Molecular recognition of wood polyphenols by phase II detoxification enzymes of the white rot Trametes versicolor

First Characterization of a Cyanobacterial Xi-Class Glutathione S-Transferase in Synechocystis PCC 6803

Glutathione S-transferases (GSTs) are evolutionarily conserved enzymes crucial for cell detoxication. They are viewed as having evolved in cyanobacteria, the ancient photosynthetic prokaryotes that colonize our planet and play a crucial role for its biosphere. Xi-class GSTs, characterized by their specific glutathionyl-hydroquinone reductase activity, have been observed in prokaryotes, fungi and plants, but have not yet been studied in cyanobacteria. In this study, we have analyzed the presumptive Xi-class GST, designated as Slr0605, of the unicellular model cyanobacterium Synechocystis PCC 6803. We report that Slr0605 is a homodimeric protein that has genuine glutathionyl-hydroquinone reductase activity. Though Slr0605 is not essential for cell growth under standard photoautotrophic conditions, it plays a prominent role in the protection against not only benzoquinone, but also cobalt-excess stress. Indeed, Slr0605 acts in defense against the cobalt-elicited disturbances of iron homeostasis, iron-sulfur cluster repair, catalase activity and the level of reactive oxygen species, which are all crucial for cell life.

Microplastics pollution in the marine environment: A review of sources, impacts and mitigation

Over the past few years, microplastics (MPs) pollution in the marine environment has emerged as a significant environmental concern. Poor management practices lead to millions of tons of plastic waste entering oceans annually, primarily from land-based sources like mismanaged waste, urban runoff, and industrial activities. MPs pollution in marine environments poses a significant threat to ecosystems and human health, as it adsorbs pollutants, heavy metals, and leaches additives such as plasticizers and flame retardants, thus contributing to chemical pollution. The review article provides a comprehensive overview of MPs pollution, its sources, and impacts on marine environments, including human health, detection techniques, and strategies for mitigating microplastic contamination in marine environments. The paper provides current information on microplastic pollution in marine environments, offering insights for researchers, policymakers, and the public, as well as promoting sustainable practices to protect the environment.

Structural and Thermodynamic Insights into Dimerization Interfaces of Drosophila Glutathione Transferases

This study presents a comprehensive analysis of the dimerization interfaces of fly GSTs through sequence alignment. Our investigation revealed GSTE1 as a particularly intriguing target, providing valuable insights into the variations within Delta and Epsilon GST interfaces. The X-ray structure of GSTE1 was determined, unveiling remarkable thermal stability and a distinctive dimerization interface. Utilizing circular dichroism, we assessed the thermal stability of GSTE1 and other Drosophila GSTs with resolved X-ray structures. The subsequent examination of GST dimer stability correlated with the dimerization interface supported by findings from X-ray structural analysis and thermal stability measurements. Our discussion extends to the broader context of GST dimer interfaces, offering a generalized perspective on their stability. This research enhances our understanding of the structural and thermodynamic aspects of GST dimerization, contributing valuable insights to the field.

Probiotics an emerging therapeutic approach towards gut-brain-axis oriented chronic health issues induced by microplastics: A comprehensive review

Applications for plastic polymers can be found all around the world, often discarded without any prior care, exacerbating the environmental issue. When large waste materials are released into the environment, they undergo physical, biological, and photo-degradation processes that break them down into smaller polymer fragments known as microplastics (MPs). The time it takes for residual plastic to degrade depends on the type of polymer and environmental factors, with some taking as long as 600 years or more. Due to their small size, microplastics can contaminate food and enter the human body through food chains and webs, causing gastrointestinal (GI) tract pain that can range from local to systemic. Microplastics can also acquire hydrophobic organic pollutants and heavy metals on their surface, due to their large surface area and surface hydrophobicity. The levels of contamination on the microplastic surface are significantly higher than in the natural environment. The gut-brain axis (GB axis), through which organisms interact with their environment, regulate nutritional digestion and absorption, intestinal motility and secretion, complex polysaccharide breakdown, and maintain intestinal integrity, can be altered by microplastics acting alone or in combination with pollutants. Probiotics have shown significant therapeutic potential in managing various illnesses mediated by the gut-brain axis. They connect hormonal and biochemical pathways to promote gut and brain health, making them a promising therapy option for a variety of GB axis-mediated illnesses. Additionally, taking probiotics with or without food can reduce the production of pro-inflammatory cytokines, reactive oxygen species (ROS), neuro-inflammation, neurodegeneration, protein folding, and both motor and non-motor symptoms in individuals with Parkinson's disease. This study provides new insight into microplastic-induced gut dysbiosis, its associated health risks, and the benefits of using both traditional and next-generation probiotics to maintain gut homeostasis.

Aging and mitigation of microplastics during sewage sludge treatments: An overview

Wastewater treatment plants (WWTPs) receive large quantities of microplastics (MPs) from raw wastewater, but many MPs are trapped in the sludge. Land application of sludge is a significant source of MP pollution. Existing reviews have summarized the analysis methods of MPs in sludge and the effect of MPs on sludge treatments. However, MP aging and mitigation during sludge treatment processes are not fully reviewed. Treatment processes used to remove water, pathogenic microorganisms, and other pollutants in sewage sludge also cause surface changes and degradation in the sludge MPs, affecting the potential risk of MPs. This study integrates MP abundance and distribution in sludge and their aging and mitigation characteristics during sludge treatment processes. The abundance, composition, and distribution of sludge MPs vary significantly with WWTPs. Furthermore, MPs exhibit variable degrees of aging, including rough surfaces, enhanced adsorption potentials for pollutants, and increased leaching behavior. Various sludge treatment processes further intensify these aging characteristics. Some sludge treatments, such as hydrothermal treatment, have efficiently removed MPs from sewage sludge. It is crucial to understand the potential risk of MP aging in sludge and the degradation properties of the MP-derived products from MP degradation in-depth and develop novel MP mitigation strategies in sludge, such as combining hydrothermal treatment and biological processes.

Rattus norvegicus Glutathione Transferase Omega 1 Localization in Oral Tissues and Interactions with Food Phytochemicals

Glutathione transferases are xenobiotic-metabolizing enzymes with both glutathione-conjugation and ligandin roles. GSTs are present in chemosensory tissues and fluids of the nasal/oral cavities where they protect tissues from exogenous compounds, including food molecules. In the present study, we explored the presence of the omega-class glutathione transferase (GSTO1) in the rat oral cavity. Using immunohistochemistry, GSTO1 expression was found in taste bud cells of the tongue epithelium and buccal cells of the oral epithelium. Buccal and lingual extracts exhibited thiol-transferase activity (4.9 ± 0.1 and 1.8 ± 0.1 μM/s/mg, respectively). A slight reduction from 4.9 ± 0.1 to 4.2 ± 0.1 μM/s/mg (p < 0.05; Student's t test) was observed in the buccal extract with 100 μM GSTO1-IN-1, a specific inhibitor of GSTO1. RnGSTO1 exhibited the usual activities of omega GSTs, i.e., thiol-transferase (catalytic efficiency of 8.9 × 104 M-1·s-1), and phenacyl-glutathione reductase (catalytic efficiency of 8.9 × 105 M-1·s-1) activities, similar to human GSTO1. RnGSTO1 interacts with food phytochemicals, including bitter compounds such as luteolin (Ki = 3.3 ± 1.9 μM). Crystal structure analysis suggests that luteolin most probably binds to RnGSTO1 ligandin site. Our results suggest that GSTO1 could interact with food phytochemicals in the oral cavity.

Qualitative metabolomics-based characterization of a phenolic UDP-xylosyltransferase with a broad substrate spectrum from Lentinus brumalis

Wood-decaying fungi are the major decomposers of plant litter. Heavy sequencing efforts on genomes of wood-decaying fungi have recently been made due to the interest in their lignocellulolytic enzymes; however, most parts of their proteomes remain uncharted. We hypothesized that wood-decaying fungi would possess promiscuous enzymes for detoxifying antifungal phytochemicals remaining in the dead plant bodies, which can be useful biocatalysts. We designed a computational mass spectrometry-based untargeted metabolomics pipeline for the phenotyping of biotransformation and applied it to 264 fungal cultures supplemented with antifungal plant phenolics. The analysis identified the occurrence of diverse reactivities by the tested fungal species. Among those, we focused on O-xylosylation of multiple phenolics by one of the species tested, Lentinus brumalis. By integrating the metabolic phenotyping results with publicly available genome sequences and transcriptome analysis, a UDP-glycosyltransferase designated UGT66A1 was identified and validated as an enzyme catalyzing O-xylosylation with broad substrate specificity. We anticipate that our analytical workflow will accelerate the further characterization of fungal enzymes as promising biocatalysts.

The Glutathione System: A Journey from Cyanobacteria to Higher Eukaryotes

From bacteria to plants and humans, the glutathione system plays a pleiotropic role in cell defense against metabolic, oxidative and metal stresses. Glutathione (GSH), the γ-L-glutamyl-L-cysteinyl-glycine nucleophile tri-peptide, is the central player of this system that acts in redox homeostasis, detoxification and iron metabolism in most living organisms. GSH directly scavenges diverse reactive oxygen species (ROS), such as singlet oxygen, superoxide anion, hydrogen peroxide, hydroxyl radical, nitric oxide and carbon radicals. It also serves as a cofactor for various enzymes, such as glutaredoxins (Grxs), glutathione peroxidases (Gpxs), glutathione reductase (GR) and glutathione-S-transferases (GSTs), which play crucial roles in cell detoxication. This review summarizes what is known concerning the GSH-system (GSH, GSH-derived metabolites and GSH-dependent enzymes) in selected model organisms (Escherichia coli, Saccharomyces cerevisiae, Arabidopsis thaliana and human), emphasizing cyanobacteria for the following reasons. Cyanobacteria are environmentally crucial and biotechnologically important organisms that are regarded as having evolved photosynthesis and the GSH system to protect themselves against the ROS produced by their active photoautotrophic metabolism. Furthermore, cyanobacteria synthesize the GSH-derived metabolites, ergothioneine and phytochelatin, that play crucial roles in cell detoxication in humans and plants, respectively. Cyanobacteria also synthesize the thiol-less GSH homologs ophthalmate and norophthalmate that serve as biomarkers of various diseases in humans. Hence, cyanobacteria are well-suited to thoroughly analyze the role/specificity/redundancy of the players of the GSH-system using a genetic approach (deletion/overproduction) that is hardly feasible with other model organisms (E. coli and S. cerevisiae do not synthesize ergothioneine, while plants and humans acquire it from their soil and their diet, respectively).

Modes-of-action of antifungal compounds: Stressors and (target-site-specific) toxins, toxicants, or Toxin-stressors

Fungi and antifungal compounds are relevant to the United Nation's Sustainable Development Goals. However, the modes-of-action of antifungals-whether they are naturally occurring substances or anthropogenic fungicides-are often unknown or are misallocated in terms of their mechanistic category. Here, we consider the most effective approaches to identifying whether antifungal substances are cellular stressors, toxins/toxicants (that are target-site-specific), or have a hybrid mode-of-action as Toxin-stressors (that induce cellular stress yet are target-site-specific). This newly described 'toxin-stressor' category includes some photosensitisers that target the cell membrane and, once activated by light or ultraviolet radiation, cause oxidative damage. We provide a glossary of terms and a diagrammatic representation of diverse types of stressors, toxic substances, and Toxin-stressors, a classification that is pertinent to inhibitory substances not only for fungi but for all types of cellular life. A decision-tree approach can also be used to help differentiate toxic substances from cellular stressors (Curr Opin Biotechnol 2015 33: 228-259). For compounds that target specific sites in the cell, we evaluate the relative merits of using metabolite analyses, chemical genetics, chemoproteomics, transcriptomics, and the target-based drug-discovery approach (based on that used in pharmaceutical research), focusing on both ascomycete models and the less-studied basidiomycete fungi. Chemical genetic methods to elucidate modes-of-action currently have limited application for fungi where molecular tools are not yet available; we discuss ways to circumvent this bottleneck. We also discuss ecologically commonplace scenarios in which multiple substances act to limit the functionality of the fungal cell and a number of as-yet-unresolved questions about the modes-of-action of antifungal compounds pertaining to the Sustainable Development Goals.

Structural insights into the interactions of glutathione transferases with a nitric oxide carrier and sodium nitroprusside

Glutathione transferases are detoxification enzymes with multifaceted roles, including a role in the metabolism and scavenging of nitric oxide (NO) compounds in cells. Here, we explored the ability of Trametes versicolor glutathione transferases (GSTs) from the Omega class (TvGSTOs) to bind metal-nitrosyl compounds. TvGSTOs have been studied previously for their ligandin role and are interesting models to study protein‒ligand interactions. First, we determined the X-ray structure of the TvGSTO3S isoform bound to the dinitrosyl glutathionyl iron complex (DNGIC), a physiological compound involved in the storage of nitric oxide. Our results suggested a different binding mode compared to the one previously described in human GST Pi 1 (GSTP1). Then, we investigated the manner in which TvGSTO3S binds three nonphysiological metal-nitrosyl compounds with different metal cores (iron, ruthenium and osmium). We assayed sodium nitroprusside, a well-studied vasodilator used in cases of hypertensive crises or heart failure. Our results showed that the tested GST can bind metal-nitrosyls at two distinct binding sites. Thermal shift analysis with six isoforms of TvGSTOs identified TvGSTO6S as the best interactant. Using the Griess method, TvGSTO6S was found to improve the release of nitric oxide from sodium nitroprusside in vitro, whereas the effects of human GST alpha 1 (GSTA1) and GSTP1 were moderate. Our results open new structural perspectives for understanding the interactions of glutathione transferases with metal-nitrosyl compounds associated with the biochemical mechanisms of NO uptake/release in biological systems.

Biotechnological methods to remove microplastics: a review

Microplastics pollution is major threat to ecosystems and is impacting abiotic and biotic components. Microplastics are diverse and highly complex contaminants that transport other contaminants and microbes. Current methods to remove microplastics include biodegradation, incineration, landfilling, and recycling. Here we review microplastics with focus on sources, toxicity, and biodegradation. We discuss the role of algae, fungi, bacteria in the biodegradation, and we present biotechnological methods to enhance degradation, e.g., gene editing tools and bioinformatics.

Research Status and Application Prospects of the Medicinal Mushroom Armillaria mellea

Armillaria is one of the most common diseases underlying chronic root rot in woody plants. Although there is no particularly effective way to prevent it, soil disinfection is a common effective protective measure. However, Armillaria itself has important medicinal value and is a symbiotic fungus in the cultivation of Gastrodia elata and Polyporus umbellatus. Therefore, researching Armillaria is of great practical significance. In this review, the biological characteristics, cultivation methods, chemical components, food and medicinal value and efficacy of Armillaria were all reviewed, and its development and utilization direction were analyzed and discussed.

Impact of environmental phthalate on human health and their bioremediation strategies using fungal cell factory- A review

Phthalates are utilized as plasticizers in plastic products to enhance their durability, transparency, and elasticity. However, phthalates are not covalently bonded to the polymer matrix of the phthalate-containing products and can be gradually released into the environment through biogeochemical processes. Hence, phthalates are now pervasive in our environment, including our food. Reports suggested that phthalates exposure to the mammalian systems is linked to various health consequences. It has become vital to develop highly efficient strategies to reduce phthalates from the environment. In this context, the utilization of fungi for phthalate bioremediation (mycoremediation) is advantageous due to their highly effective enzyme secretory system. Extracellular and intracellular enzymes of fungi are believed to break down the phthalates by ester hydrolysis to produce phthalic acid and alcohol, and subsequent digestion of the benzene rings of phthalic acid and their metabolites. The present review scrutinizes and highlights the knowledge gap in phthalate prevalence, exposure to mammals, and associated human health challenges. Furthermore, discusses the role of fungi and their secretory enzymes in the biodegradation of phthalates and gives a perspective to better describe and tackle this continuous threat.

Biochemical and Structural Characterization of Chi-Class Glutathione Transferases: A Snapshot on the Glutathione Transferase Encoded by sll0067 Gene in the Cyanobacterium Synechocystis sp. Strain PCC 6803

Glutathione transferases (GSTs) constitute a widespread superfamily of enzymes notably involved in detoxification processes and/or in specialized metabolism. In the cyanobacterium Synechocsytis sp. PCC 6803, SynGSTC1, a chi-class GST (GSTC), is thought to participate in the detoxification process of methylglyoxal, a toxic by-product of cellular metabolism. A comparative genomic analysis showed that GSTCs were present in all orders of cyanobacteria with the exception of the basal order Gloeobacterales. These enzymes were also detected in some marine and freshwater noncyanobacterial bacteria, probably as a result of horizontal gene transfer events. GSTCs were shorter of about 30 residues compared to most cytosolic GSTs and had a well-conserved SRAS motif in the active site (¹⁰SRAS¹³ in SynGSTC1). The crystal structure of SynGSTC1 in complex with glutathione adopted the canonical GST fold with a very open active site because the α4 and α5 helices were exceptionally short. A transferred multipolar electron-density analysis allowed a fine description of the solved structure. Unexpectedly, Ser10 did not have an electrostatic influence on glutathione as usually observed in serinyl-GSTs. The S10A variant was only slightly less efficient than the wild-type and molecular dynamics simulations suggested that S10 was a stabilizer of the protein backbone rather than an anchor site for glutathione.

Fungal bioassays for environmental monitoring

Environmental pollutants are today a major concern and an intensely discussed topic on the global agenda for sustainable development. They include a wide range of organic compounds, such as pharmaceutical waste, pesticides, plastics, and volatile organic compounds that can be found in air, soil, water bodies, sewage, and industrial wastewater. In addition to impacting fauna, flora, and fungi, skin absorption, inhalation, and ingestion of some pollutants can also negatively affect human health. Fungi play a crucial role in the decomposition and cycle of natural and synthetic substances. They exhibit a variety of growth, metabolic, morphological, and reproductive strategies and can be found in association with animals, plants, algae, and cyanobacteria. There are fungal strains that occur naturally in soil, sediment, and water that have inherent abilities to survive with contaminants, making the organism important for bioassay applications. In this context, we reviewed the applications of fungal-based bioassays as a versatile tool for environmental monitoring.

Biochemical and Structural Insights on the Poplar Tau Glutathione Transferase GSTU19 and 20 Paralogs Binding Flavonoids

Glutathione transferases (GSTs) constitute a widespread superfamily of enzymes notably involved in xenobiotic detoxification and/or in specialized metabolism. Populus trichocarpa genome (V4.1 assembly, Phytozome 13) consists of 74 genes coding for full-length GSTs and ten likely pseudogenes. These GSTs are divided into 11 classes, in which the tau class (GSTU) is the most abundant with 54 isoforms. PtGSTU19 and 20, two paralogs sharing more than 91% sequence identity (95% of sequence similarity), would have diverged from a common ancestor of P. trichocarpa and P. yatungensis species. These enzymes display the distinctive glutathione (GSH)-conjugation and peroxidase activities against model substrates. The resolution of the crystal structures of these proteins revealed significant structural differences despite their high sequence identity. PtGSTU20 has a well-defined deep pocket in the active site whereas the bottom of this pocket is disordered in PtGSTU19. In a screen of potential ligands, we were able to identify an interaction with flavonoids. Some of them, previously identified in poplar (chrysin, galangin, and pinocembrin), inhibited GSH-conjugation activity of both enzymes with a more pronounced effect on PtGSTU20. The crystal structures of PtGSTU20 complexed with these molecules provide evidence for their potential involvement in flavonoid transport in P. trichocarpa.

Recent developments in microbial degradation of polypropylene: Integrated approaches towards a sustainable environment

Fossil-fuel-based plastics have many enticing properties, but their production has resulted in significant environmental issues that require immediate attention. Despite the fact that these polymers are manmade, some bacteria can degrade and metabolise them, suggesting that biotechnologies based on the principle of plastic biodegradation could be beneficial. Among different types of plastics, polypropylene (PP), either having low or high density, is one of the most consumed plastics (18.85%). Their debasement under natural conditions is somewhat tricky. Still, their debasement under natural conditions is rather difficult slightly. However, different scientists have still made efforts by employing other microbes such as bacteria, fungi, and guts bacteria of larvae of insects to bio-deteriorate the PP plastic. Pre-irradiation techniques (ultraviolet and gamma irradiations), compatibilizers, and bio-additives (natural fibers, starch, and polylactic acid) have been found to impact percent bio-deterioration of different PP derivatives stronglythe various. The fungal and bacterial study showed that PP macro/microplastic might serve as an energy source and sole carbon during bio-degradation. Generally, gravimetric method or physical characterization techniques such as FTIR, XRD, SEM, etc., are utilized to affirm the bio-degradation of PP plastics-based materials. However, these techniques are not enough to warrant the bio-deterioration of PP. In this regard, a new technique approach that measures the amount of carbon dioxide emitted during bacterial or fungus degradation has also been discussed. In addition, further exploration is needed on novel isolates from plastisphere environments, sub-atomic strategies to describe plastic-debasing microorganisms and improve enzymatic action strategies, and omics-based innovations to speed up plastic waste bio-deterioration.

A marine fungus Alternaria alternata FB1 efficiently degrades polyethylene

Huge quantities of plastic wastes have been accumulating in the environment causing serious ecological problems and significantly impacting the global carbon cycling. Plastic pollutions have been recognized as the most common and durable marine contaminants. Consequently, the marine environment is becoming a hot spot to screen microorganisms possessing potential plastic degradation capabilities. Here, by screening hundreds of plastic waste-associated samples, we isolated a fungus (named Alternaria alternata FB1) that possessing a prominent capability of colonizing on the polyethylene (PE) film. Through Scanning Electron Microscope (SEM) observation, we found this fungus could efficiently degrade the PE film and formed numerous obvious holes in the plastic surface. Moreover, the Fourier Transform Infrared (FTIR) imaging detected absorption peak in the vicinity of 1715 cm^-1, indicating the formation of carbonyl bonds (-CO-). Through X-Ray Diffraction (XRD) analysis, we found that the PE film treated by strain FB1 for 28 days showed an evident reduced relative crystallinity degree, resulting in a decrease from 62.79% to 52.02%. Strikingly, the molecular weight of PE film decreased 95% after 120 days treatment by strain FB1. Using GC-MS, we further clarified that a four-carbon product (named Diglycolamine) accounted for 93.28% of all degradation products. We defined 153 enzymes that potentially involved in the degradation of PE through a transcriptomic method. The degradation capabilities of two representative enzymes including a laccase (with a molecular weight about 59.49 kDa) and a peroxidase (with a molecular weight about 36.7 kDa) were verified. Lastly, a complete biodegradation process of PE was proposed. Given the extreme paucity of microorganisms and enzymes for effective degradation of PE in the present time, our study provides a compelling candidate for further investigation of degradation mechanisms and development of biodegradation products of PE.

Press water from the mechanical drying of Douglas-fir wood chips has multiple beneficial effects on lignocellulolytic fungi

BACKGROUND

The mechanical drying of wood chips is an innovative method that improves the heating value of sawmill by-products in an energy-efficient continuous process. The liquid that comes out of the wood chips as press water (PW), however, contains a variety of undissolved as well as dissolved organic substances. The disposal of the PW as wastewater would generate additional costs due to its high organic load, offsetting the benefits in energy costs associated with the enhanced heating value of the wood chips. Our research explored if the organic load in PW could be utilized as a substrate by cellulolytic filamentous fungi. Hence, using the industrially relevant Ascomycete Trichoderma reesei RUT-C30 as well as several Basidiomycete wood-rotting fungi, we examined the potential of press water obtained from Douglas-fir wood chips to be used in the growth and enzyme production media.

RESULTS

The addition of PW supernatant to liquid cultures of T. reesei RUT-C30 resulted in a significant enhancement of the endoglucanase and endoxylanase activities with a substantially shortened lag-phase. A partial replacement of Ca2+, Mg2+, K+, as well as a complete replacement of Fe2+, Mn2+, Zn2+ by supplementing PW of the liquid media was achieved without negative effects on enzyme production. Concentrations of PW above 50% showed no adverse effects regarding the achievable endoglucanase activity but affected the endoxylanase activity to some extent. Exploring the enhancing potential of several individual PW components after chemical analysis revealed that the observed lag-phase reduction of T. reesei RUT-C30 was not caused by the dissolved sugars and ions, nor the wood particles in the PW sediment, suggesting that other, so far non-identified, compounds are responsible. However, also the growth rate of several basidiomycetes was significantly enhanced by the supplementation of raw PW to the agar medium. Moreover, their cultivation in liquid cultures reduced the turbidity of the PW substantially.

CONCLUSIONS

PW was identified as a suitable media supplement for lignocellulolytic fungi, including the cellulase and xylanase producer T. reesei RUT-C30 and several wood-degrading basidiomycetes. The possibility to replace several minerals, trace elements and an equal volume of fresh water in liquid media with PW and the ability of fungal mycelia to filter out the suspended solids is a promising way to combine biological wastewater treatment with value-adding biotechnological applications.

Biodegradation of plastic polymers by fungi: a brief review

Plastic polymers are non-degradable solid wastes that have become a great threat to the whole world and degradation of these plastics would take a few decades. Compared with other degradation processes, the biodegradation process is the most effective and best way for plastic degradation due to its non-polluting mechanism, eco-friendly nature, and cost-effectiveness. Biodegradation of synthetic plastics is a very slow process that also involves environmental factors and the action of wild microbial species. In this plastic biodegradation, fungi play a pivotal role, it acts on plastics by secreting some degrading enzymes, i.e., cutinase`, lipase, and proteases, lignocellulolytic enzymes, and also the presence of some pro-oxidant ions can cause effective degradation. The oxidation or hydrolysis by the enzyme creates functional groups that improve the hydrophilicity of polymers, and consequently degrade the high molecular weight polymer into low molecular weight. This leads to the degradation of plastics within a few days. Some well-known species which show effective degradation on plastics are Aspergillus nidulans, Aspergillus flavus, Aspergillus glaucus, Aspergillus oryzae, Aspergillus nomius, Penicillium griseofulvum, Bjerkandera adusta, Phanerochaete chrysosporium, Cladosporium cladosporioides, etc., and some other saprotrophic fungi, such as Pleurotus abalones, Pleurotus ostreatus, Agaricus bisporus and Pleurotus eryngii which also helps in degradation of plastics by growing on them. Some studies say that the degradation of plastics was more effective when photodegradation and thermo-oxidative mechanisms involved with the biodegradation simultaneously can make the degradation faster and easier. This present review gives current knowledge regarding different species of fungi that are involved in the degradation of plastics by their different enzymatic mechanisms to degrade different forms of plastic polymers.

A rush to explore protein-ligand electrostatic interaction energy with Charger

The mutual penetration of electron densities between two interacting molecules complicates the computation of an accurate electrostatic interaction energy based on a pseudo-atom representation of electron densities. The numerical exact potential and multipole moment (nEP/MM) method is time-consuming since it performs a 3D integration to obtain the electrostatic energy at short interaction distances. Nguyen et al. [(2018), Acta Cryst. A74, 524-536] recently reported a fully analytical computation of the electrostatic interaction energy (aEP/MM). This method performs much faster than nEP/MM (up to two orders of magnitude) and remains highly accurate. A new program library, Charger, contains an implementation of the aEP/MM method. Charger has been incorporated into the MoProViewer software. Benchmark tests on a series of small molecules containing only C, H, N and O atoms show the efficiency of Charger in terms of execution time and accuracy. Charger is also powerful in a study of electrostatic symbiosis between a protein and a ligand. It determines reliable protein-ligand interaction energies even when both contain S atoms. It easily estimates the individual contribution of every residue to the total protein-ligand electrostatic binding energy. Glutathione transferase (GST) in complex with a benzophenone ligand was studied due to the availability of both structural and thermodynamic data. The resulting analysis highlights not only the residues that stabilize the ligand but also those that hinder ligand binding from an electrostatic point of view. This offers new perspectives in the search for mutations to improve the interaction between the two partners. A proposed mutation would improve ligand binding to GST by removing an electrostatic obstacle, rather than by the traditional increase in the number of favourable contacts.

Diversity of Omega Glutathione Transferases in mushroom-forming fungi revealed by phylogenetic, transcriptomic, biochemical and structural approaches

The Omega class of glutathione transferases (GSTs) forms a distinct class within the cytosolic GST superfamily because most of them possess a catalytic cysteine residue. The human GST Omega 1 isoform was first characterized twenty years ago, but it took years of work to clarify the roles of the human isoforms. Concerning the kingdom of fungi, little is known about the cellular functions of Omega glutathione transferases (GSTOs), although they are widely represented in some of these organisms. In this study, we re-assess the phylogeny and the classification of GSTOs based on 240 genomes of mushroom-forming fungi (Agaricomycetes). We observe that the number of GSTOs is not only extended in the order of Polyporales but also in other orders such as Boletales. Our analysis leads to a new classification in which the fungal GSTOs are divided into two Types A and B. The catalytic residue of Type-A is either cysteine or serine, while that of Type-B is cysteine. The present study focuses on Trametes versicolor GSTO isoforms that possess a catalytic cysteine residue. Transcriptomic data show that Type-A GSTOs are constitutive enzymes while Type-B are inducible ones. The crystallographic analysis reveals substantial structural differences between the two types while they have similar biochemical profiles in the tested conditions. Additionally, these enzymes have the ability to bind antioxidant molecules such as wood polyphenols in two possible binding sites as observed from X-ray structures. The multiplication of GSTOs could allow fungal organisms to adapt more easily to new environments.

Glutathione Transferases: Surrogate Targets for Discovering Biologically Active Compounds

Glutathione transferases comprise a large class of multifunctional enzymes, some involved in detoxification pathways. Since these enzymes are able to interact with potentially toxic molecules, they could be used as targets to screen for compounds with biological activity. To test this hypothesis, glutathione transferases (GSTs) from the white-rot fungus Trametes versicolor have been used to screen for antifungal molecules from a library of tropical wood extracts. The interactions between a set of six GSTs from the omega class and 116 extracts from 21 tropical species were quantified using a high-throughput thermal shift assay. A correlation between these interactions and the antifungal properties of the tested extracts was demonstrated. This approach has been extended to the fractionation of an Andira coriacea extract and led to the detection of maackiain and lapachol in this wood. Altogether, the present results supported the hypothesis that such detoxification enzymes could be used to detect biologically active molecules.

A reverse chemical ecology approach to explore wood natural durability

The natural durability of wood species, defined as their inherent resistance to wood-destroying agents, is a complex phenomenon depending on many biotic and abiotic factors. Besides the presence of recalcitrant polymers, the presence of compounds with antimicrobial properties is known to be important to explain wood durability. Based on the advancement in our understanding of fungal detoxification systems, a reverse chemical ecology approach was proposed to explore wood natural durability using fungal glutathione transferases. A set of six glutathione transferases from the white-rot Trametes versicolor were used as targets to test wood extracts from seventeen French Guiana neotropical species. Fluorescent thermal shift assays quantified interactions between fungal glutathione transferases and these extracts. From these data, a model combining this approach and wood density significantly predicts the wood natural durability of the species tested previously using long-term soil bed tests. Overall, our findings confirm that detoxification systems could be used to explore the chemical environment encountered by wood-decaying fungi and also wood natural durability.

A First Insight into North American Plant Pathogenic Fungi Armillaria Sinapina Transcriptome

Armillaria sinapina, a fungal pathogen of primary timber species of North American forests, causes white root rot disease that ultimately kills the trees. A more detailed understanding of the molecular mechanisms underlying this illness will support future developments on disease resistance and management, as well as in the decomposition of cellulosic material for further use. In this study, RNA-Seq technology was used to compare the transcriptome profiles of A. sinapina fungal culture grown in yeast malt broth medium supplemented or not with betulin, a natural compound of the terpenoid group found in abundance in white birch bark. This was done to identify enzyme transcripts involved in the metabolism (redox reaction) of betulin into betulinic acid, a potent anticancer drug. De novo assembly and characterization of A. sinapina transcriptome was performed using Illumina technology. A total of 170,592,464 reads were generated, then 273,561 transcripts were characterized. Approximately, 53% of transcripts could be identified using public databases with several metabolic pathways represented. A total of 11 transcripts involved in terpenoid biosynthesis were identified. In addition, 25 gene transcripts that could play a significant role in lignin degradation were uncovered, as well as several redox enzymes of the cytochromes P450 family. To our knowledge, this research is the first transcriptomic study carried out on A. sinapina.

Is there a role for tau glutathione transferases in tetrapyrrole metabolism and retrograde signalling in plants?

In plants, tetrapyrrole biosynthesis occurs in chloroplasts, the reactions being catalysed by stromal and membrane-bound enzymes. The tetrapyrrole moiety is a backbone for chlorophylls and cofactors such as sirohaems, haems and phytochromobilins. Owing to this diversity, the potential cytotoxicity of some precursors and the associated synthesis costs, a tight control exists to adjust the demand and the fluxes for each molecule. After synthesis, haems and phytochromobilins are incorporated into proteins found in other subcellular compartments. However, there is only very limited information about the chaperones and membrane transporters involved in the trafficking of these molecules. After summarizing evidence indicating that glutathione transferases (GST) may be part of the transport and/or degradation processes of porphyrin derivatives, we provide experimental data indicating that tau glutathione transferases (GSTU) bind protoporphyrin IX and haem moieties and use structural modelling to identify possible residues responsible for their binding in the active site hydrophobic pocket. Finally, we discuss the possible roles associated with the binding, catalytic transformation (i.e. glutathione conjugation) and/or transport of tetrapyrroles by GSTUs, considering their subcellular localization and capacity to interact with ABC transporters. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.

Fungal potential for the degradation of petroleum-based polymers: An overview of macro- and microplastics biodegradation

Petroleum-based plastic materials as pollutants raise concerns because of their impact on the global ecosystem and on animal and human health. There is an urgent need to remove plastic waste from the environment to overcome the environmental crisis of plastic pollution. This review describes the natural and unique ability of fungi to invade substrates by using enzymes that have the capacity to detoxify pollutants and are able to act on nonspecific substrates, the fungal ability to produce hydrophobins for surface coating to attach hyphae to hydrophobic substrates, and hyphal ability to penetrate three dimensional substrates. Fungal studies on macro- and microplastics biodegradation have shown that fungi are able to use these materials as the sole carbon and energy source. Further research is required on novel isolates from plastisphere ecosystems, on the use of molecular techniques to characterize plastic-degrading fungi and enhance enzymatic activity levels, and on the use of omics-based technologies to accelerate plastic waste biodegradation processes. The addition of pro-oxidants species (photosensitizers) and the reduction of biocides and antioxidant stabilizers used in the plastic manufacturing process should also be considered to promote biodegradation. Interdisciplinary research and innovative fungal strategies for plastic waste biodegradation, as well as ecofriendly manufacturing of petroleum-based plastics, may help to reduce the negative impacts of plastic waste pollution in the biosphere.

Characterization of rat glutathione transferases in olfactory epithelium and mucus

The olfactory epithelium is continuously exposed to exogenous chemicals, including odorants. During the past decade, the enzymes surrounding the olfactory receptors have been shown to make an important contribution to the process of olfaction. Mammalian xenobiotic metabolizing enzymes, such as cytochrome P450, esterases and glutathione transferases (GSTs), have been shown to participate in odorant clearance from the olfactory receptor environment, consequently contributing to the maintenance of sensitivity toward odorants. GSTs have previously been shown to be involved in numerous physiological processes, including detoxification, steroid hormone biosynthesis, and amino acid catabolism. These enzymes ensure either the capture or the glutathione conjugation of a large number of ligands. Using a multi-technique approach (proteomic, immunocytochemistry and activity assays), our results indicate that GSTs play an important role in the rat olfactory process. First, proteomic analysis demonstrated the presence of different putative odorant metabolizing enzymes, including different GSTs, in the rat nasal mucus. Second, GST expression was investigated in situ in rat olfactory tissues using immunohistochemical methods. Third, the activity of the main GST (GSTM2) odorant was studied with in vitro experiments. Recombinant GSTM2 was used to screen a set of odorants and characterize the nature of its interaction with the odorants. Our results support a significant role of GSTs in the modulation of odorant availability for receptors in the peripheral olfactory process.

The structure of Trametes versicolor glutathione transferase Omega 3S bound to its conjugation product glutathionyl-phenethylthiocarbamate reveals plasticity of its active site

Trametes versicolor glutathione transferase Omega 3S (TvGSTO3S) catalyzes the conjugation of isothiocyanates (ITC) with glutathione (GSH). Previously, this isoform was investigated in depth both biochemically and structurally. Structural analysis of complexes revealed the presence of a GSH binding site (G site) and a deep hydrophobic binding site (H site) able to bind plant polyphenols. In the present study, crystals of apo TvGSTO3S were soaked with glutathionyl-phenethylthiocarbamate, the product of the reaction between GSH and phenethyl isothiocyanate (PEITC). On the basis of this crystal structure, we show that the phenethyl moiety binds in a new site at loop β₂ -α₂ while the glutathionyl part exhibits a particular conformation that occupies both the G site and the entrance to the H site. This binding mode is allowed by a conformational change of the loop β₂ -α₂ at the enzyme active site. It forms a hydrophobic slit that stabilizes the phenethyl group at a distinct site from the previously described H site. Structural comparison of TvGSTO3S with drosophila DmGSTD2 suggests that this flexible loop could be the region that binds PEITC for both isoforms. These structural features are discussed in a catalytic context.