Engineered Glycosidase for Significantly Improved Production of Naturally Rare Vina-Ginsenoside R7

Conserved Local Structural Motifs in Glycoside Hydrolase Families Facilitate the Discovery of Functional Enzymes

Glycoside hydrolases (GHs) are vital for natural glycoside biotransformation, especially in enhancing the pharmacological effects of natural products like ginsenosides. In this study, we collected 67 microbial-derived ginsenoside-hydrolyzing enzymes from nine GH families. Despite differences in global structures, the key residues surrounding substrate binding in GH1 and GH3 exhibit conserved structural motifs. Leveraging these motifs, five GH genes from Cellulosimicrobium were cloned, and three enzymes (Cbgl496, Cbgl516, Cbgl766) were characterized. Experimental results demonstrated that Cbgl516, Cbgl766, and Cbgl841 specifically catalyzed the hydrolysis of the β(1-6) glycosidic bond in the C-20 sugar chain of ginsenoside Rb1 to yield Rd. Cbgl496 selectively catalyzed the hydrolysis of β(1-2) glycosidic bonds in the oligosaccharide chains at the C-3 position of ginsenosides Rb1, Rb2, Rb3, and Rc, thereby directionally producing the minor ginsenosides Gy XVII, Compound O, Compound Mx1, and Compound Mc1. Structural analysis of 109,994 GH1/GH3 models from AlphaFold database revealed conserved residues across various organisms, emphasizing evolutionary conservation in the 3D structure of the catalytic core region despite sequence diversity. This study underscores the importance of conserved local structural motifs in GHs, offering insights for functional enzyme screening and understanding enzyme diversity and industrial applications.

Computer-Guided Engineered Endo- and Exocleaving Glycosidase for Significantly Improving Production of Ginsenoside F1

Ginsenoside F1, a particularly rare and valuable compound known for its health benefits, requires precise deglycosylation due to the extensive glycosylation of ginsenosides in Panax notoginseng. Here, we identified that the β-d-glucosidase BglSK exhibits both endo- and exocleaving glycosidase activities with multi-6-O-glycosides, thereby facilitating the specific production of Ginsenoside F1. The variant BglSKT137A/L508A, obtained through protein engineering, displayed kcat/KM values for the reactions of ginsenoside Rg1 and notoginsenoside R1 that were increased by 13.88-fold and 108.56-fold, respectively, compared with the BglSKWT. The reduced steric hindrance and the overall increase in loop stability show a higher tendency to adopt a closed conformation and facilitate the prereaction state, which may explain the enhanced catalytic efficiency of the engineered enzyme. These beneficial mutants will deepen our understanding of mechanisms for improving glycosidase activity and provide tools for producing high-value P. notoginseng products.

Biotransformation of Ginsenoside Rb1 to Ginsenoside Rd and 7 Rare Ginsenosides Using Irpex lacteus with HPLC-HRMS/MS Identification

The biotransformation of ginsenosides using microorganisms represents a promising and ecofriendly approach for the production of rare ginsenosides. The present study reports on the biotransformation of ginsenoside Rb1 using the fungus Irpex lacteus, resulting in the production of ginsenoside Rd and seven rare ginsenosides with novel structures. Employing high-performance liquid chromatography coupled with high-resolution tandem mass spectrometry, the identities of the transformation products were rapidly determined. Two sets of isomers with molecular weights of 980.56 and 962.55 were discovered among the seven rare ginsenosides, which were generated through the isomerization of the olefin chain in the protopanaxadiol (PPD)-type ginsenoside skeleton. Each isomer exhibited characteristic fragment ions and neutral loss patterns in their tandem mass spectra, providing evidence of their unique structures. Time-course experiments demonstrated that the transformation reaction reached equilibrium after 14 days, with Rb1 initially generating Rd and compound 5, followed by the formation of other rare ginsenosides. The biotransformation process catalyzed by I. lacteus was found to involve not only the typical deglycosylation reaction at the C-20 position but also hydroxylation at the C-22 and C-23 positions, as well as hydrogenation, transfer, and cyclization of the double bond at the C-24(25) position. These enzymatic capabilities extend to the structural modification of other PPD-type ginsenosides such as Rc and Rd, revealing the potential of I. lacteus for the production of a wider range of rare ginsenosides. The transformation activities observed in I. lacteus are unprecedented among fungal biotransformations of ginsenosides. This study highlights the application of a medicinal fungi-based biotransformation strategy for the generation of rare ginsenosides with enhanced structural diversity, thereby expanding the variety of bioactive compounds derived from ginseng.

Novel glycosidase from Paenibacillus lactis 154 hydrolyzing the 28-O-β-D-glucopyranosyl ester bond of oleanane-type saponins

Oleanane-type ginsenosides are a class of compounds with remarkable pharmacological activities. However, the lack of effective preparation methods for specific rare ginsenosides has hindered the exploration of their pharmacological properties. In this study, a novel glycoside hydrolase PlGH3 was cloned from Paenibacillus lactis 154 and heterologous expressed in Escherichia coli. Sequence analysis revealed that PlGH3 consists of 749 amino acids with a molecular weight of 89.5 kDa, exhibiting the characteristic features of the glycoside hydrolase 3 family. The enzymatic characterization results of PlGH3 showed that the optimal reaction pH and temperature was 8 and 50 °C by using p-nitrophenyl-β-D-glucopyranoside as a substrate, respectively. The Km and kcat values towards ginsenoside Ro were 79.59 ± 3.42 µM and 18.52 s-1, respectively. PlGH3 exhibits a highly specific activity on hydrolyzing the 28-O-β-D-glucopyranosyl ester bond of oleanane-type saponins. The mechanism of hydrolysis specificity was then presumably elucidated through molecular docking. Eventually, four kinds of rare oleanane-type ginsenosides (calenduloside E, pseudoginsenoside RP1, zingibroside R1, and tarasaponin VI) were successfully prepared by biotransforming total saponins extracted from Panax japonicus. This study contributes to understanding the mechanism of enzymatic hydrolysis of the GH3 family and provides a practical route for the preparation of rare oleanane-type ginsenosides through biotransformation. KEY POINTS: • The glucose at C-28 in oleanane-type saponins can be directionally hydrolyzed. • Mechanisms to interpret PlGH3 substrate specificity by molecular docking. • Case of preparation of low-sugar alternative saponins by directed hydrolysis.

New insights of flavonoid glycosidases and their application in food industry

Flavonoids are significant natural nutraceuticals and a key component of dietary supplements. Given that flavonoid glycosides are more plentiful in nature and less beneficial to human health than their aglycone counterparts, they serve as potential precursors for flavonoid production. Glycosidases have shown substantial potential within the food industry, particularly in enhancing the organoleptic properties of juice, wine, and tea. When applied to food resources, glycosidases can amplify their biological activities, thereby improving the performance of functional foods. This review provides up-to-date information on flavonoid glycosidases, including their catalytic mechanisms, biochemical properties, and natural sources, as well as their applications within the food industry. The use of flavonoid glycosidases in improving food quality is also reviewed.

Structures, Biochemical Characteristics, and Functions of β-Xylosidases

The complete degradation of abundant xylan derived from plants requires the participation of β-xylosidases to produce the xylose which can be converted to xylitol, ethanol, and other valuable chemicals. Some phytochemicals can also be hydrolyzed by β-xylosidases into bioactive substances, such as ginsenosides, 10-deacetyltaxol, cycloastragenol, and anthocyanidins. On the contrary, some hydroxyl-containing substances such as alcohols, sugars, and phenols can be xylosylated by β-xylosidases into new chemicals such as alkyl xylosides, oligosaccharides, and xylosylated phenols. Thus, β-xylosidases shows great application prospects in food, brewing, and pharmaceutical industries. This review focuses on the molecular structures, biochemical properties, and bioactive substance transformation function of β-xylosidases derived from bacteria, fungi, actinomycetes, and metagenomes. The molecular mechanisms of β-xylosidases related to the properties and functions are also discussed. This review will serve as a reference for the engineering and application of β-xylosidases in food, brewing, and pharmaceutical industries.