Neoglycolipids: probes of oligosaccharide structure, antigenicity, and function

Nanolithography of biointerfaces

This article is based on the Concluding remarks made at the Faraday Discussion meeting on Nanolithography of Biointerfaces, held in London, UK, 3-5th July 2019.

Structural analyses of a hemolytic compound found in an extract of Hypsizygus marmoreus fruiting bodies at a low pH

The current study determined the structure of a hemolytic compound found in an extract from the fruiting bodies of the edible mushroom Hypsizygus marmoreus when its pH was lowered. The hemolytic compound was purified using the modified Bligh and Dyer method followed by chromatography using reversed phase and silica gel columns. Structural analyses of the purified hemolytic compound were performed using NMR and ESI-MS. The deduced structure indicated a trans,trans-5,8-docosadienoic acid calcium salt. Although numerous proteinous hemolysins from various mushrooms have been described, the current study is the first to report on a low-molecular-weight hemolytic compound derived from an H. marmoreus extract.

The neoglycolipid (NGL) technology-based microarrays and future prospects

The neoglycolipid (NGL) technology is the basis of a state-of-the-art oligosaccharide microarray system, which we offer for screening analyses to the broad scientific community. We review here the sequential development of the technology and its power in pinpointing and isolating naturally occurring ligands for glycan-binding proteins (GBPs) within glycan populations. We highlight our Designer Array approach and Beam Search Array approach for generating natural glycome arrays to identify novel ligands of biological relevance. These two microarray approaches have been applied for assignments of ligands or antigens on glucan polysaccharides for effector proteins of the immune system (Dectin-1, DC-SIGN and DC-SIGNR) and carbohydrate-binding modules (CBMs) on bacterial hydrolases. We also discuss here the more recent applications to elucidate the structure of a prostate cancer- associated antigen F77 and identify ligands for adhesins of two rotaviruses, P[10] and P[19], expressed on an epithelial mucin glycoprotein.

pH-Dependent exhibition of hemolytic activity by an extract of Hypsizygus marmoreus fruiting bodies

The current study found that an extract from the fruiting bodies of the edible mushroom Hypsizygus marmoreus exhibited hemolytic activity against sheep red blood cells when its pH was lowered. Although hemolytic activity was not detected when an extract had a neutral pH, an extract with a low pH exhibited potent hemolytic activity. The maximal hemolytic activity was exhibited by an extract with a pH of 5.5. A heat-treated extract did not exhibit hemolytic activity before its pH was lowered, and that activity was inhibited in the presence of PMSF and EDTA. The turbidity of the extract increased during lowering of its pH, and the precipitate fraction exhibited hemolytic activity. Fractionation by a modified Bligh and Dyer method and TLC analyses suggested that a hemolytic compound in the extract might be a type of lipid. These results suggest that a hemolytic lipid-like compound in an extract of H. marmoreus fruiting bodies may be released by a non-active precursor substance(s) through metalloenzyme(s) while the extract has a low pH.

Glycomics and Proteomics Approaches to Investigate Early Adenovirus-Host Cell Interactions

Adenoviruses as most viruses rely on glycan and protein interactions to attach to and enter susceptible host cells. The Adenoviridae family comprises more than 80 human types and they differ in their attachment factor and receptor usage, which likely contributes to the diverse tropism of the different types. In the past years, methods to systematically identify glycan and protein interactions have advanced. In particular sensitivity, speed and coverage of mass spectrometric analyses allow for high-throughput identification of glycans and peptides separated by liquid chromatography. Also, developments in glycan microarray technologies have led to targeted, high-throughput screening and identification of glycan-based receptors. The mapping of cell surface interactions of the diverse adenovirus types has implications for cell, tissue, and species tropism as well as drug development. Here we review known adenovirus interactions with glycan- and protein-based receptors, as well as glycomics and proteomics strategies to identify yet elusive virus receptors and attachment factors. We finally discuss challenges, bottlenecks, and future research directions in the field of non-enveloped virus entry into host cells.

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Adenovirus entry into cells is guided by specific glycan and protein interactions.

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Glycan arrays and shotgun glycomics methods are valuable technologies to identify virus–glycan interactions.

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Shotgun proteomics and ligand-based receptor capture are powerful methods for proteinaceous receptor discovery.

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A combination of shotgun glycomics and proteomics with CRISPR/Cas9 and RNAi validation holds the promise of generating a systems biology view of virus entry processes.

Presentation, presentation, presentation! Molecular-level insight into linker effects on glycan array screening data

Changes in cell-surface glycan patterns are markers of the presence of many different disease and cancer types, offering a relatively untapped niche for glycan-targeting reagents and therapeutics in diagnosis and treatment. Of paramount importance for the success of any glycan-targeting reagent is the ability to specifically recognize the target among the plethora of different glycans that exist in the human body. The preeminent technique for defining specificity is glycan array screening, in which a glycan-binding protein (GBP) can be simultaneously screened against multiple glycans. Glycan array screening has provided unparalleled insight into GBP specificity, but data interpretation suffers from difficulties in identifying false-negative binding arising from altered glycan presentation, associated with the linker used to conjugate the glycan to the surface. In this work, we model the structure and dynamics of the linkers employed in the glycan arrays developed by the Consortium for Functional Glycomics. The modeling takes into account the physical presence and surface polarity of the array, and provides a structure-based rationalization of false-negative results arising from the so-called “linker effect.” The results also serve as a guide for interpreting glycan array screening data in a biological context; in particular, we show that attempts to employ natural amino acids as linkers may be prone to unexpected artifacts compromising glycan recognition.

Carbohydrate recognition in the immune system: contributions of neoglycolipid-based microarrays to carbohydrate ligand discovery

Oligosaccharide sequences in glycomes of eukaryotes and prokaryotes are enormously diverse. The reasons are not fully understood, but there is an increasing number of examples of the involvement of specific oligosaccharide sequences as ligands in protein-carbohydrate interactions in health and, directly or indirectly, in every major disease, be it infectious or noninfectious. The pinpointing and characterizing of oligosaccharide ligands within glycomes has been one of the most challenging aspects of molecular cell biology, as oligosaccharides cannot be cloned and are generally available in limited amounts. This overview recounts the background to the development of a microarray system that is poised for surveying proteomes for carbohydrate-binding activities and glycomes for assigning the oligosaccharide ligands. Examples are selected by way of illustrating the potential of "designer" microarrays for ligand discovery at the interface of infection, immunity, and glycobiology. Particularly highlighted are sulfo-oligosaccharide and gluco-oligosaccharide recognition systems elucidated using microarrays.

Stage-specific expression and antigenicity of glycoprotein glycans isolated from the human liver fluke, Opisthorchis viverrini

Infection by Opisthorchis viverrini (liver fluke) is a major public health problem in southeastern Asia, resulting in hepatobiliary disease and cholangiocarcinoma. Fluke surface glycoconjugates are prominently presented to the host, thereby constituting a crucial immunological interface that can determine the parasite's success in establishing infection. Therefore, N- and O-linked glycoprotein glycan profiles of the infective metacercarial stage and of the mature adult were investigated by nanospray ionisation-linear ion trap mass spectrometry (NSI-MS(n)). Glycan immunogenicity was investigated by immunoblotting with serum from infected humans. Metacercariae and adult parasites exhibit similar glycan diversity, although the prevalence of individual glycans and glycan classes varies by stage. The N-glycans of the metacercaria are mostly high mannose and monofucosylated, truncated-type oligosaccharides (62.7%), with the remainder processed to complex and hybrid type glycans (37.3%). The N-linked glycan profile of the adult is also dominated by high mannose and monofucosylated, truncated-type oligosaccharides (80.0%), with a smaller contribution from complex and hybrid type glycans (20.0%). At both stages, complex and hybrid type glycans are detected as mono-, bi-, tri-, or tetra-antennary structures. In metacercariae and adults, O-linked glycans are detected as mono- to pentasaccharides. The mucin type core 1 structure, Galβ1-3GalNAc, predominates in both stages but is less prevalent in the adult than in the metacercaria. Immunogenic recognition of liver fluke glycoproteins is reduced after deglycosylation but infected human serum was unable to recognise glycans released from peptides. Therefore, the most potent liver fluke antigenic epitopes are mixed determinants, comprised of glycan and polypeptide elements.

Carbohydrate to carbohydrate interaction in development process and cancer progression

Two types of carbohydrate to carbohydrate interaction (CCI) have been known to be involved in biological processes. One is the CCI between molecules expressed on interfacing cell membranes of different cells to mediate cell to cell adhesion, and subsequently induce cell signaling, and is termed trans-CCI. It has been indicated that the Le(x) to Le(x) interaction at the morula stage in mouse embryos plays an important role in the compaction process in embryonic development. GM3 to Gg3 or GM3 to LacCer interaction has been suggested to be involved in adhesion of tumor cells to endothelial cells, which is considered a crucial step in tumor metastasis. The other is the CCI between molecules expressed within the same microdomain of the cell surface membrane, and is termed cis-CCI. The interaction between ganglioside GM3, and multi (>3) GlcNAc termini of N-linked glycans of epidermal growth factor receptor (EGFR), has been indicated as the molecular mechanism for the inhibitory effect of GM3 on EGFR activation. Also, the complex with GM3 and GM2 has been shown to inhibit the activation of hepatocyte growth factor (HGF) receptor, cMet, through its association with tetraspanin CD82, and results in the inhibition of cell motility. Since CCI research is still limited, more examples of CCI in biological processes in development, and cancer progression will be revealed in the future.

Identification of mono- and disulfated N-acetyl-lactosaminyl Oligosaccharide structures as epitopes specifically recognized by humanized monoclonal antibody HMOCC-1 raised against ovarian cancer

A humanized monoclonal antibody raised against human ovarian cancer RMG-I cells and designated as HMOCC-1 (Suzuki, N., Aoki, D., Tamada, Y., Susumu, N., Orikawa, K., Tsukazaki, K., Sakayori, M., Suzuki, A., Fukuchi, T., Mukai, M., Kojima-Aikawa, K., Ishida, I., and Nozawa, S. (2004) Gynecol. Oncol. 95, 290-298) was characterized for its carbohydrate epitope structure. Specifically, a series of co-transfections was performed using mammalian expression vectors encoding specific glycosyltransferases and sulfotransferases. These experiments identified one sulfotransferase, GAL3ST3, and one glycosyltransferase, B3GNT7, as required for HMOCC-1 antigen formation. They also suggested that the sulfotransferase CHST1 regulates the abundance and intensity of HMOCC-1 antigen. When HEK293T cells were co-transfected with GAL3ST3 and B3GNT7 expression vectors, transfected cells weakly expressed HMOCC-1 antigen. When cells were first co-transfected with GAL3ST3 and B3GNT7 and then with CHST1, the resulting cells strongly expressed HMOCC-1 antigen. However, when cells were transfected with a mixture of GAL3ST3 and CHST1 before or after transfection with B3GNT7, the number of antigen-positive cells decreased relative to the number seen with only GAL3ST3 and B3GNT7, suggesting that CHST1 plays a regulatory role in HMOCC-1 antigen formation. Because these results predicted that HMOCC-1 antigens are SO(3) → 3Galβ1 → 4GlcNAcβ1 → 3(±SO(3) → 6)Galβ1 → 4GlcNAc, we chemically synthesized mono- and disulfated and unsulfated oligosaccharides. Immunoassays using these oligosaccharides as inhibitors showed the strongest activity by disulfated tetrasaccharide, weak but positive activity by monosulfated tetrasaccharide at the terminal galactose, and no activity by nonsulfated tetrasaccharides. These results establish the HMOCC-1 epitope, which should serve as a useful reagent to further characterize ovarian cancer.

Neoglycolipid-based oligosaccharide microarray system: preparation of NGLs and their noncovalent immobilization on nitrocellulose-coated glass slides for microarray analyses

Carbohydrate microarrays, since their advent in 2002, are revolutionizing studies of the molecular basis of protein-carbohydrate interactions both in endogenous recognition systems and pathogen-host interactions. We have developed a unique carbohydrate microarray system based on the neoglycolipid (NGL) technology, a well-validated microscale approach for generating lipid-tagged oligosaccharide probes for use in carbohydrate recognition studies. This chapter provides an overview of the principles and key features of the NGL-based oligosaccharide microarrays, and describes in detail the basic techniques - from the preparation of NGL probes to the generation of microarrays using robotic arraying hardware, as well as a general protocol for probing the microarrays with carbohydrate-binding proteins.

Glycan microarrays for decoding the glycome

In the last decade, glycan microarrays have revolutionized the analysis of the specificity of glycan-binding proteins (GBPs), providing information that simultaneously illuminates the biology mediated by them and decodes the informational content of the glycome. Numerous methods have emerged for arraying glycans in a "chip" format, and glycan libraries have been assembled that address the diversity of the human glycome. Such arrays have been successfully used for analysis of GBPs, which mediate mammalian biology, host-pathogen interactions, and immune recognition of glycans relevant to vaccine production and cancer antigens. This review covers the development of glycan microarrays and applications that have provided insights into the roles of mammalian and microbial GBPs.

Preparation and analysis of glycan microarrays

Determination of the binding specificity of glycan-binding proteins (GBPs), such as lectins, antibodies, and receptors, has traditionally been difficult and laborious. The advent of glycan microarrays has revolutionized the field of glycobiology by allowing simultaneous screening of a GBP for interactions with a large set of glycans in a single format. This unit describes the theory and method for production of two types of glycan microarrays (chemo/enzymatically synthesized and naturally derived), and their application to functional glycomics to explore glycan recognition by GBPs. These procedures are amenable to various types of arrays and a wide range of GBP samples.

Neoglycolipid (NGL)-based oligosaccharide microarrays and highlights of their recent applications in studies of the molecular basis of pathogen–host interactions

Carbohydrate microarray technologies are new developments at the frontier of glycomics that are showing great promise as tools for high-throughput analysis of carbohydrate-mediated interactions and the elucidation of carbohydrate ligands involved not only in endogenous receptor systems, but also pathogen–host interactions. The main advantage of microarray analysis is that a broad range of glycan sequences can be immobilized on solid matrices as minute spots and simultaneously interrogated. Different methodologies have emerged for constructing carbohydrate microarrays. The NGL (neoglycolipid)-based oligosaccharide microarray platform is among the relatively few systems that are beyond proof-of-concept and have provided new biological information. In the present article, I dwell, in some detail, on the NGL-based microarray. Highlights are the recent applications of NGL-based microarrays that have contributed to knowledge on the molecular basis of pathogen–host interactions, namely the assignments of the carbohydrate-binding specificities of several key surface-adhesive proteins of Toxoplasma gondii and other apicomplexan parasites, and the elucidation of receptor-binding specificities of the pandemic influenza A (H1N1) 2009 (H1N1pdm) virus compared with seasonal H1N1 virus.

Glycoprotein analysis using protein microarrays and mass spectrometry

Protein glycosylation plays an important role in a multitude of biological processes such as cell-cell recognition, growth, differentiation, and cell death. It has been shown that specific glycosylation changes are key in disease progression and can have diagnostic value for a variety of disease types such as cancer and inflammation. The complexity of carbohydrate structures and their derivatives makes their study a real challenge. Improving the isolation, separation, and characterization of carbohydrates and their glycoproteins is a subject of increasing scientific interest. With the development of new stationary phases and molecules that have affinity properties for glycoproteins, the isolation and separation of these compounds have advanced significantly. In addition to detection with mass spectrometry, the microarray platform has become an essential tool to characterize glycan structure and to study glycosylation-related biological interactions, by using probes as a means to interrogate the spotted or captured glycosylated molecules on the arrays. Furthermore, the high-throughput and reproducible nature of microarray platforms have been highlighted by its extensive applications in the field of biomarker validation, where a large number of samples must be analyzed multiple times. This review covers a brief survey of the other experimental methodologies that are currently being developed and used to study glycosylation and emphasizes methodologies that involve the use of microarray platforms. This review describes recent advances in several options of microarray platforms used in glycoprotein analysis, including glycoprotein arrays, glycan arrays, lectin arrays, and antibody/lectin arrays. The translational use of these arrays in applications related to characterization of cells and biomarker discovery is also included.

Advances on the compositional analysis of glycosphingolipids combining thin-layer chromatography with mass spectrometry

Glycosphingolipids (GSLs), composed of a hydrophilic carbohydrate chain and a lipophilic ceramide anchor, play pivotal roles in countless biological processes, including infectious diseases and the development of cancer. Knowledge of the number and sequence of monosaccharides and their anomeric configuration and linkage type, which make up the principal items of the glyco code of biologically active carbohydrate chains, is essential for exploring the function of GSLs. As part of the investigation of the vertebrate glycome, GSL analysis is undergoing rapid expansion owing to the application of novel biochemical and biophysical technologies. Mass spectrometry (MS) takes part in the network of collaborations to further unravel structural and functional aspects within the fascinating world of GSLs with the ultimate aim to better define their role in human health and disease. However, a single-method analytical MS technique without supporting tools is limited yielding only partial structural information. Because of its superior resolving power, robustness, and easy handling, high-performance thin-layer chromatography (TLC) is widely used as an invaluable tool in GSL analysis. The intention of this review is to give an insight into current advances obtained by coupling supplementary techniques such as TLC and mass spectrometry. A retrospective view of the development of this concept and the recent improvements by merging (1) TLC separation of GSLs, (2) their detection with oligosaccharide-specific proteins, and (3) in situ MS analysis of protein-detected GSLs directly on the TLC plate, are provided. The procedure works on a nanogram scale and was successfully applied to the identification of cancer-associated GSLs in several types of human tumors. The combination of these two supplementary techniques opens new doors by delivering specific structural information of trace quantities of GSLs with only limited investment in sample preparation.

Multifaceted approaches including neoglycolipid oligosaccharide microarrays to ligand discovery for malectin

In this chapter, we describe the key procedures for isolation of the oligosaccharides and the preparation of neoglycolipid probes together with expression of malectin that have enabled the discovery of the highly selective binding of this newly described protein in the endoplasmic reticulum (ER) to a diglucosyl high-mannose N-glycan. This is the first indication of a bioactivity for a diglucosyl high-mannose N-glycan of the type that occurs in the ER of eukaryotic cells and which is an intermediate in the early steps of the N-glycosylation pathway of nascent proteins. The malectin story is an example of a powerful convergence of disciplines in biological sciences: (i) developmental biology, (ii) bioinformatics, (iii) recombinant protein expression, (iv) protein structural studies, (v) glucan biochemistry, and (vi) drug-assisted engineering of oligosaccharide biosynthesis, culminating in (vii) oligosaccharide "designer" microarrays, to clinch the remarkable selectivity of the binding of this newly discovered ER protein. Thus, the way is open to the identification of the role of malectin in the N-glycosylation pathway.

GM1 structure determines SV40-induced membrane invagination and infection

Incoming simian virus 40 (SV40) particles enter tight-fitting plasma membrane invaginations after binding to the carbohydrate moiety of GM1 gangliosides in the host cell plasma membrane through pentameric VP1 capsid proteins. This is followed by activation of cellular signalling pathways, endocytic internalization and transport of the virus via the endoplasmic reticulum to the nucleus. Here we show that the association of SV40 (as well as isolated pentameric VP1) with GM1 is itself sufficient to induce dramatic membrane curvature that leads to the formation of deep invaginations and tubules not only in the plasma membrane of cells, but also in giant unilamellar vesicles (GUVs). Unlike native GM1 molecules with long acyl chains, GM1 molecular species with short hydrocarbon chains failed to support such invagination, and endocytosis and infection did not occur. To conceptualize the experimental data, a physical model was derived based on energetic considerations. Taken together, our analysis indicates that SV40, other polyoma viruses and some bacterial toxins (Shiga and cholera) use glycosphingolipids and a common pentameric protein scaffold to induce plasma membrane curvature, thus directly promoting their endocytic uptake into cells.

Carbohydrate microarrays: key developments in glycobiology

Carbohydrate chains of glycoproteins, glycolipids, proteoglycans, and polysaccharides mediate processes of biological and medical importance through their interactions with complementary proteins. The unraveling of these interactions is therefore a priority in biomedical sciences. Carbohydrate microarray technology is a new development at the frontier of glycomics that is revolutionizing the study of carbohydrate-protein interactions and the elucidation of their specificities in endogenous biological processes, microbe-host interactions, and immune defense mechanisms. In this review, we briefly refer to the principles of numerous platforms since the introduction of carbohydrate microarrays in 2002, and we highlight platforms that are beyond proof-of-concept and have provided new biological information.

Identification and quantification of N-linked oligosaccharides released from glycoproteins: an inter-laboratory study

As characterization of glycosylation is required for the licensing of recombinant glycoprotein therapeutics, technique comparability must be assessed. Eleven UK laboratories (seven industrial, two regulatory or government, two academic) participated in an inter-laboratory study to analyze N-glycans present in four mixtures prepared by PNGase F cleavage of commercial glycoproteins: human alpha1-acid glycoprotein (H alpha1), bovine alpha1-acid glycoprotein (B alpha1), bovine pancreatic ribonuclease B (RNaseB), and human serum immunoglobulin G (hIgG). Participants applied their routine glycan mapping methodology using predominantly chromatography and mass spectrometry to identify and quantify components. Data interpretation focused on the relative amounts of different glycan structures present, the degree of sialylation, antennary and the galactosylation profiles, fucosylation and bisecting GlcNAc content, and the number of glycan components identified. All laboratories found high levels of sialylation for H alpha1 and B alpha1 (Z-numbers 271 +/- 24 and 224 +/- 18, respectively), but varying ratios of di-, tri-, and tetra-antennary chains. The Z-score for hIgG glycans had high variability as values obtained from mass spectrometric and chromatographic methods clustered separately. The proportion of the major penta-mannosyl chain from RNaseB was between 29 and 62%. Proportions of fucosylated and bisected GlcNAc chains from hIgG were between 58 and 96% and 9 and 23%, respectively. Mass spectrometric approaches consistently identified more glycan species, especially when both N-glycolylneuraminic acid (Neu5Gc) and N-acetylneuraminic acid (Neu5Ac) were present. These data highlight the need for well-characterized reference standards to support method validation and regulatory guidance on selection of approaches. Pharmacopoeial specifications must acknowledge method variability.

Membrane microdomains from early gastrula embryos of medaka, Oryzias latipes, are a platform of E-cadherin- and carbohydrate-mediated cell-cell interactions during epiboly

Formation of membrane microdomain is critical for cell migration (epiboly) during gastrulation of medaka fish [Adachi et al. (Biochem. Biophys. Res. Commun. 358:848-853, 2007)]. In this study, we characterized membrane microdomain from gastrula embryos to understand its roles in epiboly. A cell adhesion molecule (E-cadherin), its associated protein (beta-catenin), transducer proteins (PLCgamma, cSrc), and a cytoskeleton protein (beta-actin) were enriched in the membrane microdomain. Le(X)-containing glycolipids and glycoproteins (Le(X)-gp) were exclusively enriched in the membrane microdomain. Interestingly, the isolated membrane microdomain had the ability to bind to each other in the presence of Ca(2+). This membrane microdomain binding was achieved through the E-cadherin homophilic and the Le(X)-glycan-mediated interactions. E-cadherin and Le(X)-gp were co-localized on the same membrane microdomain, suggesting that these two interactions are operative at the same time. Thus, the membrane microdomain functions as a platform of the E-cadherin- and Le(X)-glycan-mediated cell adhesion and signal transduction.

Glycoarrays--tools for determining protein-carbohydrate interactions and glycoenzyme specificity

Carbohydrate arrays (glycoarrays) have recently emerged as a high-throughput tool for studying carbohydrate-binding proteins and carbohydrate-processing enzymes. A number of sophisticated array platforms that allow for qualitative and quantitative analysis of carbohydrate binding and modification on the array surface have been developed, including analysis by fluorescence spectroscopy, mass spectrometry and surface plasmon resonance spectroscopy. These platforms, together with examples of biologically-relevant applications are reviewed in this Feature Article.

Pseudomonas aeruginosa mucoid strain 8830 binds glycans containing the sialyl-Lewis x epitope

Pseudomonas aeruginosa infection of patients with cystic fibrosis (CF) is a leading cause of their morbidity and mortality. Pathogenesis is initiated in part by molecular interactions of P. aeruginosa with carbohydrate residues in airway mucins that accumulate in the lungs of patients with this disease. To explore the nature of the glycans recognized by a stable, mucoid, alginate-producing strain P. aeruginosa 8830 we generated a genetically modified Pa8830 expressing green fluorescent protein (Pa3380-GFP). We tested its binding to a panel of glycolipids and neoglycolipids in which selected glycans were covalently attached to dipalmitoyl phosphatidylethanolamine and analyzed on silica gel surfaces. Among all glycans tested, Pa8830-GFP bound best to sialyl-Le(x)-containing glycan NeuAc(alpha2-3)Gal(beta1-4)[Fuc(alpha1-3)]GlcNAc-R and bound weakly to H-type blood group Fucalpha1-2Galbeta1-4GlcNAc-R, sialyl-lactose, and Le(x), and exhibited little binding toward non-fucosylated derivatives. Interestingly, while Pa8830-GFP bound to the glycosphingolipid asialoGM1, it did not appear to bind to a wide variety of other glycosphingolipids including GM1, GM2, asialoGM2, and sulfatide. These results indicate that P. aeruginosa 8830 has preferential binding to sialyl-Le(x)-containing glycans and has weak recognition of related fucose- and sialic acid-containing glycans. The finding that Pa8830 binds sialyl-Le(x)-containing glycans, which occur at increased levels in mucins from CF patients, is consistent with studies of other strains of P. aeruginosa and further suggests that such glycans on CF mucins contribute to disease pathogenesis.

N-glycolyl GM1 ganglioside as a receptor for simian virus 40

Carbohydrate microarrays have emerged as powerful tools in analyses of microbe-host interactions. Using a microarray with 190 sequence-defined oligosaccharides in the form of natural glycolipids and neoglycolipids representative of diverse mammalian glycans, we examined interactions of simian virus 40 (SV40) with potential carbohydrate receptors. While the results confirmed the high specificity of SV40 for the ganglioside GM1, they also revealed that N-glycolyl GM1 ganglioside [GM1(Gc)], which is characteristic of simian species and many other nonhuman mammals, is a better ligand than the N-acetyl analog [GM1(Ac)] found in mammals, including humans. After supplementing glycolipid-deficient GM95 cells with GM1(Ac) and GM1(Gc) gangliosides and the corresponding neoglycolipids with phosphatidylethanolamine lipid groups, it was found that GM1(Gc) analogs conferred better virus binding and infectivity. Moreover, we visualized the interaction of NeuGc with VP1 protein of SV40 by molecular modeling and identified a conformation for GM1(Gc) ganglioside in complex with the virus VP1 pentamer that is compatible with its presentation as a membrane receptor. Our results open the way not only to detailed studies of SV40 infection in relation to receptor expression in host cells but also to the monitoring of changes that may occur with time in receptor usage by the virus.

Interaction of N-linked glycans, having multivalent GlcNAc termini, with GM3 ganglioside

GM3 ganglioside interacts specifically with complex-type N-linked glycans having multivalent GlcNAc termini, as shown for (1) and (2) below. (1) Oligosaccharides (OS) isolated from ConA-non-binding N-linked glycans of ovalbumin, whose structures were identified as penta-antennary complex-type with bisecting GlcNAc, having five or six GlcNAc termini (OS B1, B2), or bi-antennary complex-type having two GlcNAc termini (OS I). OS I is a structure not previously described. (2) Multi-antennary complex-type N-linked OS isolated from fetuin, treated by sialidase followed by beta-galactosidase, having three or four GlcNAc termini exposed. These OS, conjugated to phosphatidylethanolamine (PE), showed clear interaction with (3)H-labeled liposomes containing GM3, when various doses of OS-PE conjugate were adhered by drying to multi-well polystyrene plates. Interaction was clearly observed only with liposomes containing GM3, but not LacCer, Gb4, or GalNAcalpha1-3Gb4 (Forssman antigen). GM3 interaction with PE conjugate of OS B1 or B2 was stronger than that with PE conjugate of OS I. GM3 interacted clearly with PE conjugate of N-linked OS from desialylated and degalactosylated fetuin, but not native fetuin. No binding was observed to cellobiose-PE conjugate, or to OS-PE conjugate lacking GlcNAc terminus. Thus, GM3, but not other GSL liposomes, interacts with various N-linked OS having multiple GlcNAc termini, in general. These findings suggest that the concept of carbohydrate-to-carbohydrate interaction can be extended to interaction of specific types of N-linked glycans with specific GSLs. Natural occurrence of such interaction to define cell biological phenomena is under investigation.

Detection of oligosaccharide ligands for Hepatocyte growth factor/Scatter factor (HGF/SF), Keratinocyte growth factor (KGF/FGF-7), RANTES and Heparin cofactor II by neoglycolipid microarrays of glycosaminoglycan-derived oligosaccharide fragments

Neoglycolipid technology is eminently adaptable for microarray design for high-throughput detection and specificity assignments of carbohydrate-protein interactions. Dermatan sulfate (DS) is known to play an important role because of its ability to bind growth factors as well as chemokines and to modulate their biological activities during inflammation and response to injury. We prepared various iduronic acid-rich fragments from DS by complete digestion with chondroitinase ACI, and investigated whether the DS-binding proteins, such as HGF/SF, RANTES, KGF/FGF-7 and HCII, can detect their oligosaccharide ligands in a neoglycolipid microarray. First, a comparison of the intensity of binding signals obtained from chondroitin oligosaccharides with those of heparin oligosaccharides showed that our microarray system is feasible not only to single-out the oligosaccharide ligands, but also to detect the difference between an intrinsic interaction unrelated only to electrostatic interaction and non-specific electrostatic interaction. Second, HGF/SF, KGF/FGF-7 and HCII showed preferential binding to iduronic acid-rich fragments of DS oligosaccharides that are greater than 8-mers in lengths. In contrast, RANTES binding seemed to depend only on the negative charges; their binding intensity towards the DS oligosaccharides was somewhat stronger than the binding of HGF/SF, KGF/FGF-7 and HCII. Third, the use of polyvinylpyrrolidone-40 (PVP-40), ovalbumin (OV) and Tween 20 in place of BSA as a blotting agent was useful in these glycosaminoglycan dependent reactions to minimize background due to non-specific interactions.

Carbohydrate Microarrays: Survey of Fabrication Techniques

Carbohydrate microarrays are being developed in order to decipher the information content of the glycome. This postgenomic activity is necessary because of the complexity of protein biosynthesis and post-translational modifications that cannot currently be detected at the genome level. This review looks, in detail, at the experimental approaches that have been taken in the fabrication and preparation of carbohydrate microarrays, glycan arrays and glyco-chips. Tether structures, glycan solution preparation, detection methods and applications have been gathered together in a tabular format.

Development of a carbohydrate binding assay for the B-oligomer of pertussis toxin and toxoid

Pertussis toxin (PTx) is a major virulence factor produced by Bordetella pertussis and, in its detoxified form PTd, is an important component of pertussis vaccines. The in vivo histamine sensitization test (HIST) is currently used for the safety testing of these vaccines. However, an alternative test is needed because of large assay variability and ethical concerns with regard to animal usage. PTx has two functionally distinct domains: the enzymatic A-protomer and the B-oligomer that facilitates host-cell binding and entry of PTx into the cell. The development of a quantitative PTx binding assay using glycoproteins or defined oligosaccharides is reported. PTx was found to bind preferentially to multiantennary N-glycans, with the highest binding toward the fully sialylated structures. In contrast, PTd lost the ability of PTx to bind to sialylated multiantennary structures but retained some capacity to bind to neutral multiantennary structures. The developed assay was shown to be specific, sensitive, and robust and could be used for investigating the mechanisms of PTx detoxification and for monitoring PTx binding activity in vaccine formulations. This assay could also be used to complement a PTx-enzymatic assay, developed recently, and together they may form the basis of a potential alternative in vitro assay to replace the in vivo HIST.

Preparation of Neoglycolipids with Ring‐Closed Cores via Chemoselective Oxime‐Ligation for Microarray Analysis of Carbohydrate–Protein Interactions

Affinities of most oligosaccharide-protein interactions are so low that multivalent forms of ligand and protein are required for detecting interactions. The neoglycolipid (NGL) technology was designed to address the need for microscale presentation of oligosaccharides in a multivalent form for studying carbohydrate-protein interactions, and this is now the basis of a state-of-the-art carbohydrate microarray system. NGL technology involves conjugating oligosaccharides by reductive amination to the aminolipid 1,2-dihexadecyl-sn-glycero-3-phosphoethanolamine (DHPE). Other than ring-opening of the monosaccharide residues at reducing ends, oligosaccharides remain intact, and the NGLs derived from trisaccharides or larger oligosaccharides have performed well for the majority of carbohydrate-recognition systems that have the peripheral or backbone regions of oligosaccharides as recognition motifs. However, ring-opening of reducing end monosaccharides limits applicability to very short oligosaccharides (di- and trisaccharides) and, potentially, to N-glycans recognized by proteins such as Pisum sativum agglutinin (pea lectin) that require both intact core and backbone regions for strong binding. This chapter describes a method for preparing NGLs (designated AO-NGLs) from reducing oligosaccharides by chemoselective oxime-ligation to a new lipid reagent, N-aminooxyacetyl-DHPE. Microarray analyses of the AO-NGL derived from Lewis x (Le(x)) trisaccharide probed with anti-Le(x) antibodies indicate that a significant proportion of the core monosaccharide linked to lipid is in ring-closed form. Thus, AO-NGLs have broadened the applicability of NGLs as probes in studies of carbohydrate-protein interactions.

Selective Binding of the Scavenger Receptor C-type Lectin to Lewisx Trisaccharide and Related Glycan Ligands

The scavenger receptor C-type lectin (SRCL) is an endothelial receptor that is similar in organization to type A scavenger receptors for modified low density lipoproteins but contains a C-type carbohydrate-recognition domain (CRD). Fragments of the receptor consisting of the entire extracellular domain and the CRD have been expressed and characterized. The extracellular domain is a trimer held together by collagen-like and coiled-coil domains adjacent to the CRD. The amino acid sequence of the CRD is very similar to the CRD of the asialoglycoprotein receptor and other galactose-specific receptors, but SRCL binds selectively to asialo-orosomucoid rather than generally to asialoglycoproteins. Screening of a glycan array and further quantitative binding studies indicate that this selectivity results from high affinity binding to glycans bearing the Lewis(x) trisaccharide. Thus, SRCL shares with the dendritic cell receptor DC-SIGN the ability to bind the Lewis(x) epitope. However, it does so in a fundamentally different way, making a primary binding interaction with the galactose moiety of the glycan rather than the fucose residue. SRCL shares with the asialoglycoprotein receptor the ability to mediate endocytosis and degradation of glycoprotein ligands. These studies suggest that SRCL might be involved in selective clearance of specific desialylated glycoproteins from circulation and/or interaction of cells bearing Lewis(x)-type structures with the vascular endothelium.

Ligand interactions of the Coprinopsis cinerea galectins

The basidiomycete Coprinopsis cinerea (Coprinus cinereus) expresses two fruiting body-specific isolectins (CGL1 and CGL2) that belong to the family of galectins. Understanding the role of these beta-galactoside binding lectins is still in the beginning. Even though the prerequisites for substrate binding are well understood, it is not known how discrimination between potential substrates is achieved and what kind of influence this has on the function in a distinct cellular context. Precise knowledge of the expression of galectins and their ligands will aid in elucidating their function. In Coprinopsis, the developmentally regulated ligands for galectins co-localise with galectin expression in the veil surrounding the developing primordium and the outer cells of the young stipe. In addition, galectin ligands are observed in the hymenium. The subcellular localisation of the galectin ligands suggests these to be present in cellular compartments distinct from galectin transport. The sensitivity of the in situ interactions with exogenous galectin towards detergents and organic solvents infers that these ligands are lipid-borne. Accordingly, lipid fractions from primordia are shown to contain galectin-binding compounds. Based on these results and the determined binding specificity towards substituted beta-galactosides we hypothesise that beta-galactoside-containing lipids (basidiolipids) found in mushrooms are physiological ligands for the galectins in C. cinerea.

Carbohydrate arrays as tools for the glycomics revolution

Determining the roles of carbohydrates in cell biology is hindered by the tremendous efforts that must be taken either to synthesize carbohydrates chemically or to isolate them from natural sources. Several platforms have been developed to study glycobiology. These platforms include the covalent and non-covalent immobilization of carbohydrates on microtiter plates, nitrocellulose membranes, coated slides, glass slides, gold surfaces and microspheres. Each platform has both positive and negative attributes for studying carbohydrate biology, such as flexibility and the amount of material required for study. Here we discuss these techniques with the goal of developing a ‘gold standard’ in the field of glycomics.

Molecular characterization of the rat Kupffer cell glycoprotein receptor

The Kupffer cell receptor for glycoproteins has been reported to have a role in clearance of galactose- and fucose-terminated glycoproteins from circulation. Although the gene and a cDNA encoding the receptor have been described, there has been little study of the receptor protein. To address some questions about possible ligands and functions for this receptor, fragments representing portions of the extracellular domain have been expressed and characterized. The extracellular domain consists of a trimer stabilized by an extended coiled-coil of alpha-helices. The receptor displays monosaccharide-binding characteristics similar to the hepatic asialoglycoprotein receptor, but with somewhat less selectivity. The two best monosaccharide ligands are GalNAc and galactose. alpha-Methyl fucoside is a particularly poor ligand. Analysis of Kupffer cell receptor binding to glycoproteins and oligosaccharides released from them reveals highest affinity for desialylated, complex N-linked glycans. The best glycoprotein ligands contain multiple highly branched oligosaccharides. A human ortholog of the rat receptor gene does not encode a full-length protein and is not expressed in liver. These characteristics suggest that the receptor may have functions parallel to those of the hepatocyte asialoglycoprotein receptor in some (but not all) mammalian species.

Relationships between the N-glycan structures and biological activities of recombinant human erythropoietins produced using different culture conditions and purification procedures

Eight preparations of recombinant human erythropoietin (EPO) with differing isoform compositions were produced by using different culture conditions and purification procedures. The N-glycan structures of these EPOs were analysed using a recently developed profiling procedure and identified using matrix-assisted laser desorption ionization mass spectrometry. The specific activities of each of the EPOs were estimated by in vivo and in vitro mouse bioassays. The eight EPOs were found to differ in their isoform compositions (as judged by isoelectric focusing), their N-glycan profiles, and in their in vivo and in vitro bioactivities. N-glycan analyses identified at least 23 different structures among these EPOs, including bi-, tri- and tetra-antennary N-glycans, with or without fucosylation or N-acetyllactosamine extensions, and sialylated to varying degrees. Mass spectrometry also indicated the presence of N-glycans with incomplete outer chains, terminating in N-acetylglucosamine residues, and of molecular masses consistent with phosphorylated or sulphated oligomannoside structures. The tetrasialylated tetra-antennary N-glycan contents of the eight rEPOs were found to be significantly and positively correlated with their specific activities as estimated by mouse in vivo bioassay, and significantly and negatively correlated with their specific activities as estimated by mouse in vitro bioassay. It was concluded that the tetrasialylated tetra-antennary N-glycan content of EPO is a major determinant for its in vivo biological activity in the mouse.

Oligosaccharide microarrays for glycomics

Glycomics is an emerging field that was proposed at the end of the 20th century as a new concept to follow genomics and proteomics. Studies on glycans are indispensable to define complex life systems and cell communities because all living organisms consist of diverse cells, which are covered with an abundance of heterogeneous carbohydrates. Although studies on glycans are extremely difficult because of the lack of basic technologies common to DNAs and proteins, a few new aspects of glycotechnologies have now become realized in the form of "bio-chips", which include "oligosaccharide arrays" or "glyco-chips". Recently, Fukui et al. developed oligosaccharide microarrays for glycomic analysis of extensive carbohydrate-binding proteins. How and why such glyco-engineering projects have been made in the contexts of both pure and applied sciences is described.

An investigation of the interactions of E-selectin with fuco-oligosaccharides of the blood group family

This investigation is concerned with assignments of Lewis(a) (Le(a)) and Le(x) analogs on linear and branched di- to hexasaccharide backbones as components of the recognition motifs for E-selectin. The influence of the location of fucose residue(s) was investigated using 14 structurally defined and variously fucosylated oligosaccharides in biotinylated form or as neoglycolipids in static binding assays, in microwells, and on thin-layer chromatograms. Results of the two assay systems were in agreement overall and showed that the recognition motifs for E-selectin include 4-fucosyl-lacto (Le(a)) and 3-fucosyl-neo-lacto (Le(x)) sequences strictly at capping positions and not Le(x) at an internal position as a part of VIM-2 antigen sequence. There is greater potency of the Le(a) over the Le(x) series. Additional fucose residues alpha1-2-linked to neighboring galactoses or alpha1-3-linked to inner N-acetyglucosamines or to reducing-terminal glucose residues of the tetrasaccharide backbone had little or no effect on the selectin binding. E-selectin binding to the Le(a) or Le(x )capping motif on a 3-linked branch was equivalent to the binding on the corresponding linear backbone. A lack of E-selectin binding to the Le(x) motif capping a 6-linked branch and to the Le(x) trisaccharide linked to biotin via a nine-carbon spacer indicates that the -GlcNAcbeta1-3Gal- sequence on the oligosaccharide backbone adjoining the Le(x) is a part of recognition motif for E-selectin. These findings contribute to understanding the molecular basis of E-selectin recognition and could influence future designs of selectin antagonists as possible therapeutic substances.

Oligosaccharide microarrays for high-throughput detection and specificity assignments of carbohydrate-protein interactions

We describe microarrays of oligosaccharides as neoglycolipids and their robust display on nitrocellulose. The arrays are obtained from glycoproteins, glycolipids, proteoglycans, polysaccharides, whole organs, or from chemically synthesized oligosaccharides. We show that carbohydrate-recognizing proteins single out their ligands not only in arrays of homogeneous oligosaccharides but also in arrays of heterogeneous oligosaccharides. Initial applications have revealed new findings, including: (i) among O-glycans in brain, a relative abundance of the Lewis(x) sequence based on N-acetyllactosamine recognized by anti-L5, and a paucity of the Lewis(x) sequence based on poly-N-acetyllactosamine recognized by anti-SSEA-1; (ii) insights into chondroitin sulfate oligosaccharides recognized by an antiserum and an antibody (CS-56) to chondroitin sulfates; and (iii) binding of the cytokine interferon-gamma (IFN-gamma) and the chemokine RANTES to sulfated sequences such as HNK-1, sulfo-Lewis(x), and sulfo-Lewis(a), in addition to glycosaminoglycans. The approach opens the way for discovering new carbohydrate-recognizing proteins in the proteome and for mapping the repertoire of carbohydrate recognition structures in the glycome.

Synergistic interactions of the two classes of ligand, sialyl-Lewis(a/x) fuco-oligosaccharides and short sulpho-motifs, with the P- and L-selectins: implications for therapeutic inhibitor designs

The E-, L- and P-selectins are carbohydrate-recognizing cell-adhesion molecules mediating selective leucocyte recruitment in inflammation. The 3'-sialyl- and 3'-sulpho-oligosaccharides of Lewis(x) (Le(x)) and Lewis(a) (Le(a)) series are bound by them, but for high-avidity binding of P- and L-selectins to the glycoprotein counter-receptor known as P-selectin glycoprotein ligand, PSGL-1, there is a requirement for sulpho-tyrosines neighbouring a sialyl-Le(x) glycan. The two selectins can also bind 3-O- or 6-O-sulphated galacto-lipids (sulphatides). Here we compare some features of the interactions of P- and L-selectins with a novel lipid-linked sulpho-tyrosine probe, and with the sulphatides and neoglycolipids of sialyl- and sulpho-Le(x)/Le(a) fuco-oligosaccharides. The sulpho-tyrosine probe is bound by both selectins. There are close similarities in the interactions of the two selectins with sulpho-tyrosine and the sulphatides; the binding is relatively resistant to chelation of calcium ions, in contrast to the absolute requirement of calcium ions with the long fuco-oligosaccharides, including 6-sulpho-sialyl-Le(x). With both selectins, there is striking synergy in binding signals elicited by the two ligand types when presented as equimolar mixtures on a matrix. Thus, there are two operationally distinct binding sites on both L- and P-selectin; and the binding sites for sulphate groups in the two ligand types are probably distinct. When sulpho-tyrosine and sialyl-Le(x) are presented on liposomes, a potent inhibitory activity is generated toward the binding of P-selectin to HL60 cells, with 50% inhibitory concentration (IC(50)) values in the nanomolar range. These features of the lipid-linked ligand analogues, and the simple approach for their display on liposomes, may have applications in designs and screening of selectin inhibitors as anti-inflammatory compounds.

Glycan arrays for functional glycomics

Interactions between carbohydrates and proteins mediate intracellular traffic, cell adhesion, cell recognition and immune system function. Two recent papers describe how arrays of oligosaccharide and polysaccharide molecules can be used to investigate these interactions more fully.

A monoclonal antibody, MIN/3/60, that recognizes the sulpho-Lewis(x) and sulpho-Lewis(a) sequences detects a sub-population of epithelial glycans in the crypts of human colonic epithelium

Monoclonal antibodies (MAbs) directed to Lewis(x) (Le(x)) and related carbohydrate sequences have been invaluable in anticipating biological roles for these oligosaccharides by detecting the remarkable changes that occur in their expression from the earliest stages of embryogenesis, through development and sequential stages of cell differentiation and maturation. A notable impact has been in the molecular dissection of ligand-receptor interactions in key cell adhesion events at the initial stages of leukocyte recruitment in inflammation, and almost certainly in the metastasis of epithelial tumours. Antibodies that recognise Le(x) and the 3'-sialyl forms were observed to identify leukocyte subsets; these were subsequently found to match those recognized by the leukocyte-endothelium adhesion molecules, the E- and P-selectins. We now describe a MAb (rat hybridoma MIN/3/60) raised to 3'-sulpho-Le(x), a carbohydrate sequence which, in vitro, is bound not only by the E-, L-, and P-selectins, but also by the cysteine-rich domain of the macrophage endocytosis receptor. We observe that MIN/3/60 is bispecific, however; it binds 3'-sulpho-Le(a) as well as 3'-sulpho-Le(x). Nevertheless, our exploratory studies reveal that it may be a useful histochemical reagent when used in conjunction with a monospecific antibody to 3'-sulpho-Le(a). The MIN/3/60 antibody reveals a sub-population of epithelial glycans in the crypts of Lieberkühn in normal human colon.