Structural and biochemical studies of the glycosyltransferase Bs-YjiC from Bacillus subtilis

Biotransformation of Deoxynivalenol to the Novel Metabolite Deoxynivalenol-8,15-hemiketal-7-glucoside by the Bacillus subtilis Glycosyltransferase YjiC

The mycotoxin deoxynivalenol (DON) is a chronic problem in cereals in temperate areas worldwide. Above regulatory levels, DON contamination can result in significant economic loss both to the primary producer and the feed industry in terms of increased costs. Here we report the enzymatic biotransformation of DON to a novel stable metabolite by a soil-borne strain of Bacillus subtilis. Proteomic analysis of activity-enriched protein fractions from this B. subtilis strain identified the glycosyltransferase YjiC as the enzyme responsible for the observed DON biotransformation. Liquid chromatography high-resolution tandem mass spectrometry and NMR spectroscopic analysis demonstrated that YjiC glycosylates DON at the 7-hydroxyl position, producing the novel metabolite DON-8,15-hemiketal-7-glucoside (HKDON7G). In toxicity experiments, duckweed exposed to 20 μM HKDON7G showed no phytotoxicity when compared to DON. Stability testing of HKDON7G demonstrated that it is significantly more resistant to enzymatic and microbial hydrolysis compared to DON-3-glucoside. This study is the first to report a chemical modification to the 7-hydroxyl position of DON and presents a novel mechanism for the detoxification of DON-contaminated food and feed.

Identification and characteristic analysis of PavUGT48 as a novel UDP-glycosyltransferase with dual functions on anthocyanin and amygdalin biosynthesis in sweet cherry

UDP-glycosyltransferase (UGT) is essential for fruit development, but its specific role in sweet cherry fruits has not been clearly defined. This study identified a new differentially expressed UGT gene, FUN_010048, by analyzing transcriptomic data from various colored regions of bicolored fruits. The 187 UGT family members were identified in the sweet cherry genome of 'Tieton'. Notably, FUN_010084 has been renamed PavUGT48. Expression analysis revealed that PavUGT48 increased during the development of the differently colored sweet cherry fruits. Co-expression network analysis and further experiments confirmed that PavUGT48 generates cyanidin-3-O-glucoside from cyanidin using UDP-glucose (UDP-Glc) as the sugar donor, enhancing fruit coloration. Additionally, PavUGT48 facilitates the formation of amygdalin from prunasin, but it does not react with naringenin, dihydrokaempferol, or kaempferol when UDP-Glc serves as the sugar donor. These findings enhance our understanding of UGT enzymes in sweet cherries and provide a basis for improving fruit quality and developing new varieties.

Engineering of Glycosyltransferase for Efficient Biosynthesis of Salidroside

Salidroside has been widely used in the cosmetic and medicinal industries. Previously, potential glycosyltransferase UGTBS was obtained for salidroside synthesis. However, the catalytic efficiency for salidroside was undesirable. In this study, a semirational design was applied to engineer UGTBS. The quadruple mutant M4 (I62N/S129T/F168W/Y316S) showed significantly enhanced salidroside synthesis. A conversion rate of 94.7% was obtained using mutant M4, which was 2.2-fold higher than that of the wild-type. The regioselectivity of mutant M4 toward tyrosol hydroxyl was also improved, resulting in 97.9% salidroside in the total product, which was 1.2-fold higher than that of the wild type. Kinetic constants and molecular simulations indicated that increased affinity and altered conformation of the binding pocket accounted for the enhanced salidroside synthesis. Furthermore, a fed-batch cascade reaction strategy was used, and over 183 mM salidroside was obtained. The engineered mutant M4 demonstrated precise catalysis for salidroside formation.

Discovery and mechanistic exploration of promiscuous xylosyltransferase based on protein engineering

Glycosylation is an effective means to alter the structure and properties of plant compounds, influencing the pharmacological activity of natural products (NPs) to obtain highly active NPs. In nature, glucosides are the most widely distributed, while other glycosides such as xylosides are less common and present in lower quantities. This is due to the scarcity of xylosyltransferases with substrate promiscuity in nature, and the modification of their catalytic function is also quite challenging. In this study, we first performed a phylogenetic analysis of reported UDP-glycosyltransferases (UGTs) of plant and microbiological origin and identified a unique motif region from the UGTs of the Bacillus genus, which may be responsible for the broad sugar donor catalytic activity of the UGTs in the Bacillus genus. Then, utilizing protein engineering techniques, we have evolved a xylosyltransferase M3-2, which exhibited high substrate promiscuity, sugar donor promiscuity, and site selectivity, enabling the synthesis of a variety of O-glycosides. In addition, another mutant M3-1 has been engineered to alter the sugar donor specificity of the UGT, enabling the switch from UDP-Glc donor to UDP-Xyl. The improved enzymatic activity is likely attributed to stable hydrophobic interactions and hydrogen bonding interactions between the enzyme and the substrate. In order to synthesize xylosylated products more economically and efficiently, an in vitro synthetic pathway that utilizes NPs and inexpensive glucuronic acid as starting materials was designed. Through this pathway, we successfully synthesized a variety of unnatural xylosylated products belonging to O-glycosides, one of which 10a possesses excellent anti-inflammatory activity. We anticipate that this work will contribute to the future discovery and industrial production of unnatural glycosides.

Engineering regioselectivity of glycosyltransferase for efficient polydatin synthesis

Resveratrol is a promising functional ingredient applied in food products. However, low bioavailability and poor water solubility, which can be improved by glycosylation, hinder its application. A uridine diphosphate-dependent glycosyltransferase (UGT) from Bacillus subtilis 168 (named UGTBS) presents potential application for resveratrol glycosylation; nonetheless, imprecise regioselectivity renders the synthesis of resveratrol-3-O-β-D-glucoside (polydatin) difficult. Therefore, molecular evolution was applied to UGTBS. A triple mutant Y14I/I62G/M315W was developed for 3-OH glycosylation of resveratrol and polydatin accounted for 91% of the total product. Kinetic determination and molecular docking indicated that the enhancement of hydrogen bond interaction and altered conformation of the binding pocket increases the enzyme's affinity for the 3-OH group, stabilizing the enzyme-substrate intermediate and promoting polydatin formation. Furthermore, a fed-batch cascade reaction by periodic addition of resveratrol was conducted and nearly 20 mM polydatin was obtained. The mutant Y14I/I62G/M315W can be used for polydatin manufacture.

Green and Fast Synthesis of NiCo-MOF for Simultaneous Purification-Immobilization of Bienzyme to Catalyze the Synthesis of Ginsenoside Rh2

Traditional metal-organic frameworks (MOFs) preparation is generally time-consuming, polluting, and lacking specificity for enzyme immobilization. This paper introduced a facile, rapid, and green method to produce three MOFs subsequently employed to purify and coimmobilize recombinant glycosyltransferase (UGT) and recombinant sucrose synthetase (SUSy) using histidine tag (His-tag) for the specific adsorption of Ni2+ and Co2+ from MOFs. This method simplified enzyme purification from crude extracts and enabled enzymes to be reused. The results demonstrated that NiCo-MOF exhibited a higher enzyme load (115.9 mg/g) than monometallic MOFs. Additionally, the NiCo-MOF@UGT&SUSy demonstrated excellent stability and efficiently produced the rare ginsenoside Rh2 by catalyzing a coupling reaction (95.6 μg/mL), solving the problem of the substrate cost of uridine diphosphate glucose (UDPG). The NiCo-MOF@UGT&SUSy retained 68.97% of the initial activity after 10 cycles. Finally, molecular docking studies elucidated the conversion mechanism of the target product Rh2. This technique is important in the industrialization of ginsenoside production and enzyme purification.

Enzymatic Glycosylation of 4'-Hydroxychalcones: Expanding the Scope of Nature's Catalytic Potential

Chalcones, including 4'-hydroxychalcones, have garnered significant attention in the area of drug discovery due to their diverse pharmacological properties, such as anti-inflammatory, antioxidative, and anticancer effects. However, their low water solubility and bioavailability limit their efficacy in vivo. Glycosylation presents a promising approach to enhance the water solubility, stability, and metabolic properties of chalcones. This study investigates the enzymatic glycosylation of eight chemically synthesized 4'-hydroxychalcones using a diverse set of sugar glucosyltransferases from bacterial, plant, and fungal sources, alongside Glycine max sucrose synthase (GmSuSy) in a cascade reaction. Among the tested enzymes, five exhibited a remarkable versatility for glycoside production, and for large-scale biotransformation, flavonoid 7-O-glucosyltransferase Sbaic7OGT from Scutellaria baicalensis was selected as the most effective. As a result of the experiments conducted, eight trans-chalcone glycosides were obtained. During the purification of the reaction products, we also observed the isomerization of the products by simple sunlight exposure, which resulted in eight additional cis-chalcone glycosides. This study highlights the novel use of a cascade reaction involving Glycine max sucrose synthase (GmSuSy) for the efficient glycosylation of trans-4'-hydroxychalcones, alongside the unexpected discovery of cis-chalcone glycosides during the purification process.

A novel glycosyltransferase from Bacillus subtilis achieves zearalenone detoxification by diglycosylation modification

Zearalenone (ZEN), a nonsteroidal estrogenic mycotoxin produced by Fusarium spp., contaminates cereals and threatens human and animal health by inducing hepatotoxicity, immunotoxicity, and genotoxicity. In this study, a new Bacillus subtilis strain, YQ-1, with a strong ability to detoxify ZEN, was isolated from soil samples and characterized. YQ-1 was confirmed to degrade more than 46.26% of 20 μg mL-1 ZEN in Luria-Bertani broth and 98.36% in fermentation broth within 16 h at 37 °C; one of the two resulting products was ZEN-diglucoside. Under optimal reaction conditions (50 °C and pH 5.0-9.0), the reaction mixture generated by YQ-1 catalyzing ZEN significantly reduced the promoting effect of ZEN on MCF-7 cell proliferation, effectively eliminating the estrogenic toxicity of ZEN. In addition, a new glycosyltransferase gene (yqgt) from B. subtilis YQ-1 was cloned with 98% similarity to Bs-YjiC from B. subtilis 168 and over-expressed in E. coli BL21 (DE3). ZEN glycosylation activity converted 25.63% of ZEN (20 μg mL-1) to ZEN-diG after 48 h of reaction at 37 °C. The characterization of ZEN degradation by B. subtilis YQ-1 and the expression of YQGT provide a theoretical basis for analyzing the mechanism by which Bacillus spp. degrades ZEN.

The sugar donor specificity of plant family 1 glycosyltransferases

Plant family 1 glycosyltransferases (UGTs) represent a formidable tool to produce valuable natural and novel glycosides. Their regio- and stereo-specific one-step glycosylation mechanism along with their inherent wide acceptor scope are desirable traits in biotechnology. However, their donor scope and specificity are not well understood. Since different sugars have different properties in vivo and in vitro, the ability to easily glycodiversify target acceptors is desired, and this depends on our improved understanding of the donor binding site. In the aim to unlock the full potential of UGTs, studies have attempted to elucidate the structure-function relationship governing their donor specificity. These efforts have revealed a complex phenomenon, and general principles valid for multiple enzymes are elusive. Here, we review the studies of UGT donor specificity, and attempt to group the information into key concepts which can help shape future research. We zoom in on the family-defining PSPG motif, on two loop residues reported to interact with the C6 position of the sugar, and on the role of active site arginines in donor specificity. We continue to discuss attempts to alter and expand the donor specificity by enzyme engineering, and finally discuss future research directions.

High-level production of Rhodiola rosea characteristic component rosavin from D-glucose and L-arabinose in engineered Escherichia coli

Rosavin is the characteristic component of Rhodiola rosea L., an important medicinal plant used widely in the world that has been reported to possess multiple biological activities. However, the endangered status of wild Rhodiola has limited the supply of rosavin. In this work, we successfully engineered an Escherichia coli strain to efficiently produce rosavin as an alternative production method. Firstly, cinnamate: CoA ligase from Hypericum calycinum, cinnamoyl-CoA reductase from Lolium perenne, and uridine diphosphate (UDP)-glycosyltransferase (UGT) from Bacillus subtilis (Bs-YjiC) were selected to improve the titer of rosin in E. coli. Subsequently, four UGTs from the UGT91R subfamily were identified to catalyze the formation of rosavin from rosin, with SlUGT91R1 from Solanum lycopersicum showing the highest activity level. Secondly, production of rosavin was achieved for the first time in E. coli by incorporating the SlUGT91R1 and UDP-arabinose pathway, including UDP-glucose dehydrogenase, UDP-xylose synthase, and UDP-xylose 4-epimerase, into the rosin-producing stain, and the titer reached 430.5 ± 91.4 mg/L. Thirdly, a two-step pathway derived from L-arabinose, composed of L-arabinokinase and UDP-sugar pyrophosphorylase, was developed in E. coli to further optimize the supply of the precursor UDP-arabinose. Furthermore, 1203.7 ± 32.1 mg/L of rosavin was produced from D-glucose and L-arabinose using shake-flask fermentation. Finally, the production of rosavin reached 7539.1 ± 228.7 mg/L by fed-batch fermentation in a 5-L bioreactor. Thus, the microbe-based production of rosavin shows great potential for commercialization. This work provides an effective strategy for the biosynthesis of other valuable natural products with arabinose-containing units from D-glucose and L-arabinose.

A New Potent Inhibitor against α-Glucosidase Based on an In Vitro Enzymatic Synthesis Approach

Inhibiting the activity of intestinal α-glucosidase is considered an effective approach for treating type II diabetes mellitus (T2DM). In this study, we employed an in vitro enzymatic synthesis approach to synthesize four derivatives of natural products (NPs) for the discovery of therapeutic drugs for T2DM. Network pharmacology analysis revealed that the betulinic acid derivative P3 exerted its effects in the treatment of T2DM through multiple targets. Neuroactive ligand-receptor interaction and the calcium signaling pathway were identified as key signaling pathways involved in the therapeutic action of compound P3 in T2DM. The results of molecular docking, molecular dynamics (MD) simulations, and binding free energy calculations indicate that compound P3 exhibits a more stable binding interaction and lower binding energy (-41.237 kcal/mol) with α-glucosidase compared to acarbose. In addition, compound P3 demonstrates excellent characteristics in various pharmacokinetic prediction models. Therefore, P3 holds promise as a lead compound for the development of drugs for T2DM and warrants further exploration. Finally, we performed site-directed mutagenesis to achieve targeted synthesis of betulinic acid derivative. This work demonstrates a practical strategy of discovering novel anti-hyperglycemic drugs from derivatives of NPs synthesized through in vitro enzymatic synthesis technology, providing potential insights into compound P3 as a lead compound for anti-hyperglycemic drug development.

Highly efficient synthesis of mono-β-1,6-Glucosylated Rebaudioside A derivative catalyzed by glycosyltransferase YjiC

Steviol glycosides have attracted great interest because of their high levels of sweetness and safety, and absence of calories. Improvement of their sensory qualities via glycosylation modification by glycosyltransferase is a research hotspot. In this study, YjiC, a uridine diphosphate-dependent glycosyltransferase from Bacillus subtilis 168, was found with the ability to glycosylate rebaudioside A (Reb A) to produce a novel mono β-1, 6-glycosylated Reb A derivative rebaudioside L2 (Reb L2). It has an improved sweetness compared with Reb A. Next, a cascade reaction was established by combining YjiC with sucrose synthase AtSuSy from Arabidopsis thaliana for scale-up preparation of Reb L2. It shows that Reb L2 (30.94 mg/mL) could be efficiently synthesized with an excellent yield of 91.34% within 12 h. Therefore, this study provides a potential approach for the production and application of new steviol glycoside Reb L2, expanding the scope of steviol glycosides.

Highly efficient production of rebaudioside D enabled by structure-guided engineering of bacterial glycosyltransferase YojK

Owing to zero-calorie, high-intensity sweetness and good taste profile, the plant-derived sweetener rebaudioside D (Reb D) has attracted great interest to replace sugars. However, low content of Reb D in stevia rebaudiana Bertoni as well as low soluble expression and enzymatic activity of plant-derived glycosyltransferase in Reb D preparation restrict its commercial usage. To address these problems, a novel glycosyltransferase YojK from Bacillus subtilis 168 with the ability to glycosylate Reb A to produce Reb D was identified. Then, structure-guided engineering was performed after solving its crystal structure. A variant YojK-I241T/G327N with 7.35-fold increase of the catalytic activity was obtained, which allowed to produce Reb D on a scale preparation with a great yield of 91.29%. Moreover, based on the results from molecular docking and molecular dynamics simulations, the improvement of enzymatic activity of YojK-I241T/G327N was ascribed to the formation of new hydrogen bonds between the enzyme and substrate or uridine diphosphate glucose. Therefore, this study provides an engineered bacterial glycosyltransferase YojK-I241T/G327N with high solubility and catalytic efficiency for potential industrial scale-production of Reb D.

Novel Biotransformation of Maslinic Acid to MA-2-O-β-D-Glucoside by UDP-Glycosyltransferases from Bacillus subtilis

Maslinic acid (MA) is a pentacyclic triterpenoid which originates from olive and other plants. Though MA possesses multiple biological activities, it has limitations due to its poor water solubility. YojK, YjiC, and UGT109A3 UDP-glycosyltransferases (UGTs) from Bacillus subtilis (B. subtilis) were utilized to catalyze the conjugation of MA with UDP-Glucose to generate a new MA glycosylation product, MA-2-O-β-D-glucoside (MA-2-O-β-D-Glu). The experimental results indicated that the resultant water solubility of MA-2-O-β-D-Glu is 1.69 times higher than that of MA. In addition, the recombinant YojK showed maximum activity at 40 °C with a pH range of 8.0−10.0, while the recombinant YjiC showed maximum activity at 45 °C with a pH of 8.0, and the recombinant UGT109A3 showed maximum activity at 40 °C with a pH of 8.0. Mg2+ is an important factor for efficient catalysis by three recombinant glycosyltransferases. The chemical conversion rate of the recombinant YojK, YjiC, and UGT109A3 is nearly 100% at their optimum pH, temperature, and metal ions. Furthermore, eight essential residues of three UGTs for MA glycosylation modification were further determined by molecular docking and site-directed mutagenesis. Thus, efficient glycosylation modification improves the water solubility of MA and provides a new potential method for the glycosylation modification of other pentacyclic triterpenoids.

Insight into glucocorticoids glucosylation by glucosyltransferase: A combined experimental and in-silico approach

Glucosyltransferases catalyze the glucosidic bond formation by transferring a glucose molecule from an activated sugar donor to an acceptor substrate. Glucocorticoids (GCs) are adrenal-derived steroid hormones most widely used for anti-inflammatory treatments. In this study, we biotransformed two selected GCs, cortisone and prednisone, into their O-glucoside derivatives using a versatile UDP-glycosyltransferase UGT-1. Complete structural assignment of glucosylated products revealed that the bioconversion by regio-selective glucosylation of cortisone and prednisone produced cortisone 21-glucoside and prednisone 21-glucoside, respectively. We also combined molecular dynamics (MD) simulation to study the binding feature and mechanism of glucosylation. MD simulation studies showed the formation of a stable complex between protein, glucose donor, and substrate, stabilized by hydrogen bonds. Overall, we were able to provide explanations for the experimentally observed selectivity for glucosylation by integrating experimental and computational techniques.

Glycosylation of Semi-Synthetic Isoflavene Phenoxodiol with a Recombinant Glycosyltransferase from Micromonospora echinospora ATCC 27932

Glycosyltransferase (GT)-specific degenerate PCR screening followed by in silico sequence analyses of the target clone was used to isolate a member of family1 GT-encoding genes from the established fosmid libraries of soil actinomycetes Micromonospora echinospora ATCC 27932. A recombinant MeUGT1 was heterologously expressed as a His-tagged protein in E. coli, and its enzymatic reaction with semi-synthetic phenoxodiol isoflavene (as a glycosyl acceptor) and uridine diphosphate-glucose (as a glycosyl donor) created two different glycol-attached products, thus revealing that MeUGT1 functions as an isoflavonoid glycosyltransferase with regional flexibility. Chromatographic separation of product glycosides followed by the instrumental analyses, clearly confirmed these previously unprecedented glycosides as phenoxodiol-4'-α-O-glucoside and phenoxodiol-7-α-O-glucoside, respectively. The antioxidant activities of the above glycosides are almost the same as that of parental phenoxodiol, whereas their anti-proliferative activities are all superior to that of cisplatin (the most common platinum chemotherapy drug) against two human carcinoma cells, ovarian SKOV-3 and prostate DU-145. In addition, they are more water-soluble than their parental aglycone, as well as remaining intractable to the simulated in vitro digestion test, hence demonstrating the pharmacological potential for the enhanced bio-accessibility of phenoxodiol glycosides. This is the first report on the microbial enzymatic biosynthesis of phenoxodiol glucosides.

Glycosyltransferases: Mining, engineering and applications in biosynthesis of glycosylated plant natural products

UDP-Glycosyltransferases (UGTs) catalyze the transfer of nucleotide-activated sugars to specific acceptors, among which the GT1 family enzymes are well-known for their function in biosynthesis of natural product glycosides. Elucidating GT function represents necessary step in metabolic engineering of aglycone glycosylation to produce drug leads, cosmetics, nutrients and sweeteners. In this review, we systematically summarize the phylogenetic distribution and catalytic diversity of plant GTs. We also discuss recent progress in the identification of novel GT candidates for synthesis of plant natural products (PNPs) using multi-omics technology and deep learning predicted models. We also highlight recent advances in rational design and directed evolution engineering strategies for new or improved GT functions. Finally, we cover recent breakthroughs in the application of GTs for microbial biosynthesis of some representative glycosylated PNPs, including flavonoid glycosides (fisetin 3-O-glycosides, astragalin, scutellarein 7-O-glucoside), terpenoid glycosides (rebaudioside A, ginsenosides) and polyketide glycosides (salidroside, polydatin).

Docking-guided rational engineering of a macrolide glycosyltransferase glycodiversifies epothilone B

Glycosyltransferases typically display acceptor substrate flexibility but more stringent donor specificity. BsGT-1 is a highly effective glycosyltransferase to glycosylate macrolides, including epothilones, promising antitumor compounds. Here, we show that BsGT-1 has three major regions significantly influencing the glycodiversification of epothilone B based on structural molecular docking, "hot spots" alanine scanning, and site saturation mutagenesis. Mutations in the PSPG-like motif region and the C2 loop region are more likely to expand donor preference; mutations of the flexible N3 loop region located at the mouth of the substrate-binding cavity produce novel epothilone oligosaccharides. These "hot spots" also functioned in homologues of BsGT-1. The glycosides showed significantly enhanced water solubility and decreased cytotoxicity, although the glycosyl appendages of epothilone B also reduced drug permeability and attenuated antitumor efficacy. This study laid a foundation for the rational engineering of other GTs to synthesize valuable small molecules.

A thermostable glycosyltransferase from Paenibacillus polymyxa NJPI29: recombinant expression, characterization, and application in synthesis of glycosides

Glycosylation is a prominent biological mechanism, affecting the structural and functional diversity of many natural products. In this study, a novel thermostable uridine diphosphate-dependent glycosyltransferase gene PpGT1 was cloned from Paenibacillus polymyxa NJPI29 and recombinantly expressed in B. subtilis WB600. The purified PpGT1 had a molecular weight of 45 kDa, as estimated using SDS-PAGE. The PpGT1 could catalyze the glycosylation of vanillic acid, methyl vanillate, caffeic acid, cinnamic alcohol, and ferulic acid. Moreover, PpGT1 possessed good thermostability and retained 80% of its original activity even after 12 h of incubation at 45 °C. In addition, PpGT1 remained stable within a neutral to alkaline pH range as well as in the presence of metal ions. The synthesis of methyl vanillate 4-O-β-D-glucoside by purified PpGT1 reached a yield 3.58 mM in a system with pH 8.0, 45 °C, 12 mM UDP-Glc, and 4 mM methyl vanillate. 3D-structure-based amino acid sequence alignments revealed that the catalytic residues and C-terminated PSPG motif were conserved. These unusual properties indicated that PpGT1 is a candidate UGT for valuable natural product industrial applications.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13205-021-02855-z.