Combination of UDP‐Glc(NAc) 4′‐Epimerase and Galactose Oxidase in a One‐Pot Synthesis of Biotinylated Nucleotide Sugars

The enzymatic epimerization of uridine 5′‐diphospho‐α‐D ‐glucose (UDP‐Glc, 1 ) and uridine 5′‐diphospho‐N‐acetyl‐α‐D ‐glucosamine (UDP‐GlcNAc, 2 ) and the subsequent oxidation of uridine 5′‐diphospho‐α‐D ‐galactose (UDP‐Gal, 3 ) and uridine 5′‐diphospho‐N‐acetyl‐α‐D ‐galactosamine (UDP‐GalNAc, 4 ) were combined with chemical biotinylation with biotin‐ε‐amidocaproylhydrazide in a one‐pot synthesis. Analysis by CE and NMR revealed a mixture (1.0:1.4) of the biotinylated nucleotide sugars uridine 5′‐diphospho‐6‐biotin‐ε‐amidocaproylhydrazino‐α‐D ‐galactose (UDP‐6‐biotinyl‐Gal, 7) and uridine 5′‐diphospho‐6‐biotin‐ε‐amidocaproylhydrazino‐α‐D ‐glucose (UDP‐6‐biotinyl‐Glc, 9 ), respectively, in a reaction started with 1 . One product, uridine 5′‐diphospho‐6‐biotin‐ε‐amidocaproylhydrazino‐N‐acetyl‐α‐D ‐galactosamine (UDP‐6‐biotinyl‐GalNAc, 8) was formed when the reaction was initiated with 2 . It could be demonstrated for the first time that a UDP‐Glc(NAc) 4′‐epimerase (Gne from Campylobacter jejuni) and galactose oxidase from Dactylium dendroides can be used simultaneously in enzymatic catalysis. This is of particular interest since the coaction of an enzyme demanding reductive conditions and an oxygen‐dependent oxidase is unexpected.     

Thiogalactopyranosides are resistant to hydrolysis by α-galactosidases

Fluorescently tagged glycosides containing terminal α(1→3) and α(1→4)-linked thiogalactopyranosides have been prepared and tested for resistance to hydrolysis by α-galactosidases. Eight fluorescent glycosides containing either galactose or 5-thiogalactose as the terminal sugar were enzymatically synthesized using galactosyltransferases, with lactosyl glycosides as acceptors and UDP-galactose or UDP-5'-thiogalactose, respectively, as donors. The glycosides were incubated with human α-galactosidase A (CAZy family GH27, a retaining glycosidase), Bacteroides fragilis α-1,3-galactosidase (GH110, an inverting glycosidase), or homogenates of MCF-7 human breast cancer cells or NG108-15 rat glioma cells. Substrate hydrolysis was monitored by capillary electrophoresis with fluorescence detection. All compounds containing terminal O-galactose were readily degraded. Their 5-thiogalactose counterparts were resistant to hydrolysis by human α-galactosidase A and the enzymes present in the cell extracts. B. fragilis α-1,3-galactosidase hydrolyzed both thio- and O-galactoside substrates; however, the thiogalactosides were hydrolyzed at only 1-3 % of the rate of O-galactosides. The hydrolytic resistance of 5-thiogalactose was also confirmed by an in vivo study using cells in culture. The results suggest that 5-thiogalactosides may be useful tools for the study of anabolic pathways in cell extracts or in single cells.     

Azide‐ and Alkyne‐Bearing Metabolic Chemical Reporters of Glycosylation Show Structure‐Dependent Feedback Inhibition of the Hexosamine Biosynthetic Pathway

Metabolic chemical reporters (MCRs) of protein glycosylation are analogues of natural monosaccharides that bear reactive groups, like azides and alkynes. When they are added to living cells and organisms, these small molecules are biosynthetically transformed into nucleotide donor sugars and then used by glycosyltransferases to modify proteins. Subsequent installation of tags by bioorthogonal chemistries can then enable the visualization and enrichment of these glycoproteins. Although this two‐step procedure is powerful, the use of MCRs has the potential to change the endogenous production of the natural repertoire of donor sugars. A major route for the generation of these glycosyltransferase substrates is the hexosamine biosynthetic pathway (HBP), which results in uridine diphosphate N‐acetylglucosamine (UDP‐GlcNAc). Interestingly, the rate‐determining enzyme of the HBP, glutamine fructose‐6‐phosphate amidotransferase (GFAT), is feedback inhibited by UDP‐GlcNAc. This raises the possibility that a build‐up of UDP‐MCRs would block the biosynthesis of UDP‐GlcNAc, resulting in off target effects. Here, we directly test this possibility with recombinant human GFAT and a small panel of synthetic UDP‐MCRs. We find that MCRs with larger substitutions at the N‐acetyl position do not inhibit GFAT, whereas those with modifications of the 2‐ or 6‐hydroxy group do. These results further illuminate the considerations that should be applied to the use of MCRs.     

Biosynthesis of glycolipids: Incorporation of N-acetyl galactosamine by a rat brain particulate preparation

A mixture of UDP-(N-acetyl)glucosamine-1¹⁴C and UDP-(N-acetyl)galactosamine-1¹⁴C (7∶3) served as a substrate to demonstrate in young rat brain tissue the presence of enzymes which catalyzes the reactions: UDP-glcNAc⇌UDP-galNAc (E.C.5.1.3) and UDP-galNAc+ gal-glc-cer→ galNAc-gal-glc-cer+UDP. The glycolipid acceptor specificity was examined and preliminary kinetic data were obtained for the UDP-(N-acetyl)galactosamine: gal-glc-ceramide N-acetyl galactosamine transferase. The products of the reaction were identified. The relationship of this reaction to ganglioside biosynthesis is discussed. A preliminary report of this work has been presented orally at the Federation of American Societies for Experimental Biology in 1966 (41).     

Impact of N-Terminal Tags on De Novo Vimentin Intermediate Filament Assembly

Vimentin, a type III intermediate filament protein, is found in most cells along with microfilaments and microtubules. It has been shown that the head domain folds back to associate with the rod domain and this association is essential for filament assembly. The N-terminally tagged vimentin has been widely used to label the cytoskeleton in live cell imaging. Although there is previous evidence that EGFP tagged vimentin fails to form filaments but is able to integrate into a pre-existing network, no study has systematically investigated or established a molecular basis for this observation. To determine whether a tag would affect de novo filament assembly, we used vimentin fused at the N-terminus with two different sized tags, AcGFP (239 residues, 27 kDa) and 3 × FLAG (22 residues; 2.4 kDa) to assemble into filaments in two vimentin-deficient epithelial cells, MCF-7 and A431. We showed that regardless of tag size, N-terminally tagged vimentin aggregated into globules with a significant proportion co-aligning with β-catenin at cell–cell junctions. However, the tagged vimentin aggregates could form filaments upon adding untagged vimentin at a ratio of 1:1 or when introduced into cells containing pre-existing filaments. The resultant filament network containing a mixture of tagged and untagged vimentin was less stable compared to that formed by only untagged vimentin. The data suggest that placing a tag at the N-terminus may create steric hinderance in case of a large tag (AcGFP) or electrostatic repulsion in case of highly charged tag (3 × FLAG) perhaps inducing a conformational change, which deleteriously affects the association between head and rod domains. Taken together our results shows that a free N-terminus is essential for filament assembly as N-terminally tagged vimentin is not only incapable of forming filaments, but it also destabilises when integrated into a pre-existing network.     

Production of Lewis x tetrasaccharides by metabolically engineered Escherichia coli

Two tetrasaccharides carrying the trisaccharidic Lewis x motif on a GlcNAc or a Gal residue were produced on the gram-scale by high-cell-density cultures of metabolically engineered Escherichia coli strains that overexpressed the Helicobacter pylori futA gene for alpha-3 fucosyltransferase and the Neisseria meningitidis lgtB gene for beta-4 galactosyltransferase. The first compound Galbeta-4(Fucalpha-3)GlcNAcbeta-4GlcNAc was produced by glycosylation of chitinbiose, which was endogenously generated in the bacterial cytoplasm by the successive action of the rhizobial chitin-synthase NodC and the Bacillus circulans chitinase A1, whose genes were additionally expressed in the E. coli strain. The second compound, Galbeta-4(Fucalpha-3)GlcNAcbeta-3Gal, was produced from exogenously added Gal by a strain that was deficient in galactokinase activity and overexpressed the additional N. meningitidis lgtA gene for beta-3 N-acetylglucosaminyltransferase.     

N-Acetylneuraminic Acid Production in Escherichia coli Lacking N-Acetylglucosamine Catabolic Machinery

N-Acetylneuraminic acid (Neu5Ac, also referred to as sialic acid) is a nine-carbon sugar found on cell surfaces in higher animals. With key roles in inflammation, brain development, viral adhesion, and production of therapeutic glycoproteins, access to Neu5Ac is essential. We demonstrate that disruption of the N-acetylglucosamine (GlcNAc) degradation pathway by deletion of nagA and bypassing the GlmMU pathway for uridine diphosphate-GlcNAc production by expression of the Saccharomyces cerevisiae genes agm1 and uap1 improves the NeuCB-based direct cell culture approach to Neu5Ac production. The Escherichia coli strain BRL04 (nanT^?, nanA^?, and nagA^?) transformed with a polycistronic inducible expression vector encoding Agm1, Uap1, NeuB, and NeuC, cultivated in a shake-flask and fed with glycerol and GlcNAc produced Neu5Ac at 3.7 g/L (87% conversion from GlcNAc). At the 2 L bioreactor scale, production reached 7.3 g/L at a reduced conversion of 52%. These promising results suggest that this production strain is capable of generating Neu5Ac via high-density cultivation; it remains to be seen if careful control of GlcNAc feeding rate can be optimized to maximize yield.     

An Engineered Biocatalyst for the Synthesis of Glycoconjugates: Utilization of β1,3‐N‐Acetyl‐D‐glucosaminyltransferase from Streptococcus agalactiae Type Ia Expressed in Escherichia coli as a Fusion with Maltose‐Binding Protein

A fusion protein composed of β1,3‐N‐acetyl‐D ‐glucosaminyltransferase (β1,3‐GlcNAcT) from Streptococcus agalactiae type Ia and maltose‐binding protein (MBP) was produced in Escherichia coli as a soluble and highly active form. Although this fusion protein (MBP‐β1,3‐GlcNAcT) did not show any sugar‐elongation activity to some simple low‐molecular weight acceptor substrates such as galactose, Galβ(1→4)Glc (lactose), Galβ(1→4)GlcNAc (N‐acetyllactosamine), Galβ(1→4)GlcNAcβ(1→3)Galβ(1→4)Glc (lacto‐N‐tetraose), and Galβ(1→4)GlcβCer (lactosylceramide, LacCer), the multivalent glycopolymer having LacCer‐mimic branches (LacCer mimic polymer, LacCer primer) was found to be an excellent acceptor substrate for the introduction of a β‐GlcNAc residue at the O‐3 position of the non‐reducing galactose moiety by this engineered enzyme. Subsequently, the polymer having GlcNAcβ(1→3)Galβ(1→4)Glc was subjected to further enzymatic modifications by using recombinant β1,4‐D ‐galactosyltransferase (β1,4‐GalT), α2,3‐sialyltransferase (α2,3‐SiaT), α1,3‐L ‐fucosyltransferase (α1,3‐FucT), and ceramide glycanase (CGase) to afford a biologically important ganglioside; Neu5Aα(2→3)Galβ(1→4)[Fucα(1→3)]GlcNAcβ(1→3)Galβ(1→4)GlcCerα(IV3Neu5Acα,III3Fucα‐nLc4Cer) in 40% yield (4 steps). Interestingly, it was suggested that MBP‐β1,3‐GlcNAcT could also catalyze a glycosylation reaction of the LacCer mimic polymer with N‐acetyl‐D ‐galactosamine served from UDP‐GalNAc to afford a polymer carrying trisaccharide branches, GalNAcβ(1→3)Galβ(1→4)Glc. The versatility of the MBP‐β1,3‐GlcNAcT in the practical synthesis was preliminarily demonstrated by applying this fusion protein as an immobilized biocatalyst displayed on the amylose resin which is known as a solid support showing potent binding‐affinity with MBP.     

Keratanase II-catalyzed synthesis of keratan sulfate oligomers by using sugar oxazolines as transition-state analogue substrate monomers: a novel insight into the enzymatic catalysis mechanism

Keratan sulfate (KS) oligomers with well-defined structures were synthesized by keratanase II (KSase II)-catalyzed transglycosylation. N-Acetyllactosamine [Galbeta(1-->4)GlcNAc; LacNAc] oxazoline derivatives with sulfate groups at the C-6 (1 a) and both the C-6 and the C-6' (1 b) were prepared as transition-state analogue substrate monomers for KSase II. Monomer 1 a was effectively oligomerized by the enzyme under weak alkaline conditions, to give alternating 6-sulfated KS oligomers (2 a) in good yields, and with total control of regioselectivity and stereochemistry. KSase II also recognized 1 b, which provided fully 6-sulfated KS oligomers (2 b) in good yields under similar conditions. Nonsulfated LacNAc oxazoline was difficult to oligomerize enzymatically. These results imply that the catalysis mechanism of KSase II involves a sugar oxazolinium ion that requires the 6-sulfate group in the GlcNAc residue not only in hydrolysis of KS chains, but also in oligomerization of oxazoline monomers. This is the first report of KSase II-catalyzed transglycosylation to form beta(1-->3)-glycosidic bond through a substrate-assisted mechanism.     

A Tailor‐Made “Tag–Receptor” Affinity Pair for the Purification of Fusion Proteins

A novel affinity “tag–receptor” pair was developed as a generic platform for the purification of fusion proteins. The hexapeptide RKRKRK was selected as the affinity tag and fused to green fluorescent protein (GFP). The DNA fragments were designed, cloned in Pet‐21c expression vector and expressed in E. coli host as soluble protein. A solid‐phase combinatorial library based on the Ugi reaction was synthesized: 64 affinity ligands displaying complementary functionalities towards the designed tag. The library was screened by affinity chromatography in a 96‐well format for binding to the RKRKRK‐tagged GFP protein. Lead ligand A7C1 was selected for the purification of RKRKRK fusion proteins. The affinity pair RKRKRK‐tagged GFP with A7C1 emerged as a promising solution (K_a of 2.45×10⁵ M ^?1). The specificity of the ligand towards the tag was observed experimentally and theoretically through automated docking and molecular dynamics simulations.     

Efficient Chemoenzymatic Synthesis of N-Glycans with a β1,4-Galactosylated Bisecting GlcNAc Motif

In human serum immunoglobulin G (IgG), a rare modification of biantennary complex N-glycans lead to a β1,4-galactosylated bisecting GlcNAc branch. We found that the bisecting GlcNAc on a biantennary core-fucosylated N-glycan was enzymatically galactosylated under stringent reaction conditions. Further optimizations led to an efficient enzymatic approach to this particular modification for biantennary substrates. Notably, tri- and tetra-antennary complex N-glycans were not converted by bovine galactosyltransferase. An N-glycan with a galactosylated bisecting GlcNAc was linked to a lanthanide binding tag. The pseudo-contact shifts (PCS) obtained from the corresponding Dy-complex were used to calculate the conformational preferences of the rare N-glycan. Besides two extended conformations only a single folded conformation was found.     

β‐Cyclodextrin Improves Solubility and Enzymatic C‐Glucosylation of the Flavonoid Phloretin

Nothofagin is a prominent bioactive ingredient of rooibos tea. We recently reported its synthesis through a glucosyltransferase cascade reaction involving 3′‐C‐β‐D ‐glucosylation of the dihydrochalcone phloretin from uridine 5′‐diphosphate (UDP)‐glucose and in situ formation of UDP‐glucose from sucrose and catalytic amounts of UDP. Here we show that the limitation in process efficiency caused by the vanishingly low water solubility of phloretin – a major problem for biocatalytic modifications of hydrophobic natural products in general – was overcome effectively using phloretin inclusion complexation with β‐cyclodextrin. Unlike operating in a two‐phase system containing uncomplexed insoluble phloretin or using organic cosolvents, the addition of β‐cyclodextrin inclusion complexes was well tolerated regarding enzyme activity and stability. Besides enhancing the effective phloretin concentration in water (∼0.2 mM) to about 50 mM , inclusion complexation offered the additional advantage of overcoming the complex inhibition/inactivation effect of the free/microaggregated dihydrochalcone acceptor. Thus oversaturated phloretin solution was transformed in a single batch reaction in excellent conversion (99% in solution; 88% overall) and isolated yield (78%; 17.0 g L ⁻¹). The UDP‐glucose was regenerated up to ∼90 times and the nothofagin space‐time yield of 2.4 mM h⁻¹ presented an eight‐fold improvement compared to a reference reaction using 20% DMSO (dimethyl sulfoxide) and requiring controlled phloretin feed. We thus demonstrate the high potential of inclusion complexation by cyclodextrins for boosting the glycosylation of hydrophobic flavonoid‐like natural products.

     

Traceless Cleavage of Protein–Biotin Conjugates under Biologically Compatible Conditions

Biotinylation of amines is widely used to conjugate biomolecules, but either the resulting label is non‐removable or its removal leaves a tag on the molecule of interest, thus affecting downstream processes. We present here a set of reagents (RevAmines) that allow traceless, reversible biotinylation under biologically compatible, mild conditions. Release following avidin‐based capture is achieved through the cleavage of a (2‐(alkylsulfonyl)ethyl) carbamate linker under mild conditions (200 mm ammonium bicarbonate, pH 8, 16–24 h, room temperature) that regenerates the unmodified amine. The capture and release of biotinylated proteins and peptides from neutravidin, fluorescent labelling through reversible biotinylation at the cell surface and the selective enrichment of proteins from bacterial periplasm are demonstrated. The tags are easily prepared, stable and offer the potential for future application in proteomics, activity‐based protein profiling, affinity chromatography and bio‐molecule tagging and purification.     

Antibodies against Mucin‐Based Glycopeptides Affect Trypanosoma cruzi Cell Invasion and Tumor Cell Viability

This study describes the synthesis of glycopeptides NHAc[βGal]‐(Thr)₂‐[αGalNAc]‐(Thr)₂‐[αGlcNAc]‐(Thr)₂Gly‐OVA ( 1 ‐OVA) and NHAc[βGal‐αGalNAc]‐(Thr)₃‐[αLacNAc]‐(Thr)₃‐Gly‐OVA ( 2 ‐OVA) as mimetics of both T. cruzi and tumor mucin glycoproteins. These glycopeptides were obtained by solid‐phase synthesis, which involved the prior preparation of the protected glycosyl amino acids αGlcNAc‐ThrOH ( 3 ), αGalNAc‐ThrOH ( 4 ), βGal‐ThrOH ( 5 ), αLacNAc‐ThrOH ( 6 ), and βGal‐αGalNAc‐ThrOH ( 7 ) through glycosylation reactions. Immunizations of mice with glycopeptides 1 ‐OVA and 2 ‐OVA induced high antibody titers (1:16 000), as verified by ELISA tests, whereas flow cytometry assays showed the capacity of the obtained anti‐glycopeptides 1 ‐OVA and 2 ‐OVA antibodies to recognize both T. cruzi and MCF‐7 tumor cells. In addition, antisera induced by glycopeptides 1 ‐OVA and 2 ‐OVA were also able to inhibit T. cruzi fibroblast cell invasion (70 %) and to induce antibody‐mediated cellular cytotoxicity (ADCC) against MCF‐7 cells, with 50 % reduction of cell viability.     

Spatial Geometries of Self-Assembled Chitohexaose Monolayers Regulate Myoblast Fusion

Myoblast fusion into functionally-distinct myotubes to form in vitro skeletal muscle constructs under differentiation serum-free conditions still remains a challenge. Herein, we report that our microtopographical carbohydrate substrates composed of bioactive hexa-N-acetyl-d-glucosamine (GlcNAc6) modulated the efficiency of myoblast fusion without requiring horse serum or any differentiation medium during cell culture. Promotion of the differentiation of dissociated mononucleated skeletal myoblasts (C2C12; a mouse myoblast cell line) into robust myotubes was found only on GlcNAc6 micropatterns, whereas the myoblasts on control, non-patterned GlcNAc6 substrates or GlcNAc6-free patterns exhibited an undifferentiated form. We also examined the possible role of GlcNAc6 micropatterns with various widths in the behavior of C2C12 cells in early and late stages of myogenesis through mRNA expression of myosin heavy chain (MyHC) isoforms. The spontaneous contraction of myotubes was investigated via the regulation of glucose transporter type 4 (GLUT4), which is involved in stimulating glucose uptake during cellular contraction. Narrow patterns demonstrated enhanced glucose uptake rate and generated a fast-twitch muscle fiber type, whereas the slow-twitch muscle fiber type was dominant on wider patterns. Our findings indicated that GlcNAc6-mediated integrin interactions are responsible for guiding myoblast fusion forward along with myotube formation.     

Solubilizing Trityl-Type Tag To Synthesize Asx/Glx-Containing Peptides

A novel solubilizing tag system for Asp/Asn/Glu/Gln-containing peptides is described. In this method, an Asp/Glu[Dbz-Cys-NH₂]-containing peptide (Dbz: 3,4-diaminobenzoic acid) is first synthesized through fluorenylmethyloxycarbonyl (Fmoc) solid-phase peptide synthesis. The solubilizing moiety containing an oligo-Lys group is then attached to the peptide in hexafluoroisopropanol through a trityl anchor to afford a hydrophilic tagged peptide. To detach the solubilizing tag, the Dbz moiety of the tagged peptide is activated with NaNO₂, and the Asp/Asn/Glu/Gln-containing peptide is obtained through hydrolysis or ammonolysis. This synthetic approach proved to be compatible with native chemical ligation, and amyloid β-protein 1–42 was successfully synthesized by the solubilizing-tag-aided native chemical ligation–desulfurization method.     

Development of Trityl Group Anchored Solubilizing Tags for Peptide and Protein Synthesis

Recently, solubilizing tag methods (Trt-K and Trt-R method) were developed for the challenging synthesis of peptides/proteins by means of native chemical ligation. In this system, the solubilizing tag can be attached to the Cys side chain by simply mixing the tag-introducing reagent under acidic conditions. The tagged peptides/proteins exhibited high water solubility thanks to the introduction of redundant oligo-Lys/Arg. In the final reaction, the tag can be quickly and cleanly detached by a standard deprotection reaction with trifluoroacetic acid. Herein, the development and application of these methods are described.     

Glycosylation of Receptor Binding Domain of SARS-CoV-2 S-Protein Influences on Binding to Immobilized DNA Aptamers

Nucleic acid aptamers specific to S-protein and its receptor binding domain (RBD) of SARS-CoV-2 (severe acute respiratory syndrome-related coronavirus 2) virions are of high interest as potential inhibitors of viral infection and recognizing elements in biosensors. Development of specific therapy and biosensors is complicated by an emergence of new viral strains bearing amino acid substitutions and probable differences in glycosylation sites. Here, we studied affinity of a set of aptamers to two Wuhan-type RBD of S-protein expressed in Chinese hamster ovary cell line and Pichia pastoris that differ in glycosylation patterns. The expression system for the RBD protein has significant effects, both on values of dissociation constants and relative efficacy of the aptamer binding. We propose glycosylation of the RBD as the main force for observed differences. Moreover, affinity of a several aptamers was affected by a site of biotinylation. Thus, the robustness of modified aptamers toward new virus variants should be carefully tested.     

Engineering Glyco-Enzymes for Substrate Identification and Targeting

Glycoconjugates are assembled by the coordinate actions of glycosyltransferases, which add sugars, and glycosidases, which remove sugars. These glyco-enzymes comprise families of enzymes that catalyze the same reaction, making it difficult to identify the direct substrates of each isozyme. To solve this challenge, mutagenesis of glyco-enzymes has been used to enable incorporation of unnatural sugar analogs that can be employed to tag and isolate the protein substrates of an individual glycosyltransferase. A second challenge arises in efforts to determine which substrates mediate biological effects. Engineering a glycosyltransferase to target its activity toward select acceptor substrates allows deconvolution of the roles of specific glycosylation events. Similarly, glycosidases can be engineered to target specific substrates, with basic science and translational applications. This review describes recent efforts at engineering glyco-enzymes to identify and target their distinct substrates.