Showing papers on "Glycome published in 2012"
TL;DR: It is shown that fluorinated analogs of sialic acid and fucose can be taken up and metabolized to the desired donor substrate-based inhibitors inside the cell, resulting in a global, family-wide shutdown of sIALyl- and/or fucosyltransferases and remodeling of cell-surface glycans.
Abstract: Fluorinated, cell-permeable analogs of sialic acid and fucose are processed by monosaccharide salvage pathways to generate sialyl- and fucosyltransferase inhibitors intracellularly. These compounds serve as important new tools to dissect the role of glycan modifications within complex biological systems.
337 citations
TL;DR: There has been considerable recent progress in structural glycobiology with the determination of crystal structures of several important glycosyltransferase members, showing novel folds and variations around a common α/β scaffold.
188 citations
TL;DR: This chapter describes one of two immunological approaches that can be employed for screening of plant cell wall/biomass materials from diverse plants and tissues, and suggests that Glycome Profiling lends itself well to moderate to high-throughput screening.
Abstract: The native complexity of plant cell walls makes research on them challenging. Hence, it is advantageous to have a diversity of tools that can be used to analyze and characterize plant cell walls. In this chapter, we describe one of two immunological approaches that can be employed for screening of plant cell wall/biomass materials from diverse plants and tissues. This approach, Glycome Profiling, lends itself well to moderate to high-throughput screening of plant cell wall/biomass samples. Glycome Profiling is being further optimized to reduce the amount of sample required for the analysis, and to improve the sensitivity and throughput of the assay. We are optimistic that Glycome Profiling will prove to be a broadly applicable experimental approach that will find increasing application to a wide variety of studies on plant cell wall/biomass samples.
148 citations
TL;DR: This review summarizes present knowledge about the importance of alternative glycosylation of IgG and other proteins and suggests that even slight alterations in activity or intracellular localization of one or more biosynthetic enzymes are sufficient for the creation of novel glycan structures, which can then perform new functions.
132 citations
TL;DR: A library of structures for the serum glycome is constructed to aid in the rapid identification of serum glycans and will be used to rapidly identify glycans in unknown biological samples.
Abstract: Glycosylation is one of the most common post-translational modifications of proteins and has been shown to change with various pathological states including cancer Global glycan profiling of human serum based on mass spectrometry has already led to several promising markers for diseases The changes in glycan structure can result in altered monosaccharide composition as well as in the linkages between the monosaccharides High-throughput glycan structural elucidation is not possible due to the lack of a glycan template to expedite identification In an effort toward rapid profiling and identification of glycans, we have constructed a library of structures for the serum glycome to aid in the rapid identification of serum glycans N-Glycans from human serum glycoproteins are used as a standard and compiled into a library with exact structure (composition and linkage), liquid chromatography retention time, and accurate mass Development of the library relies on highly reproducible nanoLC/MS retention times Tandem MS and exoglycosidase digestions were used for structural elucidation The library currently contains over 300 entries with 50 structures completely elucidated and over 60 partially elucidated structures This database is steadily growing and will be used to rapidly identify glycans in unknown biological samples
112 citations
TL;DR: The findings suggest that high mannose glycans are the major component of cell surface glycosylation with even terminal glucoses, which means that distinguishing stem cells from other mammalian cells may be facilitated by the major difference in the glycosolation of the cell membrane.
103 citations
TL;DR: The roles of three genes encoding xylosyltransferases participating in xyloglucan biosynthesis in Arabidopsis were further investigated using reverse genetic, biochemical, and immunological approaches and it is concluded that XXT1 and XXT2 are responsible for the bulk of the xylOSylation of the glucan backbone, and at least one of these proteins must be present and active for xylglucan to be made.
Abstract: Xyloglucan is an important hemicellulosic polysaccharide in dicot primary cell walls. Most of the enzymes involved in xyloglucan synthesis have been identified. However, many important details of its synthesis in vivo remain unknown. The roles of three genes encoding xylosyltransferases participating in xyloglucan biosynthesis in Arabidopsis (Arabidopsis thaliana) were further investigated using reverse genetic, biochemical, and immunological approaches. New double mutants (xxt1 xxt5 and xxt2 xxt5) and a triple mutant (xxt1 xxt2 xxt5) were generated, characterized, and compared with three single mutants and the xxt1 xxt2 double mutant that had been isolated previously. Antibody-based glycome profiling was applied in combination with chemical and immunohistochemical analyses for these characterizations. From the combined data, we conclude that XXT1 and XXT2 are responsible for the bulk of the xylosylation of the glucan backbone, and at least one of these proteins must be present and active for xyloglucan to be made. XXT5 plays a significant but as yet uncharacterized role in this process. The glycome profiling data demonstrate that the lack of detectable xyloglucan does not cause significant compensatory changes in other polysaccharides, although changes in nonxyloglucan polysaccharide amounts cannot be ruled out. Structural rearrangements of the polysaccharide network appear responsible for maintaining wall integrity in the absence of xyloglucan, thereby allowing nearly normal plant growth in plants lacking xyloglucan. Finally, results from immunohistochemical studies, combined with known information about expression patterns of the three genes, suggest that different combinations of xylosyltransferases contribute differently to xyloglucan biosynthesis in the various cell types found in stems, roots, and hypocotyls.
101 citations
TL;DR: This review focuses on different glycomics and glycoproteomics approaches and their application for studying protein glycosylation in the immune system.
96 citations
TL;DR: Analysis of the human plasma vWF N-glycan population using advanced MS revealed approximately 100 distinct N- glycan compositions and identified a variety of structural features, including lactosaminic extensions, ABH antigens and sulfated antennae, as well as bisecting and terminal GlcNAc residues.
Abstract: vWF (von Willebrand factor) is a key component for maintenance of normal haemostasis, acting as the carrier protein of the coagulant Factor VIII and mediating platelet adhesion at sites of vascular injury. There is ample evidence that vWF glycan moieties are crucial determinants of its expression and function. Of particular clinical interest, ABH antigens influence vWF plasma levels according to the blood group of individuals, although the molecular mechanism underlying this phenomenon remains incompletely understood. The present paper reports analyses of the human plasma vWF N-glycan population using advanced MS. Glycomics analyses revealed approximately 100 distinct N-glycan compositions and identified a variety of structural features, including lactosaminic extensions, ABH antigens and sulfated antennae, as well as bisecting and terminal GlcNAc residues. We estimate that some 300 N-glycan structures are carried by human vWF. Glycoproteomics analyses mapped ten of the consensus sites known to carry N-glycans. Glycan populations were found to be distinct, although many structural features were shared across all sites. Notably, the H antigen is not restricted to particular N-glycosylation sites. Also, the Asn(2635) site, previously designated as unoccupied, was found to be highly glycosylated. The delineation of such varied glycan populations in conjunction with current models explaining vWF activity will facilitate research aimed at providing a better understanding of the influence of glycosylation on vWF function.
90 citations
TL;DR: A shotgun glycan microarray prepared from isolated human milk glycans, and studies on their recognition by viruses, antibodies, and glycan-binding proteins (GBPs), including lectins, provide novel insights into diverse recognition functions of HMGs.
87 citations
TL;DR: Observations indicate unambiguously the manifestation of a “glycome shift” upon conversion to iPSCs, which may not merely be the result of the initialization of gene expression, but could be involved in a more aggressive manner either in the acquisition or maintenance of the undifferentiated state of i PSCs.
TL;DR: Large biological variability at the population level as well as a large number of associations between different glycans and age are shown, and sex differences are much smaller in children than in adults and are present mainly during puberty.
Abstract: Despite the importance of protein glycosylation in all physiological and pathological processes and their potential as diagnostic markers and drug targets, the glycome of children is still unexplored. We analyzed N-linked plasma and IgG glycomes in 170 children and adolescents between 6 and 18 years of age. The results showed large biological variability at the population level as well as a large number of associations between different glycans and age. The plasma N-glycome of younger children was found to contain a larger proportion of large complex glycan structures (r= �0.71 for tetrasialylated glycans; r=�0.41 for trisialylated glycans) as well as an increase in disialylated biantennary structures (r= 0.55) with age. Core fucosylation and the level of agalactosylated plasma and IgG glycans decreased while digalactosylated glycans increased with age. This pattern of age-dependent changes in children differs from changes reported in adult population in both, direction and the intensity of changes. Also, sex differences are much smaller in children than in adults and are present mainly during puberty. These important observations should be accounted for when glycan-based diagnostic tests or therapeutics are being developed or evaluated.
TL;DR: Glycan A2BG2 increases the affinity of IgG to CD16 on effector cells, consequently enhancing Antibody-Dependent Cellular Cytotoxicity (ADCC) and may serve as a biomarker for the disease and may be involved in neuronal damage.
Abstract: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease caused by degeneration of upper and lower motor neurons. To date, glycosylation patterns of glycoproteins in fluids of ALS patients have not been described. Moreover, the aberrant glycosylation related to the pathogenesis of other neurodegenerative diseases encouraged us to explore the glycome of ALS patient sera. We found high levels of sialylated glycans and low levels of core fucosylated glycans in serum-derived N-glycans of patients with ALS, compared to healthy volunteer sera. Based on these results, we analyzed the IgG Fc N297-glycans, as IgG are major serum glycoproteins affected by sialylation or core fucosylation and are found in the motor cortex of ALS patients. The analyses revealed a distinct glycan, A2BG2, in IgG derived from ALS patient sera (ALS-IgG). This glycan increases the affinity of IgG to CD16 on effector cells, consequently enhancing Antibody-Dependent Cellular Cytotoxicity (ADCC). Therefore, we explore whether the Fc-N297-glycans of IgG may be involved in ALS disease. Immunostaining of brain and spinal cord tissues revealed over-expression of CD16 and co-localization of intact ALS-IgG with CD16 and in brain with activated microglia of G93A-SOD1 mice. Intact ALS-IgG enhanced effector cell activation and ADCC reaction in comparison to sugar-depleted or control IgG. ALS-IgG were localized in the synapse between brain microglia and neurons of G93A-SOD1 mice, manifesting a promising in vivo ADCC reaction. Therefore, glycans of ALS-IgG may serve as a biomarker for the disease and may be involved in neuronal damage.
TL;DR: This study represents the first demonstration of epigenetic regulation of plasma glycome composition, suggesting a potential mechanism by which epigenetic deregulation of the glycome may contribute to disease development.
Abstract: Protein glycosylation is a ubiquitous modification that affects the structure and function of proteins. Our recent genome wide association study identified transcription factor HNF1A as an important regulator of plasma protein glycosylation. To evaluate the potential impact of epigenetic regulation of HNF1A on protein glycosylation we analyzed CpG methylation in 810 individuals. The association between methylation of four CpG sites and the composition of plasma and IgG glycomes was analyzed. Several statistically significant associations were observed between HNF1A methylation and plasma glycans, while there were no significant associations with IgG glycans. The most consistent association with HNF1A methylation was observed with the increase in the proportion of highly branched glycans in the plasma N-glycome. The hypothesis that inactivation of HNF1A promotes branching of glycans was supported by the analysis of plasma N-glycomes in 61 patients with inactivating mutations in HNF1A, where the increase in plasma glycan branching was also observed. This study represents the first demonstration of epigenetic regulation of plasma glycome composition, suggesting a potential mechanism by which epigenetic deregulation of the glycome may contribute to disease development.
TL;DR: Recent developments in analytical technology and methodology as applied to the fields of glycomics and glycoproteomics are summarized, highlighting the key role that glycoscience can play in helping scientists understand disease biology.
Abstract: The glycome consists of all glycans (or carbohydrates) within a biological system, and modulates a wide range of important biological activities, from protein folding to cellular communications. The mining of the glycome for disease markers represents a new paradigm for biomarker discovery; however, this effort is severely complicated by the vast complexity and structural diversity of glycans. This review summarizes recent developments in analytical technology and methodology as applied to the fields of glycomics and glycoproteomics. Mass spectrometric strategies for glycan compositional profiling are described, as are potential refinements which allow structure-specific profiling. Analytical methods that can discern protein glycosylation at a specific site of modification are also discussed in detail. Biomarker discovery applications are shown at each level of analysis, highlighting the key role that glycoscience can play in helping scientists understand disease biology.
TL;DR: The colitis-associated glycome mediates CD4+ T cell expansion and contributes to the exacerbation of T cell–mediated intestinal inflammation.
Abstract: Immune responses are modified by a diverse and abundant repertoire of carbohydrate structures on the cell surface, which is known as the glycome. In this study, we propose that a unique glycome that can be identified through the binding of galectin-4 is created on local, but not systemic, memory CD4+ T cells under diverse intestinal inflammatory conditions, but not in the healthy state. The colitis-associated glycome (CAG) represents an immature core 1–expressing O-glycan. Development of CAG may be mediated by down-regulation of the expression of core-2 β1,6- N -acetylglucosaminyltransferase (C2GnT) 1, a key enzyme responsible for the production of core-2 O-glycan branch through addition of N -acetylglucosamine (GlcNAc) to a core-1 O-glycan structure. Mechanistically, the CAG seems to contribute to super raft formation associated with the immunological synapse on colonic memory CD4+ T cells and to the consequent stabilization of protein kinase C θ activation, resulting in the stimulation of memory CD4+ T cell expansion in the inflamed intestine. Functionally, CAG-mediated CD4+ T cell expansion contributes to the exacerbation of T cell–mediated experimental intestinal inflammations. Therefore, the CAG may be an attractive therapeutic target to specifically suppress the expansion of effector memory CD4+ T cells in intestinal inflammation such as that seen in inflammatory bowel disease.
TL;DR: Proteomic studies of the acidic fraction of ascites fluid from patients with ovarian cancer showed that this fraction was enriched in proteoglycans, with lumican, agrin, versican and dystroglycans were potential candidates, with threonine- and serine-rich domains that could carry a significant amount of O-linked glycosylation.
Abstract: The O-linked glycosylation of the main acidic high-molecular-weight glycoprotein from ascites fluid from patients with ovarian cancer were analyzed. The O-linked oligosaccharides were shown to consist of mainly highly sialylated core 1 and 2 structures with a smaller amount of sulfated core 2 structures. These structures were shown to be able to be further extended into small keratan sulfate (KS)-type oligosaccharides with up to four N-acetyllactosamine units. Proteomic studies of the acidic fraction of ascites fluid from patients with ovarian cancer showed that this fraction was enriched in proteoglycans. Among them, lumican, agrin, versican and dystroglycans were potential candidates, with threonine- and serine-rich domains that could carry a significant amount of O-linked glycosylation, including also the O-linked KS. Glycomic analysis using liquid chromatography (LC)-tandem mass spectrometry (MS/MS) also showed that the disialic acid NeuAc-NeuAc- was frequently found as the terminating structure on the O-linked core 1 and 2 oligosaccharides from one ascites sample. Also, a small amount of the epidermal growth factor (EGF)-associated O-linked fucose structure Gal-GlcNAc-Fucitol was detected with and without sialic acid in the LC-MS/MS analysis. Candidate proteins containing O-linked fucose were suggested to be proteoglycan-type molecules containing the O-linked fucose EGF consensus domain.
TL;DR: A tool is developed which is pre-loaded with glycome data as provided by the CFG and is also able to visualize local glycan profiling data for human and mouse and enable users to visualize and perform queries on their own data.
Abstract: Motivation: The development of glycomics technologies in recent years has produced a sufficient amount of data to begin analyzing the glycan structures present in various organisms and tissues. In particular, glycan profiling using mass spectrometry (MS) and tandem MS has generated a large amount of data that are waiting to be analyzed. The Consortium for Functional Glycomics (CFG) has provided a web resource for obtaining such glycan profiling data easily. Although an interactive spectrum viewer is provided on the website as a Java applet, it is not necessarily easy to search for particular glycans or to find commonalities between different tissues in a single organism, for example. Therefore, to allow users to better take advantage of the valuable glycome data that can be obtained from mass spectra and other leading technologies, we have developed a tool called Glycome Atlas which is pre-loaded with the data from the CFG and is also able to visualize local glycan profiling data for human and mouse.
Results: We have developed a tool to allow users to visualize and perform queries of glycome data. This tool, called GlycomeAtlas, is pre-loaded with glycome data as provided by the CFG. Moreover, users can load their own local glycome data into this tool to visualize and perform queries on their own data.
Availability: This tool is available at the following URL: http://www.rings.t.soka.ac.jp/GlycomeAtlas/GUI.html.
Contact: kkiyoko@soka.ac.jp
TL;DR: Glycomics, genomics, and functional studies established ZFL as a relevant cellular model for the study of glycosylation and demonstrated that this cell system was amenable to metabolic labeling using functionalized monosaccharides that permit in vivo imaging of gly cosylation processes.
Abstract: The emergence of zebrafish as a model organism for human diseases was accompanied by the development of cellular model systems that extended the possibilities for in vitro manipulation and in vivo studies after cell implantation. The exploitation of zebrafish cell systems is, however, still hampered by the lack of genomic and biochemical data. Here, we lay a path toward the efficient use of ZFL, a zebrafish liver-derived cell system, as a platform for studying glycosylation. To achieve this, we established the glycomic profile of ZFL by a combination of mass spectrometry and NMR. We demonstrated that glycoproteins were substituted by highly sialylated multiantennary N-glycans, some of them comprising the unusual zebrafish epitope Galβ1-4[Neu5Ac(α2,3)]Galβ1-4[Fuc(α1,3)]GlcNAc, and core 1 multisialylated O-glycans. Similarly, these analyses established that glycolipids were dominated by sialylated gangliosides. In parallel, analyzing the expression patterns of all putative sialyl- and fucosyltransferases, we directly correlated the identified structures to the set of enzymes involved in ZFL glycome. Finally, we demonstrated that this cell system was amenable to metabolic labeling using functionalized monosaccharides that permit in vivo imaging of glycosylation processes. Altogether, glycomics, genomics, and functional studies established ZFL as a relevant cellular model for the study of glycosylation.
TL;DR: Examining Acanthamoeba glycosylation may yield insights into virulence factors for this genus of therapeutically resistant parasites, and the glycomic potential of its asparagine-linked glycans is elucidated.
TL;DR: The regulation of 'low level' biochemical processes, ranging from gene expression and protein folding through the production of flexible glycan surface signalling fronds, appears to require systems of chemical cognition whose sophistication may rival that of high order neural process.
Abstract: Unlike the universal genetic code and ordered protein folding, direct application of Tlusty's method to the glycome produces a reducto ad absurdum: From the beginning a complicated system of chemical cognition is needed so that external information constrains and tunes what would otherwise be a monstrously large ‘glycan code error network’. Further, the glycan manufacture machinery itself must be regulated by yet other levels of chemical cognition to ensure that what is produced matches what was chosen for production. Application of a rate distortion index theorem/operator method at this second stage appears possible, permitting analytic characterization of the complicated ‘glycan spectra’ associated with cellular interactions and their dynamics. The regulation of ‘low level’ biochemical processes, ranging from gene expression and protein folding through the production of flexible glycan surface signalling fronds, appears to require systems of chemical cognition whose sophistication may rival that of high order neural process.
TL;DR: In this article, a carbohydrate microarray analysis of a number of tumor-associated carbohydrates for their serum antibody reactivities and potential immunogenicity in humans was performed, showing that IgG antibodies targeting the Man9 or Tri-/m-II autoantigens are readily detectable in the sera of men with BPH, as well as those with cancer.
Abstract: Although tumor-associated abnormal glycosylation has been recognized for decades, information regarding host recognition of the evolving tumor glycome remains elusive. We report here a carbohydrate microarray analysis of a number of tumor-associated carbohydrates for their serum antibody reactivities and potential immunogenicity in humans. These are the precursors, cores and internal sequences of N-glycans. They are usually masked by other sugar moieties and belong to a class of glyco-antigens that are normally “cryptic”. However, viral expression of these carbohydrates may trigger host immune responses. For examples, HIV-1 and SARS-CoV display Man9 clusters and tri- or multi-antennary type II (Galβ1→4GlcNAc) chains (Tri/m-II), respectively; viral neutralizing antibodies often target these sugar moieties. We asked, therefore, whether prostate tumor expression of corresponding carbohydrates triggers antibody responses in vivo. Using carbohydrate microarrays, we analyzed a panel of human sera, including 17 samples from prostate cancer patients and 12 from men with Benign Prostatic Hyperplasia (BPH). We observed that IgG antibodies targeting the Man9- or Tri-/m-II-autoantigens are readily detectable in the sera of men with BPH, as well as those with cancer. Importantly, these antibody activities were selectively increased in prostate cancer patients. Thus, human immune systems actively recognize these N-glycan cryptic carbohydrates and produce targeting antibodies. This finding shads a light on a class of previously less studied immunological targets of human cancers. Identifying the diagnostic, prognostic and therapeutic values of these targets will require further investigation.
TL;DR: This chapter describes the generation of a lectin-binding signature associated with metastatic primary breast tumours that have been resected, fixed, and embedded in paraffin.
Abstract: Since 2005, lectin microarray technology has emerged as a relatively simple yet powerful technique for the comprehensive analysis of glycoprotein glycosylation. Lectin microarrays represent a new analytical method that can be used to explore the human glycome, a unique source of markers of diseases including cancer. The lectin microarray technology is a sensitive tool with the potential to allow high-throughput analysis of cancer-associated changes in glycosylation. This chapter describes the generation of a lectin-binding signature associated with metastatic primary breast tumours that have been resected, fixed, and embedded in paraffin. Procedures concerning sample and lectin microarray preparation are explained, alongside experimental considerations and approaches to data analysis.
TL;DR: It is shown that, following liquid chromatographic separation on graphite columns, subambient pressure ionization with nanoelectrospray (SPIN)-MS can expand the serum glycome profile in comparison with the conventional atmospheric pressure electrosprays ionization (ESI)-MS with a heated capillary inlet.
Abstract: Human serum glycan profiling with mass spectrometry (MS) has been employed to study several disease conditions and is demonstrating promise in, for example, clinical biomarker discovery. However, the low glycan ionization efficiency and the large dynamic range of glycan concentrations in human sera can hinder comprehensive profiling. In particular, large glycans are problematic because they are present at low concentrations and are prone to fragmentation. Here we show that, following liquid chromatographic separation on graphite columns, subambient pressure ionization with nanoelectrospray (SPIN)-MS can expand the serum glycome profile in comparison with the conventional atmospheric pressure electrospray ionization (ESI)-MS with a heated capillary inlet. Notably, the ions generated by the SPIN interface were observed at higher charge states for approximately half of the annotated glycans. Out of a total of 130 detected glycans, 34 were only detected with the SPIN-MS, resulting in improved coverage of glycan families as well as of glycans with larger numbers of labile monosaccharides.
TL;DR: The preparation of SAMs-coated gold surface arrays presenting carbohydrate or (glyco)peptide substrates, either pre-formed or directly synthesized on-chip, and MALDI-ToF MS analysis of glycosyltransferase activities on these immobilized substrates are described.
Abstract: Glycan-processing enzymes such as glycosyltransferases and glycosidases are responsible for the makeup of the glycome. The definition of their substrate specificities is, therefore, a central task in glycomics. In addition, these enzymes are themselves useful synthetic tools for the generation of complex carbohydrate structures as an alternative to tedious chemical synthesis. There has been great interest in using microarrays for studying these glycoenzymes because it allows the specificity of the enzyme to be probed against a panel of immobilized potential substrates, and also expands the repertoire of sugar arrays available for further carbohydrate?protein interaction studies. In particular, self-assembled monolayers (SAMs) of alkanethiols on gold surfaces have proven to be a valuable platform for such studies due to their robustness and their biocompatible, well-defined structure. Furthermore, a direct observation of the change in mass of immobilized substrates due to enzymatic processing is possible through label-free MALDI-ToF MS (matrix-assisted laser desorption/ionization time-of-flight mass spectrometry) technique. In this chapter, we describe the preparation of SAMs-coated gold surface arrays presenting carbohydrate or (glyco)peptide substrates, either pre-formed or directly synthesized on-chip, and MALDI-ToF MS analysis of glycosyltransferase activities on these immobilized substrates.
TL;DR: Current progress in glycomics is focused on, including new mass spectrometry-based high-throughput techniques for glycan purification and annotation, the recent work on enhancing microarray methodologies to decipher the glycome, and the scope of glycans as disease markers.
Abstract: Carbohydrates coat most cell types and are closely involved in various biological events. Their structures are complex to analyze owing to their branched nature, the diversity of secondary modifications of monomers, and their indirect relationship to the genome. Additionally, the range of cellular milieu in which glycan modifications are found is immense. Thus, despite genomics and proteomics being highly comprehensible and manageable to most scientists, technologies to assess glycan structures rapidly are still in their infancy. Recently, interest in profiling the glycome has increased due to the potential of glycans as disease markers. Incidentally, mass spectrometry is emerging as a powerful technique for profiling the glycome. This manuscript focuses on current progress in glycomics, including new mass spectrometry-based high-throughput techniques for glycan purification and annotation, the recent work on enhancing microarray methodologies to decipher the glycome, and the scope of glycans as disease markers.
TL;DR: This chapter describes two approaches to introduce bioorthogonal chemical reporters (tags) onto cell surface fucosylated glycans and glycans bearing LacNAc disaccharides, respectively, which can then be conjugated to imaging probes via bioorthogsonal click chemistry.
Abstract: The glycome, the full complement of glycans that cells produce, is an attractive target for molecular imaging. Imaging of the glycome in living systems has recently been enabled via bioorthogonal chemical reporter-based approaches. In this chapter, we describe two approaches to introduce bioorthogonal chemical reporters (tags) onto cell surface fucosylated glycans and glycans bearing LacNAc disaccharides, respectively. The tagged glycans can then be conjugated to imaging probes via bioorthogonal click chemistry. Similar approaches can be extended to image other sectors of the glycome in living systems.
08 Nov 2012
TL;DR: A novel algorithm for aligning glycan tree structures is implemented as a web tool called MCAW (Multiple Carbohydrate Alignment with Weights), which can now be used in several other analyses of glycan structures, such as in the development ofglycan score matrices as well as in state model determination of probabilistic tree models.
Abstract: The purpose of our research is the elucidation of glycan recognition patterns. Glycans are composed of monosaccharides and have complex structures with branches due to the fact that monosaccharides have multiple potential binding positions compared to amino acids. Each monosaccharide can potentially be bound by up to five other monosaccharides, compared to two for any amino acid. Glycans are often bound to proteins and lipids on the cell surface and play important roles in biological processes. Lectins in particular are proteins that recognize and bind to glycans. In general, lectins bind to the terminal monosaccharides of glycans on glycoconjugates. However, it is suggested that some lectins recognize not only terminal monosaccharides, but also internal monosaccharides, possibly influencing the binding affinity. Such analyses are difficult without novel bioinformatics techniques. Thus, in order to better understand the glycan recognition mechanism of such biomolecules, we have implemented a novel algorithm for aligning glycan tree structures, which we provide as a web tool called MCAW (Multiple Carbohydrate Alignment with Weights). From our web tool, we have analyzed several different lectins, and our results could confirm the existence of well-known glycan motifs. Our work can now be used in several other analyses of glycan structures, such as in the development of glycan score matrices as well as in state model determination of probabilistic tree models. Therefore, this work is a fundamental step in glycan pattern analysis to progress glycobiology research.
TL;DR: N-azidoglucosamine was successfully incorporated into glycolipidic structures of Plasmodium falciparum intraerythrocytic stages providing a new method to quantify dynamic changes in the glycosylation pattern and facilitating direct mass spectrometry analyses.
TL;DR: This paper not only brings out novel segments and their respective contribution to glycomics but also highlights the great relevance of pharmacological effects of these new glycans in the current glycome era.
Abstract: Following the genome, transcriptome and proteome, the glycome has currently launched in biology bringing apparently more challenges than the first projects. The long major conception of carbohydrates as just energetically involved class of biomolecules has fallen apart as innumerable essential biological actions have been raised, impossible to be enlisted all together at once. Such actions involve not only vital roles in cell and physiology but within a different context they also include potent therapeutic actions in coagulation, thrombosis, inflammation, virosis, pathogenesis, tumorigenesis, metastasis and angiogenesis. Glycomics is so extensive project that subdivision is necessary for its progress. Specific segments of research have been created about particular bioactive sugar classes such as sialome for sialic acids, and heparanomics for heparan bioactive domains. Fucanome and galactanome must be also included in the recent glycomics age with respect to the relatively new class of marine fucose- or galactose-composing polysaccharides named sulfated fucans and sulfated galactans. These glycans are very biologically relevant since they show potent pharmacological properties in many of the above-mentioned systems; besides in sea-urchins they are responsible to control a very rare case of carbohydrate-mediated cell signaling event, the acrosome reaction. The structure of these glycans is very restricted to phyla or species of occurrence. Among all marine organisms, only invertebrates and red algae have been known so far to express high molecular weight polymers composed of well-defined structures. These structural features are unique and very rare among any bioactive polysaccharide ever studied. This would make fucanome and galactanome differential glycomics subprojects in terms of structure and phylogeny. This paper not only brings out novel segments and their respective contribution to glycomics but also highlights the great relevance of pharmacological effects of these new glycans in the current glycome era.