Veratryl alcohol oxidase from Pleurotus ostreatus participates in lignin biodegradation and prevents polymerization of laccase-oxidized substrates

Unveiling the kinetic versatility of aryl-alcohol oxidases with different electron acceptors

Introduction: Aryl-alcohol oxidase (AAO) shows a pronounced duality as oxidase and dehydrogenase similar to that described for other glucose-methanol-choline (GMC) oxidase/dehydrogenase superfamily proteins involved in lignocellulose decomposition. In this work, we detail the overall mechanism of AAOs from Pleurotus eryngii and Bjerkandera adusta for catalyzing the oxidation of natural aryl-alcohol substrates using either oxygen or quinones as electron acceptors and describe the crystallographic structure of AAO from B. adusta in complex with a product analogue. Methods: Kinetic studies with 4-methoxybenzyl and 3-chloro-4- methoxybenzyl alcohols, including both transient-state and steady-state analyses, along with interaction studies, provide insight into the oxidase and dehydrogenase mechanisms of these enzymes. Moreover, the resolution of the crystal structure of AAO from B. adusta allowed us to compare their overall folding and the structure of the active sites of both AAOs in relation to their activities. Results and Discussion: Although both enzymes show similar mechanistic properties, notable differences are highlighted in this study. In B. adusta, the AAO oxidase activity is limited by the reoxidation of the flavin, while in P. eryngii the slower step takes place during the reductive half-reaction, which determines the overall reaction rate. By contrast, dehydrogenase activity in both enzymes, irrespective of the alcohol participating in the reaction, is limited by the hydroquinone release from the active site. Despite these differences, both AAOs are more efficient as dehydrogenases, supporting the physiological role of this activity in lignocellulosic decay. This dual activity would allow these enzymes to adapt to different environments based on the available electron acceptors.

Synergistic lignin degradation between Phanerochaete chrysosporium and Fenton chemistry is mediated through iron cycling and ligninolytic enzyme induction

Removal of recalcitrant lignin from wastewater remains a critical bottleneck in multiple aspects relating to microbial carbon cycling ranging from incomplete treatment of biosolids during wastewater treatment to limited conversion of biomass feedstock to biofuels. Based on previous studies showing that the white rot fungus Phanerochaete chrysosporium and Fenton chemistry synergistically degrade lignin, we sought to determine optimum levels of Fenton addition and the mechanisms underlying this synergy. We tested the extent of degradation of lignin under different ratios of Fenton reagents and found that relatively low levels of H2O2 and Fe(II) enhanced fungal lignin degradation, achieving 80.4 ± 1.61 % lignin degradation at 1.5 mM H2O2 and 0.3 mM Fe(II). Using a combination of whole-transcriptome sequencing and iron speciation assays, we determined that at these concentrations, Fenton chemistry induced the upregulation of 80 differentially expressed genes in P. ch including several oxidative enzymes. This study underlines the importance of non-canonical, auxiliary lignin-degrading pathways in the synergy between white rot fungi and Fenton chemistry in lignin degradation. We also found that, relative to the abiotic control, P. ch. increases the availability of Fe(II) for the production of hydroxyl radicals in the Fenton reaction by recycling Fe(III) (p < 0.001), decreasing the Fe(II) inputs necessary for lignin degradation via the Fenton reaction.

Experimental evidence that lignin-modifying enzymes are essential for degrading plant cell wall lignin by Pleurotus ostreatus using CRISPR/Cas9

Lignin-modifying enzymes (LMEs), which include laccases (Lacs), manganese peroxidases (MnPs), versatile peroxidases (VPs), and lignin peroxidases (LiPs), have been considered key factors in lignin degradation by white-rot fungi because they oxidize lignin model compounds and depolymerize synthetic lignin in vitro. However, it remains unclear whether these enzymes are essential/important in the actual degradation of natural lignin in plant cell walls. To address this long-standing issue, we examined the lignin-degrading abilities of multiple mnp/vp/lac mutants of Pleurotus ostreatus. One vp2/vp3/mnp3/mnp6 quadruple-gene mutant was generated from a monokaryotic wild-type strain PC9 using plasmid-based CRISPR/Cas9. Also, two vp2/vp3/mnp2/mnp3/mnp6, two vp2/vp3/mnp3/mnp6/lac2 quintuple-gene mutants, and two vp2/vp3/mnp2/mnp3/mnp6/lac2 sextuple-gene mutants were generated. The lignin-degrading abilities of the sextuple and vp2/vp3/mnp2/mnp3/mnp6 quintuple-gene mutants on the Beech wood sawdust medium reduced drastically, but not so much for those of the vp2/vp3/mnp3/mnp6/lac2 mutants and the quadruple mutant strain. The sextuple-gene mutants also barely degraded lignin in Japanese Cedar wood sawdust and milled rice straw. Thus, this study presented evidence that the LMEs, especially MnPs and VPs, play a crucial role in the degradation of natural lignin by P. ostreatus for the first time.

Production of recombinant lytic polysaccharide monooxygenases and evaluation effect of its addition into Aspergillus fumigatus var. niveus cocktail for sugarcane bagasse saccharification

Lignocellulosic biomass is a promising alternative for producing biofuels, despite its recalcitrant nature. There are microorganisms in nature capable of efficiently degrade biomass, such as the filamentous fungi. Among them, Aspergillus fumigatus var. niveus (AFUMN) has a wide variety of carbohydrate-active enzymes (CAZymes), especially hydrolases, but a low number of oxidative enzymes in its genome. To confirm the enzymatic profile of this fungus, this study analyzed the secretome of AFUMN cultured in sugarcane bagasse as the sole carbon source. As expected, the secretome showed a predominance of hydrolytic enzymes compared to oxidative activity. However, it is known that hydrolytic enzymes act in synergy with oxidative proteins to efficiently degrade cellulose polymer, such as the Lytic Polysaccharide Monooxygenases (LPMOs). Thus, three LPMOs from the fungus Thermothelomyces thermophilus (TtLPMO9D, TtLPMO9H, and TtLPMO9O) were selected, heterologous expressed in Aspergillus nidulans, purified, and used to supplement the AFUMN secretome to evaluate their effect on the saccharification of sugarcane bagasse. The saccharification assay was carried out using different concentrations of AFUMN secretome supplemented with recombinant T. thermophilus LPMOs, as well as ascorbic acid as reducing agent for oxidative enzymes. Through a statistic design created by Design-Expert software, we were able to analyze a possible cooperative effect between these components. The results indicated that, in general, the addition of TtLPMO9D and ascorbic acid did not favor the conversion process in this study, while TtLPMO9O had a highly significant cooperative effect in bagasse saccharification compared to the control using only AFUMN secretome.

Expanding the Physiological Role of Aryl-Alcohol Flavooxidases as Quinone Reductases

Aryl-alcohol oxidases (AAOs) are members of the glucose-methanol-choline oxidase/dehydrogenase (GMC) superfamily. These extracellular flavoproteins have been described as auxiliary enzymes in the degradation of lignin by several white-rot basidiomycetes. In this context, they oxidize fungal secondary metabolites and lignin-derived compounds using O₂ as an electron acceptor, and supply H₂O₂ to ligninolytic peroxidases. Their substrate specificity, including mechanistic aspects of the oxidation reaction, has been characterized in Pleurotus eryngii AAO, taken as a model enzyme of this GMC superfamily. AAOs show broad reducing-substrate specificity in agreement with their role in lignin degradation, being able to oxidize both nonphenolic and phenolic aryl alcohols (and hydrated aldehydes). In the present work, the AAOs from Pleurotus ostreatus and Bjerkandera adusta were heterologously expressed in Escherichia coli, and their physicochemical properties and oxidizing abilities were compared with those of the well-known recombinant AAO from P. eryngii. In addition, electron acceptors different from O₂, such as p-benzoquinone and the artificial redox dye 2,6-Dichlorophenolindophenol, were also studied. Differences in reducing-substrate specificity were found between the AAO enzymes from B. adusta and the two Pleurotus species. Moreover, the three AAOs oxidized aryl alcohols concomitantly with the reduction of p-benzoquinone, with similar or even higher efficiencies than when using their preferred oxidizing-substrate, O₂. IMPORTANCE In this work, quinone reductase activity is analyzed in three AAO flavooxidases, whose preferred oxidizing-substrate is O₂. The results presented, including reactions in the presence of both oxidizing substrates-benzoquinone and molecular oxygen-suggest that such aryl-alcohol dehydrogenase activity, although less important than its oxidase activity in terms of maximal turnover, may have a physiological role during fungal decay of lignocellulose by the reduction of quinones (and phenoxy radicals) from lignin degradation, preventing repolymerization. Moreover, the resulting hydroquinones would participate in redox-cycling reactions for the production of hydroxyl free radical involved in the oxidative attack of the plant cell-wall. Hydroquinones can also act as mediators for laccases and peroxidases in lignin degradation in the form of semiquinone radicals, as well as activators of lytic polysaccharide monooxygenases in the attack of crystalline cellulose. Moreover, reduction of these, and other phenoxy radicals produced by laccases and peroxidases, promotes lignin degradation by limiting repolymerization reactions. These findings expand the role of AAO in lignin biodegradation.

Microbial lignin valorization through depolymerization to aromatics conversion

Lignin is the most abundant source of renewable aromatic biopolymers and its valorization presents significant value for biorefinery sustainability, which promotes the utilization of renewable resources. However, it is challenging to fully convert the structurally complex, heterogeneous, and recalcitrant lignin into high-value products. The in-depth research on the lignin degradation mechanism, microbial metabolic pathways, and rational design of new systems using synthetic biology have significantly accelerated the development of lignin valorization. This review summarizes the key enzymes involved in lignin depolymerization, the mechanisms of microbial lignin conversion, and the lignin valorization application with integrated systems and synthetic biology. Current challenges and future strategies to further study lignin biodegradation and the trends of lignin valorization are also discussed.

Ancestral sequence reconstruction as a tool to study the evolution of wood decaying fungi

The study of evolution is limited by the techniques available to do so. Aside from the use of the fossil record, molecular phylogenetics can provide a detailed characterization of evolutionary histories using genes, genomes and proteins. However, these tools provide scarce biochemical information of the organisms and systems of interest and are therefore very limited when they come to explain protein evolution. In the past decade, this limitation has been overcome by the development of ancestral sequence reconstruction (ASR) methods. ASR allows the subsequent resurrection in the laboratory of inferred proteins from now extinct organisms, becoming an outstanding tool to study enzyme evolution. Here we review the recent advances in ASR methods and their application to study fungal evolution, with special focus on wood-decay fungi as essential organisms in the global carbon cycling.

Vinasse odyssey: sugarcane vinasse remediation and laccase production by Trametes sp. immobilized in polyurethane foam

Vinasse is a high pollutant liquid residue from bioethanol production. Due to its toxicity, most vinasse is used not disposed of in water bodies but employed for the fertigation of sugarcane crops, potentially leading to soil salinization or heavy metal deposition. The anaerobic digestion of vinasse for energy production is the main alternative to fertigation, but the process cannot eliminate colored compounds such as melanoidins, caramels, or phenolic compounds. The treatment of raw vinasse with white-rot fungi could remove colored and persistent toxic compounds, but is generally considered cost-ineffective. We report the treatment of vinasse by an autochthonous Trametes sp. strain immobilized in polyurethane foam and the concomitant production of high titers of laccase, a high value-added product that could improve the viability of the process. The reuse of the immobilized biomass and the discoloration of raw vinasse, the concentration of phenolic compounds, BOD and COD, and the phytotoxicity of the treated vinasse were measured to assess the viability of the process and the potential use of treated vinasse in fertigation or as a complementary treatment to anaerobic digestion. Under optimal conditions (vinasse 0.25X, 30 °C, 21 days incubation, 2% glucose added in the implantation stage), immobilized Trametes sp. causes a decrease of 75% in vinasse color and total phenolic compounds, reaching 1082 U L^-1 of laccase. The fungi could be used to treat 0.50X vinasse (BOD 44,400 mg O₂ L^-1), causing a 26% decolorization and a 30% removal of phenolic compounds after 21 days of treatment with maximum laccase titers of 112 U L^-1, while reducing COD and BOD from 103,290 to 42,500 mg O₂ L^-1 (59%) and from 44,440 to 21,230 mg O₂ L^-1 (52%), respectively. The re-utilization of immobilized biomass to treat 0.50X vinasse proved to be successful, leading to the production of 361 U L^-1 of laccase with 77% decolorization, 61% degradation of phenolic compounds, and the reduction of COD and BOD by 75% and 80%, respectively. Trametes sp. also reduced vinasse phytotoxicity to Lactuca sativa seedlings. The obtained results show that the aerobic treatment of vinasse by immobilized Trametes sp. is an interesting technology that could be employed as a sole treatment for the bioremediation of vinasse, with the concomitant the production of laccase. Alternatively, the methodology could be used in combination with anaerobic digestion to achieve greater decolorization and reduction of phenolic compounds, melanoidins, and organic load.

Enzymatic bioconversion process of lignin: mechanisms, reactions and kinetics

Lignin is a wasted renewable source of biomass-derived value-added chemicals. However, due to its material resistance to degradation, it remains highly underutilized. In order to develop new, catalysed and more environment friendly reaction processes for lignin valorization, science has turned a selective concentrated attention to microbial enzymes. This present work looks at the enzymes involved with the main reference focus on the different elementary mechanisms of action/conversion rate kinetics. Pathways, like with laccases/peroxidases, employ radicals, which more readily result in polymerization than de-polymerization. The β-etherase system interaction of proteins targets β-O-4 ether covalent bond, which targets lower molecular weight product species. Enzymatic activity is influenced by a wide variety of different factors which need to be considered in order to obtain the best functionality and synthesis yields.

A Putative Lignin Copper Oxidase from Trichoderma reesei

The ability of Trichoderma reesei, a fungus widely used for the commercial production of hemicellulases and cellulases, to grow and modify technical soda lignin was investigated. By quantifying fungal genomic DNA, T. reesei showed growth and sporulation in solid and liquid cultures containing lignin alone. The analysis of released soluble lignin and residual insoluble lignin was indicative of enzymatic oxidative conversion of phenolic lignin side chains and the modification of lignin structure by cleaving the β-O-4 linkages. The results also showed that polymerization reactions were taking place. A proteomic analysis conducted to investigate secreted proteins at days 3, 7, and 14 of growth revealed the presence of five auxiliary activity (AA) enzymes in the secretome: AA6, AA9, two AA3 enzymes), and the only copper radical oxidase encoded in the genome of T. reesei. This enzyme was heterologously produced and characterized, and its activity on lignin-derived molecules was investigated. Phylogenetic characterization demonstrated that this enzyme belonged to the AA5_1 family, which includes characterized glyoxal oxidases. However, the enzyme displayed overlapping physicochemical and catalytic properties across the AA5 family. The enzyme was remarkably stable at high pH and oxidized both, alcohols and aldehydes with preference to the alcohol group. It was also active on lignin-derived phenolic molecules as well as simple carbohydrates. HPSEC and LC-MS analyses on the reactions of the produced protein on lignin dimers (SS ββ, SS βO4 and GG β5) uncovered the polymerizing activity of this enzyme, which was accordingly named lignin copper oxidase (TrLOx). Polymers of up 10 units were formed by hydroxy group oxidation and radical formation. The activations of lignin molecules by TrLOx along with the co-secretion of this enzyme with reductases and FAD flavoproteins oxidoreductases during growth on lignin suggest a synergistic mechanism for lignin breakdown.

A novel Laccase gene from Litopenaeus vannamei is involved in the immune responses to pathogen infection and oxidative stress

Laccases (Lacs) are copper-containing oxidase enzymes that are found in various plants, fungi, and microorganisms. For invertebrates, particularly insects and crustaceans, Lacs have been shown to be involved in immune responses. In shrimp, a Lac gene has been cloned and functionally characterized, which revealed that it is involved in shrimp anti-pathogen infection. In the present study, a novel Lac gene (LvLac2) was cloned from Litopenaeus vannamei. Real-time RT-PCR analysis showed that LvLac2 is induced by white spot syndrome virus (WSSV)- or Vibrio alginolyticus infection. In addition, the downregulated expression of LvLac2 decreased the cumulative mortality of WSSV- or V. alginolyticus infected shrimps. Moreover, LvLac2 is also induced by oxidative stress. Knocking down the expression of LvLac2 decreased the severity of hepatopancreatic injury caused by oxidative stress, as well as reduced the cumulative shrimp mortality during oxidative stress. Furthermore, gene reporter assays showed that the expression of LvLac2 is regulated by NF-E2-related factor 2, which is the key transcription factor of the oxidative stress response signaling pathway. Our study revealed that LvLac2 not only participates in immune responses against infections in L. vannamei but is also involved in oxidative stress responses.

A rapid method to detect and estimate the activity of the enzyme, alcohol oxidase by the use of two chemical complexes - acetylacetone (3,5-diacetyl-1,4-dihydrolutidine) and acetylacetanilide (3,5-di-N-phenylacetyl-1,4-dihydrolutidine)

A rapid and sensitive method has been devised in order to detect and estimate the synthesis of the enzyme alcohol oxidase (AOX) by fungi, by way of the use of two chemical complexes, namely, acetylacetone (3,5-diacetyl-1,4-dihydrolutidine) and acetylacetanilide (3,5-di-N-phenylacetyl-1,4-dihydrolutidine). This method involves the use of the AOX enzyme that could specifically oxidize methanol, giving rise to equimolar equivalents each of formaldehyde (HCHO) and hydrogen peroxide (H₂O₂) as the end products. Further, the formaldehyde, thus produced was allowed to interact with the neutral solutions of acetylacetone and the ammonium salt, gradually developing a yellow color, owing to the synthesis and release of 3,5-diacetyl-1,4-dihydrolutidine (yellow product; λ = 420 nm; λ_ex/em = 390/470 nm) and the product, so generated was quantified spectrophotometrically by measureing its absorbance at 412 nm. In another set up, the amount of formaldehyde produced as a sequel to the oxidation of methanol by the AOX enzyme was determined by allowing it to react with the acetylacetanilide reagent, after which the volume of the fluorescent product - 3,5-di-N-phenylacetyl-1,4-dihydrolutidine (colorless product; λ_ex/em = 390/470 nm) that was generated was estimated by measuring its emission at 460 nm (excitation wavelength at 360 nm) in a spectrophotometer. Of the various substrates tested, a commercial source of the AOX enzyme appreciably oxidizes methanol, thereby generating formaldehyde, and further reacts with acetylacetone, to give rise to a bright yellow complex, displaying a maximum activity of 1402 U/mL. Determination of the AOX activity by the use of acetylacetone and acetylacetanilide could serve as a viable alternative to the conventional alcohol oxidase-peroxidase-2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonic acid (AOX-POD-ABTS) based method. In view of this, this method appears to be invaluable for application at the various food, pharmaceutical, fuel, biosensor, biorefinery, biopolymer, biomaterial, platform chemical, and biodiesel industries.

Controllable drug release from nano-layered hollow carrier by non-human enzyme

Natural polymers are widely used in biomedical applications because of their numerous effects. Especially, plant-derived natural polymers extracted from cell walls, especially wood, which is abundant, inexpensive and nontoxic to cells, have high mechanical strength to retain their turgor pressure. Plant-derived polymers are also unaffected by enzymes present in the human body, having a strong possibility to create a polymeric structure that releases drugs only exactly where needed. Therefore, plant-derived polymers are suitable for use in drug delivery systems (DDS) as they have durability with few drug leakage issues in the body. Here, to improve drug incorporation and release efficiency, we prepared a multilayer nanofilm from tannic acid (TA) and lignin extracted from plants and wood. We used a strategy involving film degradation by tannase and laccase, which are not present in humans, to depolymerize TA and lignin, respectively. The TA and lignin film was highly stable for 7 days at pH 3-7 and was readily degraded after enzyme treatment. We also observed controllable drug release and anticancer effect from the TA and lignin hollow carriers depending on enzymatic activity. By taking advantage of plant-derived polymers and non-toxic enzymatic reactions, we have demonstrated the film growth and degradation mechanism in depth and explored their use in a smart DDS with easily controlled release kinetics, which is useful as a DDS platform.

Activities of Secreted Aryl Alcohol Quinone Oxidoreductases from Pycnoporus cinnabarinus Provide Insights into Fungal Degradation of Plant Biomass

Auxiliary activities family 3 subfamily 2 (AA3_2) from the CAZy database comprises various functions related to ligninolytic enzymes, such as fungal aryl alcohol oxidases (AAO) and glucose oxidases, both of which are flavoenzymes. The recent study of the Pycnoporus cinnabarinus CIRM BRFM 137 genome combined with its secretome revealed that four AA3_2 enzymes are secreted during biomass degradation. One of these AA3_2 enzymes, scf184803.g17, has recently been produced heterologously in Aspergillus niger Based on the enzyme's activity and specificity, it was assigned to the glucose dehydrogenases (PcinnabarinusGDH [PcGDH]). Here, we analyze the distribution of the other three AA3_2 enzymes (scf185002.g8, scf184611.g7, and scf184746.g13) to assess their putative functions. These proteins showed the highest homology with aryl alcohol oxidase from Pleurotus eryngii Biochemical characterization demonstrated that they were also flavoenzymes harboring flavin adenine dinucleotide (FAD) as a cofactor and able to oxidize a wide variety of phenolic and nonphenolic aryl alcohols and one aliphatic polyunsaturated primary alcohol. Though presenting homology with fungal AAOs, these enzymes exhibited greater efficiency in reducing electron acceptors (quinones and one artificial acceptor) than molecular oxygen and so were defined as aryl-alcohol:quinone oxidoreductases (AAQOs) with two enzymes possessing residual oxidase activity (PcAAQO2 and PcAAQO3). Structural comparison of PcAAQO homology models with P. eryngii AAO demonstrated a wider substrate access channel connecting the active-site cavity to the solvent, explaining the absence of activity with molecular oxygen. Finally, the ability of PcAAQOs to reduce radical intermediates generated by laccase from P. cinnabarinus was demonstrated, shedding light on the ligninolytic system of this fungus.

Detoxification and color removal of Congo red by a novel Dietzia sp. (DTS26) - a microcosm approach

The present study deals with the decolorization and detoxification of Congo red (CR) by a novel marine bacterium Dietzia sp. (DTS26) isolated from Divar Island, Goa, India. The maximum decolorization of 94.5% (100 mg L(-1)) was observed under static condition within 30 h at pH 8 and temperature 32±2°C. Bacterially treated samples could enhance the light intensity by 38% and the primary production levels 5 times higher than the untreated. The strain was also able to reduce COD by 86.4% within 30 h at 100 mg L(-1) of CR dye. The degraded metabolites of CR dye were analyzed by FTIR, HPLC, GC-MS and the end product closely matches with 4-amino-3-naphthol-1-sulfonate which is comparatively less toxic than CR. Bioassay experiments conducted in treated samples for Artemia franciscana showed better survival rates (after 72 h) at higher concentration of CR (500 mg L(-1)). This work suggests the potential application of DTS26 in bioremediation of dye wastes and its safe disposal into coastal environment.

High spatial resolution infrared micro-spectroscopy reveals the mechanism of leaf lignin decomposition by aquatic fungi

Organic carbon is a critical component of aquatic systems, providing energy storage and transfer between organisms. Fungi are a major decomposer group in the aquatic carbon cycle, and are one of few groups thought to be capable of breaking down woody (lignified) tissue. In this work we have used high spatial resolution (synchrotron light source) infrared micro-spectroscopy to study the interaction between aquatic fungi and lignified leaf vein material (xylem) from River Redgum trees (E. camaldulensis) endemic to the lowland rivers of South-Eastern Australia. The work provides spatially explicit evidence that fungal colonisation of leaf litter involves the oxidative breakdown of lignin immediately adjacent to the fungal tissue and depletion of the lignin-bound cellulose. Cellulose depletion occurs over relatively short length scales (5–15 µm) and highlights the likely importance of mechanical breakdown in accessing the carbohydrate content of this resource. Low bioavailability compounds (oxidized lignin and polyphenols of plant origin) remain in colonised leaves, even after fungal activity diminishes, and suggests a possible pathway for the sequestration of carbon in wetlands. The work shows that fungi likely have a critical role in the partitioning of lignified material into a biodegradable fraction that can re-enter the aquatic carbon cycle, and a recalcitrant fraction that enters long-term storage in sediments or contribute to the formation of dissolved organic carbon in the water column.

The white-rot fungus Pleurotus ostreatus secretes laccase isozymes with different substrate specificities

Four laccase isozymes (LCC1, LCC2, LCC3 and LCC4) synthesized by Pleurotus ostreatus strain V-184 were purified and characterized. LCC1 and LCC2 have molecular masses of about 60 and 65 kDa and exhibited the same pI value (3.0). Their N termini were sequenced, revealing the same amino acid sequence and homology with laccases from other microorganisms. Laccases LCC3 and LCC4 were characterized by SDS-PAGE, estimating their molecular masses around 80 and 82 kDa, respectively. By native isoelectrofocusing, their pI values were 4.7 and 4.5, respectively. When staining with ABTS and guaiacol in native polyacrilamide gels, different specificities were observed for LCC1/LCC2 and LCC3/LCC4 isozymes.

Extracellular Ligninolytic Enzymes in Bjerkandera adusta and Lentinus squarrosulus

Extracellular ligninolytic enzyme activities were determined in two white-rot fungi, Bjerkandera adusta and Lentinus squarrosulus. To investigate the activity of extracellular enzymes, cultures were incubated over a period of 20 days in nutrient rich medium (NRM) and nutrient poor medium under static and shaking conditions. Enzymatic activity was varied with media and their incubation conditions. The highest level of Aryl alcohol oxidase (AAO) was detected under shaking condition of both medium while Manganese peroxidase (MnP) activity was best in NRM under both conditions. AAO is the main oxidases enzyme in B. adusta while laccase plays important role in L. squarrosulus. MnP is the main peroxidase enzyme in both varieties.

Multi-catalysis reactions: new prospects and challenges of biotechnology to valorize lignin

Considerable effort has been dedicated to the chemical depolymerization of lignin, a biopolymer constituting a possible renewable source for aromatic value-added chemicals. However, these efforts yielded limited success up until now. Efficient lignin conversion might necessitate novel catalysts enabling new types of reactions. The use of multiple catalysts, including a combination of biocatalysts, might be necessary. New perspectives for the combination of bio- and inorganic catalysts in one-pot reactions are emerging, thanks to green chemistry-driven advances in enzyme engineering and immobilization and new chemical catalyst design. Such combinations could offer several advantages, especially by reducing time and yield losses associated with the isolation and purification of the reaction products, but also represent a big challenge since the optimal reaction conditions of bio- and chemical catalysis reactions are often different. This mini-review gives an overview of bio- and inorganic catalysts having the potential to be used in combination for lignin depolymerization. We also discuss key aspects to consider when combining these catalysts in one-pot reactions.

The use of the fungus Dichomitus squalens for degradation in rotating biological contactor conditions

Biodegradation potential of Dichomitus squalens in biofilm cultures and rotating biological contactor (RBC) was investigated. The fungus formed thick biofilms on inert and lignocellulosic supports and exhibited stable activities of laccase and manganese peroxidase to reach 40-62 and 25-32% decolorization of anthraquinone Remazol Brilliant Blue R and heterocyclic phthalocyanine dyes, respectively. The decolorization ceased when glucose concentration dropped to 1 mmol l(-1). In RBC reactor, respective decolorizations of Remazol Brilliant Blue R and heterocyclic Methylene Blue and Azure B dyes (50 mg l(-1)) attained 99%, 93%, and 59% within 7, 40 and 200 h. The fungus exhibited tolerance to coliform and non-coliform bacteria on rich organic media, the inhibition occurred only on media containing tryptone and NaCl. The degradation efficiency in RBC reactor, capability to decolorize a wide range of dye structures and tolerance to bacterial stress make D. squalens an organism applicable to remediation of textile wastewaters.

The genome of Ganoderma lucidum provides insights into triterpenes biosynthesis and wood degradation [corrected]

Background

Ganoderma lucidum (Reishi or Ling Zhi) is one of the most famous Traditional Chinese Medicines and has been widely used in the treatment of various human diseases in Asia countries. It is also a fungus with strong wood degradation ability with potential in bioenergy production. However, genes, pathways and mechanisms of these functions are still unknown.

Methodology/Principal Findings

The genome of G. lucidum was sequenced and assembled into a 39.9 megabases (Mb) draft genome, which encoded 12,080 protein-coding genes and ∼83% of them were similar to public sequences. We performed comprehensive annotation for G. lucidum genes and made comparisons with genes in other fungi genomes. Genes in the biosynthesis of the main G. lucidum active ingredients, ganoderic acids (GAs), were characterized. Among the GAs synthases, we identified a fusion gene, the N and C terminal of which are homologous to two different enzymes. Moreover, the fusion gene was only found in basidiomycetes. As a white rot fungus with wood degradation ability, abundant carbohydrate-active enzymes and ligninolytic enzymes were identified in the G. lucidum genome and were compared with other fungi.

Conclusions/Significance

The genome sequence and well annotation of G. lucidum will provide new insights in function analyses including its medicinal mechanism. The characterization of genes in the triterpene biosynthesis and wood degradation will facilitate bio-engineering research in the production of its active ingredients and bioenergy.

Removal of monomer delignification products by laccase from Trametes versicolor

The influence of a laccase from Trametes versicolor on the removal of phenolic monomers in liquid hot water pretreated wheat straw supernatants (LHW-S) was examined. Beside the total phenol content derived by Folin-Ciocalteu (FC-) assay, phenolic monomers were measured via headspace-solid phase micro-extraction (HS-SPME)/GC-MS. A notable decrease of the phenols was achieved using 0.2 and 0.5 U/mL laccase whilst higher dosage showed no improvement. Nearly all kind of monomer phenolic compounds identified in the LHW-S were found to be removed after 24h. However, acetophenone and 4-hydroxybenzaldehyde (HBA) were obviously not affected by laccase. Summarizing, three laccase reaction groups (LRG) of phenolic monomers could be classified: immediate removal (LRG-A), degradation after 1 day (LRG-B), no effect of laccase (LRG-C). Additionally, HS-SPME/GC was found to be a powerful tool to study the reaction of laccase and phenolic monomers in complex lignocellulose derived solutions.

Decolorization and biodegradation of Reactive Blue 13 by Proteus mirabilis LAG

The decolorization and biodegradation of Reactive Blue 13 (RB13), a sulphonated reactive azo dye, was achieved under static anoxic condition with a bacterial strain identified as Proteus mirabilis LAG, which was isolated from a municipal dump site soil near Lagos, Nigeria. This strain decolorized RB13 (100mg/l) within 5h. The formation of aromatic amine prior to mineralization was supported by Fourier transform infrared spectrometry (FTIR), which revealed the disappearance of certain peaks, particularly those of the aromatic C-H bending at 600-800 cm(-1). Gas chromatography-mass spectrophotometry (GCMS) analysis of the dye metabolite showed the presence of sodium-2(2-formyl-2-hydroxyvinyl) benzoate, with a tropylium cation as its base peak, this suggested the breakage of naphthalene rings in RB13. The detection of azoreductase and laccase activities suggested the enzymatic reduction of azo bonds prior to mineralization. In addition, phytotoxicity studies indicated the detoxification of RB13 to non-toxic degradation products by this strain of P. mirabilis LAG.

New oxidase from Bjerkandera arthroconidial anamorph that oxidizes both phenolic and nonphenolic benzyl alcohols

A new flavooxidase is described from a Bjerkandera arthroconidial anamorph. Its physicochemical characteristics, a monomeric enzyme containing non-covalently bound flavin adenine dinucleotide (FAD), and several catalytic properties, such as oxidation of aromatic and polyunsaturated aliphatic primary alcohols, are similar to those of Pleurotus eryngii aryl-alcohol oxidase (AAO). However, it also efficiently oxidizes phenolic benzyl and cinnamyl alcohols that are typical substrates of vanillyl-alcohol oxidase (VAO), a flavooxidase from a different family, characterized by its multimeric nature and presence of covalently-bound FAD. The enzyme also differs from P. eryngii AAO by having extremely high efficiency oxidizing chlorinated benzyl alcohols (1000-1500 s(-1) mM(-1)), a feature related to the different alcohol metabolites secreted by the Pleurotus and Bjerkandera species including chloroaromatics, and higher activity on aromatic aldehydes. What is even more intriguing is the fact that, the new oxidase is optimally active at pH 6.0 on both p-anisyl and vanillyl alcohols, suggesting a mechanism for phenolic benzyl alcohol oxidation that is different from that described in VAO, which proceeds via the substrate phenolate anion formed at basic pH. Based on the above properties, and its ADP-binding motif, partially detected after N-terminus sequencing, the new enzyme is classified as a member of the GMC (glucose-methanol-choline oxidase) oxidoreductase family oxidizing both AAO and VAO substrates.

Laccase-HBT bleaching of eucalyptus kraft pulp: influence of the operating conditions

Different operating conditions (viz. pulp consistency, oxygen pressure and treatment time) in the biobleaching of eucalyptus kraft pulp with the laccase-HBT system was tested in order to describe their effect and normalize a biobleaching protocol. A high O(2) pressure (0.6MPa) was found to result in improved laccase-assisted delignification of the pulp. Also, a high pulp consistency (10%) and a short treatment time (2h) proved the best choices with a view to obtaining good pulp properties (kappa number and ISO brightness) under essentially mild conditions. The laccase-HBT treatment was found to result in slight delignification (in the form of a 20-27% decrease in kappa number); however, an alkaline extraction stage raised delignification to 41-45%, a much higher level than those obtained in the control tests (16-23%). Also, the use of hydrogen peroxide in the extraction stage resulted in improved brightness (14-19%), but in scarcely improved delignification (4-7%). Treating the pulp with the laccase-HBT system reduced the amount of hydrogen peroxide required for subsequent alkaline bleaching by a factor of 3-4 relative to control tests.

Langmuir-Blodgett film of hydrophobin protein from Pleurotus ostreatus at the air-water interface

We present results concerning the formation of Langmuir-Blodgett (LB) films of a class I hydrophobin from Pleurotus ostreatus at the air-water interface, and their structure as Langmuir-Blodgett (LB) films when deposited on silicon substrates. LB films of the hydrophobin were investigated by atomic force microscopy (AFM). We observed that the compressed film at the air-water interface exhibits a molecular depletion even at low surface pressure. In order to estimate the surface molecular concentration, we fit the experimental isotherm with Volmer's equation describing the equation of state for molecular monolayers. We found that about (1)/ 10 of the molecules contribute to the surface film formation. When transferred on silicon substrates, compact and uniform monomolecular layers about 2.5 nm thick, comparable to a typical molecular size, were observed. The monolayers coexist with protein aggregates, under the typical rodlet form with a uniform thickness of about 5.0 nm. The observed rodlets appear to be a hydrophilic bilayer and can then be responsible for the surface molecular depletion.

FOLy: an integrated database for the classification and functional annotation of fungal oxidoreductases potentially involved in the degradation of lignin and related aromatic compounds

The breakdown of lignin by fungi is a key step during carbon recycling in terrestrial ecosystems. This process is of great interest for green and white biotechnological applications. Given the importance of these enzymatic processes, we have classified the enzymes potentially involved in lignin catabolism into sequence-based families and integrated them in a newly developed database, designated Fungal Oxidative Lignin enzymes (FOLy). Families were defined after sequence similarity searches starting from protein sequences and validated by the convergence of results with biochemical experiments reported in the literature. The resulting database was applied as a tool for the functional annotation of genomes from different fungi, namely (i) the Basidiomycota Coprinopsis cinerea, Phanerochaete chrysosporium and Ustilago maydis and (ii) the Ascomycota Aspergillus nidulans and Trichoderma reesei. Genomic comparison of the oxidoreductases of these fungi revealed significant differences in the putative enzyme arsenals. Two Ascomycota fungal genomes were annotated and new candidate genes were identified that could be useful for lignin degradation and (or) melanin synthesis, and their function investigated experimentally. This database efforts aims at providing the means to get new insights for the understanding and biotechnological exploitation of the lignin degradation. A WWW server giving access to the routinely updated FOLy classifications of enzymes potentially involved in lignin degradation can be found at http://foly.esil.univ-mrs.fr.

Polar vineyard pruning extracts increase the activity of the main ligninolytic enzymes in Lentinula edodes cultures

Lentinula edodes is considered an alternative recycling agent for agricultural wastes, and there have been several studies to understand the relationship between its growth and ligninolytic activity. We tested the effect of wood from viticulture pruning, extracted with solvents of differing polarity, on the biomass production and activity pattern of ligninolytic enzymes. The analysis was done by measuring the mycelial dry mass and enzyme activity of liquid growth medium during the culture of L. edodes, adding either single extracts or a combination of extracts. Polar extracts enhanced mycelial production, and the activity patterns of lignin peroxidase, manganese peroxidase, aryl alcohol oxidase, and laccase were comparable to their activities predicted by ligninolysis models proposed for other fungi. We conclude that the polar extracts could be useful for enhancing fungal biomass production and for modifying lignin degradation because the regulation of ligninolytic enzyme activity is differentially influenced by the polarity of the extract.

Genetically closely related but phenotypically divergent Trichoderma species cause green mold disease in oyster mushroom farms worldwide

The worldwide commercial production of the oyster mushroom Pleurotus ostreatus is currently threatened by massive attacks of green mold disease. Using an integrated approach to species recognition comprising analyses of morphological and physiological characters and application of the genealogical concordance of multiple phylogenetic markers (internal transcribed spacer 1 [ITS1] and ITS2 sequences; partial sequences of tef1 and chi18-5), we determined that the causal agents of this disease were two genetically closely related, but phenotypically strongly different, species of Trichoderma, which have been recently described as Trichoderma pleurotum and Trichoderma pleuroticola. They belong to the Harzianum clade of Hypocrea/Trichoderma which also includes Trichoderma aggressivum, the causative agent of green mold disease of Agaricus. Both species have been found on cultivated Pleurotus and its substratum in Europe, Iran, and South Korea, but T. pleuroticola has also been isolated from soil and wood in Canada, the United States, Europe, Iran, and New Zealand. T. pleuroticola displays pachybasium-like morphological characteristics typical of its neighbors in the Harzianum clade, whereas T. pleurotum is characterized by a gliocladium-like conidiophore morphology which is uncharacteristic of the Harzianum clade. Phenotype MicroArrays revealed the generally impaired growth of T. pleurotum on numerous carbon sources readily assimilated by T. pleuroticola and T. aggressivum. In contrast, the Phenotype MicroArray profile of T. pleuroticola is very similar to that of T. aggressivum, which is suggestive of a close genetic relationship. In vitro confrontation reactions with Agaricus bisporus revealed that the antagonistic potential of the two new species against this mushroom is perhaps equal to T. aggressivum. The P. ostreatus confrontation assays showed that T. pleuroticola has the highest affinity to overgrow mushroom mycelium among the green mold species. We conclude that the evolutionary pathway of T. pleuroticola could be in parallel to other saprotrophic and mycoparasitic species from the Harzianum clade and that this species poses the highest infection risk for mushroom farms, whereas T. pleurotum could be specialized for an ecological niche connected to components of Pleurotus substrata in cultivation. A DNA BarCode for identification of these species based on ITS1 and ITS2 sequences has been provided and integrated in the main database for Hypocrea/Trichoderma (www.ISTH.info).

The coprophilous mushroom Coprinus radians secretes a haloperoxidase that catalyzes aromatic peroxygenation

Coprophilous and litter-decomposing species (26 strains) of the genus Coprinus were screened for peroxidase activities by using selective agar plate tests and complex media based on soybean meal. Two species, Coprinus radians and C. verticillatus, were found to produce peroxidases, which oxidized aryl alcohols to the corresponding aldehydes at pH 7 (a reaction that is typical for heme-thiolate haloperoxidases). The peroxidase of Coprinus radians was purified to homogeneity and characterized. Three fractions of the enzyme, CrP I, CrP II, and CrP III, with molecular masses of 43 to 45 kDa as well as isoelectric points between 3.8 and 4.2, were identified after purification by anion-exchange and size exclusion chromatography. The optimum pH of the major fraction (CrP II) for the oxidation of aryl alcohols was around 7, and an H2O2 concentration of 0.7 mM was most suitable regarding enzyme activity and stability. The apparent Km values for ABTS [2,2'-azinobis(3-ethylbenzthiazolinesulfonic acid)], 2,6-dimethoxyphenol, benzyl alcohol, veratryl alcohol, and H2O2 were 49, 342, 635, 88, and 1,201 microM, respectively. The N terminus of CrP II showed 29% and 19% sequence identity to Agrocybe aegerita peroxidase (AaP) and chloroperoxidase, respectively. The UV-visible spectrum of CrP II was highly similar to that of resting-state cytochrome P450 enzymes, with the Soret band at 422 nm and additional maxima at 359, 542, and 571 nm. The reduced carbon monoxide complex showed an absorption maximum at 446 nm, which is characteristic of heme-thiolate proteins. CrP brominated phenol to 2- and 4-bromophenols and selectively hydroxylated naphthalene to 1-naphthol. Hence, after AaP, CrP is the second extracellular haloperoxidase-peroxygenase described so far. The ability to extracellularly hydroxylate aromatic compounds seems to be the key catalytic property of CrP and may be of general significance for the biotransformation of poorly available aromatic substances, such as lignin, humus, and organopollutants in soil litter and dung environments. Furthermore, aromatic peroxygenation is a promising target of biotechnological studies.

Transformation of polycyclic aromatic hydrocarbons by laccase is strongly enhanced by phenolic compounds present in soil

Efficient transformation of several polycyclic aromatic hydrocarbons (PAHs) was obtained using a fungal laccase in the presence of phenolic compounds related to those formed in nature during the turnover of lignin and humus. The effect of these natural mediators, namely vanillin, acetovanillone, acetosyringone, syringaldehyde, 2,4,6-trimethylphenol, p-coumaric acid, ferulic acid, and sinapic acid, was compared with that of synthetic mediators such as 2,2'-azinobis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) and 1-hydroxybenzotriazole (HBT). Anthracene was significantly degraded by laccase in the absence of mediators, whereas benzo[a]pyrene and pyrene were weakly transformed (less than 15% after 24 h). Vanillin, acetovanillone, 2,4,6-trimethylphenol, and, above all, p-coumaric acid strongly promoted the removal of PAHs by laccase. 9,10-Anthraquinone was the main product detected from anthracene oxidation by all the laccase-mediator systems. The yield of anthraquinone formed was directly correlated with the amount of p-coumaric acid used. This compound resulted in a better laccase mediator than ABTS and close similarity to HBT, attaining 95% removal of anthracene and benzo[a]pyrene and around 50% of pyrene within 24 h. Benzo[a]pyrene 1,6-, 3,6-, and 6,12-quinones were produced during benzo[a]pyrene oxidation with laccase and p-coumaric acid, HBT, or ABTS as mediators, although use of the latter mediator gave further oxidation products that were not produced by the two other systems.