Characterization of a novel thermostable glucose-tolerant GH1 β-glucosidase from the hyperthermophile Ignisphaera aggregans and its application in the efficient production of baohuoside I from icariin and total epimedium flavonoids

Ignisphaera cupida sp. nov., a hyperthermophilic hydrolytic archaeon from a hot spring of Uzon (Kamchatka), and emended description of the genus Ignisphaera

A novel strictly anaerobic hyperthermophilic archaeon, strain 4213-coT, was isolated from a terrestrial hot spring in the Uzon Caldera, Kamchatka (Russian Federation). Coccoid cells were present singly, in pairs, or aggregates, and occasionally were motile. The strain grew at 75-100 °C and within a pH range of 5.4-8.2 with the optimum at 92 °C and pH 6.4-6.7. Strain 4213-coT was a chemoorganoheterotroph, growing on proteinaceous substrates and mono-, di- and polysaccharides (starch, guar gum, xanthan gum). It did not require sodium chloride for growth. The complete genome of strain 4213-coT was 1.74 Mbp in size; its G+C content was 36.18 %. Genome analysis allowed to identify 25 genes encoding glycosidases involved in polysaccharide hydrolysis as well as genes of ADP-forming acetate-CoA ligase, lactate dehydrogenase and two [NiFe] hydrogenases responsible for acetate, lactate and hydrogen formation during fermentation. Moreover gene cluster encoding archaellum subunits was found. According to the phylogenomic analysis strain 4213-coT formed a species-level phylogenetic lineage within Ignisphaera genus. Our phylogenomic analysis also supports the delineation of the Ignisphaera genus into a separate family Ignisphaeraceae, as recently published. Here we propose a novel species Ignisphaera cupida, sp. nov. with type strain 4213-coT (=JCM 39446T=VKM B-3715T=UQM 41593T). Ecogenomic analysis showed that representatives of the Ignisphaera are thermophilic archaea, the majority of them were found in terrestrial hot springs and deep-sea hydrothermal vents. This study allowed a better understanding of physiology and ecology of Ignisphaeraceae - a rather understudied archaeal group.

Engineered β-glycosidase from Hyperthermophilic Sulfolobus solfataricus with Improved Rd-hydrolyzing Activity for Ginsenoside Compound K Production

Hyperthermophilic Sulfolobus solfataricus β-glycosidase (SS-βGly), with higher stability and activity than mesophilic enzymes, has potential for industrial ginsenosides biotransformation. However, its relatively low ginsenoside Rd-hydrolyzing activity limits the production of pharmaceutically active minor ginsenoside compound K (CK). In this study, first, we used molecular docking to predict the key enzyme residues that may hypothetically interact with ginsenoside Rd. Then, based on sequence alignment and alanine scanning mutagenesis approach, key variant sites were identified that might improve the enzyme catalytic efficiency. The enzyme catalytic efficiency (kcat/Km) and substrate affinity (Km) of the N264D variant enzyme for ginsenoside Rd increased by 60% and decreased by 17.9% compared with WT enzyme, respectively, which may be due to a decrease in the binding free energy (∆G) between the variant enzyme and substrate Rd. In addition, Markov state models (MSM) analysis during the whole 1000-ns MD simulations indicated that altering N264 to D made the variant enzyme achieve a more stable SS-βGly conformational state than the wild-type (WT) enzyme and corresponding Rd complex. Under identical conditions, the relative activities and the CK conversion rates of the N264D enzyme were 1.7 and 1.9 folds higher than those of the WT enzyme. This study identified an excellent hyperthermophilic β-glycosidase candidate for industrial biotransformation of ginsenosides.

Biochemical and in silico structural properties of a thermo-acid stable β-glucosidase from Beauveria bassiana

β-glucosidase hydrolyses the glycosidic bonds in cellobiose and cello-oligosaccharides, a critical step in the saccharification for biofuel production. Hence, the aim of this study was to gain insights into the biochemical and structural properties of a β-glucosidase from Beauveria bassiana, an entomopathogenic fungus. The β-glucosidase was purified to homogeneity using salt precipitation, ultrafiltration, and chromatographic techniques, attaining a specific activity of 496 U/mg. The molecular mass of the enzyme was then estimated via SDS-PAGE to be 116 kDa, while its activity pattern was confirmed by zymography using 4-methylumbelliferyl-β-d-glucopyranoside. Furthermore, the pH optima and temperature of the enzyme were found to be pH 5.0 and 60 °C respectively; its activity was significantly enhanced by Mg2+ and Na+ and was found to be relatively moderate in the presence of ethanol and dichloromethane. Molecular docking of the modelled B. bassiana β-glucosidase structure with the substrates, viz., 4-nitrophenyl β-d-glucopyranoside and cellobiose, revealed the binding affinity energies of -7.2 and -6.2 (kcal mol-1), respectively. Furthermore, the computational study predicted Lys-657, Asp-658, and Arg-1000 as the core amino acid residues in the catalytic site of the enzyme. This is the first investigation into a purified β-glucosidase from B. bassiana, providing valuable insights into the functional properties of carbohydrases from entomopathogenic fungal endophytes.

Exploring the diversity of β-glucosidase: Classification, catalytic mechanism, molecular characteristics, kinetic models, and applications

High-value chemicals and energy-related products can be produced from biomass. Biorefinery technology offers a sustainable and cost-effective method for this high-value conversion. β-glucosidase is one of the key enzymes in biorefinery processes, catalyzing the production of glucose from aryl-glycosides and cello-oligosaccharides via the hydrolysis of β-glycosidic bonds. Although β-glucosidase plays a critical catalytic role in the utilization of cellulosic biomass, its efficacy is often limited by substrate or product inhibitions, low thermostability, and/or insufficient catalytic activity. To provide a detailed overview of β-glucosidases and their benefits in certain desired applications, we collected and summarized extensive information from literature and public databases, covering β-glucosidases in different glycosidase hydrolase families and biological kingdoms. These β-glucosidases show differences in amino acid sequence, which are translated into varying degrees of the molecular properties critical in enzymatic applications. This review describes studies on the diversity of β-glucosidases related to the classification, catalytic mechanisms, key molecular characteristics, kinetics models, and applications, and highlights several β-glucosidases displaying high stability, activity, and resistance to glucose inhibition suitable for desired biotechnological applications.

Biochemical characteristics of Myceliophthora thermophila recombinant β-glucosidase (MtBgl3c) applicable in cellulose bioconversion

The GH3 β-glucosidase gene of Myceliophthora thermophila (MtBgl3c) has been cloned and heterologously expressed in E. coli for the first time. This study highlights the important characteristics of recombinant MtBgl3c (rMtBgl3c) which make it a promising candidate in industrial applications. Optimization of the production of rMtBgl3c led to 28,000 U L-1. On purification, it has a molecular mass of ∼100 kDa. It is a broad substrate specific thermostable enzyme that exhibits pH and temperature optima at 5.0 and 55 °C, respectively. The amino acid residues Asp287 and Glu514 act as nucleophile and catalytic acid/base, respectively in the enzyme catalysis. Its low Km value (1.28 mM) indicates a high substrate affinity as compared to those previously reported. The rMtBgl3c displays a synergistic action with the commercial enzyme cocktail in the saccharification of sugarcane bagasse suggesting its utility in the cellulose bioconversion. Tolerance to solvents, detergents as well as glucose make this enzyme applicable in wine, detergent, paper and textile industries too.

Advancements in the Biotransformation and Biosynthesis of the Primary Active Flavonoids Derived from Epimedium

Epimedium is a classical Chinese herbal medicine, which has been used extensively to treat various diseases, such as sexual dysfunction, osteoporosis, cancer, rheumatoid arthritis, and brain diseases. Flavonoids, such as icariin, baohuoside I, icaritin, and epimedin C, are the main active ingredients with diverse pharmacological activities. Currently, most Epimedium flavonoids are extracted from Epimedium plants, but this method cannot meet the increasing market demand. Biotransformation strategies promised huge potential for increasing the contents of high-value Epimedium flavonoids, which would promote the full use of the Epimedium herb. Complete biosynthesis of major Epimedium flavonoids by microbial cell factories would enable industrial-scale production of Epimedium flavonoids. This review summarizes the structures, pharmacological activities, and biosynthesis pathways in the Epimedium plant, as well as the extraction methods of major Epimedium flavonoids, and advancements in the biotransformation and complete microbial synthesis of Epimedium flavonoids, which would provide valuable insights for future studies on Epimedium herb usage and the production of Epimedium flavonoids.

Flavonoids as Aglycones in Retaining Glycosidase-Catalyzed Reactions: Prospects for Green Chemistry

Flavonoids and their glycosides are abundant in many plant-based foods. The (de)glycosylation of flavonoids by retaining glycoside hydrolases has recently attracted much interest in basic and applied research, including the possibility of altering the glycosylation pattern of flavonoids. Research in this area is driven by significant differences in physicochemical, organoleptic, and bioactive properties between flavonoid aglycones and their glycosylated counterparts. While many flavonoid glycosides are present in nature at low levels, some occur in substantial quantities, making them readily available low-cost glycosyl donors for transglycosylations. Retaining glycosidases can be used to synthesize natural and novel glycosides, which serve as standards for bioactivity experiments and analyses, using flavonoid glycosides as glycosyl donors. Engineered glycosidases also prove valuable for the synthesis of flavonoid glycosides using chemically synthesized activated glycosyl donors. This review outlines the bioactivities of flavonoids and their glycosides and highlights the applications of retaining glycosidases in the context of flavonoid glycosides, acting as substrates, products, or glycosyl donors in deglycosylation or transglycosylation reactions.

Multidisciplinary strategies to enhance therapeutic effects of flavonoids from Epimedii Folium: Integration of herbal medicine, enzyme engineering, and nanotechnology

Flavonoids such as baohuoside I and icaritin are the major active compounds in Epimedii Folium (EF) and possess excellent therapeutic effects on various diseases. Encouragingly, in 2022, icaritin soft capsules were approved to reach the market for the treatment of hepatocellular carcinoma (HCC) by National Medical Products Administration (NMPA) of China. Moreover, recent studies demonstrate that icaritin can serve as immune-modulating agent to exert anti-tumor effects. Nonetheless, both production efficiency and clinical applications of epimedium flavonoids have been restrained because of their low content, poor bioavailability, and unfavorable in vivo delivery efficiency. Recently, various strategies, including enzyme engineering and nanotechnology, have been developed to increase productivity and activity, improve delivery efficiency, and enhance therapeutic effects of epimedium flavonoids. In this review, the structure-activity relationship of epimedium flavonoids is described. Then, enzymatic engineering strategies for increasing the productivity of highly active baohuoside I and icaritin are discussed. The nanomedicines for overcoming in vivo delivery barriers and improving therapeutic effects of various diseases are summarized. Finally, the challenges and an outlook on clinical translation of epimedium flavonoids are proposed.

Screening and characterizing flavone synthases and its application in biosynthesizing vitexin from naringenin by a one-pot enzymatic cascade

C-glycosylated flavonoids are important structural derivatives of flavonoids and have a variety of physiological activities. Flavone synthase is a key enzyme for producing C-glycosylated flavonoids. In this study, three flavone synthase genes were cloned, overexpressed and characterized in E. coli. By analyzing the enzymatic properties of the enzymes, Aethusa cynapium flavone synthase (AcFNS) was better than Apium graveolens flavone synthase (AgFNS) and Petroselinum crispum flavone synthase (PcFNS) in terms of catalytic ability, organic solvent tolerance and stability. Then, a one-pot enzymatic cascade was developed to synthesize vitexin from naringenin by using AcFNS, C-glycosyltransferase (TcCGT) from Trollius chinensis, and sucrose synthase (GmSUS) from Glycine max. The effects of enzyme ratios, substrate concentrations, cofactors, and reaction conditions on vitexin production were determined. The highest vitexin production reached 935.6 mg/L with a corresponding molar conversion of 78.7 % for (2 S)-naringenin. Thus, this is the first report of a one-pot enzymatic cascade for vitexin production from naringenin in vitro.

UPLC-MS/MS method for simultaneously determining nucleosides and methyl-nucleosides in liver mRNA of Epimedin C-induced liver injury mouse model

Background

Epimedin C, one of the main active ingredients of Epimedium, has been reported to have potential hepatotoxicity. However, the mechanism of Epimedin C-induced liver injury has not been studied. mRNA methylation, mainly including N6-methyladenosine and N5-methylcytidine, is implicated in the regulation of many biological processes and diseases. The study of quantifying mRNA methylation alterations in Epimedin C-induced liver injury mice may contribute to clarify the mechanism of its hepatotoxicity. Therefore, an analysis method needs to be established to determine nucleoside and methyl-nucleoside levels in liver mRNA.

Methods

An ultra-high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method was developed and validated to simultaneously determine six nucleosides (adenosine, uridine, cytidine, guanosine, N6-methyladenosine and N5-methylcytidine) in liver mRNA. Besides, the Epimedin C-induced liver injury mouse model was studied by intragastrical administration Epimedin C at a daily dose of 10 or 40 mg/kg for 4 weeks. The nucleoside samples of the mice liver mRNA were prepared and separated on an UPLC column using 0.1% formic acid water and methanol after enzymatic digestion. Then the sample was detected by a Qtrap 6500 mass spectrometer.

Results

In this method, calibration curves of the six nucleosides showed good linearity over their concentration ranges. The linear ranges were 40–20,000 pg/mL for adenosine, cytidine, N6-methyladenosine and N5-methylcytidine, 0.2–100 ng/mL for guanosine, and 2–1000 ng/mL for uridine. Epimedin C-induced liver injury mouse model was successfully established,which could be proved by the elevation of serum aminotransferase levels, and the increased inflammatory cell infiltration as well as vacuolar degeneration in liver. The N6-methyladenosine and N5-methylcytidine levels, and the ratios of N6-methyladenosine to adenosine and N5-methylcytidine to cytidine of the mice liver mRNA were all significantly increased after Epimedin C treatment.

Conclusion

The established method was successfully applied to the determination of six nucleosides levels in liver mRNA of the Epimedin C-induced liver injury mice model and the control group. The results indicated that mRNA methylation might be associated with Epimedin C-induced liver injury. This study will facilitate the mechanism research on the hepatotoxicity of Epimedin C.

Biosynthesis of 3'-O-methylisoorientin from luteolin by selecting O-methylation/C-glycosylation motif

Glycosylation and methylation of flavonoids are the main types of structural modifications and can endow flavonoids with greater stability, bioactivity, and bioavailability. In this study, five types of O-methyltransferases were screened for producing O-methylated luteolin, and the biosynthesis strategy of 3'-O-methylisoorientin from luteolin was determined. To improve the production of 3'-O-methylluteolin, the S-adenosyl-l-methionine synthesis pathway was reconstructed in the recombinant strain by introducing S-adenosyl-l-methionine synthetase genes. After optimizing the conversion conditions, maximal 3'-O-methylluteolin production reached 641 ± 25 mg/L with a corresponding molar conversion of 76.5 %, which was the highest titer of methylated flavonoids reported to date in Escherichia coli. 3'-O-Methylluteolin (127 mg) was prepared from 250 mL of the broth by silica gel column chromatography and preparative HPLC with a yield of 79.4 %. Subsequently, we used the biocatalytic cascade of Gentiana triflora C-glycosyltransferase (Gt6CGT) and Glycine max sucrose synthase (GmSUS) to biosynthesize 3'-O-methylisoorientin from 3'-O-methylluteolin in vitro. By optimizing the coupled reaction conditions and using the fed-batch operation, maximal 3'-O-methylisoorientin production reached 226 ± 8 mg/L with a corresponding molar conversion of 98 %. Therefore, this study provides an efficient method for the production of novel 3'-O-methylisoorientin and the biosynthesis strategy for methylated C-glycosylation flavonoids by selective O-methylation/C-glycosylation motif on flavonoids.

Characterization of a glucose-stimulated β-glucosidase from Microbulbifer sp. ALW1

Glucose-tolerant and/or glucose-stimulated β-glucosidase is of great interest for its industrial utilization in enzymatic digestion of lignocellulosic biomass for biofuel production. In this study, a new gene of β-glucosidase MaGlu1A was cloned from an alginate-degrading marine bacterium Microbulbifer sp. ALW1. The gene of MaGlu1A encoded a 472-amino acid protein classified into the glycosyl hydrolase family 1 (GH1). The recombinant β-glucosidase was overexpressed and purified from Escherichia coli with a molecular mass of 65.0 kDa. Structure analysis illustrated the catalytic acid/base residue Glu186 and nucleophilic residue Glu370 in the enzyme. MaGlu1A displayed optimal activity at 40 °C and pH 4.5, respectively. It had substrate preference to the aryl-β-glycosidic bonds with glucose, fucose, and galactose moieties, in addition to cellobiose. MaGlu1A demonstrated strong stimulation to the supplemental glucose. Site-directed mutagenesis suggested an essential role of Asn242 in glucose stimulation. The enzymatic characterization of MaGlu1A provides general information about its catalytic properties facilitating its practical applications.

Orientin and vitexin production by a one-pot enzymatic cascade of a glycosyltransferase and sucrose synthase

Orientin and vitexin, important components of bamboo-leaf extracts, are C-glycosylflavones which exhibit a number of interesting biological properties. In this work, we developed an efficient biocatalytic cascade for orientin and vitexin production consisting of Trollius chinensis C-glycosyltransferase (TcCGT) and Glycine max sucrose synthase (GmSUS). In order to relieve the bottleneck of the biocatalytic cascade, the biocatalytic efficiency, reaction condition compatibilities and the ratio of the enzymes were determined. We found that the specific activity of TcCGT was significantly influenced by enzyme dose and Triton X-100 or Tween 20 (0.2%). Co-culture of BL21-TcCGT-Co and BL21-GmSUS-Co affected the catalytic efficiency of TcCGT and GmSUS, and the maximum orientin production rate reached 47 μM/min at the inoculation ratio of 9:1. The optimal pH and temperature for the biocatalytic cascade were pH 7.5 and 30 °C, respectively. Moreover, the high dose of the enzymes can improve the tolerance of biocatalytic cascade to substrate inhibition in the one-pot reaction. By using a fed-batch strategy, maximal titers of orientin and vitexin reached 7090 mg/L with a corresponding molar conversion of 98.7% and 5050 mg/L with a corresponding molar conversion of 97.3%, respectively, which is the highest titer reported to date. Therefore, the method described herein for efficient production of orientin and vitexin by modulating catalytic efficiencies of enzymes can be widely used for the C-glycosylation of flavonoids.

High-level expression of a novel multifunctional GH3 family β-xylosidase/α-arabinosidase/β-glucosidase from Dictyoglomus turgidum in Escherichia coli

A novel β-xylosidase Dt-2286 from Dictyoglomus turgidum was cloned and overexpressed in Escherichia coli BL21 (DE3). Dt-2286 belonging to glycoside hydrolase (GH) family 3 encodes a polypeptide with 762 amino acid residues with a molecular weight of 85.1 kDa. By optimization of the growth and induction conditions, the activity of β-xylosidase reached 273 U/mL, which is the highest yield reported to date from E. coli in a shake-flask. The optimal activities of the purified Dt-2286 were found at pH 5.0 and 98 °C. It also shows excellent thermostable/haloduric/organic solvent-tolerance. Dt-2286 was revealed to be a multifunctional enzyme with β-xylosidase, α-arabinofuranoside, α-arabinopyranoside and β-glucosidase activities, and K_cat/K_m was 5245.316 mM^-1 s^-1, 2077.353 mM^-1 s^-1, 1626.454 mM^-1 s^-1, and 470.432 mM^-1 s^-1 respectively. Dt-2286 showed significant synergistic effects on the degradation of xylans, releasing more reduced sugars (up to 15.08 fold) by simultaneous addition with endoxylanase. Moreover, this enzyme has good activity in the hydrolysis of epimedium B, demonstrating its versatility in practical applications.

A novel β-glucosidase from a hot-spring metagenome shows elevated thermal stability and tolerance to glucose and ethanol

β-glucosidase causes hydrolysis of β-1,4-glycosidic bond in glycosides and oligosaccharides. It is an industrially important enzyme owing to its potential in biomass processing applications. In this study, computational screening of an extreme temperature aquatic habitat metagenomic resource was done, leading to the identification of a novel gene, bgl_M, encoding a β-glucosidase. The comparative protein sequence and homology structure analyses designated it as a GH1 family β-glucosidase. The bgl_M gene was expressed in a heterologous host, Escherichia coli. The purified protein, Bgl_M, was biochemically characterized for β-glucosidase activity. Bgl_M exhibited noteworthy hydrolytic potential towards cellobiose and lactose. Bgl_M, showed substantial catalytic activity in the pH range of 5.0-7.0 and at the temperature 40 °C-70 °C. The enzyme was found quite stable at 50 °C with a loss of hardly 20% after 40 h of heat exposure. Furthermore, any drastically negative effect was not observed on the enzyme's activity in the presence of metal ions, non-ionic surfactants, metal chelating, and denaturing agents. A significantly high glucose tolerance, retaining 80% relative activity at 1 M, and 40% at 5 M glucose, and ethanol tolerance, exhibiting 80% relative activity in 10% ethanol, enrolled Bgl_M as a promising enzyme for cellulose saccharification. Furthermore, its ability to catalyze the hydrolysis of daidzin and polydatin ascertained it as an admirably suited biocatalyst for enhancement of nutritional values in soya and wine industries.