Engineering a versatile tandem repeat-type α2-6sialic acid-binding lectin

Lectins as versatile tools to explore cellular glycosylation

Lectins are naturally occurring carbohydrate-binding proteins that are ubiquitous in nature and highly selective for their, often incompletely characterised, binding partners. From their discovery in the late 1880s to the present day, they have provided a broad palette of versatile tools for exploring the glycosylation of cells and tissues and for uncovering the myriad functions of glycosylation in biological systems. The technique of lectin histochemistry, used to map the glycosylation of tissues, has been instrumental in revealing the changing profile of cellular glycosylation in development, health and disease. It has been especially enlightening in revealing fundamental alterations in cellular glycosylation that accompany cancer development and metastasis, and has facilitated the identification of glycosylated biomarkers that can predict prognosis and may have utility in development of early detection and screening, Moreover, it has led to insights into the functional role of glycosylation in healthy tissues and in the processes underlying disease. Recent advances in biotechnology mean that our understanding of the precise binding partners of lectins is improving and an ever-wider range of lectins are available, including recombinant human lectins and lectins with enhanced, engineered properties. Moreover, use of traditional histochemistry to support a broad range of cutting-edge technologies and the development of high throughout microarray platforms opens the way for ever more sophisticated mapping - and understanding - of the glycome.

Lectin Histochemistry: Historical Perspectives, State of the Art, and Future Directions

Lectins, discovered more than 100 years ago and defined by their ability to selectively recognize specific carbohydrate structures, are ubiquitous in living organisms. Their precise functions are as yet under-explored and incompletely understood but they are clearly involved, through recognition of their binding partners, in a myriad of biological mechanisms involved in cell identity, adhesion, signaling, and growth regulation in health and disease. Understanding the complex "sugar code" represented by the "glycome" is a major challenge and at the forefront of current biological research. Lectins have been widely employed in histochemical studies to map glycosylation in cells and tissues. Here, a brief history of the discovery of lectins and early developments in their use is presented along with a selection of some of the most interesting and significant discoveries to emerge from the use of lectin histochemistry. Further, an evaluation of the next generation of lectin-based technologies is presented, including the potential for designing recombinant lectins with more precisely defined binding characteristics, linking lectin-based studies with other technologies to answer fundamental questions in glycobiology and approaches to exploring the interactions of lectins with their binding partners in more detail.

One, two, many: Strategies to alter the number of carbohydrate binding sites of lectins

Carbohydrates are more than an energy-storage. They are ubiquitously found on cells and most proteins, where they encode biological information. Lectins bind these carbohydrates and are essential for translating the encoded information into biological functions and processes. Hundreds of lectins are known, and they are found in all domains of life. For half a century, researchers have been preparing variants of lectins in which the binding sites are varied. In this way, the traits of the lectins such as the affinity, avidity and specificity towards their ligands as well as their biological efficacy were changed. These efforts helped to unravel the biological importance of lectins and resulted in improved variants for biotechnological exploitation and potential medical applications. This review gives an overview on the methods for the preparation of artificial lectins and complexes thereof and how reducing or increasing the number of binding sites affects their function.

Self-Assembling Lectin Nano-Block Oligomers Enhance Binding Avidity to Glycans

Lectins, carbohydrate-binding proteins, are attractive biomolecules for medical and biotechnological applications. Many lectins have multiple carbohydrate recognition domains (CRDs) and strongly bind to specific glycans through multivalent binding effect. In our previous study, protein nano-building blocks (PN-blocks) were developed to construct self-assembling supramolecular nanostructures by linking two oligomeric proteins. A PN-block, WA20-foldon, constructed by fusing a dimeric four-helix bundle de novo protein WA20 to a trimeric foldon domain of T4 phage fibritin, self-assembled into several types of polyhedral nanoarchitectures in multiples of 6-mer. Another PN-block, the extender PN-block (ePN-block), constructed by tandemly joining two copies of WA20, self-assembled into cyclized and extended chain-type nanostructures. This study developed novel functional protein nano-building blocks (lectin nano-blocks) by fusing WA20 to a dimeric lectin, Agrocybe cylindracea galectin (ACG). The lectin nano-blocks self-assembled into various oligomers in multiples of 2-mer (dimer, tetramer, hexamer, octamer, etc.). The mass fractions of each oligomer were changed by the length of the linkers between WA20 and ACG. The binding avidity of the lectin nano-block oligomers to glycans was significantly increased through multivalent effects compared with that of the original ACG dimer. Lectin nano-blocks with high avidity will be useful for various applications, such as specific cell labeling.

Strategies and Tactics for the Development of Selective Glycan-Binding Proteins

The influences of glycans impact all biological processes, disease states, and pathogenic interactions. Glycan-binding proteins (GBPs), such as lectins, are decisive tools for interrogating glycan structure and function because of their ease of use and ability to selectively bind defined carbohydrate epitopes and glycosidic linkages. GBP reagents are prominent tools for basic research, clinical diagnostics, therapeutics, and biotechnological applications. However, the study of glycans is hindered by the lack of specific and selective protein reagents to cover the massive diversity of carbohydrate structures that exist in nature. In addition, existing GBP reagents often suffer from low affinity or broad specificity, complicating data interpretation. There have been numerous efforts to expand the GBP toolkit beyond those identified from natural sources through protein engineering, to improve the properties of existing GBPs or to engineer novel specificities and potential applications. This review details the current scope of proteins that bind carbohydrates and the engineering methods that have been applied to enhance the affinity, selectivity, and specificity of binders.

Towards structure-focused glycoproteomics

Facilitated by advances in the separation sciences, mass spectrometry and informatics, glycoproteomics, the analysis of intact glycopeptides at scale, has recently matured enabling new insights into the complex glycoproteome. While diverse quantitative glycoproteomics strategies capable of mapping monosaccharide compositions of N- and O-linked glycans to discrete sites of proteins within complex biological mixtures with considerable sensitivity, quantitative accuracy and coverage have become available, developments supporting the advancement of structure-focused glycoproteomics, a recognised frontier in the field, have emerged. Technologies capable of providing site-specific information of the glycan fine structures in a glycoproteome-wide context are indeed necessary to address many pending questions in glycobiology. In this review, we firstly survey the latest glycoproteomics studies published in 2018–2020, their approaches and their findings, and then summarise important technological innovations in structure-focused glycoproteomics. Our review illustrates that while the O-glycoproteome remains comparably under-explored despite the emergence of new O-glycan-selective mucinases and other innovative tools aiding O-glycoproteome profiling, quantitative glycoproteomics is increasingly used to profile the N-glycoproteome to tackle diverse biological questions. Excitingly, new strategies compatible with structure-focused glycoproteomics including novel chemoenzymatic labelling, enrichment, separation, and mass spectrometry-based detection methods are rapidly emerging revealing glycan fine structural details including bisecting GlcNAcylation, core and antenna fucosylation, and sialyl-linkage information with protein site resolution. Glycoproteomics has clearly become a mainstay within the glycosciences that continues to reach a broader community. It transpires that structure-focused glycoproteomics holds a considerable potential to aid our understanding of systems glycobiology and unlock secrets of the glycoproteome in the immediate future.

Application of Lectin Microarrays for Biomarker Discovery

Many proteins in living organisms are glycosylated. As their glycan patterns exhibit protein-, cell-, and tissue-specific heterogeneity, changes in the glycosylation levels could serve as useful indicators of various pathological and physiological states. Thus, the identification of glycoprotein biomarkers from specific changes in the glycan profiles of glycoproteins is a trending field. Lectin microarrays provide a new glycan analysis platform, which enables rapid and sensitive analysis of complex glycans without requiring the release of glycans from the protein. Recent developments in lectin microarray technology enable high-throughput analysis of glycans in complex biological samples. In this review, we will discuss the basic concepts and recent progress in lectin microarray technology, the application of lectin microarrays in biomarker discovery, and the challenges and future development of this technology. Given the tremendous technical advancements that have been made, lectin microarrays will become an indispensable tool for the discovery of glycoprotein biomarkers.

Recent approaches for directly profiling cell surface sialoform

Sialic acids (SAs) are nine-carbon monosaccharides existing at the terminal location of glycan structures on the cell surface and secreted glycoconjugates. The expression levels and linkages of SAs on cells and tissues, collectively known as sialoform, present the hallmark of the cells and tissues of different systems and conditions. Accordingly, detecting or profiling cell surface sialoforms is very critical for understanding the function of cell surface glycans and glycoconjugates and even the molecular mechanisms of their underlying biological processes. Further, it may provide therapeutic and diagnostic applications for different diseases. In the past decades, several kinds of SA-specific binding molecules have been developed for detecting and profiling specific sialoforms of cells and tissues; the experimental materials have expanded from frozen tissue to living cells; and the analytical technologies have advanced from histochemistry to fluorescent imaging, flow cytometry and microarrays. This review summarizes the recent bioaffinity approaches for directly detecting and profiling specific SAs or sialylglycans, and their modifications of different cells and tissues.

Lectin engineering: the possible and the actual

Lectins are a widespread group of sugar-binding proteins occurring in all types of organisms including animals, plants, bacteria, fungi and even viruses. According to a recent report, there are more than 50 lectin scaffolds (∼Pfam), for which three-dimensional structures are known and sugar-binding functions have been confirmed in the literature, which far exceeds our view in the twentieth century (Fujimoto et al. 2014 Methods Mol. Biol. 1200, 579-606 (doi:10.1007/978-1-4939-1292-6_46)). This fact suggests that new lectins will be discovered either by a conventional screening approach or just by chance. It is also expected that new lectin domains including those found in enzymes as carbohydrate-binding modules will be generated in the future through evolution, although this has never been attempted on an experimental level. Based on the current state of the art, various methods of lectin engineering are available, by which lectin specificity and/or stability of a known lectin scaffold can be improved. However, the above observation implies that any protein scaffold, including those that have never been described as lectins, may be modified to acquire a sugar-binding function. In this review, possible approaches to confer sugar-binding properties on synthetic proteins and peptides are described.

Deciphering Protein Glycosylation by Computational Integration of On-chip Profiling, Glycan-array Data, and Mass Spectrometry

The difficulty in uncovering detailed information about protein glycosylation stems from the complexity of glycans and the large amount of material needed for the experiments. Here we report a method that gives information on the isomeric variants of glycans in a format compatible with analyzing low-abundance proteins. On-chip glycan modification and probing (on-chip gmap) uses sequential and parallel rounds of exoglycosidase cleavage and lectin profiling of microspots of proteins, together with algorithms that incorporate glycan-array analyses and information from mass spectrometry, when available, to computationally interpret the data. In tests on control proteins with simple or complex glycosylation, on-chip gmap accurately characterized the relative proportions of core types and terminal features of glycans. Subterminal features (monosaccharides and linkages under a terminal monosaccharide) were accurately probed using a rationally designed sequence of lectin and exoglycosidase incubations. The integration of mass information further improved accuracy in each case. An alternative use of on-chip gmap was to complement the mass spectrometry analysis of detached glycans by specifying the isomers that comprise the glycans identified by mass spectrometry. On-chip gmap provides the potential for detailed studies of glycosylation in a format compatible with clinical specimens or other low-abundance sources.

Studying the Structural Significance of Galectin Design by Playing a Modular Puzzle: Homodimer Generation from Human Tandem-Repeat-Type (Heterodimeric) Galectin-8 by Domain Shuffling

Tissue lectins are emerging (patho)physiological effectors with broad significance. The capacity of adhesion/growth-regulatory galectins to form functional complexes with distinct cellular glycoconjugates is based on molecular selection of matching partners. Engineering of variants by changing the topological display of carbohydrate recognition domains (CRDs) provides tools to understand the inherent specificity of the functional pairing. We here illustrate its practical implementation in the case of human tandem-repeat-type galectin-8 (Gal-8). It is termed Gal-8 (NC) due to presence of two different CRDs at the N- and C-terminal positions. Gal-8N exhibits exceptionally high affinity for 3'-sialylated/sulfated β-galactosides. This protein is turned into a new homodimer, i.e., Gal-8 (NN), by engineering. The product maintained activity for lactose-inhibitable binding of glycans and glycoproteins. Preferential association with 3'-sialylated/sulfated (and 6-sulfated) β-galactosides was seen by glycan-array analysis when compared to the wild-type protein, which also strongly bound to ABH-type epitopes. Agglutination of erythrocytes documented functional bivalency. This result substantiates the potential for comparative functional studies between the variant and natural Gal-8 (NC)/Gal-8N.

Characterization of Cryptopygus antarcticus endo-β-1,4-glucanase from Bombyx mori expression systems

Endo-β-1,4-glucanase (CaCel) from Antarctic springtail, Cryptopygus antarcticus, a cellulase with high activity at low temperature, shows potential industrial use. To obtain sufficient active cellulase for characterization, CaCel gene was expressed in Bombyx mori-baculovirus expression systems. Recombinant CaCel (rCaCel) has been expressed in Escherichia coli (Ec-CaCel) at temperatures below 10°C, but the expression yield was low. Here, rCaCel with a silkworm secretion signal (Bm-CaCel) was successfully expressed and secreted into pupal hemolymph and purified to near 90% purity by Ni-affinity chromatography. The yield and specific activity of rCaCel purified from B. mori were estimated at 31 mg/l and 43.2 U/mg, respectively, which is significantly higher than the CaCel yield obtained from E. coli (0.46 mg/l and 35.8 U/mg). The optimal pH and temperature for the rCaCels purified from E. coli and B. mori were 3.5 and 50°C. Both rCaCels were active at a broad range of pH values and temperatures, and retained more than 30% of their maximal activity at 0°C. Oligosaccharide structural analysis revealed that Bm-CaCel contains elaborated N- and O-linked glycans, whereas Ec-CaCel contains putative O-linked glycans. Thermostability of Bm-CaCel from B. mori at 60°C was higher than that from E. coli, probably due to glycosylation.

Lectin engineering, a molecular evolutionary approach to expanding the lectin utilities

In the post genomic era, glycomics—the systematic study of all glycan structures of a given cell or organism—has emerged as an indispensable technology in various fields of biology and medicine. Lectins are regarded as “decipherers of glycans”, being useful reagents for their structural analysis, and have been widely used in glycomic studies. However, the inconsistent activity and availability associated with the plant-derived lectins that comprise most of the commercially available lectins, and the limit in the range of glycan structures covered, have necessitated the development of innovative tools via engineering of lectins on existing scaffolds. This review will summarize the current state of the art of lectin engineering and highlight recent technological advances in this field. The key issues associated with the strategy of lectin engineering including selection of template lectin, construction of a mutagenesis library, and high-throughput screening methods are discussed.

The detection and discovery of glycan motifs in biological samples using lectins and antibodies: new methods and opportunities

Recent research has uncovered unexpected ways that glycans contribute to biology, as well as new strategies for combatting disease using approaches involving glycans. To make full use of glycans for clinical applications, we need more detailed information on the location, nature, and dynamics of glycan expression in vivo. Such studies require the use of specimens acquired directly from patients. Effective studies of clinical specimens require low-volume assays, high precision measurements, and the ability to process many samples. Assays using affinity reagents-lectins and glycan-binding antibodies-can meet these requirements, but further developments are needed to make the methods routine and effective. Recent advances in the use of glycan-binding proteins involve improved determination of specificity using glycan arrays; the availability of databases for mining and analyzing glycan array data; lectin engineering methods; and the ability to quantitatively interpret lectin measurements. Here, we describe many of the challenges and opportunities involved in the application of these new approaches to the study of biological samples. The new tools hold promise for developing methods to improve the outcomes of patients afflicted with diseases characterized by aberrant glycan expression.

Podocalyxin is a glycoprotein ligand of the human pluripotent stem cell-specific probe rBC2LCN

In comprehensive glycome analysis with a high-density lectin microarray, we have previously shown that the recombinant N-terminal domain of the lectin BC2L-C from Burkholderia cenocepacia (rBC2LCN) binds exclusively to undifferentiated human induced pluripotent stem (iPS) cells and embryonic stem (ES) cells but not to differentiated somatic cells. Here we demonstrate that podocalyxin, a heavily glycosylated type 1 transmembrane protein, is a glycoprotein ligand of rBC2LCN on human iPS cells and ES cells. When analyzed by DNA microarray, podocalyxin was found to be highly expressed in both iPS cells and ES cells. Western and lectin blotting revealed that rBC2LCN binds to podocalyxin with a high molecular weight of more than 240 kDa in undifferentiated iPS cells of six different origins and four ES cell lines, but no binding was observed in either differentiated mouse feeder cells or somatic cells. The specific binding of rBC2LCN to podocalyxin prepared from a large set of iPS cells (138 types) and ES cells (15 types) was also confirmed using a high-throughput antibody-overlay lectin microarray. Alkaline digestion greatly reduced the binding of rBC2LCN to podocalyxin, indicating that the major glycan ligands of rBC2LCN are presented on O-glycans. Furthermore, rBC2LCN was found to exhibit significant affinity to a branched O-glycan comprising an H type 3 structure (Ka, 2.5 × 10(4) M(-1)) prepared from human 201B7 iPS cells, indicating that H type 3 is a most probable potential pluripotency marker. We conclude that podocalyxin is a glycoprotein ligand of rBC2LCN on human iPS cells and ES cells.

Lectin microarrays: concept, principle and applications

The lectin microarray is a novel platform for glycan analysis, having emerged only in recent years. Unlike other conventional methods, e.g., liquid chromatography and mass spectrometry, it enables rapid and high-sensitivity profiling of complex glycan features without the need for liberation of glycans. Target samples include an extensive range of glycoconjugates involved in cells, tissues, body fluids, as well as synthetic glycans and their mimics. Various procedures for rapid differential glycan profiling have been developed for glycan-related biomarkers. Such glycoproteomics targeting allows precise diagnosis of chronic diseases potentially related to cancer. Application of this method to evaluation of various types of stem cells resulted in the discovery of a new pluripotent cell-specific glycan marker. To explore this technology a more fundamental and extensive understanding of lectins is necessary in relation to the structural uniqueness of glycans. In this chapter, the essence of the lectin microarray is described with some focus on an evanescent-field-activated fluorescence detection principle as a system to achieve in situ (i.e., washing free) aqueous-phase observation under equilibrium conditions. The developed lectin microarray system allows even researchers with poor experience in glycan profiling to perform extensive high-throughput analysis targeting various forms of glycans and even cells.

Binding sugars: from natural lectins to synthetic receptors and engineered neolectins

The large diversity and complexity of glycan structures together with their crucial role in many biological or pathological processes require the development of new high-throughput techniques for analyses. Lectins are classically used for characterising, imaging or targeting glycoconjugates and, when printed on microarrays, they are very useful tools for profiling glycomes. Development of recombinant lectins gives access to reliable and reproducible material, while engineering of new binding sites on existing scaffolds allows tuning of specificity. From the accumulated knowledge on protein-carbohydrate interactions, it is now possible to use nucleotide and peptide (bio)synthesis for producing new carbohydrate-binding molecules. Such a biomimetic approach can also be addressed by boron chemistry and supra-molecular chemistry for the design of fully artificial glycosensors.

Integrated approach toward the discovery of glyco-biomarkers of inflammation-related diseases

Glycobiology has contributed tremendously to the discovery and characterization of cancer-related biomarkers containing glycans (i.e., glyco-biomarkers) and a more detailed understanding of cancer biology. It is now recognized that most chronic diseases involve some elements of chronic inflammation; these include cancer, Alzheimer's disease, and metabolic syndrome (including consequential diabetes mellitus and cardiovascular diseases). By extending the knowledge and experience of the glycobiology community regarding cancer biomarker discovery, we should be able to contribute to the discovery of diagnostic/prognostic glyco-biomarkers of other chronic diseases that involve chronic inflammation. Future integration of large-scale "omics"-type data (e.g., genomics, epigenomics, transcriptomics, proteomics, and glycomics) with computational model building, or a systems glycobiology approach, will facilitate such efforts.

Lectin-based structural glycomics: a practical approach to complex glycans

Glycans exist in nature in various forms of glycoconjugates, i.e., glycoproteins, glycolipids, and glycosaminoglycans, either in soluble or membrane-bound forms. One of their prominent properties distinguished from nucleic acids and proteins is "heterogeneity" largely attributed to their inherent features of biosynthesis. In general, various methods based on the physicochemical principles have been taken for their separation and structural determination although all of them require prior liberation of glycans and appropriate labeling. On the other hand, a series of carbohydrate-binding proteins, or "lectins," have extensively been used in a more direct manner for cell typing, histochemical staining, and glycoprotein fractionation. Although most procedures conventionally used are useful, unfortunately they lack "throughput" comparable to a performance required for current omics studies. Recently, a novel technique called lectin microarray has attracted increasing attention from not only glycoscientists but also researchers in other fields, because it is straightforward and also informative. The method is innovating in that it enables direct approach to glycoconjugates such as glycoproteins and even cells without liberation of glycans from the core substrate, and therefore can be effectively applied for the sake of differential profiling in various fields. Concept, strategy, and technical advancement of lectin microarray are described. Also, as an introduction to glycomics, the authors explain the motivation to challenge this theme.

Glycan and lectin microarrays for glycomics and medicinal applications

Three different array formats to study a challenging field of glycomics are presented here, based on the use of a panel of immobilized glycan or lectins, and on in silico computational approach. Glycan and lectin arrays are routinely used in combination with other analytical tools to decipher a complex nature of glycan-mediated recognition responsible for signal transduction of a broad range of biological processes. Fundamental aspects of the glycan and lectin array technology are discussed, with the focus on the choice and availability of the biorecognition elements, fabrication protocols, and detection platforms involved. Moreover, practical applications of both technologies especially in the field of clinical diagnostics are provided. The future potential of a complementary in silico array technology to reveal details of the protein-glycan-binding profiles is discussed here.

A versatile technology for cellular glycomics using lectin microarray

All cells in nature are covered with a dense and complex array of glycans. The total glycan repertoire expressed on cells, "the cellular glycome," varies at every level of biological organization, and in response to intrinsic and extrinsic stimuli. The cellular glycome is often referred to as the "cell face," which reflects the condition and type of the cell. In other words, cells can be discriminated in detail by characterization of their individual cellular glycome. Based on this concept, we describe our strategy for profiling the cellular glycome using lectin microarray followed by lectin-based cell discrimination using Chinese hamster ovary cells and their glycosylation-defective mutants (Lec1, Lec2, and Lec8) as models. The results add to the understanding and applications of "Cellular Glycomics."