Substrate Characterization of Bacteroides fragilis α1,3/4-Fucosyltransferase Enabling Access to Programmable One-Pot Enzymatic Synthesis of KH-1 Antigen

Engineering Escherichia coli for Highly Efficient Biosynthesis of Lacto-N-difucohexaose II through De Novo GDP-l-fucose Pathway

Lacto-N-difucohexaose II (LNDFH II) is a typical fucosylated human milk oligosaccharide and can be enzymatically produced from lacto-N-tetraose (LNT) by a specific α1,3/4-fucosyltransferase from Helicobacter pylori DMS 6709, referred to as FucT14. Previously, we constructed an engineered Escherichia coli BL21(DE3) with a single plasmid for highly efficient biosynthesis of LNT. In this study, two additional plasmids harboring the de novo GDP-L-fucose pathway module and FucT14, respectively, were further introduced to construct the strain for successful biosynthesis of LNDFH II. FucT14 was actively expressed, and the engineered strain produced LNDFH II as the major product, lacto-N-fucopentaose (LNFP) V as the minor product, and a trace amount of LNFP II and 3-fucosyllactose as very minor products. Additional expression of the α1,3-fucosyltransferase FutM1 from a Bacteroidaceae bacterium from the gut metagenome could obviously enhance the LNDFH II biosynthesis. After optimization of induction conditions, the maximum titer reached 3.011 g/L by shake-flask cultivation. During the fed-batch cultivation, LNDFH II was highly efficiently produced with the highest titer of 18.062 g/L and the productivity yield of 0.301 g/L·h.

Highly-efficient in vivo production of lacto-N-fucopentaose V by a regio-specific α1,3/4-fucosyltransferase from Bacteroides fragilis NCTC 9343

Lacto-N-fucopentaose V (LNFP V) is a typical human milk pentasaccharide. Multi-enzymatic in vitro synthesis of LNFP V from lactose was reported, however, microbial cell factory approach to LNFP V production has not been reported yet. In this study, the biosynthetic pathway of LNFP V was examined in Escherichia coli. The previously constructed E. coli efficiently producing lacto-N-tetraose was used as the starting strain. GDP-fucose pathway module and a regio-specific glycosyltransferase with α1,3-fucosylation activity were introduced to realize the efficient synthesis of LNFP V. The α1,3/4-fucosyltransferase from Bacteroides fragilis was selected as the best enzyme for in vivo biosynthesis of LNFP V from nine candidates, with the highest titer and the lowest by-product accumulation. A beneficial variant K128D was obtained to further enhance LNFP V titer using computer-assisted site-directed mutagenesis. The final strain EW10 could produce 25.68 g/L LNFP V by fed-batch cultivation, with the productivity of 0.56 g/L·h.

Utilization of glycosyltransferases as a seamless tool for synthesis and modification of the oligosaccharides-A review

Glycosyltransferases (GTs) catalyze the transfer of active monosaccharide donors to carbohydrates to create a wide range of oligosaccharide structures. GTs display strong regioselectivity and stereoselectivity in producing glycosidic bonds, making them extremely valuable in the in vitro synthesis of oligosaccharides. The synthesis of oligosaccharides by GTs often gives high yields; however, the enzyme activity may experience product inhibition. Additionally, the higher cost of nucleotide sugars limits the usage of GTs for oligosaccharide synthesis. In this review, we comprehensively discussed the structure and mechanism of GTs based on recent literature and the CAZY website data. To provide innovative ideas for the functional studies of GTs, we summarized several remarkable characteristics of GTs, including folding, substrate specificity, regioselectivity, donor sugar nucleotides, catalytic reversibility, and differences between GTs and GHs. In particular, we highlighted the recent advancements in multi-enzyme cascade reactions and co-immobilization of GTs, focusing on overcoming problems with product inhibition and cost issues. Finally, we presented various types of GT that have been successfully used for oligosaccharide synthesis. We concluded that there is still an opportunity for improvement in enzymatically produced oligosaccharide yield, and future research should focus on improving the yield and reducing the production cost.

An Overview of Sugar Nucleotide-Dependent Glycosyltransferases for Human Milk Oligosaccharide Synthesis

Human milk oligosaccharides (HMOs) have received increasing attention because of their special effects on infant health and commercial value as the new generation of core components in infant formula. Currently, large-scale production of HMOs is generally based on microbial synthesis using metabolically engineered cell factories. Introduction of the specific glycosyltransferases is essential for the construction of HMO-producing engineered strains in which the HMO-producing glycosyltransferases are generally sugar nucleotide-dependent. Four types of glycosyltransferases have been used for typical glycosylation reactions to synthesize HMOs. Soluble expression, substrate specificity, and regioselectivity are common concerns of these glycosyltransferases in practical applications. Screening of specific glycosyltransferases is an important research topic to solve these problems. Molecular modification has also been performed to enhance the catalytic activity of various HMO-producing glycosyltransferases and to improve the substrate specificity and regioselectivity. In this article, various sugar nucleotide-dependent glycosyltransferases for HMO synthesis were overviewed, common concerns of these glycosyltransferases were described, and the future perspectives of glycosyltransferase-related studies were provided.

Biosynthesis of Human Milk Oligosaccharides: Enzyme Cascade and Metabolic Engineering Approaches

Human milk oligosaccharides (HMOs) have unique beneficial effects for infants and are considered as the new gold standard for premium infant formula. They are a collection of unconjugated glycans, and more than 200 distinct structures have been identified. Generally, HMOs are enzymatically produced by elongation and/or modification from lactose via stepwise glycosylation. Each glycosylation requires a specific glycosyltransferase (GT) and the corresponding nucleotide sugar donor. In this review, the typical HMO-producing GTs and the one-pot multienzyme modules for generating various nucleotide sugar donors are introduced, the principles for designing the enzyme cascade routes for HMO synthesis are described, and the important metabolic engineering strategies for mass production of HMOs are also reviewed. In addition, the future research directions in biotechnological production of HMOs were prospected.

Efficient production of lacto-N-fucopentaose III in engineered Escherichia coli using α1,3-fucosyltransferase from Parabacteroides goldsteinii

Lacto-N-fucopentaose III (LNFP III) is a human milk oligosaccharide (HMO) with potential health benefits in infants, including in immune development and modulation of the intestinal environment. Low-cost fermentative production of various HMOs from lactose by engineered Escherichia coli has attracted attention, but few reports have investigated long-chain HMO production, such as of the pentasaccharide LNFP III. LNFP III is synthesized by α1,3-fucosyltransfer reaction to the glucosamine (GlcNAc) moiety in the lacto-N-neotetraose (LNnT) skeleton by α1,3-fucosyltransferase (α1,3-FucT). However, the known α1,3-FucTs also transfer fucose to the reducing terminal glucose moiety of LNnT or the starting material lactose, resulting in various byproducts. Here, we found a useful α1,3-FucT from Parabacteroides goldsteinii (PgsFucT), which is only reactive for GlcNAc in the N-acetyllactosamine (LacNAc) skeleton in vivo. On the basis of sequence alignment with a FucT of known structure, we also generated α1,3-FucT variants with altered reactivity for LacNAc or lactose. An E. coli strain heterologously expressing PgsFucT accumulated 3.84 g/L of LNFP III after 48 h of culture in a 3-L jar-fermenter. The amounts of various byproduct sugars were remarkably decreased compared with a strain expressing the previously characterized α1,3-fucT from Bacteroides fragilis.

Biosynthesis of human milk oligosaccharides via metabolic engineering approaches: current advances and challenges

Human milk oligosaccharides (HMOs) are structurally complex unconjugated glycans that are the third largest solid component in human milk. HMOs have drawn increasing attention because of their beneficial effects to infant health. Of the more than 200 HMOs, only less than 10 have been used in medical or food industries. Although HMO research has been becoming increasingly intensive and booming, the limited availability of HMOs still cannot meet the demand in health effect research and large-scale application. Therefore, efficient synthetic approaches and strategies for HMO production are urgently needed. The goal of this review is to highlight recent advances in microbial cell factory development for HMO biosynthesis. Key challenges in representative HMO production are also highlighted. The further perspectives in general HMO biosynthesis are discussed.

Pathway Optimization and Uridine 5'-Triphosphate Regeneration for Enhancing Lacto-N-Tetraose Biosynthesis in Engineered Escherichia coli

Recently, human milk oligosaccharides (HMOs) have attracted increasing attention and display great commercial importance, especially for the infant formula industry. Lacto-N-tetraose (LNT) is an important neutral HMO commercially added in infant formula and a core structure for synthesizing complex HMOs. Previously, a novel LNT-generating β-1,3-galactosyltransferase from Pseudogulbenkiania ferrooxidans was identified and used for construction of an LNT-producing engineered Escherichia coli. In this work, LNT biosynthesis was further enhanced by pathway optimization and uridine 5'-triphosphate (UTP) regeneration. The main strategies included genomic integration of UDP-glucose 4-epimerase-encoding gene, fine-tuning of the LNT pathway-related genes, blocking of competitive pathways related to UDP-galactose, and overexpression of UTP supply related genes. The maximal LNT titer reached 6.16 and 57.5 g/L by shake-flask and fed-batch fermentation, respectively.

Chemoenzymatic Synthesis of Asymmetrically Branched Human Milk Oligosaccharide Lacto-N-Hexaose

We herein reported the first chemoenzymatic synthesis of lacto-N-hexaose (LNH) by combining chemical carbohydrate synthesis with a selectively enzymatic glycosylation strategy. A tetrasaccharide core structure GlcNH₂β1→3 (GlcNAcβ1→6) Galβ1→4Glc, a key precursor for subsequent enzymatic glycan extension toward asymmetrically branched human milk oligosaccharides, was synthesized in this work. When the order of galactosyltransferase-catalyzed reactions was appropriately arranged, the β1,4-galactosyl and β1,3-galactosyl moieties could be sequentially assembled on the C6-arm and C3-arm of the tetrasaccharide, respectively, to achieve an efficient LNH synthesis. Lacto-N-neotetraose (LNnH), another common human milk oligosaccharide, was also synthesized en route to the target LNH.

Occurrence, functional properties, and preparation of 3-fucosyllactose, one of the smallest human milk oligosaccharides

Human milk oligosaccharides (HMOs) are receiving wide interest and high attention due to their health benefits, especially for newborns. The HMOs-fortified products are expected to mimic human milk not only in the kinds of added oligosaccharides components but also the appropriate proportion between these components, and further provide the nutrition and physiological effects of human milk to newborns as closely as possible. In comparison to intensively studied 2'-fucosyllactose (2'-FL), 3-fucosyllactose (3-FL) has less attention in almost all respects. Nerveless, 3-FL naturally occurs in breast milk and increases roughly over the course of lactation with a nonnegligible content, and plays an irreplaceable role in human milk and delivers functional properties to newborns. According to the safety evaluation, 3-FL shows no acute oral toxicity, genetic toxicity, and subchronic toxicity. It has been approved as generally recognized as safe (GRAS). Biological production of 3-FL can be realized by enzymatic and cell factory approaches. The α1,3- or α1,3/4-fucosyltransferase is the key enzyme for 3-FL biosynthesis. Various metabolic engineering strategies have been applied to enhance 3-FL yield using cell factory approach. In conclusion, this review gives an overview of the recent scientific literatures regarding occurrence, bioactive properties, safety evaluation, and biotechnological preparation of 3-FL.

Functional glyco-metagenomics elucidates the role of glycan-related genes in environments

BACKGROUND

Glycan-related genes play a fundamental role in various processes for energy acquisition and homeostasis maintenance while adapting to the environment in which the organism exists; however, their role in the microbiome in the environment is unclear.

METHODS

Sequence alignment was performed between known glycan-related genes and complete genomes of microorganisms, and optimal parameters for identifying glycan-related genes were determined based on the alignments. Using the constructed scheme (> 90% of identity and > 25 aa of alignment length), glycan-related genes in various environments were identified from 198 different metagenome data.

RESULTS

As a result, we identified 86.73 million glycan-related genes from the metagenome data. Among the 12 environments classified in this study, the percentage of glycan-related genes was high in the human-associated environment, suggesting that these environments utilize glycan metabolism better than other environments. On the other hand, the relative abundances of both glycoside hydrolases and glycosyltransferases surprisingly had a coverage of over 80% in all the environments. These glycoside hydrolases and glycosyltransferases were classified into two groups of (1) general enzyme families identified in various environments and (2) specific enzymes found only in certain environments. The general enzyme families were mostly from genes involved in monosaccharide metabolism, and most of the specific enzymes were polysaccharide degrading enzymes.

CONCLUSION

These findings suggest that environmental microorganisms could change the composition of their glycan-related genes to adapt the processes involved in acquiring energy from glycans in their environments. Our functional glyco-metagenomics approach has made it possible to clarify the relationship between the environment and genes from the perspective of carbohydrates, and the existence of glycan-related genes that exist specifically in the environment.

Enzymatic modular assembly of hybrid Lewis antigens

The enzymatic synthesis of hybrid Lewis antigens including KH-1 (Lewis y-Lewis x-Lactose, Ley-Lex-Lac), Lewis a-Lewis x-Lactose (Lea-Lex-Lac), and Lewis b-Lewis x-Lactose (Leb-Lex-Lac) has been achieved using a facile enzymatic modular assembly strategy. Starting from a readily available tetrasaccharide, 3 complex hybrid Lewis antigens were achieved in over 40% total yields in less than 5 linear steps of sequential enzymatic glycosylation using 6 enzyme modules. The regio-selective fucosylation was achieved by simply controlling the donor-acceptor ratio. This strategy provides an easy access to these biologically important complex hybrid Lewis antigens at preparative scales.

Physiological effects, biosynthesis, and derivatization of key human milk tetrasaccharides, lacto-N-tetraose, and lacto-N-neotetraose

Human milk oligosaccharides (HMOs) have recently attracted ever-increasing interest because of their versatile physiological functions. In HMOs, two tetrasaccharides, lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT), constitute the essential components, each accounting 6% (w/w) of total HMOs. Also, they serve as core structures for fucosylation and sialylation, generating functional derivatives and elongation generating longer chains of core structures. LNT, LNnT, and their fucosylated and/or sialylated derivatives account for more than 30% (w/w) of total HMOs. For derivatization, LNT and LNnT can be modified into a series of complex fucosylated and/or sialylated HMOs by transferring fucose residues at α1,2-, α1,3-, and α1,3/4-linkage and/or sialic acid residues at α2,3- and α2,6-linkage. Such structural diversity allows these HMOs to possess great commercial value and an application potential in the food and pharmaceutical industries. In this review, we first elaborate the physiological functions of these tetrasaccharides and derivatives. Next, we extensively review recent developments in the biosynthesis of LNT, LNnT, and their derivatives in vitro and in vivo by employing advanced enzymatic reaction systems and metabolic engineering strategies. Finally, future perspectives in the synthesis of these HMOs using enzymatic and metabolic engineering approaches are presented.

Synthesis of N-Acetyllactosamine and N-Acetyllactosamine-Based Bioactives

N-Acetyllactosamine (LacNAc) or more specifically β-d-galactopyranosyl-1,4-N-acetyl-d-glucosamine is a unique acyl-amino sugar and a key structural unit in human milk oligosaccharides, an antigen component of many glycoproteins, and an antiviral active component for the development of effective drugs against viruses. LacNAc is useful itself and as a basic building block for producing various bioactive oligosaccharides, notably because this synthesis may be used to add value to dairy lactose. Despite a significant amount of information in the literature on the benefits, structures, and types of different LacNAc-derived oligosaccharides, knowledge about their effective synthesis for large-scale production is still in its infancy. This work provides a comprehensive analysis of existing production strategies for LacNAc and important LacNAc-based structures, including sialylated LacNAc as well as poly- and oligo-LacNAc. We conclude that direct extraction from milk is too complex, while chemical synthesis is also impractical at an industrial scale. Microbial routes have application when multiple step reactions are needed, but the major route to large-scale biochemical production will likely lie with enzymatic routes, particularly those using β-galactosidases (for LacNAc synthesis), sialidases (for sialylated LacNAc synthesis), and β-N-acetylhexosaminidases (for oligo-LacNAc synthesis). Glycosyltransferases, especially for the biosynthesis of extended complex LacNAc structures, could also play a major role in the future. In these cases, immobilization of the enzyme can increase stability and reduce cost. Processing parameters, such as substrate concentration and purity, acceptor/donor ratio, water activity, and temperature, can affect product selectivity and yield. More work is needed to optimize these reaction parameters and in the development of robust, thermally stable enzymes to facilitate commercial production of these important bioactive substances.

Biological strategies for oligo/polysaccharide synthesis: biocatalyst and microbial cell factory

Oligosaccharides and polysaccharides constitute the principal components of carbohydrates, which are important biomacromolecules that demonstrate considerable bioactivities. However, the variety and structural complexity of oligo/polysaccharides represent a major challenge for biological and structural explorations. To access structurally defined oligo/polysaccharides, biological strategies using glycoenzyme biocatalysts have shown remarkable synthetic potential attributed to their regioselectivity and stereoselectivity that allow mild, structurally controlled reaction without addition of protecting groups necessary in chemical strategies. This review summarizes recent biotechnological approaches of oligo/polysaccharide synthesis, which mainly includes in vitro enzymatic synthesis and cell factory synthesis. We have discussed the important factors involved in the production of nucleotide sugars. Furthermore, the strategies established in the cell factory and enzymatic syntheses are summarized, and we have highlighted concepts like metabolic flux rebuilding and regulation, enzyme engineering, and route design as important strategies. The research challenges and prospects are also outlined and discussed.

Effective Separation of Human Milk Glycosides using Carbon Dioxide Supercritical Fluid Chromatography

Carbohydrate purification remains problematic due to the intrinsic diversity of structural isomers present in nature. Although liquid chromatography-based techniques are suitable for analyzing or preparing most glycan structures acquired either from natural sources or through chemical or enzymatic synthesis, the separation of regioisomers or linkage isomers with a clear resolution remains challenging. Herein, a carbon dioxide supercritical fluid chromatography (SFC) method was devised to resolve 18 human milk glycosides: oligomers (disaccharides to hexasaccharides), fucosylated regioisomers (lacto-N-fucopentaose I, III, and V; lacto-N-neofucopentaose V; lacto-N-difucohexaose III; blood group H₁ antigen; and TF-LNnT), and connectivity isomers (lacto-N-tetraose/lacto-N-neotetraose and para-lacto-N-hexaose/para-lacto-N-neohexaose/type-1 hexasaccharide). The analysis of these glycosides represents a major limitation associated with conventional carbohydrate analysis. The unprecedented resolution achieved by the SFC method indicates the suitability of this key technology for revealing complex human milk glycomes.

Recent progress in synthesis of carbohydrates with sugar nucleotide-dependent glycosyltransferases

Sugar nucleotide-dependent glycosyltransferases (GTs) are key enzymes that catalyze the formation of glycosidic bonds in nature. They have been increasingly applied in the synthesis of complex carbohydrates and glycoconjugates with or without in situ generation of sugar nucleotides. Human GTs are becoming more accessible and new bacterial GTs have been identified and characterized. An increasing number of crystal structures elucidated for GTs from mammalian and bacterial sources facilitate structure-based design of mutants as improved catalysts for synthesis. Automated platforms have also been developed for chemoenzymatic synthesis of carbohydrates. Recent progress in applying sugar nucleotide-dependent GTs in enzymatic and chemoenzymatic synthesis of mammalian glycans and glycoconjugates, bacterial surface glycans, and glycosylated natural products from bacteria and plants are reviewed.

Enzymatic modular synthesis and microarray assay of poly-N-acetyllactosamine derivatives

A facile enzymatic modular assembly strategy for the preparative-scale synthesis of poly-N-acetyllactosamine (poly-LacNAc) glycans with varied lengths and designed sialylation and/or fucosylation patterns is described. These glycans were printed as a microarray to investigate their interactions with a panel of glycan binding proteins (GBPs). Binding affinities revealed that the avidity of GBPs could be largely affected by the length and the patterns of sialylation and fucosylation.