Fungal Enzymes for Bio-Products from Sustainable and Waste Biomass

Identification of a novel forkhead transcription factor MtFKH1 for cellulase and xylanase gene expression in Myceliophthora thermophila (ATCC 42464)

Myceliophthora thermophila is a thermophilic fungus, known to produce industrially important enzymes in biorefineries. The mechanism underlying cellulase and xylanase expression in filamentous fungi is a complex regulatory network controlled by numerous transcription factors (TFs). These TFs in M. thermophila remain unclear. Here, we identified and characterised a novel cellulase and xylanase regulator MtFKH1 in M. thermophila through comparative transcriptomic and genetic analyses. Five of the eight potential TFs, which showed differential expression levels when grown on Avicel and glucose, were successfully deleted using the newly designed CRISPR/Cas9 system. This system identified the forkhead TF MtFKH1. The disruption of Mtfkh1 elevated the cellulolytic and xylanolytic enzyme activities, whereas the overexpression of Mtfkh1 led to considerable decrease in cellulase and xylanase production in M. thermophila cultivated on Avicel. The loss of Mtfkh1 also exhibited an impairment in sporulation in M. thermophila. Real-time quantitative reverse transcription PCR (RT-qPCR) and the electrophoretic mobility shift assays (EMSAs) demonstrated that MtFKH1 regulates the gene expression and specifically bind to the promoter regions of genes encoding β-glucosidase (bgl1/MYCTH_66804), cellobiohydrolase (cbh1/MYCTH_109566), and xylanase (xyn1/MYCTH_112050), respectively. Furthermore, DNase I footprinting analysis identified binding motif of MtFKH1 in the upstream region of Mtbgl1, with strongest binding affinity. Finally, transcriptomic profiling and Gene Ontology (GO) enrichment analyses of Mtfkh1 deletion mutant revealed that the regulon of MtFKH1 were significantly prevalent in hydrolase activity (acting on glycosyl bonds), polysaccharide binding, and carbohydrate metabolic process functional categories. These findings expand our knowledge on how forkhead transcription factor regulates lignocellulose degradation and provide a novel target for engineering of fungal cell factories with the hyperproduction of cellulase and xylanase.

Structural and Biochemical Insights into Lignin-Oxidizing Activity of Bacterial Peroxidases against Soluble Substrates and Kraft Lignin

Great interest has recently been drawn to the production of value-added products from lignin; however, its recalcitrance and high chemical complexity have made this challenging. Dye-decolorizing peroxidases and catalase-peroxidases are among the enzymes that are recognized to play important roles in environmental lignin oxidation. However, bacterial lignin-oxidizing enzymes remain less characterized compared to related proteins from fungi. In this study, screening of 18 purified bacterial peroxidases against the general chromogenic substrate 2,2'-azinobis(3-ethylbenzthiazoline-6-sulfonate) (ABTS) revealed the presence of peroxidase activity in all proteins. Agarose plate-based screens with kraft lignin identified detectable and high lignin oxidation activity in 15 purified proteins. Crystal structures were determined for the DyP-type peroxidases FC2591 from Frankia casuarinae, PF3257 from Pseudomonas fluorescens, and PR9465 from Pseudomonas rhizosphaerae. The structures revealed the presence of hemes with bound oxygens coordinated by conserved His, Arg, and Asp residues as well as three molecular tunnels connecting the heme with the protein surface. Structure-based site-directed mutagenesis of FC2591 identified at least five active site residues as essential for oxidase activity against both ABTS and lignin, whereas the S370A mutant protein showed a three- to 4-fold activity increase with both substrates. HPLC analysis of reaction products of the wild-type FC2591 and S370A mutant proteins with the model lignin dimer guaiacylglycerol-β-guaiacyl ether and kraft lignin revealed the formation of products consistent with the radical coupling of the reaction intermediates. Thus, this study identified novel bacterial heme peroxidases with lignin oxidation activity and provided further insights into our understanding of these enzymes.

In situ imaging of LPMO action on plant tissues

Lytic polysaccharide monooxygenases (LPMOs) are copper-dependent enzymes that oxidatively cleave recalcitrant polysaccharides such as cellulose. Several studies have reported LPMO action in synergy with other carbohydrate-active enzymes (CAZymes) for the degradation of lignocellulosic biomass but direct LPMO action at the plant tissue level remains challenging to investigate. Here, we have developed a MALDI-MS imaging workflow to detect oxidised oligosaccharides released by a cellulose-active LPMO at cellular level on maize tissues. Using this workflow, we imaged LPMO action and gained insight into the spatial variation and relative abundance of oxidised and non-oxidised oligosaccharides. We reveal a targeted action of the LPMO related to the composition and organisation of plant cell walls.

Renewable hemicellulose-based materials for value-added applications

The importance of renewable resources and environmentally friendly materials has grown globally in recent time. Hemicellulose is renewable lignocellulosic materials that have been the subject of substantial valorisation research. Due to its distinctive benefits, including its wide availability, low cost, renewability, biodegradability, simplicity of chemical modification, etc., it has attracted increasing interest in a number of value-added fields. In this review, a systematic summarizes of the structure, extraction method, and characterization technique for hemicellulose-based materials was carried out. Also, their most current developments in a variety of value-added adsorbents, biomedical, energy-related, 3D-printed materials, sensors, food packaging applications were discussed. Additionally, the most recent challenges and prospects of hemicellulose-based materials are emphasized and examined in-depth. It is anticipated that in the near future, persistent scientific efforts will enable the renewable hemicellulose-based products to achieve practical applications.

Plant-derived citronellol can significantly disrupt cell wall integrity maintenance of Colletotrichum camelliae

Anthracnose, a fungal disease, commonly infects tea plants and severely impacts the yield and quality of tea. One method for controlling anthracnose is the application of citronellol, a plant extract that exhibits broad-spectrum antimicrobial activity. Herein, the physiological and biochemical mechanism by which citronellol controls anthracnose caused by Colletotrichum camelliae was investigated. Citronellol exhibited excellent antifungal activity based on direct and indirect mycelial growth inhibition assays, with EC50 values of 76.88 mg/L and 29.79 μL/L air, respectively. Citronellol also exhibited good control effects on C. camelliae in semi-isolated leaf experiments. Optical and scanning electron microscopy revealed that citronellol caused C. camelliae mycelia to thin, fracture, fold and deform. Transmission electron microscopy revealed that the mycelial cell walls collapsed inward and separated, and the organelles became blurred after treatment with citronellol. The sensitivity of C. camelliae to calcofluor white staining was significantly enhanced by citronellol, while PI staining showed minimal fluorescence, and the relative conductivity of mycelia were not significantly different. Under citronellol treatment, the expression levels of β-1,3-glucanase, chitin synthase, and chitin deacetylase-related genes were significantly decreased, while the expression levels of chitinase genes were increased, leading to lower chitinase activity and increased β-1,3-glucanase activity. Therefore, citronellol disrupted the cell wall integrity of C. camelliae and inhibited normal mycelial growth.

Versatile Applications of Brewer's Spent Grain: Solid-State Fermentation and Nutritional Added Value

Brewer's spent grain (BSG) is a major by-product in the beer-brewing process which contributes to 85% of the entire generated by-product in the brewing process. BSG is rich in proteins, and most of the malt proteins (74-78%) remain insoluble in BSG after the mashing process. Solid-state fermentation (SSF) is a promising bioprocess that enables microorganisms to survive in environments with minimal water and has shown to enhance the nutritional composition of BSG. In this review, the potential application of protein, amino acids (proline, threonine, and serine), phenolic contents, and soluble sugars (glucose, fructose, xylose, arabinose, and cellobiose) extracted from BSG by various microorganisms using SSF is explored. Incorporation of BSG into animal feed, human diets, and as a substrate for microorganisms are the prospects that could be implemented in the industrial scale. This review also discussed various advances to improve the fermentation yield such as symbiotic fermentation, the addition of nitrogen supplements, and an optimal mixture of the agro-industrial waste substrate. Future perspectives on SSF are also addressed to provide important ideas for immediate and future studies. However, challenges include optimizing SSF conditions and design of bioreactors, and operational costs must be addressed in the future to overcome current obstacles. Overall, this mini review highlights the potential benefits of BSG utilization and SSF in a sustainable way.

Powerful cell wall biomass degradation enzymatic system from saprotrophic Aspergillus fumigatus

Cell wall biomass, Earth's most abundant natural resource, holds significant potential for sustainable biofuel production. Composed of cellulose, hemicellulose, lignin, pectin, and other polymers, the plant cell wall provides essential structural support to diverse organisms in nature. In contrast, non-plant species like insects, crustaceans, and fungi rely on chitin as their primary structural polysaccharide. The saprophytic fungus Aspergillus fumigatus has been widely recognized for its adaptability to various environmental conditions. It achieves this by secreting different cell wall biomass degradation enzymes to obtain essential nutrients. This review compiles a comprehensive collection of cell wall degradation enzymes derived from A. fumigatus, including cellulases, hemicellulases, various chitin degradation enzymes, and other polymer degradation enzymes. Notably, these enzymes exhibit biochemical characteristics such as temperature tolerance or acid adaptability, indicating their potential applications across a spectrum of industries.

Lignocellulolytic Enzymes Production by Four Wild Filamentous Fungi for Olive Stones Valorization: Comparing Three Fermentation Regimens

Lignocellulolytic enzymes play a crucial role in efficiently converting lignocellulose into valuable platform molecules in various industries. However, they are limited by their production yields, costs, and stability. Consequently, their production by producers adapted to local environments and the choice of low-cost raw materials can address these limitations. Due to the large amounts of olive stones (OS) generated in Morocco which are still undervalued, Penicillium crustosum, Fusarium nygamai, Trichoderma capillare, and Aspergillus calidoustus, are cultivated under different fermentation techniques using this by-product as a local lignocellulosic substrate. Based on a multilevel factorial design, their potential to produce lignocellulolytic enzymes during 15 days of dark incubation was evaluated. The results revealed that P. crustosum expressed a maximum total cellulase activity of 10.9 IU/ml under sequential fermentation (SF) and 3.6 IU/ml of β-glucosidase activity under submerged fermentation (SmF). F. nygamai recorded the best laccase activity of 9 IU/ml under solid-state fermentation (SSF). Unlike T. capillare, SF was the inducive culture for the former activity with 7.6 IU/ml. A. calidoustus produced, respectively, 1,009 μg/ml of proteins and 11.5 IU/ml of endoglucanase activity as the best results achieved. Optimum cellulase production took place after the 5th day under SF, while ligninases occurred between the 9th and the 11th days under SSF. This study reports for the first time the lignocellulolytic activities of F. nygamai and A. calidoustus. Furthermore, it underlines the potential of the four fungi as biomass decomposers for environmentally-friendly applications, emphasizing the efficiency of OS as an inducing substrate for enzyme production.

The development and nutritional quality of Lyophyllum decastes affected by monochromatic or mixed light provided by light-emitting diode

Edible fungi has certain photo-sensitivity during the mushroom emergence stage, but there has been few relevant studies on the responses of Lyophyllum decastes to different light quality. L. decastes were planted in growth chambers with different light qualities that were, respectively, white light (CK), monochromatic red light (R), monochromatic blue light (B), mixed red and blue light (RB), and the mixture of far-red and blue light (FrB). The photo-sensitivity of L. decastes was investigated by analyzing the growth characteristics, nutritional quality, extracellular enzymes as well as the light photoreceptor genes in mushroom exposed to different light treatments. The results showed that R led to mycelium degeneration, fungal skin inactivation and failure of primordial formation in L. decastes. The stipe length, stipe diameter, pileus diameter and the weight of fruiting bodies exposed to RB significantly increased by 8.0, 28.7, 18.3, and 58.2% respectively, compared to the control (p < 0.05). B significantly decreased the stipe length and the weight of fruiting body, with a decrease of 8.5 and 20.2% respectively, compared to the control (p < 0.05). Increased color indicators and deepened simulated color were detected in L. decastes pileus treated with B and FrB in relative to the control. Meanwhile, the expression levels of blue photoreceptor genes such as WC-1, WC-2 and Cry-DASH were significantly up-regulated in mushroom exposed to B and FrB (p < 0.05). Additionally, the contents of crude protein and crude polysaccharide in pileus treated with RB were, respectively, increased by 26.5 and 9.4% compared to the control, while those in stipes increased by 5.3 and 58.8%, respectively. Meanwhile, the activities of extracellular enzyme such as cellulase, hemicellulase, laccase, manganese peroxidase, lignin peroxidase and amylase were significant up-regulated in mushroom subjected to RB (p < 0.05), which may promote the degradation of the culture materials. On the whole, the largest volume and weight as well as the highest contents of nutrients were all detected in L. decastes treated with RB. The study provided a theoretical basis for the regulation of light environment in the industrial production of high quality L. decastes.

Exploring class III cellobiose dehydrogenase: sequence analysis and optimized recombinant expression

BACKGROUND

Cellobiose dehydrogenase (CDH) is an extracellular fungal oxidoreductase with multiple functions in plant biomass degradation. Its primary function as an auxiliary enzyme of lytic polysaccharide monooxygenase (LPMO) facilitates the efficient depolymerization of cellulose, hemicelluloses and other carbohydrate-based polymers. The synergistic action of CDH and LPMO that supports biomass-degrading hydrolases holds significant promise to harness renewable resources for the production of biofuels, chemicals, and modified materials in an environmentally sustainable manner. While previous phylogenetic analyses have identified four distinct classes of CDHs, only class I and II have been biochemically characterized so far.

RESULTS

Following a comprehensive database search aimed at identifying CDH sequences belonging to the so far uncharacterized class III for subsequent expression and biochemical characterization, we have curated an extensive compilation of putative CDH amino acid sequences. A sequence similarity network analysis was used to cluster them into the four distinct CDH classes. A total of 1237 sequences encoding putative class III CDHs were extracted from the network and used for phylogenetic analyses. The obtained phylogenetic tree was used to guide the selection of 11 cdhIII genes for recombinant expression in Komagataella phaffii. A small-scale expression screening procedure identified a promising cdhIII gene originating from the plant pathogen Fusarium solani (FsCDH), which was selected for expression optimization by signal peptide shuffling and subsequent production in a 5-L bioreactor. The purified FsCDH exhibits a UV-Vis spectrum and enzymatic activity similar to other characterized CDH classes.

CONCLUSION

The successful production and functional characterization of FsCDH proved that class III CDHs are catalytical active enzymes resembling the key properties of class I and class II CDHs. A detailed biochemical characterization based on the established expression and purification strategy can provide new insights into the evolutionary process shaping CDHs and leading to their differentiation into the four distinct classes. The findings have the potential to broaden our understanding of the biocatalytic application of CDH and LPMO for the oxidative depolymerization of polysaccharides.

Engineering A-type Dye-Decolorizing Peroxidases by Modification of a Conserved Glutamate Residue

Dye-decolorizing peroxidases (DyPs) are recently identified microbial enzymes that have been used in several Biotechnology applications from wastewater treatment to lignin valorization. However, their properties and mechanism of action still have many open questions. Their heme-containing active site is buried by three conserved flexible loops with a putative role in modulating substrate access and enzyme catalysis. Here, we investigated the role of a conserved glutamate residue in stabilizing interactions in loop 2 of A-type DyPs. First, we did site saturation mutagenesis of this residue, replacing it with all possible amino acids in bacterial DyPs from Bacillus subtilis (BsDyP) and from Kitasatospora aureofaciens (KaDyP1), the latter being characterized here for the first time. We screened the resulting libraries of variants for activity towards ABTS and identified variants with increased catalytic efficiency. The selected variants were purified and characterized for activity and stability. We furthermore used Molecular Dynamics simulations to rationalize the increased catalytic efficiency and found that the main reason is the electron channeling becoming easier from surface-exposed tryptophans. Based on our findings, we also propose that this glutamate could work as a pH switch in the wild-type enzyme, preventing intracellular damage.

Genomic characterization and expression profiling of the lytic polysaccharide monooxygenases AA9 family in thermophilic fungi Thermothelomyces fergusii in response to carbon source media

Enhancing enzyme activity and stability in biomass degradation can improve substrate saccharification and, increases biorefinery efficiency. For the first time, we identified 20 lytic polysaccharide monooxygenases (LPMOs) AA9 genes in the genome of Thermothelomyces fergusii. Our results showed that TfAA9 was categorized into LPMOs1, LPMOs2, and LPMOs3 subgroups based on protein diversity. Protein- 3D structure analysis showed strong interactions between Myceliophthora thermophila AA9 proteins and 17 TfAA9 proteins. Gene ontology analysis indicated a high enrichment of cellulase activity in TfAA9 genes. KEGG pathways analysis revealed the role of TfAA9 proteins in the endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose. Numerous TfAA9s gene transcripts were up-regulated on avicel, cellobiose, and glucose, with a higher proportion on avicel. Protein concentration, endoglucanase, and cellulase activity were also boosted on avicel. However, limited fungal biomass was observed on avicel, despite the abundance of AA9 LPMOs in the T. fergusii genome. These findings expand our understanding of fungal AA9 genes and their role in lignocellulolytic degradation. The disparity between biomass and enzymatic activity suggests screening TfAA9 genes for highly active enzymes and redundant genes via heterologous expression. In short, functional characterization of these genes could contribute to improving the saccharification process of industrial raw materials.

Fungal bioprocessing for circular bioeconomy: Exploring lignocellulosic waste valorization

The rising global demand for sustainable and eco-friendly practices has led to a burgeoning interest in circular bioeconomy, wherein waste materials are repurposed into valuable resources. Lignocellulosic waste, abundant in agricultural residues and forestry by-products, represents a significant untapped resource. This article explores the potential of fungal-mediated processes for the valorisation of lignocellulosic waste, highlighting their role in transforming these recalcitrant materials into bio-based products. The articles delve into the diverse enzymatic and metabolic capabilities of fungi, which enable them to efficiently degrade and metabolise lignocellulosic materials. The paper further highlights key fungal species and their mechanisms involved in the breakdown of complex biomass, emphasising the importance of understanding their intricate biochemical pathways for optimising waste conversion processes. The key insights of the article will significantly contribute to advancing the understanding of fungal biotechnology for circular bioeconomy applications, fostering a paradigm shift towards a more resource-efficient and environmentally friendly approach to waste management and bio-based product manufacturing.

Clustered surface amino acid residues modulate the acid stability of GH10 xylanase in fungi

Acidic xylanases are widely used in industries such as biofuels, animal feeding, and fruit juice clarification due to their tolerance to acidic environments. However, the factors controlling their acid stability, especially in GH10 xylanases, are only partially understood. In this study, we identified a series of thermostable GH10 xylanases with optimal temperatures ranging from 70 to 90 °C, and among these, five enzymes (Xyn10C, Xyn10RE, Xyn10TC, Xyn10BS, and Xyn10PC) exhibited remarkable stability at pH 2.0. Our statistical analysis highlighted several factors contributing to the acid stability of GH10 xylanases, including electrostatic repulsion, π-π stacking, ionic bonds, hydrogen bonds, and Van der Waals interactions. Furthermore, through mutagenesis studies, we uncovered that acid stability is influenced by a complex interplay of amino acid residues. The key amino acid sites determining the acid stability of GH10 xylanases were thus elucidated, mainly concentrated in two surface regions behind the enzyme active center. Notably, the critical residues associated with acid stability markedly enhanced Xyn10RE's thermostability by more than sixfold, indicating a potential acid-thermal interplay in GH10 xylanases. This study not only reported a series of valuable genes but also provided a range of modification targets for enhancing the acid stability of GH10 xylanases. KEY POINTS: • Five acid stable and thermostable GH10 xylanases were reported. • The key amino acid sites, mainly forming two enriched surface regions behind the enzyme active center, were identified responsible for acid stability of GH10 xylanases. • The finding revealed interactive amino acid sites, offering a pathway for synergistic enhancement of both acid stability and thermostability in GH10 xylanase modifications.

Enzymatic and biophysical characterization of a novel modular cellulosomal GH5 endoglucanase multifunctional from the anaerobic gut fungus Piromyces finnis

Cellulases from anaerobic fungi are enzymes less-studied biochemically and structurally than cellulases from bacteria and aerobic fungi. Currently, only thirteen GH5 cellulases from anaerobic fungi were biochemically characterized and two crystal structures were reported. In this context, here, we report the functional and biophysical characterization of a novel multi-modular cellulosomal GH5 endoglucanase from the anaerobic gut fungus Piromyces finnis (named here PfGH5). Multiple sequences alignments indicate that PfGH5 is composed of a GH5 catalytic domain and a CBM1 carbohydrate-binding module connected through a CBM10 dockerin module. Our results showed that PfGH5 is an endoglucanase from anaerobic fungus with a large spectrum of activity. PfGH5 exhibited preference for hydrolysis of oat β-glucan, followed by galactomannan, carboxymethyl cellulose, mannan, lichenan and barley β-glucan, therefore displaying multi-functionality. For oat β-glucan, PfGH5 reaches its optimum enzymatic activity at 40 °C and pH 5.5, with Km of 7.1 μM. Ion exchange chromatography analyzes revealed the production of oligosaccharides with a wide degree of polymerization indicated that PfGH5 has endoglucanase activity. The ability to bind and cleave different types of carbohydrates evidence the potential of PfGH5 for use in biotechnology and provide a useful basis for future investigation and application of new anaerobic fungi enzymes.

Optimization of enzymatic saccharification of industrial wastes using a thermostable and halotolerant endoglucanase through Box-Behnken experimental design

This study describes the production, characterization and application of an endoglucanase from Penicillium roqueforti using lignocellulosic agro-industrial wastes as the substrate during solid-state fermentation. The endoglucanase was generated after culturing with different agro-industrial wastes for 96 h without any pretreatment. The highest activity was obtained at 50 °C and pH 4.0. Additionally, the enzyme showed stability in the temperature and pH ranges of 40-80 °C and 4.0-5.0, respectively. The addition of Ca2+, Zn2+, Mg2+, and Cu2+ increased enzymatic activity. Halotolerance as a characteristic of the enzyme was confirmed when its activity increased by 35% on addition of 2 M NaCl. The endoglucanase saccharified sugarcane bagasse, coconut shell, wheat bran, cocoa fruit shell, and cocoa seed husk. The Box-Behnken design was employed to optimize fermentable sugar production by evaluating the following parameters: time, substrate, and enzyme concentration. Under ideal conditions, 253.19 mg/g of fermentable sugars were obtained following the saccharification of wheat bran, which is 41.5 times higher than that obtained without optimizing. This study presents a thermostable, halotolerant endoglucanase that is resistant to metal ions and organic solvents with the potential to be applied in producing fermentable sugars for manufacturing biofuels from agro-industrial wastes.

Biodegradation of agave Comiteco bagasse by Pleurotus spp.: a source of cellulases useful in hydrolytic treatment to produce reducing sugars

This study aimed to determine the production parameters of five strains of Pleurotus spp. during their cultivation on agave Comiteco bagasse, as well as the feasibility of using cellulolytic extracts to produce reducing sugars in the same bagasse. After cultivation, the basidiome production parameters varied between 41.2 and 65.7% (biological efficiency), 0.17 and 0.30 (yield), 0.60 and 0.90% (production rate), 16.4 and 41.1% (Bioconversion) and 9.4 and 21.3 g (mean mushroom weight). At day 15 of growth, P. djamor showed the highest β-glucosidase activity (43.95 ± 4.5 IU/g); on day 33. The same strain had the highest endoglucanase activity (21.12 ± 0.5 IU/ml). Both extracts were partially purified, and the kinetic parameters Vmax and Km were estimated (20.83 µmole/ml sec and 232.01 µmole/ml for β-glucosidase and 685.01 µmole/ml sec and 1,240.34 µmole/ml for endoglucanase). In the enzymatic hydrolysis assay, the highest concentration of reducing sugars (43.13 ± 1.09 g/L; 0.21 g/g bagasse) was obtained by a mixture of the two partially purified extracts acting synergistically after 48 h and with a pH adjustment. The results suggest that the use of agave Comiteco bagasse for cultivating edible mushrooms while obtaining cellulolytic extracts is an alternative treatment for waste reduction and valorization of agro-industrial by-products.

A novel transcriptional repressor specifically regulates xylanase gene 1 in Trichoderma reesei

BACKGROUND

The well-known industrial fungus Trichoderma reesei has an excellent capability of secreting a large amount of cellulases and xylanases. The induced expression of cellulase and xylanase genes is tightly controlled at the transcriptional level. However, compared to the intensive studies on the intricate regulatory mechanism of cellulase genes, efforts to understand how xylanase genes are regulated are relatively limited, which impedes the further improvement of xylanase production by T. reesei via rational strain engineering.

RESULTS

To identify transcription factors involved in regulating xylanase gene expression in T. reesei, yeast one-hybrid screen was performed based on the promoters of two major extracellular xylanase genes xyn1 and xyn2. A putative transcription factor named XTR1 showing significant binding capability to the xyn1 promoter but not that of xyn2, was successfully isolated. Deletion of xtr1 significantly increased the transcriptional level of xyn1, but only exerted a minor promoting effect on that of xyn2. The xylanase activity was increased by ~ 50% with XTR1 elimination but the cellulase activity was hardly affected. Subcellular localization analysis of XTR1 fused to a green fluorescence protein demonstrated that XTR1 is a nuclear protein. Further analyses revealed the precise binding site of XTR1 and nucleotides critical for the binding within the xyn1 promoter. Moreover, competitive EMSAs indicated that XTR1 competes with the essential transactivator XYR1 for binding to the xyn1 promoter.

CONCLUSIONS

XTR1 represents a new transcriptional repressor specific for controlling xylanase gene expression. Isolation and functional characterization of this new factor not only contribute to further understanding the stringent regulatory network of xylanase genes, but also provide important clues for boosting xylanase biosynthesis in T. reesei.

Oleaginous yeasts for biochemicals, biofuels and food from lignocellulose-hydrolysate and crude glycerol

Microbial lipids produced from lignocellulose and crude glycerol (CG) can serve as sustainable alternatives to vegetable oils, whose production is, in many cases, accompanied by monocultures, land use changes or rain forest clearings. Our projects aim to understand the physiology of microbial lipid production by oleaginous yeasts, optimise the production and establish novel applications of microbial lipid compounds. We have established methods for fermentation and intracellular lipid quantification. Following the kinetics of lipid accumulation in different strains, we found high variability in lipid formation even between very closely related oleaginous yeast strains on both, wheat straw hydrolysate and CG. For example, on complete wheat straw hydrolysate, we saw that one Rhodotorula glutinis strain, when starting assimilating D-xylosealso assimilated the accumulated lipids, while a Rhodotorula babjevae strain could accumulate lipids on D-xylose. Two strains (Rhodotorula toruloides CBS 14 and R. glutinis CBS 3044) were found to be the best out of 27 tested to accumulate lipids on CG. Interestingly, the presence of hemicellulose hydrolysate stimulated glycerol assimilation in both strains. Apart from microbial oil, R. toruloides also produces carotenoids. The first attempts of extraction using the classical acetone-based method showed that β-carotene is the major carotenoid. However, there are indications that there are also substantial amounts of torulene and torularhodin, which have a very high potential as antioxidants.

In Situ Formed ROS-Responsive Hydrogel with STING Agonist and Gemcitabine to Intensify Immunotherapy against Pancreatic Ductal Adenocarcinoma

Immunotherapy, the most revolutionary anticancer strategy, faces major obstacles in yielding desirable outcomes in pancreatic ductal adenocarcinoma (PDAC) due to the highly immunosuppressive tumor microenvironment (TME). Meanwhile, when used alone, the traditional first-line chemotherapeutic agent gemcitabine (GEM) in PDAC treatment is also insufficient to achieve lasting efficacy. In this study, a reactive oxygen species degradable hydrogel system, denoted as GEM-STING@Gel, is engineered to codeliver gemcitabine and the stimulator of interferon genes (STING) agonist DMXAA (5,6-dimethylxanthenone-4-acetic acid) into the tumor site. In this work, the strategy addresses the major challenges of current immunotherapies with a facile platform, which can synergistically activate innate immunity and promote the cytotoxic T lymphocytes infiltration at the tumor site, thereby modulating the immunosuppressive TME. Further, the efficient therapeutic potency of the immunotherapy is confirmed in an orthotopic postsurgical model, unleashing the translational potential to prevent tumor recurrence after surgical resection. This study underscores the advantages of this integrative strategy that combines chemotherapy, immunotherapy, and biomaterial-based hydrogel, including improved therapeutic efficacy, operational convenience, and superior biosafety.

Improving the cellobiose hydrolysis activity of glucose-stimulating β-glucosidase Bgl2A

β-Glucosidases with high catalytic activity and glucose tolerant properties possess promising applications in lignocellulose-based industries. To obtain enzymes possessing these properties, a semi-rational strategy was employed to engineer the glucose-stimulating β-glucosidase Bgl2A for high cellobiose hydrolysis activity. A total of 18 mutants were constructed. A22S, V224D, and A22S/V224D exhibited high specific activities of 272.06, 237.60, and 239.29 U/mg toward cellobiose, which were 2.5- to 2.8-fold of Bgl2A. A22S, V224D, and A22S/V224D exhibited increased k_cat values, which were 2.7- to 3.1-fold of Bgl2A. A22S and V224D maintained glucose-stimulating property, whereas A22S/V224D lost it. Using 150 g/L cellobiose as the substrate, the amount of glucose produced by A22S was the highest, yielding 129.70 g/L glucose after 3 h reaction at 35 °C. The synergistic effects of the engineered enzymes with commercial cellulase on hydrolyzing cellulose were investigated. Supplemented with the commercial cellulase and A22S, the highest glucose amount of 23.30 g/L was yielded from cellulose with hydrolysis rate of 21.02 %. Given its high cellobiose hydrolysis activity and glucose-stimulating properties, A22S can be used as a component of enzyme cocktail to match mesophilic cellulases for efficient cellulose hydrolysis.

Constitutive overexpression of cellobiohydrolase 2 in Trichoderma reesei reveals its ability to initiate cellulose degradation

Cellulose degradation results from the synergistic effect of different enzymes, but which enzyme is involved in the initial stage of cellulose degradation is still not well understood. Cellobiohydrolase 2 (CBH2) attached to the conidial surface is possibly associated with the initial stage. However, its specific mechanism is still incompletely known. This study explored the potential role of CBH2 in initiating cellulose degradation using a constitutive overexpression strategy. First, the CBH2-overexpression Trichoderma reesei strains Qgc2-5 and Qrc2-40 were constructed using the constitutive promoters Pgpd1 and PrpS30, respectively. It was found that cbh2 was expressed at a high level under the glucose conditions and was significantly higher than that of the parental strain QM9414 at the early stage of 29 h when cellulose was used as the carbon source. Particularly, the constitutive overexpression of cbh2 caused the strong expression of major cellulase-encoding genes (cbh1, eg1, and eg2) and the rapid decomposition of cellulosic material. Meanwhile, the scanning electron microscope showed that the groove-like structure of the cellulose surface was eroded seriously owing to CBH2 overexpression, which caused the cellulose surface to be smooth. These results showed that the overexpression of CHB2 caused the major cellulase enzymes to be expressed and contributed to cellulose degradation, showing the potential role of CBH2 in the initial stage of the cellulose hydrolytic process.

Orientation of Cel5A and Xyn10B in a fusion construct is important in facilitating synergistic degradation of plant biomass polysaccharides

One approach to achieve efficient and economical saccharification of plant biomass would be using thermostable and multifunctional enzymes from hyperthermophiles such as Thermotoga maritima. Thus, the bifunctional constructs, Cel5A-Xyn10B and Xyn10B-Cel5A, were produced by fusing cellulase Cel5A at the N- and C-terminals of xylanase Xyn10B, respectively. The Cel5A-Xyn10B fusion construct showed cellulase activity of 1483 U μmol^-1 against carboxymethyl cellulose, which was nearly the same as that of Cel5A in the free form. However, xylanase activity of this construct increased by 2-fold against beechwood xylan as compared to that of Xyn10B in free form. The synergistic effect between Cel5A and Xyn10B in the form of Cel5A-Xyn10B fusion resulted an overall increase in the release of reducing sugars. However, Xyn10B-Cel5A showed about 60% decrease in activities of both the component enzymes as compared to their activities in the free form. Both the fusion constructs were active in a wide range of pH from 4.0 to 9.0 and temperatures from 50 to 90 °C. Nearly 80% of cellulase and xylanase activities were retained in Cel5A-Xyn10B fusion after incubation at 60 °C for 1 h. Secondary structures of the component enzymes were retained in the Cel5A-Xyn10B fusion as observed by circular dichroism spectroscopy. Docking and simulation studies suggested that the enhanced xylanase activity in Cel5A-Xyn10B was due to the high binding energy, favorable orientation of the active sites, as well as relative positioning of the active site residues of Cel5A and Xyn10B in closer vicinity, which facilitated the substrate channeling.

Potential of lignocellulose degrading microorganisms for agricultural residue decomposition in soil: A review

Lignocellulosic crop residues (LCCRs) hold a significant share of the terrestrial biomass, estimated at 5 billion Mg per annum globally. A massive amount of these LCCRs are burnt in many countries resulting in immense environmental pollution; hence, its proper disposal in a cost-effective and eco-friendly manner is a significant challenge. Among the different options for management of LCCRs, the use of lignocellulose degrading microorganisms (LCDMOs), like fungi and bacteria, has emerged as an eco-friendly and effective way for its on-site disposal. LCDMOs achieve degradation through various mechanisms, including multiple supportive enzymes, causing oxidative attacks by which recalcitrance of lignocellulose material is reduced, paving the way to further activity by depolymerizing enzymes. This improves the physical properties of soil, recycles plant nutrients, promotes plant growth and thus helps improve productivity. Rapid and proper microbial degradation may be achieved through the correct combination of the LCDMOs, supplementing nutrients and controlling different factors affecting microbial activity in the field. The review is a critical discussion of previous studies revealing the potential of individuals or a set of LCDMOs, factors controlling the rate of degradation and the key researchable areas for better understanding of the role of these decomposers for future use.

Impact of Cellulolytic Fungi on Biodegradation of Hemp Shives and Corn Starch-Based Composites with Different Flame-Retardants

Biocomposite boards (BcBs) composed of hemp shives and corn starch are known as thermal insulating or structural building materials. Therefore, they must be stable during exploitation. However, BcBs are exposed to microorganisms present in the environment, and it is of great interest to investigate the biodegradation behaviour of these materials. This work identified microorganisms growing on BcBs that contain either Flovan CGN or expandable graphite as flame retardants and selected fungi such as Rhizopus oryzae and Aspergillus fumigatus to test the way they affect the materials of interest. For this purpose, the enzymatic activity of cellulases and amylases produced by these organisms were determined. In addition, the apparent density as well as compressive strength of the affected boards were evaluated. The results showed that apparent density and compressive strength deteriorated in BcB composition with the Flovan CGN flame retardant. At the same time, the level of deterioration was lower when the expandable graphite was used, suggesting that it also acts as an antimicrobial agent. A scanning electronic microscopy analysis was employed to monitor the growth of microorganisms in the BcBs. Such analysis demonstrated that, regardless of BcB composition, fungi easily penetrate into the middle layers of the material.

Use of carbohydrate-directed enzymes for the potential exploitation of sugarcane bagasse to obtain value-added biotechnological products

Microorganisms, such as fungi and bacteria, are crucial players in the production of enzymatic cocktails for biomass hydrolysis or the bioconversion of plant biomass into products with industrial relevance. The biotechnology industry can exploit lignocellulosic biomass for the production of high-value chemicals. The generation of biotechnological products from lignocellulosic feedstock presents several bottlenecks, including low efficiency of enzymatic hydrolysis, high cost of enzymes, and limitations on microbe metabolic performance. Genetic engineering offers a route for developing improved microbial strains for biotechnological applications in high-value product biosynthesis. Sugarcane bagasse, for example, is an agro-industrial waste that is abundantly produced in sugar and first-generation processing plants. Here, we review the potential conversion of its feedstock into relevant industrial products via microbial production and discuss the advances that have been made in improving strains for biotechnological applications.

X-Ray Scattering Reveals Two Mechanisms of Cellulose Microfibril Degradation by Filamentous Fungi

Mushroom-forming fungi (Agaricomycetes) employ enzymatic and nonenzymatic cellulose degradation mechanisms, the latter presumably relying on Fenton-generated radicals. The effects of the two mechanisms on the cellulose microfibrils structure remain poorly understood. We examined cellulose degradation caused by litter decomposers and wood decomposers, including brown-rot and white-rot fungi and one fungus with uncertain wood decay type, by combining small- and wide-angle X-ray scattering. We also examined the effects of commercial enzymes and Fenton-generated radicals on cellulose using the same method. We detected two main degradation or modification mechanisms. The first characterized the mechanism used by most fungi and resembled enzymatic cellulose degradation, causing simultaneous microfibril thinning and decreased crystalline cellulose. The second mechanism was detected in one brown-rot fungus and one litter decomposer and was characterized by patchy amorphogenesis of crystalline cellulose without substantial thinning of the fibers. This pattern did not resemble the effect of Fenton-generated radicals, suggesting a more complex mechanism is involved in the destruction of cellulose crystallinity by fungi. Furthermore, our results showed a mismatch between decay classifications and cellulose degradation patterns and that even within litter decomposers two degradation mechanisms were found, suggesting higher functional diversity under current ecological classifications of fungi.

IMPORTANCE Cellulose degradation by fungi plays a fundamental role in terrestrial carbon cycling, but the mechanisms by which fungi cope with the crystallinity of cellulose are not fully understood. We used X-ray scattering to analyze how fungi, a commercial enzyme mix, and a Fenton reaction-generated radical alter the crystalline structure of cellulose. Our data revealed two mechanisms involved in crystalline cellulose degradation by fungi: one that results in the thinning of the cellulose fibers, resembling the enzymatic degradation of cellulose, and one that involves amorphogenesis of crystalline cellulose by yet-unknown pathways, resulting in a patchy-like degradation pattern. These results pave the way to a deeper understanding of cellulose degradation and the development of novel ways to utilize crystalline cellulose.

Research Progress on Lignocellulosic Biomass Degradation Catalyzed by Enzymatic Nanomaterials

Lignocellulose biomass (LCB) has extensive applications in many fields such as bioenergy, food, medicines, and raw materials for producing value-added products. One of the keys to efficient utilization of LCB is to obtain directly available oligo- and monomers (e.g., glucose). With the characteristics of easy recovery and separation, high efficiency, economy, and environmental protection, immobilized enzymes have been developed as heterogeneous catalysts to degrade LCB effectively. In this review, applications and mechanisms of LCB-degrading enzymes are discussed, and the nanomaterials and methods used to immobilize enzymes are also discussed. Finally, the research progress of lignocellulose biodegradation catalyzed by nano-enzymes was discussed.

Extracellular Enzyme of Endophytic Fungi Isolated from Ziziphus spina Leaves as Medicinal Plant

Endophytic fungi live inside plants or any part of them without creating any visible pathogenic signs. Endophytic fungi are found within medicinal plants and have shown strong biologic activity, such as anticancer and antioxidant activities, as well as producing extracellular enzymes. In this study, different fungal strains were isolated from the leaves of the medicinal plant Ziziphus spina, including Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger, Cladosporium sp., Rhizopus sp., and Mucor sp. Extracellular enzymes have been quantified using agar plate-based methods in which fungi were grown in specified growth media to detect the enzymes produced. The results showed that A. niger has the highest ability to produce amylase, Cladosporium sp. has the highest ability to produce protease and pectinase, Rhizopus and Mucor sp. have the highest ability to produce cellulase, and A. niger and Cladosporium sp. have the same ability to produce lipase and laccase. The ability of medicinal plant endophytic fungi to produce extracellular enzymes has great therapeutic potential in clinical microbiology. Some of the isolates showed great activity in secreting particular enzymes, indicating that the enzymes of these fungi could be used in a variety of applications.

Exploring the multi-level regulation of lignocellulases in the filamentous fungus Trichoderma guizhouense NJAU4742 from an omics perspective

BACKGROUND

Filamentous fungi are highly efficient at deconstructing plant biomass by secreting a variety of enzymes, but the complex enzymatic regulation underlying this process is not conserved and remains unclear.

RESULTS

In this study, cellulases and xylanases could specifically respond to Avicel- and xylan-induction, respectively, in lignocellulose-degrading strain Trichoderma guizhouense NJAU4742, however, the differentially regulated cellulases and xylanases were both under the absolute control of the same TgXyr1-mediated pathway. Further analysis showed that Avicel could specifically induce cellulase expression, which supported the existence of an unknown specific regulator of cellulases in strain NJAU4742. The xylanase secretion is very complex, GH10 endoxylanases could only be induced by Avicel, while, other major xylanases were significantly induced by both Avicel and xylan. For GH10 xylanases, an unknown specific regulator was also deduced to exist. Meanwhile, the post-transcriptional inhibition was subsequently suggested to stop the Avicel-induced xylanases secretion, which explained the specifically high xylanase activities when induced by xylan in strain NJAU4742. Additionally, an economical strategy used by strain NJAU4742 was proposed to sense the environmental lignocellulose under the carbon starvation condition, that only slightly activating 4 lignocellulose-degrading genes before largely secreting all 33 TgXyr1-controlled lignocellulases if confirming the existence of lignocellulose components.

CONCLUSIONS

This study, aiming to explore the unknown mechanisms of plant biomass-degrading enzymes regulation through the combined omics analysis, will open directions for in-depth understanding the complex carbon utilization in filamentous fungi.

Role of ascomycete and basidiomycete fungi in meeting established and emerging sustainability opportunities: a review

Fungal biomass is the future's feedstock. Non-septate Ascomycetes and septate Basidiomycetes, famously known as mushrooms, are sources of fungal biomass. Fungal biomass, which on averagely comprises about 34% protein and 45% carbohydrate, can be cultivated in bioreactors to produce affordable, safe, nontoxic, and consistent biomass quality. Fungal-based technologies are seen as attractive, safer alternatives, either substituting or complementing the existing standard technology. Water and wastewater treatment, food and feed, green technology, innovative designs in buildings, enzyme technology, potential health benefits, and wealth production are the key sectors that successfully reported high-efficiency performances of fungal applications. This paper reviews the latest technical know-how, methods, and performance of fungal adaptation in those sectors. Excellent performance was reported indicating high potential for fungi utilization, particularly in the sectors, yet to be utilized and improved on the existing fungal-based applications. The expansion of fungal biomass in the industrial-scale application for the sustainability of earth and human well-being is in line with the United Nations' Sustainable Development Goals.

Isolation and characterization of a mesophilic cellulolytic endophyte Preussia africana from Juniperus oxycedrus

The medicinal plant Juniperus oxycedrus is less recognized for the diversity of its fungal endophytes and their potential to produce extracellular enzymes. The present study is the first report on the isolation and identification of a mesophilic endophytic strain JO-A, Preussia africana, from fresh stems of the J. oxycedrus endemic tree in the Ifrane region-Morocco, and the evaluation of its ability to produce cellulases. A one-time multi-parameter one-factor screening was optimized to select factors that enhance cellulase production in P. africana. The maximum production of both CMCase and FPase activities were 1.913 IU.mL^-1 and 0.885 IU.mL^-1, respectively, when the medium was supplemented with 2% w/v glucose. These remarkable titers were tenfold greater than those obtained under the initial non-optimized conditions. This mesophilic P. africana JO-A strain grows and actively produces cellulases at 37 °C demonstrating its great potential for various biotechnology applications. The cellulolytic extract showed the highest enzymatic activities at pH 5.0 and 50 °C with a half-life of 24 h at 50 °C.

Endophytic fungi: a potential source of industrial enzyme producers

Microbial enzymes have gained interest for their widespread use in various industries and medicine due to their stability, ease of production, and optimization. Endophytic fungi in plant tissues produce a wide range of secondary metabolites and enzymes, which exhibit a variety of biological activities. The present review illustrates promising applications of enzymes produced by endophytic fungi and discusses the characteristic features of the enzymes, application of the endophytic fungal enzymes in therapeutics, agriculture, food, and biofuel industries. Endophytic fungi producing ligninolytic enzymes have possible biotechnological applications in lignocellulosic biorefineries. The global market of industrially important enzymes, challenges, and future prospects are illustrated. However, the commercialization of endophytic fungal enzymes for industrial purposes is yet to be explored. The present review suggests that endophytic fungi can produce various enzymes and may become a novel source for upscaling the production of enzymes of industrial use.

Biochemical biorefinery: A low-cost and non-waste concept for promoting sustainable circular bioeconomy

The transition from a fossil-based linear economy to a circular bioeconomy is no longer an option but rather imperative, given worldwide concerns about the depletion of fossil resources and the demand for innovative products that are ecocompatible. As a critical component of sustainable development, this discourse has attracted wide attention at the regional and international levels. Biorefinery is an indispensable technology to implement the blueprint of the circular bioeconomy. As a low-cost, non-waste innovative concept, the biorefinery concept will spur a myriad of new economic opportunities across a wide range of sectors. Consequently, scaling up biorefinery processes is of the essence. Despite several decades of research and development channeled into upscaling biorefinery processes, the commercialization of biorefinery technology appears unrealizable. In this review, challenges limiting the commercialization of biorefinery technologies are discussed, with a particular focus on biofuels, biochemicals, and biomaterials. To counteract these challenges, various process intensification strategies such as consolidated bioprocessing, integrated biorefinery configurations, the use of highly efficient bioreactors, simultaneous saccharification and fermentation, have been explored. This study also includes an overview of biomass pretreatment-generated inhibitory compounds as platform chemicals to produce other essential biocommodities. There is a detailed examination of the technological, economic, and environmental considerations of a sustainable biorefinery. Finally, the prospects for establishing a viable circular bioeconomy in Nigeria are briefly discussed.

Elimination of the Sugar Transporter GAT1 Increased Xylanase I Production in Trichoderma reesei

The filamentous fungus Trichoderma reesei secretes large quantities of cellulases and hemicellulases that have found wide applications in industry. Compared with extensive studies on the mechanism controlling cellulase gene expression, less is known about the regulatory mechanism behind xylanase gene expression. Herein, several putative sugar transporter encoding genes that showed significant upregulation on xylan were identified in T. reesei. Deletion of one such gene, gat1, resulted in increased xylanase production but hardly affected cellulase induction. Further analyses demonstrated that deletion of gat1 markedly increased XYNI production at the transcriptional level and only exerted a minor effect on XYNII synthesis. In contrast, overexpressing gat1 caused a continuous decrease in xyn1 expression. Deletion of gat1 also affected the expression of xyn1 and pectinase genes when T. reesei was cultivated with galacturonic acid as the sole carbon source. Transcriptome analyses of Δgat1 and its parental strain identified 255 differentially expressed genes that are enriched in categories of glycoside hydrolases, lipid metabolism, transporters, and transcriptional factors. The results thus implicate a repressive role of the sugar transporter GAT1 in xyn1 expression and reveal that distinct regulatory mechanisms may exist in controlling the expression of different xylanase genes in T. reesei.

Lytic polysaccharide monooxygenases (LPMOs) producing microbes: A novel approach for rapid recycling of agricultural wastes

Out of the huge quantity of agricultural wastes produced globally, rice straw is one of the most abundant ligno-cellulosic waste. For efficient utilization of these wastes, several cost-effective biological processes are available. The practice of field level in-situ or ex-situ decomposition of rice straw is having less degree of adoption due to its poor decomposition ability within a short time span between rice harvest and sowing of the next crop. Agricultural wastes including rice straw are in general utilized by using lignocellulose degrading microbes for industrial metabolite or compost production. However, bioconversion of crystalline cellulose and lignin present in the waste, into simple molecules is a challenging task. To resolve this issue, researchers have identified a novel new generation microbial enzyme i.e., lytic polysaccharide monooxygenases (LPMOs) and reported that the combination of LPMOs with other glycolytic enzymes are found efficient. This review explains the progress made in LPMOs and their role in lignocellulose bioconversion and the possibility of exploring LPMOs producers for rapid decomposition of agricultural wastes. Also, it provides insights to identify the knowledge gaps in improving the potential of the existing ligno-cellulolytic microbial consortium for efficient utilization of agricultural wastes at industrial and field levels.

Fungal Proteases as Emerging Biocatalysts to Meet the Current Challenges and Recent Developments in Biomedical Therapies: An Updated Review

With the increasing world population, demand for industrialization has also increased to fulfill humans' living standards. Fungi are considered a source of essential constituents to produce the biocatalytic enzymes, including amylases, proteases, lipases, and cellulases that contain broad-spectrum industrial and emerging applications. The present review discussed the origin, nature, mechanism of action, emerging aspects of genetic engineering for designing novel proteases, genome editing of fungal strains through CRISPR technology, present challenges and future recommendations of fungal proteases. The emerging evidence revealed that fungal proteases show a protective role to many environmental exposures and discovered that an imbalance of protease inhibitors and proteases in the epithelial barriers leads to the protection of chronic eosinophilic airway inflammation. Moreover, mitoproteases recently were found to execute intense proteolytic processes that are crucial for mitochondrial integrity and homeostasis function, including mitochondrial biogenesis, protein synthesis, and apoptosis. The emerging evidence revealed that CRISPR/Cas9 technology had been successfully developed in various filamentous fungi and higher fungi for editing of specific genes. In addition to medical importance, fungal proteases are extensively used in different industries such as foods to prepare butter, fruits, juices, and cheese, and to increase their shelf life. It is concluded that hydrolysis of proteins in industries is one of the most significant applications of fungal enzymes that led to massive usage of proteomics.

Engineering interventions in industrial filamentous fungal cell factories for biomass valorization

Filamentous fungi possess versatile capabilities for synthesizing a variety of valuable bio compounds, including enzymes, organic acids and small molecule secondary metabolites. The advancements of genetic and metabolic engineering techniques and the availability of sequenced genomes discovered their potential as expression hosts for recombinant protein production. Remarkably, plant-biomass degrading filamentous fungi show the unique capability to decompose lignocellulose, an extremely recalcitrant biopolymer. The basic biochemical approaches have motivated several industrial processes for lignocellulose biomass valorisation into fermentable sugars and other biochemical for biofuels, biomolecules, and biomaterials. The review gives insight into current trends in engineering filamentous fungi for enzymes, fuels, and chemicals from lignocellulose biomass. This review describes the variety of enzymes and compounds that filamentous fungi produce, engineering of filamentous fungi for biomass valorisation with a special focus on lignocellulolytic enzymes and other bulk chemicals.

The enzyme interactome concept in filamentous fungi linked to biomass valorization

Biomass represents an abundant and inexpensive source of sugars and aromatic compounds that can be used as raw materials for conversion into value-added bioproducts. Filamentous fungi are sources of plant cell wall degrading enzymes in nature. Understanding the interactions between enzymes is crucial for optimizing biomass degradation processes. Herein, the concept of the interactome is presented as a holistic approach that depicts the interactions among enzymes, substrates, metabolites, and inhibitors. The interactome encompasses several stages of biomass degradation, starting with the sensing of the substrate and the subsequent synthesis of hydrolytic and oxidative enzymes (fungus-substrate interaction). Enzyme-enzyme interactions are exemplified in the complex processes of lignocellulosic biomass degradation. The enzyme-substrate-metabolite-inhibitor interaction also provides a better understanding of biomass conversion, allowing bioproduct production from recalcitrant agro-industrial residues, thus bringing greater value to residual biomass. Finally, technological applications are presented for optimizing the interactome at various levels.

Enhancement of the enzymatic hydrolysis efficiency of wheat bran using the Bacillus strains and their consortium

In the downstream process, the bioconversion of lignocellulosic biomass can be improved by applying a biological pretreatment procedure using microorganisms to produce hydrolytic enzymes to modify the recalcitrant structure of lignocellulose. In this study, various Bacillus strains (B. subtilis B.01162 and B.01212, B. coagulans B.01123 and B.01139, B. cereus B.00076 and B.01718, B. licheniformis B.01223 and B.01231) were evaluated for the degrading capacity of wheat bran in the submerged medium using enzymatic activities, reducing sugars and weight loss as indicators. The obtained results revealed that the B. subtilis B.01162, B. coagulans B.01123 and B. cereus B.00076 could be promising degraders for the wheat bran pretreatment. Besides, the application of their consortium (the combination of 2-3 Bacillus species) showed the positive effects on cellulose bioconversion compared with monocultures. Among them, the mixture of B. subtilis B.01162 and B. coagulans B.01123 increased significantly the cellulase, endo-glucanase, and xylanase enzyme activity resulting in accelerating the lignocellulose degradation. Our results served a very good base for the development of microbial consortium for biological pretreatment of lignocellulosic raw materials.

A simple and direct ionic chromatography method to monitor galactose oxidase activity

Galactose oxidase (GalOx, EC.1.1.3.9) is one of the most extensively studied copper radical oxidases (CROs). The reaction catalyzed by GalOx leads to the oxidation of the C-6 hydroxyl group of galactose and galactosides (including galactosylated polysaccharides and glycoproteins) to the corresponding aldehydes, coupled to the reduction of dioxygen to hydrogen peroxide. Despite more than 60 years of research including mechanistic studies, enzyme engineering and application development, GalOx activity remains primarily monitored by indirect measurement of the co-product hydrogen peroxide. Here, we describe a simple direct method to measure GalOx activity through the identification of galactosylated oxidized products using high-performance anion-exchange chromatography coupled to pulsed amperometric detection (HPAEC-PAD). Using galactose and lactose as representative substrates, we were able to separate and detect the C-6 oxidized products, which were confirmed by LC-MS and NMR analyses to exist in their hydrated (geminal-diol) forms. We show that the HPAEC-PAD method is superior to other methods in terms of sensitivity as we could detect down to 0.08 μM of Lac^OX (eq. 30 μg L⁻¹). We believe the method will prove useful for qualitative detection of galactose oxidase activity in biological samples or for quantitative purposes to analyze enzyme kinetics or to compare enzyme variants in directed evolution programs.

Galactose oxidase (GalOx, EC.1.1.3.9) is one of the most extensively studied copper radical oxidases. Here, we show it can be monitored through the release of oxidized galactosylated products using a simple, direct and sensitive HPAEC-PAD method.

A Comprehensive Insight into Fungal Enzymes: Structure, Classification, and Their Role in Mankind's Challenges

Enzymes have played a crucial role in mankind's challenges to use different types of biological systems for a diversity of applications. They are proteins that break down and convert complicated compounds to produce simple products. Fungal enzymes are compatible, efficient, and proper products for many uses in medicinal requests, industrial processing, bioremediation purposes, and agricultural applications. Fungal enzymes have appropriate stability to give manufactured products suitable shelf life, affordable cost, and approved demands. Fungal enzymes have been used from ancient times to today in many industries, including baking, brewing, cheese making, antibiotics production, and commodities manufacturing, such as linen and leather. Furthermore, they also are used in other fields such as paper production, detergent, the textile industry, and in drinks and food technology in products manufacturing ranging from tea and coffee to fruit juice and wine. Recently, fungi have been used for the production of more than 50% of the needed enzymes. Fungi can produce different types of enzymes extracellularly, which gives a great chance for producing in large amounts with low cost and easy viability in purified forms using simple purification methods. In the present review, a comprehensive trial has been advanced to elaborate on the different types and structures of fungal enzymes as well as the current status of the uses of fungal enzymes in various applications.

Xylanolytic Enzymes in Pulp and Paper Industry: New Technologies and Perspectives

The pulp and paper industry discharges massive amount of wastewater containing hazardous organochlorine compounds released during different processing stages. Therefore, some cost-effective and nonpolluting practices such as enzymatic treatments are required for the potential mitigation of effluents released in the environment. Various xylanolytic enzymes such as xylanases, laccases, cellulases and hemicellulases are used to hydrolyse raw materials in the paper manufacturing industry. These enzymes are used either individually or in combination, which has the efficient potential to be considered for bio-deinking and bio-bleaching components. They are highly dynamic, renewable, and high in specificity for enhancing paper quality. The xylanase act on the xylan and cellulases act on the cellulose fibers, and thus increase the bleaching efficacy of paper. Similarly, hemicellulase enzyme like endo-xylanases, arabinofuranosidase and β-D-xylosidases have been described as functional properties towards the biodegradation of biomass. In contrast, laccase enzymes act as multi-copper oxidoreductases, bleaching the paper by the oxidation and reduction process. Laccases possess low redox potential compared to other enzymes, which need some redox mediators to catalyze. The enzymatic process can be affected by various factors such as pH, temperature, metal ions, incubation periods, etc. These factors can either increase or decrease the efficiency of the enzymes. This review draws attention to the xylanolytic enzyme-based advanced technologies for pulp bleaching in the paper industry.

A Lignocellulolytic Colletotrichum sp. OH with Broad-Spectrum Tolerance to Lignocellulosic Pretreatment Compounds and Derivatives and the Efficiency to Produce Hydrogen Peroxide and 5-Hydroxymethylfurfural Tolerant Cellulases

Fungal endophytes are an emerging source of novel traits and biomolecules suitable for lignocellulosic biomass treatment. This work documents the toxicity tolerance of Colletotrichum sp. OH toward various lignocellulosic pretreatment-derived inhibitors. The effects of aldehydes (vanillin, p-hydroxybenzaldehyde, furfural, 5-hydroxymethylfurfural; HMF), acids (gallic, formic, levulinic, and p-hydroxybenzoic acid), phenolics (hydroquinone, p-coumaric acid), and two pretreatment chemicals (hydrogen peroxide and ionic liquid), on the mycelium growth, biomass accumulation, and lignocellulolytic enzyme activities, were tested. The reported Colletotrichum sp. OH was naturally tolerant to high concentrations of single inhibitors like HMF (IC50; 17.5 mM), levulinic acid (IC50; 29.7 mM), hydroquinone (IC50; 10.76 mM), and H2O2 (IC50; 50 mM). The lignocellulolytic enzymes displayed a wide range of single and mixed inhibitor tolerance profiles. The enzymes β-glucosidase and endoglucanase showed H2O2- and HMF-dependent activity enhancements. The enzyme β-glucosidase activity was 34% higher in 75 mM and retained 20% activity in 125 mM H2O2. Further, β-glucosidase activity increased to 24 and 32% in the presence of 17.76 and 8.8 mM HMF. This research suggests that the Colletotrichum sp. OH, or its enzymes, can be used to pretreat plant biomass, hydrolyze it, and remove inhibitory by-products.

Biodegradation of Keratin-Rich Husbandry Waste as a Path to Sustainable Agriculture

Every year, the size of the human population grows; with it, the need for agricultural products increases. This leads to an increment in the volume of waste, including hard-to-degrade keratin-rich ones, such as feathers. Currently, most of the agro-industrial complex protein by-products are utilized by incineration, landfilling, and chemical hydrolysis. Such methods do not meet modern trends in the development of a sustainable economy, negatively affecting the environment and humans, and preventing the reusing of waste. An alternative is biodegradation, which consists of the application of living organisms and their enzymes to recycle by-products. This approach is not only sustainable, but also makes it possible to obtain products of waste hydrolysis that are in demand for the manufacture of fertilizers and feed additives. This brings the development of agriculture closer to a circular economy and makes the recycling process more profitable. This review article emphasizes the significance of keratinolytic microorganisms and keratinases for the improvement of green methods for processing hard-to-degrade protein waste of the agro-industrial complex, which is necessary for sustainable economic development.