diseased limbs. Therapy using stem cell-derived exosomes that contain multiple proangiogenic and promyogenic factors represents a promising strategy. Yet the therapeutic efficacy is not optimal because exosomes alone cannot efficiently rescue and recruit endothelial and skeletal muscle cells and restore their functions under hyperglycemic and ischemic conditions. To address these limitations, we fabricated ischemic-limb-targeting stem cell-derived exosomes and oxygen-releasing nanoparticles and codelivered them in order to recruit endothelial and skeletal muscle cells, improve cell survival under ischemia before vasculature is established, and restore cell morphogenic function under high glucose and ischemic conditions. The exosomes and oxygen-releasing nanoparticles, delivered by intravenous injection, specifically accumulated in the ischemic limbs. Following 4 weeks of delivery, the exosomes and released oxygen synergistically stimulated angiogenesis and muscle regeneration without inducing substantial inflammation and reactive oxygen species overproduction. Our work demonstrates that codelivery of exosomes and oxygen is a promising treatment solution for saving diabetic ischemic limbs.

Genome-Wide Identification and Expression Analysis of Catalase Gene Families in Triticeae

Aerobic metabolism in plants results in the production of hydrogen peroxide (H2O2), a significant and comparatively stable non-radical reactive oxygen species (ROS). H2O2 is a signaling molecule that regulates particular physiological and biological processes (the cell cycle, photosynthesis, plant growth and development, and plant responses to environmental challenges) at low concentrations. Plants may experience oxidative stress and ultimately die from cell death if excess H2O2 builds up. Triticum dicoccoides, Triticum urartu, and Triticum spelta are different ancient wheat species that present different interesting characteristics, and their importance is becoming more and more clear. In fact, due to their interesting nutritive health, flavor, and nutritional values, as well as their resistance to different parasites, the cultivation of these species is increasingly important. Thus, it is important to understand the mechanisms of plant tolerance to different biotic and abiotic stresses by studying different stress-induced gene families such as catalases (CAT), which are important H2O2-metabolizing enzymes found in plants. Here, we identified seven CAT-encoding genes (TdCATs) in Triticum dicoccoides, four genes in Triticum urartu (TuCATs), and eight genes in Triticum spelta (TsCATs). The accuracy of the newly identified wheat CAT gene members in different wheat genomes is confirmed by the gene structures, phylogenetic relationships, protein domains, and subcellular location analyses discussed in this article. In fact, our analysis showed that the identified genes harbor the following two conserved domains: a catalase domain (pfam00199) and a catalase-related domain (pfam06628). Phylogenetic analyses showed that the identified wheat CAT proteins were present in an analogous form in durum wheat and bread wheat. Moreover, the identified CAT proteins were located essentially in the peroxisome, as revealed by in silico analyses. Interestingly, analyses of CAT promoters in those species revealed the presence of different cis elements related to plant development, maturation, and plant responses to different environmental stresses. According to RT-qPCR, Triticum CAT genes showed distinctive expression designs in the studied organs and in response to different treatments (salt, heat, cold, mannitol, and ABA). This study completed a thorough analysis of the CAT genes in Triticeae, which advances our knowledge of CAT genes and establishes a framework for further functional analyses of the wheat gene family.

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.

Selection, Identification, and Transcript Expression Analysis of Antioxidant Enzyme Genes in Neoseiulus barkeri after Short-Term Heat Stress

Phytoseiid mite Neoseiulus barkeri is a crucial biological control agent utilized to control pest mites and many insects in crops all over the world. However, they are vulnerable to multiple environmental pressures, with high-temperature stress being the most significant challenge. Heat stress disrupts the balance of reactive oxygen species (ROS) levels in organisms, resulting in oxidative stress within the body. Antioxidant enzymes play a crucial role in effectively neutralizing and clearing ROS. In this study, comparative transcriptomics and quantitative real-time PCR (qRT-PCR) were employed to assess the impact of short-term heat stress on the transcript expression of antioxidant enzyme genes in N. barkeri. We primarily identified four antioxidant enzyme genes (NbSOD, NbPrx, NbCAT, and NbGPX) in N. barkeri after exposure to short-term heat stress. Then, new data on the expression patterns of these genes were generated. RNA sequencing and bioinformatics analysis revealed that NbSOD belongs to the Fe/Mn family of superoxide dismutase (SOD), which was identified as MnSOD. NbPrx was classified as a 1-Cys peroxiredoxin of the peroxidase family, whereas NbCAT was recognized as a classical catalase, and NbGPX was determined as cytoplasmic glutathione peroxidase-1 (GPX1). Transcriptional expression analysis of these four genes was conducted at different high temperatures: 36 °C, 38 °C, and 40 °C for 2, 4, and 6 h. The results also showed that all four genes exhibited significant up-regulation in response to short-term heat stress. Similarly, the highest expression levels for NbSOD, NbPrx, and NbCAT were observed at 40 °C for 4 h. However, NbGPX displayed its maximum expression value at 38 °C for 4 h. Overall, the obtained data suggest that short-term heat stress increases levels of ROS generated inside living organisms, which disrupts the oxidative balance and leads to alterations in the expression levels of antioxidant enzyme genes.

Antioxidant defense of Deinococcus radiodurans: how does it contribute to extreme radiation resistance?

PURPOSE

Deinococcus radiodurans is an extremely radioresistant bacterium characterized by D10 of 10 kGy, and able to grow luxuriantly under chronic ionizing radiation of 60 Gy/h. The aim of this article is to review the antioxidant system of D. radiodurans and its possible role in the unusual resistance of this bacterium to ionizing radiation.

CONCLUSIONS

The unusual radiation resistance of D. radiodurans has apparently evolved as a side effect of the adaptation of this extremophile to other damaging environmental factors, especially desiccation. The antioxidant proteins and low-molecular antioxidants (especially low-molecular weight Mn2+ complexes and carotenoids, in particular, deinoxanthin), as well as protein and non-protein regulators, are important for the antioxidant defense of this species. Antioxidant protection of proteins from radiation inactivation enables the repair of DNA damage caused by ionizing radiation.

Enzymatic Hydroxylation of Aliphatic C-H Bonds by a Mn/Fe Cofactor

The aerobic oxidation of carbon-hydrogen (C-H) bonds in biology is currently known to be accomplished by a limited set of cofactors that typically include heme, nonheme iron, and copper. While manganese cofactors perform difficult oxidation reactions, including water oxidation within Photosystem II, they are generally not known to be used for C-H bond activation, and those that do catalyze this important reaction display limited intrinsic reactivity. Here we report that the 2-aminoisobutyric acid hydroxylase from Rhodococcus wratislaviensis, AibH1H2, requires manganese to functionalize a strong, aliphatic C-H bond (BDE = 100 kcal/mol). Structural and spectroscopic studies of this enzyme reveal a redox-active, heterobimetallic manganese-iron active site at the locus of O2 activation and substrate coordination. This result expands the known reactivity of biological manganese-iron cofactors, which was previously restricted to single-electron transfer or stoichiometric protein oxidation. Furthermore, the AibH1H2 cofactor is supported by a protein fold distinct from typical bimetallic oxygenases, and bioinformatic analyses identify related proteins abundant in microorganisms. This suggests that many uncharacterized monooxygenases may similarly require manganese to perform oxidative biochemical tasks.

White clover from the exclusion zone of the Chernobyl NPP: Morphological, biochemical, and genetic characteristics

A comprehensive study of the biological effects of chronic radiation exposure (8 μGy/h) in populations of white clover (Trifolium repens L.) from the Chernobyl exclusion zone was carried out. White clover is one of the most important pasture legumes, having many agricultural applications. Studies at two reference and three radioactively contaminated plots showed no stable morphological effects in white clover at this level of radiation exposure. Increased activities of catalase and peroxidases were found in some impacted plots. Auxin concentration was enhanced in the radioactively contaminated plots. Genes involved in the maintenance of water homeostasis and photosynthetic processes (TIP1 and CAB1) were upregulated at radioactively contaminated plots.

Catalase: A critical node in the regulation of cell fate

Catalase (CAT) is an extensively studied if somewhat enigmatic enzyme that is at the heart of eukaryotic antioxidant systems with a canonical role in peroxisomal function. The CAT family of proteins exert control over a wide range of plant growth and defence processes. CAT proteins are subject to many types of post-translational modification (PTM), which modify activity, ligand binding, stability, compartmentation and function. The CAT interactome involves many cytosolic and nuclear proteins that appear to be essential for protein functions. Hence, the CAT network of roles extends far beyond those associated with peroxisomal metabolism. Some pathogen effector proteins are able to redirect CAT to the nucleus and recent evidence indicates CAT can traffic to the nucleus in the absence of exogenous proteins. While the mechanisms that target CAT to the nucleus are not understood, CAT activity in the cytosol and nucleus is promoted by interactions with nucleoredoxin. Here we discuss recent findings that have been pivotal in generating a step change in our understanding of CAT functions in plant cells.

The Biomodified Lignin Platform: A Review

A reliance on fossil fuel has led to the increased emission of greenhouse gases (GHGs). The excessive consumption of raw materials today makes the search for sustainable resources more pressing than ever. Technical lignins are mainly used in low-value applications such as heat and electricity generation. Green enzyme-based modifications of technical lignin have generated a number of functional lignin-based polymers, fillers, coatings, and many other applications and materials. These bio-modified technical lignins often display similar properties in terms of their durability and elasticity as fossil-based materials while also being biodegradable. Therefore, it is possible to replace a wide range of environmentally damaging materials with lignin-based ones. By researching publications from the last 20 years focusing on the latest findings utilizing databases, a comprehensive collection on this topic was crafted. This review summarizes the recent progress made in enzymatically modifying technical lignins utilizing laccases, peroxidases, and lipases. The underlying enzymatic reaction mechanisms and processes are being elucidated and the application possibilities discussed. In addition, the environmental assessment of novel technical lignin-based products as well as the developments, opportunities, and challenges are highlighted.

Effect of Redox Potential on Diiron-Mediated Disproportionation of Hydrogen Peroxide

Heme and nonheme dimanganese catalases are widely distributed in living organisms to participate in antioxidant defenses that protect biological systems from oxidative stress. The key step in these processes is the disproportionation of H₂O₂ to O₂ and water, which can be interpreted via two different mechanisms, namely via the formation of high-valent oxoiron(IV) and peroxodimanganese(III) or diiron(III) intermediates. In order to better understand the mechanism of this important process, we have chosen such synthetic model compounds that can be used to map the nature of the catalytically active species and the factors influencing their activities. Our previously reported μ-1,2-peroxo-diiron(III)-containing biomimics are good candidates, as both proposed reactive intermediates (Fe^IVO and Fe^III₂(μ-O₂)) can be derived from them. Based on this, we have investigated and compared five heterobidentate-ligand-containing model systems including the previously reported and fully characterized [Fe^II(L^1-4)₃]²⁺ (L¹ = 2-(2'-pyridyl)-1H-benzimidazole, L² = 2-(2'-pyridyl)-N-methyl-benzimidazole, L³ = 2-(4-thiazolyl)-1H-benzimidazole and L⁴ = 2-(4'-methyl-2'-pyridyl)-1H-benzimidazole) and the novel [Fe^II(L⁵)₃]²⁺ (L⁵ = 2-(1H-1,2,4-triazol-3-yl)-pyridine) precursor complexes with their spectroscopically characterized μ-1,2-peroxo-diiron(III) intermediates. Based on the reaction kinetic measurements and previous computational studies, it can be said that the disproportionation reaction of H₂O₂ can be interpreted through the formation of an electrophilic oxoiron(IV) intermediate that can be derived from the homolysis of the O-O bond of the forming μ-1,2-peroxo-diiron(III) complexes. We also found that the disproportionation rate of the H₂O₂ shows a linear correlation with the Fe^III/Fe^II redox potential (in the range of 804 mV-1039 mV vs. SCE) of the catalysts controlled by the modification of the ligand environment. Furthermore, it is important to note that the two most active catalysts with L³ and L⁵ ligands have a high-spin electronic configuration.

Hydrogen sulfide signaling in plants

SIGNIFICANCE

Hydrogen sulfide (H2S) is a multitasking potent regulator that facilitates plant growth, development, and responses to environmental stimuli.

RECENT ADVANCES

The important beneficial effects of H2S in various aspects of plant physiology aroused the interest of this chemical for agriculture. Protein cysteine persulfidation has been recognized as the main redox regulatory mechanism of H2S signaling. An increasing number of studies, including large-scale proteomic analyses and function characterizations, have revealed that H2S-mediated persulfidations directly regulate protein functions, altering downstream signaling in plants. To date, the importance of H2S-mediated persufidation in several abscisic acid signaling-controlling key proteins has been assessed as well as their role in stomatal movements, largely contributing to the understanding of the plant H2S-regulatory mechanism.

CRITICAL ISSUES

The molecular mechanisms of the H2S sensing and transduction in plants remain elusive. The correlation between H2S-mediated persulfidation with other oxidative posttranslational modifications of cysteines are still to be explored.

FUTURE DIRECTIONS

Implementation of advanced detection approaches for the spatiotemporal monitoring of H2S levels in cells and the current proteomic profiling strategies for the identification and quantification of the cysteine site-specific persulfidation will provide insight into the H2S signaling in plants.

Enzymatic Hydroxylation of Aliphatic C-H Bonds by a Mn/Fe Cofactor

Manganese cofactors activate strong chemical bonds in many essential enzymes. Yet very few manganese-dependent enzymes are known to functionalize ubiquitous carbon-hydrogen (C-H) bonds, and those that catalyze this important reaction display limited intrinsic reactivity. Herein, we report that the 2-aminoisobutyric acid hydroxylase from Rhodococcus wratislaviensis requires manganese to functionalize a C-H bond possessing a bond dissociation enthalpy (BDE) exceeding 100 kcal/mol. Structural and spectroscopic studies of this enzyme reveal a redox-active, heterobimetallic manganese-iron active site that utilizes a manganese ion at the locus for O ₂ activation and substrate coordination. Accordingly, this enzyme represents the first documented Mn-dependent monooxygenase in biology. Related proteins are widespread in microorganisms suggesting that many uncharacterized monooxygenases may utilize manganese-containing cofactors to accomplish diverse biological tasks.

Antioxidant enzymes that target hydrogen peroxide are conserved across the animal kingdom, from sponges to mammals

Oxygen is the sustenance of aerobic life and yet is highly toxic. In early life, antioxidants functioned solely to defend against toxic effects of reactive oxygen species (ROS). Later, as aerobic metabolisms evolved, ROS became essential for signalling. Thus, antioxidants are multifunctional and must detoxify, but also permit ROS signalling for vital cellular processes. Here we conduct metazoan-wide genomic assessments of three enzymatic antioxidant families that target the predominant ROS signaller, hydrogen peroxide: namely, monofunctional catalases (CAT), peroxiredoxins (PRX), and glutathione peroxidases (GPX). We reveal that the two most evolutionary ancient families, CAT and PRX, exhibit metazoan-wide conservation. In the basal animal lineage, sponges (phylum Porifera), we find all three antioxidant families, but with GPX least abundant. Poriferan CATs are distinct from bilaterian CATs, but the evolutionary divergence is small. Amongst PRXs, subfamily PRX6 is the most conserved, whilst subfamily AhpC-PRX1 is the largest; PRX4 is the only core member conserved from sponges to mammals and may represent the ancestral animal AhpC-PRX1. Conversely, for GPX, the most recent family to arise, only the cysteine-dependent subfamily GPX7 is conserved across metazoans, and common across Porifera. Our analyses illustrate that the fundamental functions of antioxidants have resulted in gene conservation throughout the animal kingdom.

Using Front-Face Fluorescence Spectroscopy and Biochemical Analysis of Honey to Assess a Marker for the Level of Varroa destructor Infestation of Honey Bee (Apis mellifera) Colonies

Varroa destructor is a parasitic mite responsible for the loss of honey bee (Apis mellifera) colonies. This study aimed to find a promising marker in honey for the bee colony infestation level using fluorescence spectroscopy and biochemical analyses. We examined whether the parameters of the honey samples' fluorescence spectra and biochemical parameters, both related to proteins and phenolics, may be connected with the level of honey bee colonies' infestation. The infestation level was highly positively correlated with the catalase activity in honey (r = 0.936). Additionally, the infestation level was positively correlated with the phenolic spectral component (r = 0.656), which was tentatively related to the phenolics in honey. No correlation was found between the diastase activity in honey and the colonies' infestation level. The results indicate that the catalase activity in honey and the PFC1 spectral component may be reliable markers for the V. destructor infestation level of the colonies. The obtained data may be related to the honey yield obtained from the apiaries.

The catalase-peroxidase PiCP1 plays a critical role in abiotic stress resistance, pathogenicity and asexual structure development in Phytophthora infestans

Catalase-peroxidase is a heme oxidoreductase widely distributed in bacteria and lower eukaryotes. In this study, we identified a catalase-peroxidase PiCP1 (PITG_05579) in Phytophthora infestans. PiCP1 had catalase/peroxidase and secretion activities and was highly expressed in sporangia and upregulated in response to oxidative and heat stresses. Compared with wild type, PiCP1-silenced transformants (STs) had decreased catalase activity, reduced oxidant stress resistance and damped cell wall integrity. In contrast, PiCP1-overexpression transformants (OTs) demonstrated increased tolerance to abiotic stresses and induced the upregulation of PR genes in the host salicylic acid pathway. The high concentration of PiCP1 can also induced callose deposition in plant tissue. Importantly, both STs and OTs have severely reduced sporangia formation and zoospore releasing rate, but the sporangia germination rate and type varied depending on environmental conditions. Comparative sequence analyses show that catalase-peroxidases are broadly distributed and highly conserved among soil-borne plant parasitic oomycetes, but not in freshwater-inhabiting or strictly plants-inhabiting oomycetes. In addition, we found that silencing PiCP1 downregulated the expression of PiCAT2. These results revealed the important roles of PiCP1 in abiotic stress resistance, pathogenicity and in regulating asexual structure development in response to environmental change. Our findings provide new insights into catalase-peroxidase functions in eukaryotic pathogens.

Free Radicals and Oxidative Stress: Signaling Mechanisms, Redox Basis for Human Diseases, and Cell Cycle Regulation

Free radicals contain one or more unpaired electrons in their valence shell, thus making them unstable, short-lived, and highly reactive species. Excessive generation of these free radicals ultimately leads to oxidative stress causing oxidation and damage to significant macromolecules in the living system and essentially disrupting signal transduction pathways and antioxidants equilibrium. At lower concentrations, ROS serves as "second messengers," influencing many physiological processes in the cell. However, higher concentrations beyond cell capacity cause oxidative stress, contributing to human pathologies such as diabetes, cancer, Parkinson's disease, cardiovascular diseases, cataract, asthma, hypertension, atherosclerosis, arthritis, and Alzheimer's disease. Signaling pathways such as NF-κB, MAPKs, PI3K/Akt/ mTOR, and Keap1-Nrf2- ARE modulate the detrimental effects of oxidative stress by increasing the expression of cellular antioxidant defenses, phase II detoxification enzymes, and decreased production of ROS. Free radicals such as H2O2 are indeed needed for the advancement of the cell cycle as these molecules influence DNA, proteins, and enzymes in the cell cycle pathway. In the course of cell cycle progression, the cellular redox environment becomes more oxidized, moving from the G1 phase, becoming higher in G2/M and moderate in the S phase. Signals in the form of an increase in cellular pro-oxidant levels are required, and these signals are often terminated by a rise in the amount of antioxidants and MnSOD with a decrease in the level of cyclin D1 proteins. Therefore, understanding the mechanism of cell cycle redox regulation will help in the therapy of many diseases.

Protein-protein interactions in plant antioxidant defense

The regulation of reactive oxygen species (ROS) levels in plants is ensured by mechanisms preventing their over accumulation, and by diverse antioxidants, including enzymes and nonenzymatic compounds. These are affected by redox conditions, posttranslational modifications, transcriptional and posttranscriptional modifications, Ca²⁺, nitric oxide (NO) and mitogen-activated protein kinase signaling pathways. Recent knowledge about protein-protein interactions (PPIs) of antioxidant enzymes advanced during last decade. The best-known examples are interactions mediated by redox buffering proteins such as thioredoxins and glutaredoxins. This review summarizes interactions of major antioxidant enzymes with regulatory and signaling proteins and their diverse functions. Such interactions are important for stability, degradation and activation of interacting partners. Moreover, PPIs of antioxidant enzymes may connect diverse metabolic processes with ROS scavenging. Proteins like receptor for activated C kinase 1 may ensure coordination of antioxidant enzymes to ensure efficient ROS regulation. Nevertheless, PPIs in antioxidant defense are understudied, and intensive research is required to define their role in complex regulation of ROS scavenging.

The antihyperglycemic effect of pulsed electric field-extracted polysaccharide of Kaempferia elegans officinale on streptozotocin induced diabetic mice

Kaempferia elegans polysaccharide (KEP) was extracted using a high-voltage pulsed electric field-assisted hot water method. Its physicochemical properties, in vitro activity and hypoglycemic effect was investigated. Experiments were undertaken with diabetic mice models and the potential mechanism of KEP to improve blood glucose levels was unveiled through measurements of relevant indicators in the serum and liver of the mice. Results showed that KEP is mainly composed of glucose, rhamnose, arabinose, and galactose. It has certain DPPH and ABTS free radical scavenging ability and good α-glucosidase inhibitory ability, indicating that KEP has the potential to improve blood glucose levels in diabetes patients. The experimental results of KEP treatment on mice showed that KEP could control the continuous increase of fasting blood glucose levels. The potential mechanisms behind this blood glucose level control composes of (1) increasing the glucokinase and C peptide levels and decreasing Glucose-6-phosphatase content for improving key enzyme activity in the glucose metabolism pathway. This promotes the consumption of blood glucose during glycolysis, thereby inhibiting the production of endogenous glucose in gluconeogenesis pathway; (2) reducing triglyceride, total cholesterol, low density lipoprotein cholesterol, and increasing high density lipoprotein cholesterol content, for regulating blood lipid indicators to normal levels; and (3) by improving the activities of catalase, glutathione peroxidase, and antioxidant enzymes superoxide dismutase for further improving the antioxidant defense system in the body to reduce blood glucose.

Maternal catalase supplementation regulates fatty acid metabolism and antioxidant ability of lactating sows and their offspring

Introduction and methods

As a crucial antioxidant enzyme, catalase (CAT) could destroy the cellular hydrogen peroxide to mitigate oxidative stress. The current study aimed to investigate the effects of maternal CAT supplementation from late gestation to day 14 of lactation on antioxidant ability and fatty acids metabolism with regard to the sow-piglet-axis. On day 95 of gestation, forty sows were divided into control (CON) group (fed a basal diet) and CAT group (fed a basal diet supplemented with 660 mg/kg CAT), the feeding experiment ended on day 14 of lactation.

Results

The lactating sows in the CAT group produced more milk, and had higher antioxidant enzymes activity including POD and GSH-Px (P < 0.05), lower content of serum LDL as well as plasmic C18:3n3 content (P < 0.05). Additionally, maternal CAT supplementation improved offspring's body weight at day 14 of nursing period and ADG (P < 0.05), and regulated the antioxidant ability as evidenced by decreased related enzymes activity such as T-AOC and CAT and changed genes expression level. It significantly affected lipid metabolism of suckling piglets manifested by increasing the serum ALT, CHOL, and LDL (P < 0.05) level and modulating plasma medium- and long-chain fatty acids (MCFAs and LCFAs), as well as regulating the genes expression involved in lipid metabolism.

Conclusion

Maternal CAT supplementation could regulate the fatty acid composition and enhance the antioxidant ability of sows and offspring during the lactating period and further promote the growth of suckling piglets. These findings might provide a reference value for the utilization of CAT as supplement for mother from late pregnancy to lactation period to promote the fatty acid metabolism of offspring.

Placing human gene families into their evolutionary context

Following the draft sequence of the first human genome over 20 years ago, we have achieved unprecedented insights into the rules governing its evolution, often with direct translational relevance to specific diseases. However, staggering sequence complexity has also challenged the development of a more comprehensive understanding of human genome biology. In this context, interspecific genomic studies between humans and other animals have played a critical role in our efforts to decode human gene families. In this review, we focus on how the rapid surge of genome sequencing of both model and non-model organisms now provides a broader comparative framework poised to empower novel discoveries. We begin with a general overview of how comparative approaches are essential for understanding gene family evolution in the human genome, followed by a discussion of analyses of gene expression. We show how homology can provide insights into the genes and gene families associated with immune response, cancer biology, vision, chemosensation, and metabolism, by revealing similarity in processes among distant species. We then explain methodological tools that provide critical advances and show the limitations of common approaches. We conclude with a discussion of how these investigations position us to gain fundamental insights into the evolution of gene families among living organisms in general. We hope that our review catalyzes additional excitement and research on the emerging field of comparative genomics, while aiding the placement of the human genome into its existentially evolutionary context.

Metal-binding proteins and cross-linking in the defensive glue of the slug Arion subfuscus

The role of metals in forming the primary cross-links in slug glue was investigated. Several metal-binding proteins were identified in the defensive glue produced by the slug Arion subfuscus. Notably, the C-lectins that are unique to the glue are iron-binding proteins. This is unusual for C-lectins. Dissociating these proteins from iron does not affect the glue's stiffness. Similarly, several proteins that can bind to zinc were identified, but dissociating the proteins from zinc did not weaken the glue. These results suggest that metal coordination is not involved in the primary cross-links of this hydrogel glue. The stable cross-links that provide stiffness are more likely to be created by a catalytic event involving protein oxidation. Cross-linking was unexpectedly difficult to prevent. Collecting the glue into a large volume of ice-cold buffer with reagents aimed at inhibiting oxidative cross-linking caused a slight loss of cross-linking, as demonstrated by the appearance of uncross-linked proteins in native gel electrophoresis. Notable among these was a protein that is normally heavily oxidized (asmp165). Nevertheless, this effect was not large, suggesting that the primary cross-links form before secretion.

Characterization and genomic analysis of two novel psychrotolerant Acidithiobacillus ferrooxidans strains from polar and subpolar environments

The bioleaching process is carried out by aerobic acidophilic iron-oxidizing bacteria that are mainly mesophilic or moderately thermophilic. However, many mining sites are located in areas where the mean temperature is lower than the optimal growth temperature of these microorganisms. In this work, we report the obtaining and characterization of two psychrotolerant bioleaching bacterial strains from low-temperature sites that included an abandoned mine site in Chilean Patagonia (PG05) and an acid rock drainage in Marian Cove, King George Island in Antarctic (MC2.2). The PG05 and MC2.2 strains showed significant iron-oxidation activity and grew optimally at 20°C. Genome sequence analyses showed chromosomes of 2.76 and 2.84 Mbp for PG05 and MC2.2, respectively, and an average nucleotide identity estimation indicated that both strains clustered with the acidophilic iron-oxidizing bacterium Acidithiobacillus ferrooxidans. The Patagonian PG05 strain had a high content of genes coding for tolerance to metals such as lead, zinc, and copper. Concordantly, electron microscopy revealed the intracellular presence of polyphosphate-like granules, likely involved in tolerance to metals and other stress conditions. The Antarctic MC2.2 strain showed a high dosage of genes for mercury resistance and low temperature adaptation. This report of cold-adapted cultures of the At. ferrooxidans species opens novel perspectives to satisfy the current challenges of the metal bioleaching industry.

Integrating Genome-Resolved Metagenomics with Trait-Based Process Modeling to Determine Biokinetics of Distinct Nitrifying Communities within Activated Sludge

Conventional bioprocess models for wastewater treatment are based on aggregated bulk biomass concentrations and do not incorporate microbial physiological diversity. Such a broad aggregation of microbial functional groups can fail to predict ecosystem dynamics when high levels of physiological diversity exist within trophic guilds. For instance, functional diversity among nitrite-oxidizing bacteria (NOB) can obfuscate engineering strategies for their out-selection in activated sludge (AS), which is desirable to promote energy-efficient nitrogen removal. Here, we hypothesized that different NOB populations within AS can have different physiological traits that drive process performance, which we tested by estimating biokinetic growth parameters using a combination of highly replicated respirometry, genome-resolved metagenomics, and process modeling. A lab-scale AS reactor subjected to a selective pressure for over 90 days experienced resilience of NOB activity. We recovered three coexisting Nitrospira population genomes belonging to two sublineages, which exhibited distinct growth strategies and underwent a compositional shift following the selective pressure. A trait-based process model calibrated at the NOB genus level better predicted nitrite accumulation than a conventional process model calibrated at the NOB guild level. This work demonstrates that trait-based modeling can be leveraged to improve our prediction, control, and design of functionally diverse microbiomes driving key environmental biotechnologies.

Parasitemia and elevation as predictors of hemoglobin concentration and antioxidant capacity in two sympatric lizards

Studies which quantify the influence of abiotic factors on physiological variation are paramount to comprehend organismal responses to diverse environments. We studied three physiological aspects of metabolism in two sympatric and ecologically similar European lizard species, Podarcis muralis and Iberolacerta horvathi, across an 830-m elevational gradient. We collected blood samples and tail tips from adult lizards, which were analyzed for parasitemia, hemoglobin concentration, potential metabolic activity and catalase activity. Hemoglobin concentration was higher in males than females and it increased across elevation in one of the studied species - P. muralis. Parasitemia was not an important predictor of the variation in hemoglobin concentration, which suggests that blood parasites do not constraint the aerobic capacity of the lizards. On the other hand, catalase activity reflected increased antioxidant activity in the presence of higher parasitemia, possibly acting as an adaptive mechanism to reduce oxidative stress during immune activation. Potential metabolic activity, as a proxy for maximum respiratory enzymatic capacity, did not differ between species or sexes nor was it affected by elevation or levels of parasitemia. The results provide insight into the relationships between physiological, biotic, and environmental traits in sympatric lizards.

Stable Dried Catalase Particles Prepared by Electrospraying

Therapeutic proteins and peptides are clinically important, offering potency while reducing the potential for off-target effects. Research interest in developing therapeutic polypeptides has grown significantly during the last four decades. However, despite the growing research effort, maintaining the stability of polypeptides throughout their life cycle remains a challenge. Electrohydrodynamic (EHD) techniques have been widely explored for encapsulation and delivery of many biopharmaceuticals. In this work, we explored monoaxial electrospraying for encapsulation of bovine liver catalase, investigating the effects of the different components of the electrospraying solution on the integrity and bioactivity of the enzyme. The catalase was successfully encapsulated within polymeric particles made of polyvinylpyrrolidone (PVP), dextran, and polysucrose. The polysorbate 20 content within the electrospraying solution (50 mM citrate buffer, pH 5.4) affected the catalase loading—increasing the polysorbate 20 concentration to 500 μg/mL resulted in full protein encapsulation but did not prevent loss in activity. The addition of ethanol (20% v/v) to a fully aqueous solution improves the electrospraying process by reducing surface tension, without loss of catalase activity. The polymer type was shown to have the greatest impact on preserving catalase activity within the electrosprayed particles. When PVP was the carrier there was no loss in activity compared with fresh aqueous solutions of catalase. The optimum particles were obtained from a 20% w/v PVP or 30% w/v PVP-trehalose (1:1 w/w) solution. The addition of trehalose confers stability advantages to the catalase particles. When trehalose-PVP particles were stored at 5 °C, enzymatic activity was maintained over 3 months, whereas for the PVP-only analogue a 50% reduction in activity was seen. This demonstrates that processing catalase by monoaxial electrospraying can, under optimised conditions, result in stable polymeric particles with no loss of activity.

Characterization and Comparative Genomic Analysis of a Highly Colistin-Resistant Chryseobacterium gallinarum: a Rare, Uncommon Pathogen

For the first time, we describe the whole genome of a yellow-pigmented, capsule-producing, pathogenic, and colistin-resistant Chryseobacterium gallinarum strain MGC42 isolated from a patient with urinary tract infection in India. VITEK 2 automated system initially identified this isolate as C. indologenes. However, 16S rRNA gene sequencing revealed that MGC42 shared 99.67% sequence identity with C. gallinarum–type strain DSM 27622. The draft genome of the strain MGC42 was 4,455,926 bp long with 37.08% Guanine-Cytosine (GC) content and was devoid of any plasmid. Antibiotic resistance, virulence, and toxin genes were predicted by implementing a machine learning classifier. Potential homologs of 340 virulence genes including hemolysin secretion protein D, metalloprotease, catalase peroxidases and autotransporter adhesins, type VI secretion system (T6SS) spike proteins, and 27 toxin factors including a novel toxin domain Ntox23 were identified in the genome. Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs of 110 transporter proteins were predicted that were in agreement with moderate efflux activity. Twelve antibiotic resistance genes including two potentially novel putative β-lactamase genes sharing low similarity with known β-lactamase genes were also identified in the genome of this strain. The strain MGC42 was also resistant to several classes of antibiotics along with carbapenems and polymyxin. We also identified mutations in the orthologs of pmrB (M384T) and lpxD (I66V) that might be responsible for colistin resistance. The MGC42 strain shared 683 core genes with other environmental and clinical strains of Chryseobacterium species. Our findings suggest that the strain MGC42 is a multidrug-resistant, virulent pathogen and recommend 16S rRNA gene sequencing to identify clinical specimens of Chryseobacterium species.

Molecular characteristics of the multi-functional FAO enzyme ACAD9 illustrate the importance of FADH2 /NADH ratios for mitochondrial ROS formation

A decade ago I postulated that ROS formation in mitochondria was influenced by different FADH₂ /NADH (F/N) ratios of catabolic substrates. Thus, fatty acid oxidation (FAO) would give higher ROS formation than glucose oxidation. Both the emergence of peroxisomes and neurons not using FAO, could be explained thus. ROS formation in NADH:ubiquinone oxidoreductase (Complex I) comes about by reverse electron transport (RET) due to high QH₂ levels, and scarcity of its electron-acceptor (Q) during FAO. The then new, unexpected, finding of an FAO enzyme, ACAD9, being involved in complex I biogenesis, hinted at connections in line with the hypothesis. Recent findings about ACAD9's role in regulation of respiration fit with predictions the model makes: cementing connections between ROS production and F/N ratios. I describe how ACAD9 might be central to reversing the oxidative damage in complex I resulting from FAO. This seems to involve two distinct, but intimately connected, ACAD9 characteristics: (i) its upregulation of complex I biogenesis, and (ii) releasing FADH₂ , with possible conversion into FMN, the crucial prosthetic group of complex I.

HDA-2-Containing Complex Is Required for Activation of Catalase-3 Expression in Neurospora crassa

It is essential for aerobic organisms to maintain the homeostasis of intracellular reactive oxygen species (ROS) for survival and adaptation to the environment. In line with other eukaryotes, the catalase of Neurospora crassa is an important enzyme for clearing ROS, and its expression is tightly regulated by the growth phase and various oxidative stresses. Our study reveals that, in N. crassa, histone deacetylase 2 (HDA-2) and its catalytic activity positively regulate the expression of the catalase-3 (cat-3) gene. HDA-2, SIF-2, and SNT-1 may form a subcomplex with such a regulation role. As expected, deletion of HDA-2 or SIF-2 subunit increased acetylation levels of histone H4, indicating that loss of HDA-2 complex fails to deacetylate H4 at the cat-3 locus. Furthermore, loss of HDA-2 or its catalytic activity led to dramatic decreases of TFIIB and RNA polymerase II (RNAP II) recruitment at the cat-3 locus and also resulted in high deposition of H2A.Z at the promoter and transcription start site (TSS) regions of the cat-3 gene. Collectively, this study strongly demonstrates that the HDA-2-containing complex activates the transcription of the cat-3 gene by facilitating preinitiation complex (PIC) assembly and antagonizing the inhibition of H2A.Z at the cat-3 locus through H4 acetylation. IMPORTANCE Clearance of reactive oxygen species (ROS) is critical to the survival of aerobic organisms. In the model filamentous fungus Neurospora crassa, catalase-3 (cat-3) expression is activated in response to H₂O₂-induced ROS stress. We found that histone deacetylase 2 (HDA-2) positively regulates cat-3 transcription in N. crassa; this is widely divergent from the classical repressive role of most histone deacetylases. Like HDA-2, the SIF-2 or SNT-1 subunit of HDA-2-containing complex plays a positive role in cat-3 transcription. Furthermore, we also found that HDA-2-containing complex provides an appropriate chromatin environment to facilitate PIC assembly and to antagonize the inhibition role of H2A.Z at the cat-3 locus through H4 acetylation. Taken together, our results establish a mechanism for how the HDA-2-containing complex regulates transcription of the cat-3 gene in N. crassa.

Evolution and functional diversification of catalase genes in the green lineage

Background

Catalases (CATs) break down hydrogen peroxide into water and oxygen to prevent cellular oxidative damage, and play key roles in the development, biotic and abiotic stresses of plants. However, the evolutionary relationships of the plant CAT gene family have not been systematically reported.

Results

Here, we conducted genome-wide comparative, phylogenetic, and structural analyses of CAT orthologs from 29 out of 31 representative green lineage species to characterize the evolution and functional diversity of CATs. We found that CAT genes in land plants were derived from core chlorophytes and detected a lineage-specific loss of CAT genes in Fabaceae, suggesting that the CAT genes in this group possess divergent functions. All CAT genes were split into three major groups (group α, β1, and β2) based on the phylogeny. CAT genes were transferred from bacteria to core chlorophytes and charophytes by lateral gene transfer, and this led to the independent evolution of two types of CAT genes: α and β types. Ten common motifs were detected in both α and β groups, and β CAT genes had five unique motifs, respectively. The findings of our study are inconsistent with two previous hypotheses proposing that (i) new CAT genes are acquired through intron loss and that (ii) the Cys-343 residue is highly conserved in plants. We found that new CAT genes in most higher plants were produced through intron acquisition and that the Cys-343 residue was only present in monocots, Brassicaceae and Pp_CatX7 in P. patens, which indicates the functional specificity of the CATs in these three lineages. Finally, our finding that CAT genes show high overall sequence identity but that individual CAT genes showed developmental stage and organ-specific expression patterns suggests that CAT genes have functionally diverged independently.

Conclusions

Overall, our analyses of the CAT gene family provide new insights into their evolution and functional diversification in green lineage species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08621-6.

Tomato methionine sulfoxide reductase B2 functions in drought tolerance by promoting ROS scavenging and chlorophyll accumulation through interaction with Catalase 2 and RBCS3B

Reactive oxygen species (ROS) are inevitably generated in aerobic organisms as by-products of common metabolism and as the result of defense and development. ROS readily oxidizes methionine (Met) residues of proteins to form Met-R-sulfoxide or Met-S-sulfoxide (MetSO), resulting in protein inactivation or malfunction. Although it is known that MetSO can be reverted to Met by methionine sulfoxide reductase (Msr), the mechanism how Msr interacts with its target proteins is poorly understood. In this study, two target proteins of tomato MsrB2 (SlMsrB2), catalase 2 (CAT2) and the Rubisco small subunit RBCS3B, were identified. Silencing of SlMsrB2 by RNA interference (RNAi) in tomato led to decreased drought tolerance, accompanied by increased ROS accumulation and chlorophyll degradation. By contrast, overexpression of SlMsrB2 in tomato significantly reduced ROS accumulation and enhanced drought tolerance. Protein interaction analysis showed that SlMsrB2 interacts with CAT2 and RBCS3B in vitro and in planta. Silencing of CAT2 by RNAi and RBCS3B by virus-induced gene silencing (VIGS) resulted in development of pale green leaves and enhanced ROS accumulation in tomato plants. These results demonstrate that SlMsrB2 functions in drought tolerance and promotes chlorophyll accumulation by modulating ROS accumulation.

Basidiomycota Fungi and ROS: Genomic Perspective on Key Enzymes Involved in Generation and Mitigation of Reactive Oxygen Species

Our review includes a genomic survey of a multitude of reactive oxygen species (ROS) related intra- and extracellular enzymes and proteins among fungi of Basidiomycota, following their taxonomic classification within the systematic classes and orders, and focusing on different fungal lifestyles (saprobic, symbiotic, pathogenic). Intra- and extracellular ROS metabolism-involved enzymes (49 different protein families, summing 4170 protein models) were searched as protein encoding genes among 63 genomes selected according to current taxonomy. Extracellular and intracellular ROS metabolism and mechanisms in Basidiomycota are illustrated in detail. In brief, it may be concluded that differences between the set of extracellular enzymes activated by ROS, especially by H2O2, and involved in generation of H2O2, follow the differences in fungal lifestyles. The wood and plant biomass degrading white-rot fungi and the litter-decomposing species of Agaricomycetes contain the highest counts for genes encoding various extracellular peroxidases, mono- and peroxygenases, and oxidases. These findings further confirm the necessity of the multigene families of various extracellular oxidoreductases for efficient and complete degradation of wood lignocelluloses by fungi. High variations in the sizes of the extracellular ROS-involved gene families were found, however, among species with mycorrhizal symbiotic lifestyle. In addition, there are some differences among the sets of intracellular thiol-mediation involving proteins, and existence of enzyme mechanisms for quenching of intracellular H2O2 and ROS. In animal- and plant-pathogenic species, extracellular ROS enzymes are absent or rare. In these fungi, intracellular peroxidases are seemingly in minor role than in the independent saprobic, filamentous species of Basidiomycota. Noteworthy is that our genomic survey and review of the literature point to that there are differences both in generation of extracellular ROS as well as in mechanisms of response to oxidative stress and mitigation of ROS between fungi of Basidiomycota and Ascomycota.

Investigation of the Importance of Protein 3D Structure for Assessing Conservation of Lysine Acetylation Sites in Protein Homologs

Acetylation is a protein post-translational modification (PTM) that can affect a variety of cellular processes. In bacteria, two PTM Nε-acetylation mechanisms have been identified: non-enzymatic/chemical acetylation via acetyl phosphate or acetyl coenzyme A and enzymatic acetylation via protein acetyltransferases. Prior studies have shown that extensive acetylation of Nε-lysine residues of numerous proteins from a variety of bacteria occurs via non-enzymatic acetylation. In Escherichia coli, new Nε-lysine acetyltransferases (KATs) that enzymatically acetylate other proteins have been identified, thus expanding the repertoire of protein substrates that are potentially regulated by acetylation. Therefore, we designed a study to leverage the wealth of structural data in the Protein Data Bank (PDB) to determine: (1) the 3D location of lysine residues on substrate proteins that are acetylated by E. coli KATs, and (2) investigate whether these residues are conserved on 3D structures of their homologs. Five E. coli KAT substrate proteins that were previously identified as being acetylated by YiaC and had 3D structures in the PDB were selected for further analysis: adenylate kinase (Adk), isocitrate dehydrogenase (Icd), catalase HPII (KatE), methionyl-tRNA formyltransferase (Fmt), and a peroxide stress resistance protein (YaaA). We methodically compared over 350 protein structures of these E. coli enzymes and their homologs; to accurately determine lysine residue conservation requires a strategy that incorporates both flexible structural alignments and visual inspection. Moreover, our results revealed discrepancies in conclusions about lysine residue conservation in homologs when examining linear amino acid sequences compared to 3D structures.

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.

Comparative Analysis of Three Trypanosomatid Catalases of Different Origin

Most trypanosomatid flagellates do not have catalase. In the evolution of this group, the gene encoding catalase has been independently acquired at least three times from three different bacterial groups. Here, we demonstrate that the catalase of Vickermania was obtained by horizontal gene transfer from Gammaproteobacteria, extending the list of known bacterial sources of this gene. Comparative biochemical analyses revealed that the enzymes of V. ingenoplastis, Leptomonas pyrrhocoris, and Blastocrithidia sp., representing the three independent catalase-bearing trypanosomatid lineages, have similar properties, except for the unique cyanide resistance in the catalase of the latter species.