Broadening the synthetic potential of disaccharide phosphorylases through enzyme engineering

Engineered production of bioactive polyphenolic O-glycosides

Polyphenolic compounds (such as quercetin and resveratrol) possess potential medicinal values due to their various bioactivities, but poor water solubility hinders their health benefits to humankind. Glycosylation is a well-known post-modification method to biosynthesize natural product glycosides with improved hydrophilicity. Glycosylation has profound effects on decreasing toxicity, increasing bioavailability and stability, together with changing bioactivity of polyphenolic compounds. Therefore, polyphenolic glycosides can be used as food additives, therapeutics, and nutraceuticals. Engineered biosynthesis provides an environmentally friendly and cost-effective approach to generate polyphenolic glycosides through the use of various glycosyltransferases (GTs) and sugar biosynthetic enzymes. GTs transfer the sugar moieties from nucleotide-activated diphosphate sugar (NDP-sugar) donors to sugar acceptors such as polyphenolic compounds. In this review, we systematically review and summarize the representative polyphenolic O-glycosides with various bioactivities and their engineered biosynthesis in microbes with different biotechnological strategies. We also review the major routes towards NDP-sugar formation in microbes, which is significant for producing unusual or novel glycosides. Finally, we discuss the trends in NDP-sugar based glycosylation research to promote the development of prodrugs that positively impact human health and wellness.

Disaccharide phosphorylases: Structure, catalytic mechanisms and directed evolution

Disaccharide phosphorylases (DSPs) are carbohydrate-active enzymes with outstanding potential for the biocatalytic conversion of common table sugar into products with attractive properties. They are modular enzymes that form active homo-oligomers. From a mechanistic as well as a structural point of view, they are similar to glycoside hydrolases or glycosyltransferases. As the majority of DSPs show strict stereo- and regiospecificities, these enzymes were used to synthesize specific disaccharides. Currently, protein engineering of DSPs is pursued in different laboratories to broaden the donor and acceptor substrate specificities or improve the industrial particularity of naturally existing enzymes, to eventually generate a toolbox of new catalysts for glycoside synthesis. Herein we review the characteristics and classifications of reported DSPs and the glycoside products that they have been used to synthesize.

Phosphorylase-catalyzed bottom-up synthesis of short-chain soluble cello-oligosaccharides and property-tunable cellulosic materials

Cellulose-based materials are produced industrially in countless varieties via top-down processing of natural lignocellulose substrates. By contrast, cellulosic materials are only rarely prepared via bottom up synthesis and oligomerization-induced self-assembly of cellulose chains. Building up a cellulose chain via precision polymerization is promising, however, for it offers tunability and control of the final chemical structure. Synthetic cellulose derivatives with programmable material properties might thus be obtained. Cellodextrin phosphorylase (CdP; EC 2.4.1.49) catalyzes iterative β-1,4-glycosylation from α-d-glucose 1-phosphate, with the ability to elongate a diversity of acceptor substrates, including cellobiose, d-glucose and a range of synthetic glycosides having non-sugar aglycons. Depending on the reaction conditions leading to different degrees of polymerization (DP), short-chain soluble cello-oligosaccharides (COS) or insoluble cellulosic materials are formed. Here, we review the characteristics of CdP as bio-catalyst for synthetic applications and show advances in the enzymatic production of COS and reducing end-modified, tailored cellulose materials. Recent studies reveal COS as interesting dietary fibers that could provide a selective prebiotic effect. The bottom-up synthesized celluloses involve chains of DP ≥ 9, as precipitated in solution, and they form ~5 nm thick sheet-like crystalline structures of cellulose allomorph II. Solvent conditions and aglycon structures can direct the cellulose chain self-assembly towards a range of material architectures, including hierarchically organized networks of nanoribbons, or nanorods as well as distorted nanosheets. Composite materials are also formed. The resulting materials can be useful as property-tunable hydrogels and feature site-specific introduction of functional and chemically reactive groups. Therefore, COS and cellulose obtained via bottom-up synthesis can expand cellulose applications towards product classes that are difficult to access via top-down processing of natural materials.

Engineering of cellobiose phosphorylase for the defined synthesis of cellotriose

Cellodextrins are non-digestible oligosaccharides that have attracted interest from the food industry as potential prebiotics. They are typically produced through the partial hydrolysis of cellulose, resulting in a complex mixture of oligosaccharides with a varying degree of polymerisation (DP). Here, we explore the defined synthesis of cellotriose as product since this oligosaccharide is believed to be the most potent prebiotic in the mixture. To that end, the cellobiose phosphorylase (CBP) from Cellulomonas uda and the cellodextrin phosphorylase (CDP) from Clostridium cellulosi were evaluated as biocatalysts, starting from cellobiose and α-d-glucose 1-phosphate as acceptor and donor substrate, respectively. The CDP enzyme was shown to rapidly elongate the chains towards higher DPs, even after extensive mutagenesis. In contrast, an optimised variant of CBP was found to convert cellobiose to cellotriose with a molar yield of 73%. The share of cellotriose within the final soluble cellodextrin mixture (DP2-5) was 82%, resulting in a cellotriose product with the highest purity reported to date. Interestingly, the reaction could even be initiated from glucose as acceptor substrate, which should further decrease the production costs.

Key points

• Cellobiose phosphorylase is engineered for the production of cellotriose.

• Cellotriose is synthesised with the highest purity and yield to date.

• Both cellobiose and glucose can be used as acceptor for cellotriose production.

Product solubility control in cellooligosaccharide production by coupled cellobiose and cellodextrin phosphorylase

Soluble cellodextrins (linear β‐1,4‐d‐gluco‐oligosaccharides) have interesting applications as ingredients for human and animal nutrition. Their bottom‐up synthesis from glucose is promising for bulk production, but to ensure a completely water‐soluble product via degree of polymerization (DP) control (DP ≤ 6) is challenging. Here, we show biocatalytic production of cellodextrins with DP centered at 3 to 6 (~96 wt.% of total product) using coupled cellobiose and cellodextrin phosphorylase. The cascade reaction, wherein glucose was elongated sequentially from α‐d‐glucose 1‐phosphate (αGlc1‐P), required optimization and control at two main points. First, kinetic and thermodynamic restrictions upon αGlc1‐P utilization (200 mM; 45°C, pH 7.0) were effectively overcome (53% → ≥90% conversion after 10 hrs of reaction) by in situ removal of the phosphate released via precipitation with Mg²⁺. Second, the product DP was controlled by the molar ratio of glucose/αGlc1‐P (∼0.25; 50 mM glucose) used in the reaction. In optimized conversion, soluble cellodextrins in a total product concentration of 36 g/L were obtained through efficient utilization of the substrates used (glucose: 98%; αGlc1‐P: ∼80%) after 1 hr of reaction. We also showed that, by keeping the glucose concentration low (i.e., 1–10 mM; 200 mM αGlc1‐P), the reaction was shifted completely towards insoluble product formation (DP ∼9–10). In summary, this study provides the basis for an efficient and product DP‐controlled biocatalytic synthesis of cellodextrins from expedient substrates.

Development and Application of a High-Throughput Functional Metagenomic Screen for Glycoside Phosphorylases

Glycoside phosphorylases (GPs) catalyze the reversible phosphorolysis of glycosidic bonds, releasing sugar 1-phosphates. To identify a greater range of these under-appreciated enzymes, we have developed a high-throughput functional screening method based on molybdenum blue formation. In a proof-of-principle screen focused on cellulose-degrading GPs we interrogated ∼23,000 large insert (fosmid) clones sourced from microbial communities inhabiting two separate environments and identified seven novel GPs from carbohydrate active enzyme family GH94 and one from GH149. Characterization identified cellobiose phosphorylases, cellodextrin phosphorylases, laminaribiose phosphorylases, and a β-1,3-glucan phosphorylase. To demonstrate the versatility of the screening method, varying substrate combinations were used to identify GP activity from families GH13, GH65, GH112, and GH130 in addition to GH94 and GH149. These pilot screen and substrate versatility results provide a screening paradigm platform for recovering diverse GPs from uncultivated microbial communities acting on different substrates with considerable potential to unravel previously unknown degradative pathways within microbiomes.

Harnessing glycoenzyme engineering for synthesis of bioactive oligosaccharides

Combined with chemical synthesis, the use of glycoenzyme biocatalysts has shown great synthetic potential over recent decades owing to their remarkable versatility in terms of substrates and regio- and stereoselectivity that allow structurally controlled synthesis of carbohydrates and glycoconjugates. Nonetheless, the lack of appropriate enzymatic tools with requisite properties in the natural diversity has hampered extensive exploration of enzyme-based synthetic routes to access relevant bioactive oligosaccharides, such as cell-surface glycans or prebiotics. With the remarkable progress in enzyme engineering, it has become possible to improve catalytic efficiency and physico-chemical properties of enzymes but also considerably extend the repertoire of accessible catalytic reactions and tailor novel substrate specificities. In this review, we intend to give a brief overview of the advantageous use of engineered glycoenzymes, sometimes in combination with chemical steps, for the synthesis of natural bioactive oligosaccharides or their precursors. The focus will be on examples resulting from the three main classes of glycoenzymes specialized in carbohydrate synthesis: glycosyltransferases, glycoside hydrolases and glycoside phosphorylases.

Rational design of an improved transglucosylase for production of the rare sugar nigerose

The sucrose phosphorylase from Bifidobacterium adolescentis (BaSP) can be used as a transglucosylase for the production of rare sugars. We designed variants of BaSP for the efficient synthesis of nigerose from sucrose and glucose, thereby adding to the inventory of rare sugars that can conveniently be produced from bulk sugars.

Glucansucrase Gtf180-ΔN of Lactobacillus reuteri 180: enzyme and reaction engineering for improved glycosylation of non-carbohydrate molecules

Glucansucrases have a broad acceptor substrate specificity and receive increased attention as biocatalysts for the glycosylation of small non-carbohydrate molecules using sucrose as donor substrate. However, the main glucansucrase-catalyzed reaction results in synthesis of α-glucan polysaccharides from sucrose, and this strongly impedes the efficient glycosylation of non-carbohydrate molecules and complicates downstream processing of glucosylated products. This paper reports that suppressing α-glucan synthesis by mutational engineering of the Gtf180-ΔN enzyme of Lactobacillus reuteri 180 results in the construction of more efficient glycosylation biocatalysts. Gtf180-ΔN mutants (L938F, L981A, and N1029M) with an impaired α-glucan synthesis displayed a substantial increase in monoglycosylation yields for several phenolic and alcoholic compounds. Kinetic analysis revealed that these mutants possess a higher affinity for the model acceptor substrate catechol but a lower affinity for its mono-α-d-glucoside product, explaining the improved monoglycosylation yields. Analysis of the available high resolution 3D crystal structure of the Gtf180-ΔN protein provided a clear understanding of how mutagenesis of residues L938, L981, and N1029 impaired α-glucan synthesis, thus yielding mutants with an improved glycosylation potential.

Converting bulk sugars into prebiotics: semi-rational design of a transglucosylase with controlled selectivity

Bad sugars in, good sugar out: an engineered sucrose phosphorylase for the production of kojibiose from sucrose and glucose.

Enzymatic Glycosylation of Phenolic Antioxidants: Phosphorylase-Mediated Synthesis and Characterization

Although numerous biologically active molecules exist as glycosides in nature, information on the activity, stability, and solubility of glycosylated antioxidants is rather limited to date. In this work, a wide variety of antioxidants were glycosylated using different phosphorylase enzymes. The resulting antioxidant library, containing α/β-glucosides, different regioisomers, cellobiosides, and cellotriosides, was then characterized. Glycosylation was found to significantly increase the solubility and stability of all evaluated compounds. Despite decreased radical-scavenging abilities, most glycosides were identified to be potent antioxidants, outperforming the commonly used 2,6-bis(1,1-dimethylethyl)-4-methylphenol (BHT). Moreover, the point of attachment, the anomeric configuration, and the glycosidic chain length were found to influence the properties of these phenolic glycosides.

Engineering the specificity of trehalose phosphorylase as a general strategy for the production of glycosyl phosphates

A two-step process is reported for the anomeric phosphorylation of galactose, using trehalose phosphorylase as biocatalyst. The monosaccharide enters this process as acceptor but can subsequently be released from the donor side, thanks to the non-reducing nature of the disaccharide intermediate. A key development was the creation of an optimized enzyme variant that displays a strict specificity (99%) for β-galactose 1-phosphate as product.

Biotechnological advances in UDP-sugar based glycosylation of small molecules

Glycosylation of small molecules like specialized (secondary) metabolites has a profound impact on their solubility, stability or bioactivity, making glycosides attractive compounds as food additives, therapeutics or nutraceuticals. The subsequently growing market demand has fuelled the development of various biotechnological processes, which can be divided in the in vitro (using enzymes) or in vivo (using whole cells) production of glycosides. In this context, uridine glycosyltransferases (UGTs) have emerged as promising catalysts for the regio- and stereoselective glycosylation of various small molecules, hereby using uridine diphosphate (UDP) sugars as activated glycosyldonors. This review gives an extensive overview of the recently developed in vivo production processes using UGTs and discusses the major routes towards UDP-sugar formation. Furthermore, the use of interconverting enzymes and glycorandomization is highlighted for the production of unusual or new-to-nature glycosides. Finally, the technological challenges and future trends in UDP-sugar based glycosylation are critically evaluated and summarized.

Role of glycoside phosphorylases in mannose foraging by human gut bacteria

To metabolize both dietary fiber constituent carbohydrates and host glycans lining the intestinal epithelium, gut bacteria produce a wide range of carbohydrate-active enzymes, of which glycoside hydrolases are the main components. In this study, we describe the ability of phosphorylases to participate in the breakdown of human N-glycans, from an analysis of the substrate specificity of UhgbMP, a mannoside phosphorylase of the GH130 protein family discovered by functional metagenomics. UhgbMP is found to phosphorolyze β-D-Manp-1,4-β-D-GlcpNAc-1,4-D-GlcpNAc and is also a highly efficient enzyme to catalyze the synthesis of this precious N-glycan core oligosaccharide by reverse phosphorolysis. Analysis of sequence conservation within family GH130, mapped on a three-dimensional model of UhgbMP and supported by site-directed mutagenesis results, revealed two GH130 subfamilies and allowed the identification of key residues responsible for catalysis and substrate specificity. The analysis of the genomic context of 65 known GH130 sequences belonging to human gut bacteria indicates that the enzymes of the GH130_1 subfamily would be involved in mannan catabolism, whereas the enzymes belonging to the GH130_2 subfamily would rather work in synergy with glycoside hydrolases of the GH92 and GH18 families in the breakdown of N-glycans. The use of GH130 inhibitors as therapeutic agents or functional foods could thus be considered as an innovative strategy to inhibit N-glycan degradation, with the ultimate goal of protecting, or restoring, the epithelial barrier.

Structure of novel enzyme in mannan biodegradation process 4-O-β-D-mannosyl-D-glucose phosphorylase MGP

The crystal structure of a novel component of the mannan biodegradation system, 4-O-β-D-mannosyl-D-glucose phosphorylase (MGP), was determined to a 1.68-Å resolution. The structure of the enzyme revealed a unique homohexameric structure, which was formed by using two helices attached to the N-terminus and C-terminus as a tab for sticking between subunits. The structures of MGP complexes with genuine substrates, 4-O-β-D-mannosyl-D-glucose and phosphate, and the product D-mannose-1-phosphate were also determined. The complex structures revealed that the invariant residue Asp131, which is supposed to be the general acid/base, did not exist close to the glycosidic Glc-O4 atom, which should be protonated in the catalytic reaction. Also, no solvent molecule that might mediate a proton transfer from Asp131 was observed in the substrate complex structure, suggesting that the catalytic mechanism of MGP is different from those of known disaccharide phosphorylases.

Engineering the acceptor specificity of trehalose phosphorylase for the production of trehalose analogs

Trehalose (α-D-glucopyranosyl-(1,1)-α-D-glucopyranoside) is widely used in the food industry, thanks to its protective effect against freezing and dehydration. Analogs of trehalose have the additional benefit that they are not digested and thus do not contribute to our caloric intake. Such trehalose analogs can be produced with the enzyme trehalose phosphorylase, when it is applied in the reverse, synthetic mode. Despite the enzyme's broad acceptor specificity, its catalytic efficiency for alternative monosaccharides is much lower than for glucose. For galactose, this difference is shown here to be caused by a lower K(m) whereas the k(cat) for both substrates is equal. Consequently, increasing the affinity was attempted by enzyme engineering of the trehalose phosphorylase from Thermoanaerobacter brockii, using both semirational and random mutagenesis. While a semirational approach proved unsuccessful, high-throughput screening of an error-prone PCR library resulted in the discovery of three beneficial mutations that lowered K(m) two- to three-fold. In addition, it was found that mutation of these positions also leads to an improved catalytic efficiency for mannose and fructose, suggesting their involvement in acceptor promiscuity. Combining the beneficial mutations did not further improve the affinity, and even resulted in a decreased catalytic activity and thermostability. Therefore, enzyme variant R448S is proposed as new biocatalyst for the industrial production of lactotrehalose (α-D-glucopyranosyl-(1,1)-α-D-galactopyranoside).

3-O-α-D-glucopyranosyl-L-rhamnose phosphorylase from Clostridium phytofermentans

We found an unreported activity of phosphorylase catalyzed by a protein (Cphy1019) belonging to glycoside hydrolase family 65 (GH65) from Clostridium phytofermentans. The recombinant Cphy1019 produced in Escherichia coli did not phosphorolyze α-linked glucobioses, such as trehalose (α1-α1), kojibiose (α1-2), nigerose (α1-3), and maltose (α1-4), which are typical substrates for GH65 enzymes. In reverse phosphorolysis, Cphy1019 utilized only l-rhamnose as the acceptor among various sugars examined with β-d-glucose 1-phosphate as the donor. The reaction product was determined to be 3-O-α-d-glucopyranosyl-l-rhamnose, indicating strict α1-3 regioselectivity. We propose 3-O-α-d-glucopyranosyl-l-rhamnose: phosphate β-d-glucosyltransferase as the systematic name and 3-O-α-d-glucopyranosyl-l-rhamnose phosphorylase as the short name for this novel GH65 phosphorylase.