Enzyme cascades for the synthesis of nucleotide sugars: Updates to recent production strategies

One-Pot Hetero-Di-C-Glycosylation of the Natural Polyphenol Phloretin by a Single C-Glycosyltransferase With Broad Sugar Substrate Specificity

The structural motif of hetero-di-C-glycosyl compound is prominent in plant polyphenol natural products and involves two different glycosyl residues (e.g., β-d-glucosyl, β-d-xylosyl) attached to carbons of the same phenolic ring. Polyphenol hetero-di-C-glycosides attract attention as specialized ingredients of herbal medicines and their tailored synthesis by enzymatic C-glycosylation is promising to overcome limitations of low natural availability and to expand molecular diversity to new-to-nature glycoside structures. However, installing these di-C-glycoside structures with synthetic precision and efficiency is challenging. Here we have characterized the syntheses of C-β-galactosyl-C-β-glucosyl and C-β-glucosyl-C-β-xylosyl structures on the phloroglucinol ring of the natural polyphenol phloretin, using kumquat (Fortunella crassifolia) C-glycosyltransferase (FcCGT). The FcCGT uses uridine 5'-diphosphate (UDP)-galactose (5 mU/mg) and UDP-xylose (0.3 U/mg) at lower activity than UDP-glucose (3 U/mg). The 3'-C-β-glucoside (nothofagin) is ~10-fold less reactive than non-glycosylated phloretin with all UDP-sugars, suggesting the practical order of hetero-di-C-glycosylation as C-galactosylation or C-xylosylation of phloretin followed by C-glucosylation of the resulting mono-C-glycoside. Each C-glycosylation performed in the presence of twofold excess of UDP-sugar proceeds to completion and appears to be effectively irreversible, as evidenced by the absence of glycosyl residue exchange at extended reaction times. Synthesis of C-β-glucosyl-C-β-xylosyl phloretin is shown at 10 mM concentration in quantitative conversion using cascade reaction of FcCGT and UDP-xylose synthase, allowing for in situ formation of UDP-xylose from the more expedient donor substrate UDP-glucuronic acid. The desired di-C-glycoside with Xyl or Gal was obtained as a single product of the synthesis and its structure was confirmed by NMR.

Protein Fusion of Biosynthetic Enzymes and a Thermo-Responsive Polypeptide Expedites Facile Access to Biocatalysts for Nucleotide Sugars

Nucleotide sugars (NSs) are essential building blocks for the enzymatic assembly of glycans. In this study, we established a preparation and recycling avenue to the biocatalysts for the enzymatic synthesis of NSs. This approach involves fusing two enzymes into a bifunctional chimera and using elastin-like polypeptides (ET64) as a purification tag, which allows for easy recovery of these biocatalysts without the need for chromatography. We successfully constructed and obtained five bifunctional fusion enzymes (GalK-USP-ET64, GlmU-NahK-ET64, ManC-NahK-ET64, FKP-ET64, and NanA-CSS-ET64) for the synthesis of five common NSs (UDP-Gal, UDP-GlcNAc, GDP-Man, GDP-Fuc, and CMP-Neu5Ac). These enzymes were obtained using the Inverse Transition Cycling (ITC) process in yields ranging from 60 to 124 mg per liter of fermentation. The enzymatic synthesis of NSs was carried out on a scale from hundreds of milligrams to multiple grams using these biocatalysts. Furthermore, we investigated the reusability of these biocatalysts by recycling them from the reaction solution using the ITC process. The recycling of GalK-USP-ET64, GlmU-NahK-ET64, FKP-ET64, and NanA-CSS-ET64 was effectively achieved for 15, 13, 3, and 4 times, respectively. These biocatalysts could be used not only for the enzymatic synthesis of NSs but also for the chemoenzymatic synthesis of glycan biomolecules when coupled with glycosyltransferases.

Enzyme cascades for nucleotide sugar regeneration in glycoconjugate synthesis

Leloir glycosyltransferases are instrumental in the synthesis of glycoconjugates. Nucleotide sugars as their donor substrates are still considered expensive making preparative enzymatic syntheses economically unattractive. The review highlights the development and advancements of in situ regeneration cycles that utilize nucleotides as byproducts from glycosyltransferase reactions to synthesize respective nucleotide sugars. This approach reduces costs and avoids inhibition of Leloir glycosyltransferases. Regeneration cycles for ten nucleotide sugars are explored emphasizing enzyme cascades from salvage pathways and nucleotide biosynthesis. Additionally, the review highlights advancements involving sucrose synthase for the in situ regeneration of nucleotide sugars from sucrose. Sucrose synthase as the first example of a reversible glycosyltransferase reaction paved the way to establish economic syntheses of glycosylated natural products. Important aspects like enzyme immobilization and protein fusion to optimize processes are discussed. Overall, the review underscores the significance of advanced in situ regeneration cycles for nucleotide sugars for cost-effective access to high-value glycoconjugates. KEY POINTS: • Enzyme cascades for in situ regeneration of nucleotide sugars • Effective cycles for large-scale synthesis of glycoconjugates • Regeneration of nucleotide sugars from sucrose by sucrose synthase.

Use of Crithidia fasciculata extract for the facile enzymatic synthesis of GDP-L-[3H]Fucose

For studies involving glycosyltransferases and nucleotide sugar transporters, radioactive nucleotide sugars are critical reagents. Of these, GDP-L-[3H]Fucose is currently commercially unavailable. Here, we present a facile approach for the preparation of GDP-[3H]-L-Fucose, using the enzymatic machinery present in the cytosol of the non-infectious and easily cultivated protozoan, Crithidia fasciculata, and its purification by solid phase extraction ion exchange chromatography.

Human Milk Oligosaccharides: Decoding Their Structural Variability, Health Benefits, and the Evolution of Infant Nutrition

Human milk oligosaccharides (HMOs), the third most abundant solid component in human milk, vary significantly among women due to factors such as secretor status, race, geography, season, maternal nutrition and weight, gestational age, and delivery method. In recent studies, HMOs have been shown to have a variety of functional roles in the development of infants. Because HMOs are not digested by infants, they act as metabolic substrates for certain bacteria, helping to establish the infant's gut microbiota. By encouraging the growth of advantageous intestinal bacteria, these sugars function as prebiotics and produce short-chain fatty acids (SCFAs), which are essential for gut health. HMOs can also specifically reduce harmful microbes and viruses binding to the gut epithelium, preventing illness. HMO addition to infant formula is safe and promotes healthy development, infection prevention, and microbiota. Current infant formulas frequently contain oligosaccharides (OSs) that differ structurally from those found in human milk, making it unlikely that they would reproduce the unique effects of HMOs. However, there is a growing trend in producing OSs resembling HMOs, but limited data make it unclear whether HMOs offer additional therapeutic benefits compared to non-human OSs. Better knowledge of how the human mammary gland synthesizes HMOs could direct the development of technologies that yield a broad variety of complex HMOs with OS compositions that closely mimic human milk. This review explores HMOs' complex nature and vital role in infant health, examining maternal variation in HMO composition and its contributing factors. It highlights recent technological advances enabling large-scale studies on HMO composition and its effects on infant health. Furthermore, HMOs' multifunctional roles in biological processes such as infection prevention, brain development, and gut microbiota and immune response regulation are investigated. The structural distinctions between HMOs and other mammalian OSs in infant formulas are discussed, with a focus on the trend toward producing more precise replicas of HMOs found in human milk.

Enzymatic Routes to Designer Hemicelluloses for Use in Biobased Materials

Various enzymes can be used to modify the structure of hemicelluloses directly in vivo or following extraction from biomass sources, such as wood and agricultural residues. Generally, these enzymes can contribute to designer hemicelluloses through four main strategies: (1) enzymatic hydrolysis such as selective removal of side groups by glycoside hydrolases (GH) and carbohydrate esterases (CE), (2) enzymatic cross-linking, for instance, the selective addition of side groups by glycosyltransferases (GT) with activated sugars, (3) enzymatic polymerization by glycosynthases (GS) with activated glycosyl donors or transglycosylation, and (4) enzymatic functionalization, particularly via oxidation by carbohydrate oxidoreductases and via amination by amine transaminases. Thus, this Perspective will first highlight enzymes that play a role in regulating the degree of polymerization and side group composition of hemicelluloses, and subsequently, it will explore enzymes that enhance cross-linking capabilities and incorporate novel chemical functionalities into saccharide structures. These enzymatic routes offer a precise way to tailor the properties of hemicelluloses for specific applications in biobased materials, contributing to the development of renewable alternatives to conventional materials derived from fossil fuels.

Advanced enzymatic multigram-scale production of nucleotide sugars in a continuous fed-batch membrane reactor

Enzymatic production of nucleotide sugars on a multigram scale presents a challenge, as only a few processes have been reported for large-scale nucleotide sugar production. They rely primarily on batch synthesis and employ exceptional amounts of enzymes. This study introduces a novel approach for the multigram-scale production of nucleotide sugars with a continuous fed-batch membrane reactor. We successfully synthesized five main nucleotide sugars: UDP-Gal, UDP-GalNAc, UDP-GlcA, GDP-Man, and CMP-Neu5Ac on a multigram scale. Efficient biocatalyst utilization results in high performance, including space-time yield (STY, g*L-1h-1), total turnover number (TTN, g product per g enzyme), and an efficient product formation rate (g/h) suitable for industrially relevant bioprocesses. The established continuous-fed batch reactor system produced up to 8.2 g CMP-Neu5Ac in three consecutive productions in less than 15 h with satisfying TTNs of 91 gProduct/gEnzyme. Continuous production of UDP-GlcA over 28 h resulted in a final product amount of 14.8 g and TTN of 493 gP/gE. This process enables the production of nucleotide sugars with stable product formation, requiring minimal technical equipment for multigram quantities of nucleotide sugars at the laboratory scale. Notably, the system exhibited robustness and flexibility, allowing its application to various enzymatic nucleotide sugar synthesis cascades.

Unlocking Industrial Potential: Phase-Transition Coimmobilization of Multienzyme Systems for High-Efficiency Uridine Diphosphate Galactose Production

Transitioning from batch to continuous industrial production often improves the economic returns and production efficiency. Immobilization is a critical strategy that can facilitate this shift. This study refined the previously established method for synthesizing uridine diphosphate galactose (UDP-Gal) by employing thermophilic enzymes. Three thermophilic enzymes (galactokinase, uridine diphosphate glucose pyrophosphorylase, and inorganic pyrophosphatase) were coimmobilized on the pH-responsive carrier Eudragit S-100, promoting enzyme recovery and reuse while their industrial potential was assessed. The coimmobilization system efficiently catalyzed UDP-Gal production, yielding 13.69 mM in 1.5 h, attaining a UTP conversion rate of 91.2% and a space-time yield (STY) of 5.16 g/L/h. Moreover, the system exhibited exceptional reproducibility, retaining 58.9% of its initial activity after five cycles. This research highlighted promising prospects for coimmobilization in industrial synthesis and proposed a novel methodology for enhancing UDP-Gal production in the industry. In addition, the phase-transition property of Eudragit S-100 paves the way for further exploration with the one-pot synthesis of poorly soluble galactosides.

Process Development for the Enzymatic Gram-Scale Production of the Unnatural Nucleotide Sugar UDP-6-Azido-GalNAc

Azido sugars hold great promise as substrates in numerous click-chemistry applications. However, the synthesis of activated azido sugars is limited by cost and complexity. Conventional chemical activation methods are intricate and time-consuming. In response, we have developed a process for the large-scale production of UDP-6-azido-GalNAc through enzymatic nucleotide sugar synthesis on a gram scale. Our optimization strategies encompassed refining the process parameters of an enzyme cascade featuring NahK from Bifidobacterium longum and AGX1 from Homo sapiens. Using the repetitive-batch-mode technology, we synthesized up to 2.1 g of UDP-6-azido-GalNAc, achieving yields up to 97 % in five consecutive batch cycles using a single enzyme batch. The synthesis process demonstrated to have total turnover numbers (TTNs) between 4.4-4.8 g of product per gram of enzyme (gP/gE) and STYs ranging from 1.7-2.4 g per liter per hour (g*L-1*h-1). By purification of a product solution pool containing 2.6 g (4.1 mmol) UDP-6-azido-GalNAc, 2.1 g (2,122.1 mg) UDP-6-azido-GalNAc (sodium salt) with a purity of 99.96 % (HPLC) were obtained. The overall recovery after purification was 81 % (3.32 mmol). Our work establishes a robust production platform for the gram-scale synthesis of unnatural nucleotide sugars, opening new avenues for applications in glycan engineering.

Directional co-immobilization of artificial multimeric-enzyme complexes as a robust biocatalyst for biosynthesis curcumin glucosides and regeneration of UDP-glucose

Site-directed protein immobilization allows the homogeneous orientation of proteins while maintaining high activity, which is advantageous for various applications. In this study, the use of SpyCatcher/SpyTag technology and magnetic nickel ferrite (NiFe2O4 NPs) nanoparticles were used to prepare a site-directed immobilization of BsUGT2m from Bacillus subtilis and AtSUSm from Arabidopsis thaliana for enhancing curcumin glucoside production with UDP-glucose regeneration from sucrose and UDP. The immobilization of self-assembled multienzyme complex (MESAs) enzymes were characterized for immobilization parameters and stability, including thermal, pH, storage stability, and reusability. The immobilized MESAs exhibited a 2.5-fold reduction in UDP consumption, enhancing catalytic efficiency. Moreover, the immobilized MESAs demonstrated high storage and temperature stability over 21 days at 4 °C and 25 °C, outperforming their free counterparts. Reusability assays showed that the immobilized MESAs retained 78.7 % activity after 10 cycles. Utilizing fed-batch technology, the cumulative titer of curcumin 4'-O-β-D-glucoside reached 6.51 mM (3.57 g/L) and 9.45 mM (5.18 g/L) for free AtSUSm/BsUGT2m and immobilized MESAs, respectively, over 12 h. This study demonstrates the efficiency of magnetic nickel ferrite nanoparticles in co-immobilizing enzymes, enhancing biocatalysts' catalytic efficiency, reusability, and stability.

Combining an Enhanced Polyphosphate Kinase-Driven UDP-Glucose Regeneration System with the Screening of Key Glycosyltransferases for Efficient In Vitro Synthesis of Nucleoside Disaccharides

Nucleoside disaccharides are essential glycosides that naturally occur in specific living organisms. This study developed an enhanced UDP-glucose regeneration system to facilitate the in vitro multienzyme synthesis of nucleoside disaccharides by integrating it with nucleoside-specific glycosyltransferases. The system utilizes maltodextrin and polyphosphate as cost-effective substrates for UDP-glucose supply, catalyzed by α-glucan phosphorylase (αGP) and UDP-glucose pyrophosphorylase (UGP). To address the low activity of known polyphosphate kinases (PPKs) in the UDP phosphorylation reaction, a sequence-driven screening identified RhPPK with high activity against UDP (>1000 U/mg). Computational design further led to the creation of a double mutant with a 2566-fold increase in thermostability at 50 °C. The enhanced UDP-glucose regeneration system increased the production rate of nucleoside disaccharide synthesis by 25-fold. In addition, our UDP-glucose regeneration system is expected to be applied to other glycosyl transfer reactions.

Recent advances of 3-fucosyllactose in health effects and production

Human milk oligosaccharides (HMOs) have been recognized as gold standard for infant development. 3-Fucosyllactose (3-FL), being one of the Generally Recognized as Safe HMOs, represents a core trisaccharide within the realm of HMOs; however, it has received comparatively less attention in contrast to extensively studied 2'-fucosyllactose. The objective of this review is to comprehensively summarize the health effects of 3-FL, including its impact on gut microbiota proliferation, antimicrobial effects, immune regulation, antiviral protection, and brain maturation. Additionally, the discussion also covers the commercial application and regulatory approval status of 3-FL. Lastly, an organized presentation of large-scale production methods for 3-FL aims to provide a comprehensive guide that highlights current strategies and challenges in optimization.

Engineering a Robust UDP-Glucose Pyrophosphorylase for Enhanced Biocatalytic Synthesis via ProteinMPNN and Ancestral Sequence Reconstruction

UDP-glucose is a key metabolite in carbohydrate metabolism and plays a vital role in glycosyl transfer reactions. Its significance spans across the food and agricultural industries. This study focuses on UDP-glucose synthesis via multienzyme catalysis using dextrin, incorporating UTP production and ATP regeneration modules to reduce costs. To address thermal stability limitations of the key UDP-glucose pyrophosphorylase (UGP), a deep learning-based protein sequence design approach and ancestral sequence reconstruction are employed to engineer a thermally stable UGP variant. The engineered UGP variant is significantly 500-fold more thermally stable at 60 °C and has a half-life of 49.8 h compared to the wild-type enzyme. MD simulations and umbrella sampling calculations provide insights into the mechanism behind the enhanced thermal stability. Experimental validation demonstrates that the engineered UGP variant can produce 52.6 mM UDP-glucose within 6 h in an in vitro cascade reaction. This study offers practical insights for efficient UDP-glucose synthesis methods.

Efficient One-Pot Synthesis of Uridine Diphosphate Galactose Employing a Trienzyme System

The limited availability of high-cost nucleotide sugars is a significant constraint on the application of their downstream products (glycosides and prebiotics) in the food or pharmaceutical industry. To better solve the problem, this study presented a one-pot approach for the biosynthesis of UDP-Gal using a thermophilic multienzyme system consisting of GalK, UGPase, and PPase. Under optimal conditions, a 2 h reaction resulted in a UTP conversion rate of 87.4%. In a fed-batch reaction with Gal/ATP = 20 mM:10 mM, UDP-Gal accumulated to 33.76 mM with a space-time yield (STY) of 6.36 g/L·h-1 after the second feeding. In repetitive batch synthesis, the average yield of UDP-Gal over 8 cycles reached 10.80 g/L with a very low biocatalyst loading of 0.002 genzymes/gproduct. Interestingly, Galk (Tth0595) could synthesize Gal-1P using ADP as a donor of phosphate groups, which had never been reported before. This approach possessed the benefits of high synthesis efficiency, low cost, and superior reaction system stability, and it provided new insights into the rapid one-pot synthesis of UDP-Gal and high-value glycosidic compounds.

Strategies for Automated Enzymatic Glycan Synthesis (AEGS)

Glycans are the most abundant biopolymers on earth and are constituents of glycoproteins, glycolipids, and proteoglycans with multiple biological functions. The availability of different complex glycan structures is of major interest in biotechnology and basic research of biological systems. High complexity, establishment of general and ubiquitous synthesis techniques, as well as sophisticated analytics, are major challenges in the development of glycan synthesis strategies. Enzymatic glycan synthesis with Leloir-glycosyltransferases is an attractive alternative to chemical synthesis as it can achieve quantitative regio- and stereoselective glycosylation in a single step. Various strategies for synthesis of a wide variety of different glycan structures has already be established and will exemplarily be discussed in the scope of this review. However, the application of enzymatic glycan synthesis in an automated system has high demands on the equipment, techniques, and methods. Different automation approaches have already been shown. However, while these techniques have been applied for several glycans, only a few strategies are able to conserve the full potential of enzymatic glycan synthesis during the process - economical and enzyme technological recycling of enzymes is still rare. In this review, we show the major challenges towards Automated Enzymatic Glycan Synthesis (AEGS). First, we discuss examples for immobilization of glycans or glycosyltransferases as an important prerequisite for the embedment and implementation in an enzyme reactor. Next, improvement of bioreactors towards automation will be described. Finally, analysis and monitoring of the synthesis process are discussed. Furthermore, automation processes and cycle design are highlighted. Accordingly, the transition of recent approaches towards a universal automated glycan synthesis platform will be projected. To this end, this review aims to describe essential key features for AEGS, evaluate the current state-of-the-art and give thought- encouraging impulses towards future full automated enzymatic glycan synthesis.

Ubiquitin Degradation of the AICAR Transformylase/IMP Cyclohydrolase Ade16 Regulates the Sexual Reproduction of Cryptococcus neoformans

F-box protein is a key protein of the SCF E3 ubiquitin ligase complex, responsible for substrate recognition and degradation through specific interactions. Previous studies have shown that F-box proteins play crucial roles in Cryptococcus sexual reproduction. However, the molecular mechanism by which F-box proteins regulate sexual reproduction in C. neoformans is unclear. In the study, we discovered the AICAR transformylase/IMP cyclohydrolase Ade16 as a substrate of Fbp1. Through protein interaction and stability experiments, we demonstrated that Ade16 is a substrate for Fbp1. To examine the role of ADE16 in C. neoformans, we constructed the iADE16 strains and ADE16^OE strains to analyze the function of Ade16. Our results revealed that the iADE16 strains had a smaller capsule and showed growth defects under NaCl, while the ADE16^OE strains were sensitive to SDS but not to Congo red, which is consistent with the stress phenotype of the fbp1Δ strains, indicating that the intracellular protein expression level after ADE16 overexpression was similar to that after FBP1 deletion. Interestingly, although iADE16 strains can produce basidiospores normally, ADE16^OE strains can produce mating mycelia but not basidiospores after mating, which is consistent with the fbp1Δmutant strains, suggesting that Fbp1 is likely to regulate the sexual reproduction of C. neoformans through the modulation of Ade16. A fungal nuclei development assay showed that the nuclei of the ADE16^OE strains failed to fuse in the bilateral mating, indicating that Ade16 plays a crucial role in the regulation of meiosis during mating. In summary, our findings have revealed a new determinant factor involved in fungal development related to the post-translational regulation of AICAR transformylase/IMP cyclohydrolase.

Advances in the Synthesis and Analysis of Biologically Active Phosphometabolites

Phosphorus-containing metabolites cover a large molecular diversity and represent an important domain of small molecules which are highly relevant for life and represent essential interfaces between biology and chemistry, between the biological and abiotic world. The large but not unlimited amount of phosphate minerals on our planet is a key resource for living organisms on our planet, while the accumulation of phosphorus-containing waste is associated with negative effects on ecosystems. Therefore, resource-efficient and circular processes receive increasing attention from different perspectives, from local and regional levels to national and global levels. The molecular and sustainability aspects of a global phosphorus cycle have become of much interest for addressing the phosphorus biochemical flow as a high-risk planetary boundary. Knowledge of balancing the natural phosphorus cycle and the further elucidation of metabolic pathways involving phosphorus is crucial. This requires not only the development of effective new methods for practical discovery, identification, and high-information content analysis, but also for practical synthesis of phosphorus-containing metabolites, for example as standards, as substrates or products of enzymatic reactions, or for discovering novel biological functions. The purpose of this article is to review the advances which have been achieved in the synthesis and analysis of phosphorus-containing metabolites which are biologically active.