Clustered O-Glycans of IgA1: DEFINING MACRO- AND MICROHETEROGENEITY BY USE OF ELECTRON CAPTURE/TRANSFER DISSOCIATION*

IgA nephropathy (IgAN) is the most common primary glomerulonephritis in the world. Aberrantly glycosylated IgA1, with galactose (Gal)-deficient hinge region (HR) O-glycans, plays a pivotal role in the pathogenesis of the disease. It is not known whether the glycosylation defect occurs randomly or preferentially at specific sites. We have described the utility of activated ion-electron capture dissociation (AI-ECD) mass spectrometric analysis of IgA1 O-glycosylation. However, locating and characterizing the entire range of O-glycan attachment sites are analytically challenging due to the clustered serine and threonine residues in the HR of IgA1 heavy chain. To address this problem, we analyzed all glycoforms of the HR glycopeptides of a Gal-deficient IgA1 myeloma protein, mimicking the aberrant IgA1 in patients with IgAN, by use of a combination of IgA-specific proteases + trypsin and AI-ECD Fourier transform ion cyclotron resonance (FT-ICR) tandem mass spectrometry (MS/MS). The IgA-specific proteases provided a variety of IgA1 HR fragments that allowed unambiguous localization of all O-glycosylation sites in the six most abundant glycoforms, including the sites deficient in Gal. Additionally, this protocol was adapted for on-line liquid chromatography (LC)-AI-ECD MS/MS and LC-electron transfer dissociation MS/MS analysis. Our results thus represent a new clinically relevant approach that requires ECD/electron transfer dissociation-type fragmentation to define the molecular events leading to pathogenesis of a chronic kidney disease. Furthermore, this work offers generally applicable principles for the analysis of clustered sites of O-glycosylation.Glycosylation is one of the most common post-translational modifications of proteins. It is estimated that over half of mammalian proteins are glycosylated. Patients with several autoimmune disorders, chronic inflammatory diseases, and some infectious diseases exhibit abnormal glycosylation of serum immunoglobulins and other glycoproteins (1–5). The biological functions of these modifications in health and disease have become a significant area of interest in biomedical research (6). A subset of these glycoproteins has clustered sites of O-glycosylation with serine- and threonine-rich stretches within the amino acid sequence. Mucins, such as membrane-associated MUC1, are perhaps the best known family of proteins that are heavily O-glycosylated. Their altered expression and aberrant glycosylation have made them potential targets as biomarkers for early detection of cancer (7). Immunoglobulin A1 (IgA1)1 contains both O- and N-glycans (Fig. 1). Aberrant O-glycosylation of IgA1 is involved in the pathogenesis of IgA nephropathy (IgAN) and the closely related Henoch-Schönlein purpura nephritis (1, 8). Interestingly, the aberrantly glycosylated molecules, IgA1 in IgAN and MUC1 in cancer, are recognized by the immune system as neoepitopes as evidenced by formation of specific antibodies (9–11). Mucin-like bacterial surface proteins exhibit similar properties: the molecules have clustered bacterial O-glycans that mediate cellular adhesion, and blocking antibodies target these glycan-containing epitopes (12).Open in a separate windowFig. 1.IgA1 structural elements. IgA1 has N-linked glycans (filled circles) and O-linked glycans (open circles). The O-glycosylated sites are in the HR between the first and second constant region domains of the heavy chains. The HR is a Pro-rich segment with nine possible sites of O-glycan attachment. Underlined serine and threonine residues are usually glycosylated (31). Arrows show cleavage sites of trypsin and IgA-specific proteases.An O-glycosylated protein from a single source contains a population of variably O-glycosylated isoforms that show a distinct distribution of microheterogeneity of the O-glycan chains in terms of number, sites of attachment, and composition. Characterizing these clustered sites and understanding how the distributions change under different biological conditions or disease states are an analytical challenge. Enzymatic or chemical release of O-glycans is not selective. The heterogeneity, composition, and quantitative aspects of different O-glycan chains can be assessed and quantified by gas chromatographic and/or mass spectrometric techniques. However, the site-specific information and context of location and composition of adjacent chains are lost. Carbohydrate-specific lectin analysis of O-glycoproteins can provide information on glycan composition and comparative differences between samples, such as those from healthy controls and patients with various disease states. We have successfully demonstrated this in the analysis of IgA1 O-glycans from patients with IgAN versus healthy controls and disease controls (13–15). This included proximal assessment of sites with galactose (Gal)-deficient O-glycans after digests with IgA-specific proteases (8). Several studies have demonstrated the value of mass spectrometry (MS) in identifying Gal-deficient IgA1 in patients with IgAN (16–21), including our work that demonstrated the first direct localization of native sites of O-glycan chains in the hinge region (HR) of IgA1 by use of electron capture dissociation (ECD) (20, 22). ECD and the more recently developed electron transfer dissociation (ETD) have been used to identify sites of O-glycosylation on a variety of proteins (23–26). This includes the analysis of sites of O-glycosylation by on-line LC-ECD/ETD MS/MS methods (23, 26, 27).IgAN is the most common primary glomerulonephritis worldwide (28) with about 20–40% of patients developing end stage renal failure. It is characterized by mesangial deposits of IgA1-containing immune complexes (28). The distinctive O-glycan chains of IgA1 molecules play a pivotal role in the pathogenesis of IgAN (1, 10, 14–16, 29, 30). IgA1 contains an HR between the first and second heavy chain constant region domains with a high content of Ser, Thr, and Pro. This segment usually has three to five O-glycan chains per HR (31) (see Fig. 1). Aberrantly glycosylated IgA1, deficient in Gal in some of the O-glycans in the HR, in serum is rare in healthy individuals but is present at elevated levels in IgAN patients (13, 15). This distinctive IgA1 is in circulating immune complexes (8, 10, 15) and in the glomerular deposits of IgAN patients (16, 29). The absence of Gal apparently leads to the exposure of neoepitopes, including terminal and sialylated N-acetylgalactosamine (GalNAc) residues (9, 10). These epitopes are recognized by naturally occurring anti-glycan IgG or IgA1 antibodies and, consequently, circulating immune complexes are formed (9, 10, 15) that can deposit in the glomerular mesangia. To identify the pathogenic forms of IgA1, a thorough analysis of O-glycan microheterogeneity, including identification of the attachment sites, will be required.In this work, we demonstrate the complete analysis of O-glycoform microheterogeneity and site localization of the glycoforms in a naturally Gal-deficient IgA1 (Ale) myeloma protein that mimics the nephritogenic IgA1 in patients with IgAN (8, 9). Reversed phase (RP) LC FT-ICR MS successfully identified 10 distinct IgA1 HR fragments representing >99% of total IgA1. AI-ECD of the six most abundant IgA1 HR glycoforms (>95% of total IgA1) was accomplished with three distinct IgA-specific protease + trypsin digestions, identifying sites of Gal deficiency across four distinct IgA1 O-glycoforms. Based on the success of the ECD fragmentation of these IgA1 HR fragments, we adapted the analysis for on-line LC-MS/MS methods for both ECD and ETD. The variety of IgA1 HR proteolytic fragments provides a practical set of guidelines for the ECD/ETD analysis of clustered sites of O-glycosylation on this and other proteins. These results also provide insight into the order of attachment of the O-glycans in the IgA1 HR.     

Association of Cell Surface Mucins with Galectin-3 Contributes to the Ocular Surface Epithelial Barrier

Maintenance of an intact mucosal barrier is critical to preventing damage to and infection of wet-surfaced epithelia. The mechanism of defense has been the subject of much investigation, and there is evidence now implicating O-glycosylated mucins on the epithelial cell surface. Here we investigate a new role for the carbohydrate-binding protein galectin-3 in stabilizing mucosal barriers through its interaction with mucins on the apical glycocalyx. Using the surface of the eye as a model system, we found that galectin-3 colocalized with two distinct membrane-associated mucins, MUC1 and MUC16, on the apical surface of epithelial cells and that both mucins bound to galectin-3 affinity columns in a galactose-dependent manner. Abrogation of the mucin-galectin interaction in four different mucosal epithelial cell types using competitive carbohydrate inhibitors of galectin binding, β-lactose and modified citrus pectin, resulted in decreased levels of galectin-3 on the cell surface with concomitant loss of barrier function, as indicated by increased permeability to rose bengal diagnostic dye. Similarly, down-regulation of mucin O-glycosylation using a stable tetracycline-inducible RNA interfering system to knockdown c1galt1 (T-synthase), a critical galactosyltransferase required for the synthesis of core 1 O-glycans, resulted in decreased cell surface O-glycosylation, reduced cell surface galectin-3, and increased epithelial permeability. Taken together, these results suggest that galectin-3 plays a key role in maintaining mucosal barrier function through carbohydrate-dependent interactions with cell surface mucins.Mucosal surfaces comprise more than 400 m² of the total surface area in humans (compared with 1.8 m² for skin) and are, thus, by far the largest area of contact with the environment (1). Epithelial cells in mucosal surfaces are continuously faced with the critical function of forming a protective apical barrier that prevents cellular damage and infection while allowing the exchange of molecules with the extracellular milieu. Loss of barrier function is ascribed to numerous mucosal pathologies, such as dry eye (a disease affecting more than 5 million people in the United States), severe asthma, and inflammatory bowel disease (2–4). Integral to the apical surface of mucosal epithelia are cell surface-associated mucins, a group of high molecular weight glycoproteins defined by the presence of long amino-terminal, extracellular domains containing extensive sites for O-glycan attachment. O-Glycosylation is the most abundant post-translational modification of mucins and constitutes up to 80% of mucin''s mass. It is thought that specific cell surface mucins and their O-glycans provide protection to the mucosal surface (5). Data from knock-out mice deficient in cell surface mucin MUC1 and core 3 β-1,3-N-acetylglucosaminyltransferase, an enzyme involved in the synthesis of mucin-type O-glycans in human colon, indicate the requirement for mucins and their O-glycans in maintaining barrier integrity in the gastrointestinal tract and the eye (6–9). However, the mechanism by which cell surface-associated mucins and their O-glycans contribute to forming the mucosal barrier on the epithelial glycocalyx remains poorly characterized.Galectins are a family of animal β-galactoside-binding lectins, defined by their evolutionarily conserved carbohydrate recognition domain (10, 11). As many as 15 galectins have been identified in mammals, and they are widely distributed among different types of cells and tissues (12). Galectins have been implicated in numerous biological processes, including tumor cell adhesion and progression, immunity, inflammation, wound healing, and development (11, 13, 14). Galectin-3 is a 35-kDa protein originally identified as Mac-2, a cell surface antigen expressed on murine thioglycollate-elicited peritoneal macrophages (15). It is now established that galectin-3, like other galectins, can interact in a multivalent fashion and cross-link glycan ligands on cell surface receptors, such as with epidermal growth factor receptors and α5β1 integrin, to generate molecular lattices (16, 17). In this study we investigate whether galectin-3 participates in mucosal barrier function through its interaction with cell surface-associated mucins. We demonstrate here that two distinct cell surface mucins, MUC1 and MUC16, interact with galectin-3 on the apical surface of epithelial cells and that carbohydrate-mediated mucin-galectin-3 interactions play an important role in maintaining mucosal barrier function.     

Exploring the N-glycosylation Pathway in Chlamydomonas reinhardtii Unravels Novel Complex Structures

Chlamydomonas reinhardtii is a green unicellular eukaryotic model organism for studying relevant biological and biotechnological questions. The availability of genomic resources and the growing interest in C. reinhardtii as an emerging cell factory for the industrial production of biopharmaceuticals require an in-depth analysis of protein N-glycosylation in this organism. Accordingly, we used a comprehensive approach including genomic, glycomic, and glycoproteomic techniques to unravel the N-glycosylation pathway of C. reinhardtii. Using mass-spectrometry-based approaches, we found that both endogenous soluble and membrane-bound proteins carry predominantly oligomannosides ranging from Man-2 to Man-5. In addition, minor complex N-linked glycans were identified as being composed of partially 6-O-methylated Man-3 to Man-5 carrying one or two xylose residues. These findings were supported by results from a glycoproteomic approach that led to the identification of 86 glycoproteins. Here, a combination of in-source collision-induced dissodiation (CID) for glycan fragmentation followed by mass tag-triggered CID for peptide sequencing and PNGase F treatment of glycopeptides in the presence of ¹⁸O-labeled water in conjunction with CID mass spectrometric analyses were employed. In conclusion, our data support the notion that the biosynthesis and maturation of N-linked glycans in the endoplasmic reticulum and Golgi apparatus occur via a GnT I-independent pathway yielding novel complex N-linked glycans that maturate differently from their counterparts in land plants.Chlamydomonas reinhardtii is a green alga that is used as a model organism for studying a number of biological processes such as photosynthesis, flagellar assembly and function, organelle biosynthesis, phototaxis, and circadian rhythms (1). Studies on glycosylation pathways in C. reinhardtii have been mostly focused on O-glycosylation processing, as the cell wall of this organism consists of a vast framework of O-glycosylated hydroxyproline-rich glycoproteins (2, 3). More recently, Bollig et al. even demonstrated that O-glycans from C. reinhardtii cell wall glycoproteins contain arabinose and galactose, the latter being in the furanose form (4). In contrast, the N-glycosylation pathway, although a major post-translational modification step in the maturation of secreted proteins in eukaryotes, has received very little attention so far. In N-glycan processing, a Man₅GlcNAc₂-PP-dolichololigosaccharide intermediate is first assembled onto a dolichol pyrophosphate on the cytosolic face of the endoplasmic reticulum (ER).¹ After translocation of this intermediate by a flippase, the biosynthesis continues in the lumen of the ER until a Glc₃Man₉GlcNAc₂-PP-dolichol N-glycan precursor is completed (5). This precursor is then transferred by the oligosaccharyltransferase (OST) multisubunit complex onto the asparagine residues of the consensus Asn-X-Ser/Thr sequences of a protein (5). The precursor is then deglucosylated/reglucosylated to ensure the quality control of the neosynthesized protein through the interaction with ER-resident chaperones such as calnexin and calreticulin. These ER events are crucial for the proper folding of secreted proteins (6), conserved in eukaryotes investigated so far, and involve a limited number of oligomannoside N-glycans. In contrast, the evolutionary adaptation of N-glycan processing in the Golgi apparatus gives rise to a large variety of organism-specific complex structures (7). Type I mannosidases located in this compartment first degrade the oligosaccharide precursor into oligomannoside N-glycans ranging from Man₉GlcNAc₂ (Man-9) to Man₅GlcNAc₂ (Man-5). N-acetylglucosaminyltransferase I (GnT I) then transfers a first GlcNAc residue on the α(1,3)-mannose arm of Man-5 to initiate the synthesis of polyantennary complex-type N-glycans (7).To date, a few studies carried out in Chlorophycaea using on-blot affinodetection or a combination of exoglycosidase digestions and two-dimensional HPLC separation have suggested that proteins secreted by these microalgae harbor mainly oligomannosides or mature N-glycans having a core xylose residue (8–10). Deeper insight into the structure of glycans N-linked to proteins secreted by two algal species, Porphyridium sp. and Phaeodactylum tricornutum, has been recently reported. A cell wall glycoprotein from the red microalgae Porphyridium sp. was found to carry Man-8 and Man-9 oligomannosides containing 6-O-methyl mannose and substituted by one or two xylose residues (11). In contrast, glycans N-linked to proteins secreted by the diatom P. tricornutum can be processed through a GnT I-dependent pathway into paucimannosidic oligosaccharides (12).In contrast to glycomic analysis, which focuses on the structure of N-linked oligosaccharides irrespective of the carrier proteins, glycoproteomics is used to characterize and determine the cell localization of individual proteins carrying these carbohydrate post-translational modifications. Whereas mammalian N-glycoproteomes have been studied extensively down to tissue- and cell-type-specific levels (13–17), less information is available regarding the N-glycoproteomes of plants and green algae (18, 19). The use of glycoproteomic approaches could help unravel the identity of endogenous glycoproteins from C. reinhardtii. As this green alga possesses many animal-like features (20), glycoproteomic analyses will help provide information concerning similarities and differences relative to not only mammalian but also vascular plant N-glycosylation pathways and glycoprotein trafficking.Recently, microalgae have emerged as an alternative system for the production of biopharmaceuticals, which represents a multibillion-dollar industry worldwide (21). The high expense and complicating factor of potential virus contamination encountered with commonly used expression systems have driven scientists to seek alternatives such as C. reinhardtii cells. Actually, they are cheap, easy to grow, safe, and scalable for the production of a high amount of proteins, making them ideal hosts for industrial production (22). Several studies have already demonstrated that the green alga C. reinhardtii is a convenient platform for producing recombinant proteins, including those of human origin (23). For example, a large single-chain antibody directed against glycoprotein D of the herpes simplex virus (24) and full-length IgG1 monoclonal antibodies directed against anthrax protective antigen 83 (25) have been successfully expressed in the chloroplast of transgenic C. reinhardtii cells. The production of secreted therapeutic proteins such as erythropoietin has also been evaluated (26). In contrast to the expression of proteins in the chloroplast, protein post-translational modifications such as N-glycosylation acquired by the secreted recombinant protein are a major concern for biopharmaceuticals, as more than half of the approved ones are glycosylated (27). Moreover, glycosylation is a critical quality attribute for biopharmaceuticals, because the presence and structures of the N-glycans are required for their biological activity, stability, and half-life (28, 29). However, given that unsuitable N-glycan structures can induce immune responses in humans (30–32) and generate adverse reactions, as reported for α(1,3)-Gal epitope on therapeutic drugs like cetuximab (33), it is essential to take into account the N-glycosylation capacity for an optimal expression system. Therefore, a suitable expression system should allow the production of glycomolecules harboring N-glycans and/or O-glycans compatible with human therapeutical applications and better efficacy of the therapeutic drug (34).In this study, we used a comprehensive approach including genomic, glycomic, and glycoproteomic analyses to investigate the N-glycosylation pathway occurring in C. reinhardtii. Our results revealed that the biosynthesis and maturation of N-glycans occur in the ER and Golgi apparatus through a GnT I-independent pathway and yield novel complex structures in addition to oligomannoside N-glycans.     

The GlycoFilter: A Simple and Comprehensive Sample Preparation Platform for Proteomics,N-Glycomics and Glycosylation Site Assignment

Current strategies to study N-glycoproteins in complex samples are often discrete, focusing on either N-glycans or N-glycosites enriched by sugar-based techniques. In this study we report a simple and rapid sample preparation platform, the GlycoFilter, which allows a comprehensive characterization of N-glycans, N-glycosites, and proteins in a single workflow. Both PNGase F catalyzed de-N-glycosylation and trypsin digestions are accelerated by microwave irradiation and performed sequentially in a single spin filter. Both N-glycans and peptides (including de-N-glycosylated peptides) are separately collected by filtration. The condition to effectively collect complex and heterogeneous N-glycans was established on model glycoproteins, bovine ribonuclease B, bovine fetuin, and human serum IgG. With this platform, the N-glycome, N-glycoproteome and proteome of human urine and plasma were characterized. Overall, a total of 865 and 295 N-glycosites were identified from three pairs of urine and plasma samples, respectively. Many sites were defined unambiguously as partially occupied by the detection of their nonsugar-modified peptides (128 from urine and 61 from plasma), demonstrating that partial occupancy of N-glycosylation occurs frequently. Given the likely high prevalence and variability of partial occupancy, glycoprotein quantification based exclusively on deglycosylated peptides may lead to inaccurate quantification.N-glycosylation is one of the most abundant post-translational modifications of proteins. It is estimated that more than 50% of human proteins are N-glycosylated (1). This type of modification is critical to many fundamental biologic and pathologic processes such as: structural modulation of proteins, cell-cell signaling and interactions, pathogen-host recognition, and tumor progression (2, 3). Inherently, N-glycans are extremely heterogeneous, and subtle variations in the composition or structure may induce dramatic biological consequences (4, 5). Because of their heterogeneity, N-glycans typically need to be released from the parent glycoproteins to be accurately characterized or quantified (3, 6).Identifying the sugar-modified position (glycosite) in a glycoprotein is also critical to understanding the biological role of N-glycosylation (7). Current methods that determine glycosites often use sugar-based enrichment techniques, such as hydrazide chemistry (8) or lectin affinity (9). The extracted glycoproteins or glycopeptides are subjected to de-N-glycosylation, and the deglycosylated peptides are then sequenced by liquid chromatography-tandem MS (LC-MS/MS) to characterize the previously glycosylated sites with a standard bottom-up proteomic approach (10). Filtration has been previously applied to collect peptides (FASP) (11) and deglycosylated peptides after lectin-enrichment (N-glyco FASP) (12). Although these enrichment techniques can identify low-abundant glycosites because of the enrichment selectivity (13), typically they are not feasible for characterization of the N-glycome, because glycans are oxidized and altered when coupled to the hydrazide groups (8), and the selective affinity of the lectin usually biases the N-glycome.N-glycosylation is often considered “irreversible” once a glycoprotein is exported into the extracellular matrix. The addition of a dolichol-linked N-glycan precursor (Glc₃Man₉GlcNAc₂) onto a nascent peptide is an enzyme-catalyzed and nontemplate driven process (2). However, the likelihood and efficiency of this addition are impacted by many factors including: (1) the concentration and activity of oligosaccharyltransferase (2, 14), (2) the availability of dolichol-linked N-glycan precursor (2, 14), (3) the length of time the glycosylated region is unfolded during passage across the endoplasmic reticulum membrane (2, 14), (4) the accessibility of the glycosite, which is greatly impacted by neighboring amino acids (15), and (5) the conformation of a glycosylated protein (correctly folded or not) (14). Because of these variables, the majority of the common N-glycosylation consensus motif (Asn-XXX-Ser/Thr, in which XXX is any amino acid except proline) in human proteins are not actually modified by a sugar chain (15).Furthermore, a glycosite may be partially occupied (PO),¹ a state in which both the glycosylated (sugar-modified asparagine) and nonglycosylated (nonsugar-modified asparagine) forms coexist. For example, human corticosteroid-binding globulin, a major plasma glycoprotein with six N-glycosites, has variable degrees in occupancy among its six glycosites (ranging from 70 to 99.5%) that also seem to change with pregnancy (16). Although the biological implications of partial occupancy in N-glycosylation are not well understood, to date, there are no well-defined strategies that can readily identify PO glycosites, particularly in a complex mixture. Current sugar-based enrichment methodologies alone are typically incapable of determining whether a particular glycosite is partially occupied or not, because the nonglycosylated peptides are typically removed.Here we demonstrate a simple, rapid but comprehensive sample preparation platform, the GlycoFilter, which collects N-glycans and peptides separately in a single spin filter device. We demonstrate that glycans, including large acidic glycans, can be effectively separated and captured using a simple shift in pH combined with filtration. Although the lectin-based enrichment method of N-glyco FASP also uses a filtration principle to identify lectin-specific glycosites (12), this platform enables efficient downstream characterization of the N-glycans, N-glycosites, and the remaining proteome of a simple or complex biological sample. Furthermore, the GlycoFilter has the additional nonbiased capability to identify PO N-glycosites using a standard LC-MS/MS approach.     

Identification and Quantification of Glycoproteins Using Ion-Pairing Normal-phase Liquid Chromatography and Mass Spectrometry

Glycoprotein structure determination and quantification by MS requires efficient isolation of glycopeptides from a proteolytic digest of complex protein mixtures. Here we describe that the use of acids as ion-pairing reagents in normal-phase chromatography (IP-NPLC) considerably increases the hydrophobicity differences between non-glycopeptides and glycopeptides, thereby resulting in the reproducible isolation of N-linked high mannose type and sialylated glycopeptides from the tryptic digest of a ribonuclease B and fetuin mixture. The elution order of non-glycopeptides relative to glycopeptides in IP-NPLC is predictable by their hydrophobicity values calculated using the Wimley-White water/octanol hydrophobicity scale. O-linked glycopeptides can be efficiently isolated from fetuin tryptic digests using IP-NPLC when N-glycans are first removed with PNGase. IP-NPLC recovers close to 100% of bacterial N-linked glycopeptides modified with non-sialylated heptasaccharides from tryptic digests of periplasmic protein extracts from Campylobacter jejuni 11168 and its pglD mutant. Label-free nano-flow reversed-phase LC-MS is used for quantification of differentially expressed glycopeptides from the C. jejuni wild-type and pglD mutant followed by identification of these glycoproteins using multiple stage tandem MS. This method further confirms the acetyltransferase activity of PglD and demonstrates for the first time that heptasaccharides containing monoacetylated bacillosamine are transferred to proteins in both the wild-type and mutant strains. We believe that IP-NPLC will be a useful tool for quantitative glycoproteomics.Protein glycosylation is a biologically significant and complex post-translational modification, involved in cell-cell and receptor-ligand interactions (1–4). In fact, clinical biomarkers and therapeutic targets are often glycoproteins (5–9). Comprehensive glycoprotein characterization, involving glycosylation site identification, glycan structure determination, site occupancy, and glycan isoform distribution, is a technical challenge particularly for quantitative profiling of complex protein mixtures (10–13). Both N- and O-glycans are structurally heterogeneous (i.e. a single site may have different glycans attached or be only partially occupied). Therefore, the MS¹ signals from glycopeptides originating from a glycoprotein are often weaker than from non-glycopeptides. In addition, the ionization efficiency of glycopeptides is low compared with that of non-glycopeptides and is often suppressed in the presence of non-glycopeptides (11–13). When the MS signals of glycopeptides are relatively high in simple protein digests then diagnostic sugar oxonium ion fragments produced by, for example, front-end collisional activation can be used to detect them. However, when peptides and glycopeptides co-elute, parent ion scanning is required to selectively detect the glycopeptides (14). This can be problematic in terms of sensitivity, especially for detecting glycopeptides in digests of complex protein extracts.Isolation of glycopeptides from proteolytic digests of complex protein mixtures can greatly enhance the MS signals of glycopeptides using reversed-phase LC-ESI-MS (RPLC-ESI-MS) or MALDI-MS (15–24). Hydrazide chemistry is used to isolate, identify, and quantify N-linked glycopeptides effectively, but this method involves lengthy chemical procedures and does not preserve the glycan moieties thereby losing valuable information on glycan structure and site occupancy (15–17). Capturing glycopeptides with lectins has been widely used, but restricted specificities and unspecific binding are major drawbacks of this method (18–21). Under reversed-phase LC conditions, glycopeptides from tryptic digests of gel-separated glycoproteins have been enriched using graphite powder medium (22). In this case, however, a second digestion with proteinase K is required for trimming down the peptide moieties of tryptic glycopeptides so that the glycopeptides (typically <5 amino acid residues) essentially resemble the glycans with respect to hydrophilicity for subsequent separation. Moreover, the short peptide sequences of the proteinase K digest are often inadequate for de novo sequencing of the glycopeptides.Glycopeptide enrichment under normal-phase LC (NPLC) conditions has been demonstrated using various hydrophilic media and different capture and elution conditions (23–28). NPLC allows either direct enrichment of peptides modified by various N-linked glycan structures using a ZIC®-HILIC column (23–27) or targeting sialylated glycopeptides using a titanium dioxide micro-column (28). However, NPLC is neither effective for enriching less hydrophilic glycopeptides, e.g. the five high mannose type glycopeptides modified by 7–11 monosaccharide units from a tryptic digest of ribonuclease b (RNase B), nor for enriching O-linked glycopeptides of bovine fetuin using a ZIC-HILIC column (23). The use of Sepharose medium for enriching glycopeptides yielded only modest recovery of glycopeptides (28). In addition, binding of hydrophilic non-glycopeptides with these hydrophilic media contaminates the enriched glycopeptides (23, 28).We have recently developed an ion-pairing normal-phase LC (IP-NPLC) method to enrich glycopeptides from complex tryptic digests using Sepharose medium and salts or bases as ion-pairing reagents (29). Though reasonably effective the technique still left room for significant improvement. For example, the method demonstrated relatively modest glycopeptide selectivity, providing only 16% recovery for high mannose type glycopeptides (29). Here we report on a new IP-NPLC method using acids as ion-pairing reagents and polyhydroxyethyl aspartamide (A) as the stationary phase for the effective isolation of tryptic glycopeptides. The method was developed and evaluated using a tryptic digest of RNase B and fetuin mixture. In addition, we demonstrate that O-linked glycopeptides can be effectively isolated from a fetuin tryptic digest by IP-NPLC after removal of the N-linked glycans by PNGase F.The new IP-NPLC method was used to enrich N-linked glycopeptides from the tryptic digests of protein extracts of wild-type (wt) and PglD mutant strains of Campylobacter jejuni NCTC 11168. C. jejuni has a unique N-glycosylation system that glycosylates periplasmic and inner membrane proteins containing the extended N-linked sequon, D/E-X-N-X-S/T, where X is any amino acid other than proline (30–32). The N-linked glycan of C. jejuni has been previously determined to be GalNAc-α1,4-GalNAc-α1,4-[Glcβ1,3]-GalNAc-α1,4-GalNAc-α1,4-GalNAc-α1,3-Bac-β1 (BacGalNAc₅Glc residue mass: 1406 Da), where Bac is 2,4-diacetamido-2,4,6-trideoxyglucopyranose (30). In addition, the glycan structure of C. jejuni is conserved, unlike in eukaryotic systems (30–32). IP-NPLC recovered close to 100% of the bacterial N-linked glycopeptides with virtually no contamination of non-glycopeptides. Furthermore, we demonstrate for the first time that acetylation of bacillosamine is incomplete in the wt using IP-NPLC and label-free MS.     

Diversity Within the O-linked Protein Glycosylation Systems of Acinetobacter Species

The opportunistic human pathogen Acinetobacter baumannii is a concern to health care systems worldwide because of its persistence in clinical settings and the growing frequency of multiple drug resistant infections. To combat this threat, it is necessary to understand factors associated with disease and environmental persistence of A. baumannii. Recently, it was shown that a single biosynthetic pathway was responsible for the generation of capsule polysaccharide and O-linked protein glycosylation. Because of the requirement of these carbohydrates for virulence and the non-template driven nature of glycan biogenesis we investigated the composition, diversity, and properties of the Acinetobacter glycoproteome. Utilizing global and targeted mass spectrometry methods, we examined 15 strains and found extensive glycan diversity in the O-linked glycoproteome of Acinetobacter. Comparison of the 26 glycoproteins identified revealed that different A. baumannii strains target similar protein substrates, both in characteristics of the sites of O-glycosylation and protein identity. Surprisingly, glycan micro-heterogeneity was also observed within nearly all isolates examined demonstrating glycan heterogeneity is a widespread phenomena in Acinetobacter O-linked glycosylation. By comparing the 11 main glycoforms and over 20 alternative glycoforms characterized within the 15 strains, trends within the glycan utilized for O-linked glycosylation could be observed. These trends reveal Acinetobacter O-linked glycosylation favors short (three to five residue) glycans with limited branching containing negatively charged sugars such as GlcNAc3NAcA4OAc or legionaminic/pseudaminic acid derivatives. These observations suggest that although highly diverse, the capsule/O-linked glycan biosynthetic pathways generate glycans with similar characteristics across all A. baumannii.Acinetobacter baumannii is an emerging opportunistic pathogen of increasing significance to health care institutions worldwide (1–3). The growing number of identified multiple drug resistant (MDR)¹ strains (2–4), the ability of isolates to rapidly acquire resistance (3, 4), and the propensity of this agent to survive harsh environmental conditions (5) account for the increasing number of outbreaks in intensive care, burn, or high dependence health care units since the 1970s (2–5). The burden on the global health care system of MDR A. baumannii is further exacerbated by standard infection control measures often being insufficient to quell the spread of A. baumannii to high risk individuals and generally failing to remove A. baumannii from health care institutions (5). Because of these concerns, there is an urgent need to identify strategies to control A. baumannii as well as understand the mechanisms that enable its persistence in health care environments.Surface glycans have been identified as key virulence factors related to persistence and virulence within the clinical setting (6–8). Acinetobacter surface carbohydrates were first identified and studied in A. venetianus strain RAG-1, leading to the identification of a gene locus required for synthesis and export of the surface carbohydrates (9, 10). These carbohydrate synthesis loci are variable yet ubiquitous in A. baumannii (11, 12). Comparison of 12 known capsule structures from A. baumannii with the sequences of their carbohydrate synthesis loci has provided strong evidence that these loci are responsible for capsule synthesis with as many as 77 distinct serotypes identified by molecular serotyping (11). Because of the non-template driven nature of glycan synthesis, the identification and characterization of the glycans themselves are required to confirm the true diversity. This diversity has widespread implications for Acinetobacter biology as the resulting carbohydrate structures are not solely used for capsule biosynthesis but can be incorporated and utilized by other ubiquitous systems, such as O-linked protein glycosylation (13, 14).Although originally thought to be restricted to species such as Campylobacter jejuni (15, 16) and Neisseria meningitidis (17), bacterial protein glycosylation is now recognized as a common phenomenon within numerous pathogens and commensal bacteria (18, 19). Unlike eukaryotic glycosylation where robust and high-throughput technologies now exist to enrich (20–22) and characterize both the glycan and peptide component of glycopeptides (23–25), the diversity (glycan composition and linkage) within bacterial glycosylation systems makes few technologies broadly applicable to all bacterial glycoproteins. Because of this challenge a deeper understanding of the glycan diversity and substrates of glycosylation has been largely unachievable for the majority of known bacterial glycosylation systems. The recent implementation of selective glycopeptide enrichment methods (26, 27) and the use of multiple fragmentation approaches (28, 29) has facilitated identification of an increasing number of glycosylation substrates independent of prior knowledge of the glycan structure (30–33). These developments have facilitated the undertaking of comparative glycosylation studies, revealing glycosylation is widespread in diverse genera and far more diverse then initially thought. For example, Nothaft et al. were able to show N-linked glycosylation was widespread in the Campylobacter genus and that two broad groupings of the N-glycans existed (34).During the initial characterization of A. baumannii O-linked glycosylation the use of selective enrichment of glycopeptides followed by mass spectrometry analysis with multiple fragmentation technologies was found to be an effective means to identify multiple glycosylated substrates in the strain ATCC 17978 (14). Interestingly in this strain, the glycan utilized for protein modification was identical to a single subunit of the capsule (13) and the loss of either protein glycosylation or glycan synthesis lead to decreases in biofilm formation and virulence (13, 14). Because of the diversity in the capsule carbohydrate synthesis loci and the ubiquitous distribution of the PglL O-oligosaccharyltransferase required for protein glycosylation, we hypothesized that the glycan variability might be also extended to O-linked glycosylation. This diversity, although common in surface carbohydrates such as the lipopolysaccharide of numerous Gram-negative pathogens (35), has only recently been observed within bacterial proteins glycosylation system that are typically conserved within species (36) and loosely across genus (34, 37).In this study, we explored the diversity within the O-linked protein glycosylation systems of Acinetobacter species. Our analysis complements the recent in silico studies of A. baumannii showing extensive glycan diversity exists in the carbohydrate synthesis loci (11, 12). Employing global strategies for the analysis of glycosylation, we experimentally demonstrate that the variation in O-glycan structure extends beyond the genetic diversity predicted by the carbohydrate loci alone and targets proteins of similar properties and identity. Using this knowledge, we developed a targeted approach for the detection of protein glycosylation, enabling streamlined analysis of glycosylation within a range of genetic backgrounds. We determined that; O-linked glycosylation is widespread in clinically relevant Acinetobacter species; inter- and intra-strain heterogeneity exist within glycan structures; glycan diversity, although extensive results in the generation of glycans with similar properties and that the utilization of a single glycan for capsule and O-linked glycosylation is a general feature of A. baumannii but may not be a general characteristic of all Acinetobacter species such as A. baylyi.     

A Comparative Study of Lectin Affinity Based Plant N-Glycoproteome Profiling Using Tomato Fruit as a Model

Lectin affinity chromatography (LAC) can provide a valuable front-end enrichment strategy for the study of N-glycoproteins and has been used to characterize a broad range eukaryotic N-glycoproteomes. Moreover, studies with mammalian systems have suggested that the use of multiple lectins with different affinities can be particularly effective. A multi-lectin approach has also been reported to provide a significant benefit for the analysis of plant N-glycoproteins; however, it has yet to be determined whether certain lectins, or combinations of lectins are optimal for plant N-glycoproteome profiling; or whether specific lectins show preferential association with particular N-glycosylation sites or N-glycan structures. We describe here a comparative study of three mannose-binding lectins, concanavalin A, snowdrop lectin, and lentil lectin, to profile the N-glycoproteome of mature green stage tomato (Solanum lycopersicum) fruit pericarp. Through coupling lectin affinity chromatography with a shotgun proteomics strategy, we identified 448 putative N-glycoproteins, whereas a parallel lectin affinity chromatography plus hydrophilic interaction chromatography analysis revealed 318 putative N-glycosylation sites on 230 N-glycoproteins, of which 100 overlapped with the shotgun analysis, as well as 17 N-glycan structures. The use of multiple lectins substantially increased N-glycoproteome coverage and although there were no discernible differences in the structures of N-glycans, or the charge, isoelectric point (pI) or hydrophobicity of the glycopeptides that differentially bound to each lectin, differences were observed in the amino acid frequency at the −1 and +1 subsites of the N-glycosylation sites. We also demonstrated an alternative and complementary in planta recombinant expression strategy, followed by affinity MS analysis, to identify the putative N-glycan structures of glycoproteins whose abundance is too low to be readily determined by a shotgun approach, and/or combined with deglycosylation for predicted deamidated sites, using a xyloglucan-specific endoglucanase inhibitor protein as an example.N-glycosylation is one of the most heterogeneous and common post-translational modifications of eukaryotic proteins and one that affects many aspects of protein targeting, enzymatic properties, stability and intermolecular interactions (1–3). There is therefore considerable interest in developing robust and sensitive high throughput analytical pipelines to isolate and structurally characterize N-glycoprotein populations (2, 4–8), allowing glycoprotein identification and analysis of the glycosylation site occupancy and N-glycan structure. To this end, lectin affinity chromatography (LAC)¹ is increasingly popular: specifically, various lectins are known to have different binding affinities for N-glycans and so the selective binding of N-glycoproteins in complex protein extracts to these lectins and their subsequent release allows a critical enrichment step before sequencing and glycan analysis by MS (9).As a refinement of this approach, the use of multiple lectin affinity chromatography (MLAC) in yeast and animal studies (4, 6, 10), using different proteomic platforms, has been shown to increase the numbers of isolated N-glycoproteins or N-glycopeptides. Collectively, these studies of taxonomically diverse eukaryotic N-glycoproteomes suggest a general conservation of the glycosylation site (N-X-S/T, where X can be any amino acid except proline), as well as conserved features of three-dimensional protein structure (4, 6, 10). Although there have been several studies to determine the structural basis of the binding specificity of specific lectins to yeast and animal N-glycoproteins (11), larger scale N-glycoproteomic analyses have typically not attempted to determine whether a particular combination of lectins provides optimal enrichment, or whether specific features, such as N-glycan structure or amino acid sequence at and around the N-glycosylation site, are associated with different lectins. Therefore, systematic comparative studies are essential to determine whether particular lectins can be optimal for specific tissues, organs, and organisms.LAC has also been used in plant N-glycoprotein analyses to enrich for populations of cell wall localized proteins (8, 12, 13) and a recent report (13) described the application of MLAC to map substantial numbers of N-glycosylation sites in a range of key experimental model organisms, included the plant Arabidopsis thaliana. Using a LTQ-Orbitrap Velos mass spectrometer, the authors identified 2186 unique N-glycosylation sites in proteins extracted from five different arabidopsis organs (13), which represents a substantial increase in the number of identified N-glycosylation sites that have resulted from previous plant N-glycoprotein studies. However, the particular analytical platform that was used did not allow the structural characterization of the N-glycans or N-glycopeptides (13). Indeed, certain features of N-glycopeptides, such as poor fragmentation, heterogeneity and a large dynamic range in most complex mixtures often limits the structural analysis of N-glycans in high throughput systematic analyses (2). It is also important to note that the structures of plant N-glycans differ from those of animals and yeast, as exemplified by the presence of β-1, 2-xylose and α-1, 3-fucose and the complete absence of multiantennary N-glycans and sialic acid in plant N-glycoproteins (1, 14). Therefore, assumptions that are made with regard to the lectin binding of animal and yeast proteins do not necessarily apply to those from plants. Consequently, there is a need to investigate the structural basis of lectin binding to plant N-glycoproteins. Moreover, the limitations of typical shotgun based profiling approaches in identifying and characterizing low abundance N-glycoproteins in complex protein extracts need to be addressed to allow more comprehensive plant N-glycoproteome profiling.In the present study we address both these issues using mature green stage tomato (Solanum lycopersicum) fruit pericarp as an experimental model to carry out a comparative analysis of N-glycoproteins associated with each of three mannose-binding lectins: concanavalin A (ConA), snowdrop lectin (GNA), and lentil lectin (LCH). Fruit development is associated with substantial cell wall metabolism and the expression of many wall localized N-glycoproteins (8) and tomato in particular represents an excellent model for studies of fleshy fruits and cell wall N-glycoproteins (15). We established an MLAC analytical pipeline that included shotgun proteomic profiling and deglycosylation and deamidation analysis, to allow the determination of N-glycoprotein protein identity, N-glycosylation site and N-glycan structures. This information was then used to establish whether a combination of lectins is indeed advantageous for the study of plant N-glycoproteomes, and to assess whether any of these structural characteristics result in predictable preferential binding to specific lectins. From these studies it became evident that large dynamic range of N-glycoprotein abundance was a significant limiting factor in the structural determination of the tomato, and that there was a bias toward the detection of highly abundant N-glycopeptides. We therefore evaluated the use of an in planta recombinant expression strategy, combined with affinity purification MS (AP-MS), as a means to characterize the N-glycan structures of glycoproteins whose abundance is too low to be readily determined via the primary shotgun pipeline, using a tomato xyloglucan-specific endoglucanase inhibitor protein (XEGIP) as a test case.     

The Antiretroviral Lectin Cyanovirin-N Targets Well-Known and Novel Targets on the Surface of Entamoeba histolytica Trophozoites

Entamoeba histolytica, the protist that causes amebic dysentery and liver abscess, has a truncated Asn-linked glycan (N-glycan) precursor composed of seven sugars (Man₅GlcNAc₂). Here, we show that glycoproteins with unmodified N-glycans are aggregated and capped on the surface of E. histolytica trophozoites by the antiretroviral lectin cyanovirin-N and then replenished from large intracellular pools. Cyanovirin-N cocaps the Gal/GalNAc adherence lectin, as well as glycoproteins containing O-phosphodiester-linked glycans recognized by an anti-proteophosphoglycan monoclonal antibody. Cyanovirin-N inhibits phagocytosis by E. histolytica trophozoites of mucin-coated beads, a surrogate assay for amebic virulence. For technical reasons, we used the plant lectin concanavalin A rather than cyanovirin-N to enrich secreted and membrane proteins for mass spectrometric identification. E. histolytica glycoproteins with occupied N-glycan sites include Gal/GalNAc lectins, proteases, and 17 previously hypothetical proteins. The latter glycoproteins, as well as 50 previously hypothetical proteins enriched by concanavalin A, may be vaccine targets as they are abundant and unique. In summary, the antiretroviral lectin cyanovirin-N binds to well-known and novel targets on the surface of E. histolytica that are rapidly replenished from large intracellular pools.Entamoeba histolytica causes amebic dysentery and liver abscess in the developing world (10, 20, 29). We are interested in E. histolytica glycoproteins containing Asn-linked glycans (N-glycans) for numerous reasons. E. histolytica makes an N-glycan precursor that contains 7 sugars (Man₅GlcNAc₂-PP-dolichol) rather than 14 sugars (Glc₃Man₉GlcNAc₂-PP-dolichol) made by most animals, plants, and fungi (21, 31, 44). E. histolytica N-glycans are used for quality control of glycoprotein folding in the endoplasmic reticulum (ER) lumen, and there is positive selection for sites of N-linked glycosylation in secreted and membrane proteins of E. histolytica (5, 11, 53).Unprocessed Man₅GlcNAc₂, by far the most abundant E. histolytica N-glycan, is present on the plasma membrane and vesicular membranes (31). The antiretroviral lectin cyanovirin-N, which is specific for α-1,2-linked mannose present on unprocessed N-glycans, binds E. histolytica N-glycans and forms aggregates or caps on the surface of E. histolytica trophozoites (1, 25, 31, 44, 45). E. histolytica glycoproteins are also capped by the plant lectin concanavalin A (ConA), which has a broader carbohydrate specificity (mannose and glucose) than cyanovirin-N (3, 16, 18, 19). Heavy subunits of the Gal/GalNAc lectin, the most important E. histolytica vaccine candidate, have 7 to 10 potential sites for N-linked glycosylation (32, 39, 43). Inhibition of N-glycan synthesis results in Gal/GalNAc lectins that are unable to bind to sugars on host epithelial cells.Carbohydrates appear to be an important target on the surface of E. histolytica as anti-proteophosphoglycan (PPG) monoclonal antibodies bind to O-phosphodiester-linked glycans and protect animal models from amebic infection (6, 33, 35, 40, 48). Lectin affinity columns are a powerful method for enriching unique parasite glycoproteins that may be identified by mass spectrometry (MS) of tryptic fragments (17, 55). For example, we recently used the plant lectin wheat germ agglutinin to dramatically enrich glycoproteins with short N-glycans of Giardia (42).The goal of the present studies was to explore further the interaction of the antiretroviral lectin cyanovirin-N with E. histolytica trophozoites in vitro. Questions asked included the following: Are E. histolytica glycoproteins with N-glycans replenished on the plasma membrane after capping with cyanovirin-N? What is the effect of cyanovirin-N capping on other amebic virulence factors and/or vaccine candidates (e.g., the Gal/GalNAc lectin and PPG)? Is capping by cyanovirin-N mediated by actin, as described for capping by the Gal/GalNAc lectin and ConA? What is the effect of the cyanovirin-N on amebic phagocytosis of mucin-coated beads, a surrogate assay for virulence? Which trophozoite glycoproteins are potential targets of cyanovirin-N (identified by mass spectrometry of lectin-enriched E. histolytica proteins)? Are any of them potential vaccine candidates?     

A Universal Chemical Enrichment Method for Mapping the Yeast N-glycoproteome by Mass Spectrometry (MS)

Glycosylation is one of the most common and important protein modifications in biological systems. Many glycoproteins naturally occur at low abundances, which makes comprehensive analysis extremely difficult. Additionally, glycans are highly heterogeneous, which further complicates analysis in complex samples. Lectin enrichment has been commonly used, but each lectin is inherently specific to one or several carbohydrates, and thus no single or collection of lectin(s) can bind to all glycans. Here we have employed a boronic acid-based chemical method to universally enrich glycopeptides. The reaction between boronic acids and sugars has been extensively investigated, and it is well known that the interaction between boronic acid and diols is one of the strongest reversible covalent bond interactions in an aqueous environment. This strong covalent interaction provides a great opportunity to catch glycopeptides and glycoproteins by boronic acid, whereas the reversible property allows their release without side effects. More importantly, the boronic acid-diol recognition is universal, which provides great capability and potential for comprehensively mapping glycosylation sites in complex biological samples. By combining boronic acid enrichment with PNGase F treatment in heavy-oxygen water and MS, we have identified 816 N-glycosylation sites in 332 yeast proteins, among which 675 sites were well-localized with greater than 99% confidence. The results demonstrated that the boronic acid-based chemical method can effectively enrich glycopeptides for comprehensive analysis of protein glycosylation. A general trend seen within the large data set was that there were fewer glycosylation sites toward the C termini of proteins. Of the 332 glycoproteins identified in yeast, 194 were membrane proteins. Many proteins get glycosylated in the high-mannose N-glycan biosynthetic and GPI anchor biosynthetic pathways. Compared with lectin enrichment, the current method is more cost-efficient, generic, and effective. This method can be extensively applied to different complex samples for the comprehensive analysis of protein glycosylation.Glycosylation is an extremely important protein modification that frequently regulates protein folding, trafficking, and stability. It is also involved in a wide range of cellular events (1) such as immune response (2, 3), cell proliferation (4), cell-cell interactions (5), and signal transduction (6). Aberrant protein glycosylation is believed to have a direct correlation with the development of several diseases, including diabetes, infectious diseases, and cancer (7–11). Secretory proteins frequently get glycosylated, including those in body fluids such as blood, saliva, and urine (12, 13). Samples containing these proteins can be easily obtained and used for diagnostic and therapeutic purposes. Several glycoproteins have previously been identified as biomarkers, including Her2/Neu in breast cancer (14), prostate-specific antigen (PSA) in prostate cancer (15), and CA125 in ovarian cancer (16, 17), which highlights the clinical importance of identifying glycoproteins as indicators or biomarkers of diseases. Therefore, effective methods for systematic analysis of protein glycosylation are essential to understand the mechanisms of glycobiology, identify drug targets and discover biomarkers.Approximately half of mammalian cell proteins are estimated to be glycosylated at any given time (18). There have been many reports regarding identification of protein glycosylation sites and elucidation of glycan structures (19–30). Glycan structure analysis can lead to potential therapeutic and diagnostic applications (31, 32), but it is also critical to identify which proteins are glycosylated as well as the sites at which the modification occurs. Despite progress in recent years, the large-scale analysis of protein glycosylation sites using MS-based proteomics methods is still a challenge. Without an effective enrichment method, the low abundance of glycoproteins prohibits the identification of the majority of sites using the popular intensity-dependent MS sequence method.About a decade ago, a very beautiful and elegant method based on hydrazide chemistry was developed to enrich glycopeptides. Hydrazide conjugated beads reacted with aldehydes formed from the oxidation of cis-diols in glycans (33). This method has been extensively applied to many different types of biological samples (34–41). Besides the hydrazide-based enrichment method, lectins have also been frequently used to enrich glycopeptides or glycoproteins before MS analysis (28, 29, 42–46). However, there are many different types of lectins, and each is specific to certain glycans (47, 48). Therefore, no combination of lectins can bind to all glycosylated peptides or proteins, which prevents comprehensive analysis of protein glycosylation. Because of the complexity of biological samples, effective enrichment methods are critical for the comprehensive analysis of protein glycosylation before MS analysis.One common feature of all glycoproteins and glycopeptides is that they contain multiple hydroxyl groups in their glycans. From a chemistry point of view, this can be exploited to effectively enrich them. Ideally, chemical enrichment probes must have both strong and specific interactions with multiple hydroxyl groups. The reaction between boronic acids and 1,2- or 1,3-cis-diols in sugars has been extensively studied (49–52) and applied for the small-scale analysis of glycoproteins (53–55). Furthermore, boronate affinity chromatography has been employed for the analysis of nonenzymatically glycated peptides (56, 57). Boronic acid-based chemical enrichment methods are expected to have great potential for global analysis of glycopeptides when combined with modern MS-based proteomics techniques. However, the method has not yet been used for the comprehensive analysis of protein N-glycosylation in complex biological samples (58).Yeast is an excellent model biological system that has been extensively used in a wide range of experiments. Last year, two papers reported the large-scale analysis of protein N-glycosylation in yeast (59, 60). In one study, a new MS-based method was developed based on N-glycopeptide mass envelopes with a pattern via metabolic incorporation of a defined mixture of N-acetylglucosamine isotopologs into N-glycans. Peptides with the recoded envelopes were specifically targeted for fragmentation, facilitating high confidence site mapping (59). Using this method, 133 N-glycosylation sites were confidently identified in 58 yeast proteins. When combined with an effective enrichment method, this MS-based analysis will provide a more complete coverage of the N-glycoproteome. The other work combined lectin enrichment with digestion by two enzymes (Glu_c and trypsin) to increase the peptide coverage, and 516 well-localized N-glycosylation sites were identified in 214 yeast proteins by MS (60).Here we have comprehensively identified protein N-glycosylation sites in yeast by combining a boronic acid-based chemical enrichment method with MS-based proteomics techniques. Magnetic beads conjugated with boronic acid were systematically optimized to selectively enrich glycosylated peptides from yeast whole cell lysates. The enriched peptides were subsequently treated with Peptide-N4-(N-acetyl-beta-glucosaminyl)asparagine amidase (PNGase F)¹ in heavy-oxygen water. Finally, peptides were analyzed by an on-line LC-MS system. Over 800 protein N-glycosylation sites were identified in the yeast proteome, which clearly demonstrates that the boronic acid-based chemical method is an effective enrichment method for large-scale analysis of protein glycosylation by MS.     

Affinity Enrichment and Characterization of Mucin Core-1 Type Glycopeptides from Bovine Serum

The lack of consensus sequence, common core structure, and universal endoglycosidase for the release of O-linked oligosaccharides makes O-glycosylation more difficult to tackle than N-glycosylation. Structural elucidation by mass spectrometry is usually inconclusive as the CID spectra of most glycopeptides are dominated by carbohydrate-related fragments, preventing peptide identification. In addition, O-linked structures also undergo a gas-phase rearrangement reaction, which eliminates the sugar without leaving a telltale sign at its former attachment site. In the present study we report the enrichment and mass spectrometric analysis of proteins from bovine serum bearing Galβ1–3GalNAcα (mucin core-1 type) structures and the analysis of O-linked glycopeptides utilizing electron transfer dissociation and high resolution, high mass accuracy precursor ion measurements. Electron transfer dissociation (ETD) analysis of intact glycopeptides provided sufficient information for the identification of several glycosylation sites. However, glycopeptides frequently feature precursor ions of low charge density (m/z > ∼850) that will not undergo efficient ETD fragmentation. Exoglycosidase digestion was utilized to reduce the mass of the molecules while retaining their charge. ETD analysis of species modified by a single GalNAc at each site was significantly more successful in the characterization of multiply modified molecules. We report the unambiguous identification of 21 novel glycosylation sites. We also detail the limitations of the enrichment method as well as the ETD analysis.Glycosylation is among the most prevalent post-translational modifications of proteins; it is estimated that over half of all proteins undergo glycosylation during their lifespan (1). Glycosylation of secreted proteins and the extracellular part of membrane proteins occurs in the endoplasmic reticulum and the contiguous Golgi complex. The side chains of Trp, Asn, and Thr/Ser residues can be modified, termed as C-, N-, and O-glycosylation, respectively (2, 3). In addition, O-glycosylation also occurs within the nucleus and the cytosol: a single GlcNAc residue modifies Ser and Thr residues. O-GlcNAc glycosylation fulfills a regulatory/signaling function similar to phosphorylation (4).From an analytical point of view, C-glycosylation is the simplest. A consensus sequence has been defined: WXXW where the first Trp is modified, and the modification, a Man moiety, readily survives sample preparation and mass spectrometric analysis, including collisional activation (5). Investigation of N-glycosylation is also facilitated by several factors. First, N-glycosylation again has a well defined consensus sequence: NX(S/T/C) where the middle amino acid cannot be Pro (6). Second, there is a universal core glycan structure: GlcNAc₂Man₃; and this core is conserved across species. Third, a specific endoglycosidase, peptide N-glycosidase F, has been identified. This enzyme cleaves the carbohydrate structure from the peptide, leaving behind a diagnostic sign: the Asn residue is hydrolyzed to Asp, inducing a mass shift of +1 Da. By contrast, analysis of O-glycosylation is hampered by a lack of (i) a consensus sequence, (ii) a universal core structure, and (iii) a universal endoglycosidase or gentle chemical hydrolysis method to facilitate analysis.Glycosylation shows a high degree of species and tissue specificity; the same site may be modified by a wide variety of different glycan structures, and unmodified variants of the protein may occur simultaneously (7–9). Disease and physiological changes also may alter the glycosylation pattern (10–12). The biological role(s) of glycosylation has been studied extensively (13–15), although such studies are seriously hampered by the difficulties of glycosylation analysis.Most secreted proteins are glycosylated; and thus, mammalian serum is rich in glycoproteins. On the other hand, O-linked glycoproteins represent a small percentage of the serum protein content. Glycoproteins may display a befuddling heterogeneity both in site specificity and site occupancy. Thus, the enrichment of modified proteins or peptides is necessary for their characterization, and different techniques have been tested for this purpose. Lectin affinity chromatography is a popular method for selective isolation of glycoproteins and glycopeptides. Concanavalin A can be used to isolate oligomannose type glycopeptides (16), wheat germ agglutinin is applied for GlcNAc-containing compounds (16, 17), and jacalin is selective for core-1 type O-glycopeptides (18, 19). Lectins with preferential affinity for fucosylated and sialylated structures can also be utilized (12). Non-selective capture of glycopeptides can be performed using hydrophilic interaction chromatography (20, 21) or size exclusion chromatography (22). A recent approach applies porous graphite columns for semiselective enrichment (23), whereas the acidic character of sialylated glycopeptides has also been exploited via titanium dioxide-mediated enrichment (24). Finally vicinal cis-diols can be selectively captured using boronic acid derivatives (25–27). All methods described here provide some glycopeptide enrichment from non-glycosylated peptide background, but all also suffer from significant non-selective binding. N-Linked glycoproteins may also be selectively captured on hydrazide resin following periodate oxidation (28). This approach requires enzymatic deglycosylation to release the captured peptides for analysis, therefore excluding the determination of the carbohydrate structure.Intact glycopeptide characterization still represents a significant challenge. Edman degradation, either alone or in combination with mass spectrometry, has been utilized for such tasks (29, 30). CID analysis of O-linked glycopeptides has limited utility. (i) MS/MS analysis cannot differentiate between the isomeric carbohydrate units and usually does not reveal the linkage positions and the configuration of the glycosidic bonds. (ii) Such spectra are typically dominated by abundant product ions associated with carbohydrate fragmentation, namely non-reducing end oxonium ions and product ions formed via sequential neutral losses of sugar residues from the precursor ions. (iii) The glycan is cleaved from the peptide via a gas-phase rearrangement reaction, and as a result the peptide itself and most peptide fragments (if any) are detected partially or completely deglycosylated (31–33). Recently a different approach, the combination of positive and negative ion mode infrared multiphoton dissociation, was found to provide conclusive structural assignment for some O-linked glycopeptides (34). However, two novel MS/MS techniques, electron capture dissociation (ECD),¹ which is performed in FT-ICR mass spectrometers (35), and electron transfer dissociation (ETD), which is performed in various ion trapping devices (36), may represent the real breakthrough. In both cases an electron is transferred to multiply protonated peptide cations, triggering peptide fragmentation at the covalent bond between the amino group and the α-carbon, producing mostly c and radical z· product ions while leaving the side chains intact. ETD is typically more efficient than ECD and thus leads to more comprehensive fragmentation. In addition, ETD can be performed in ion traps and thus, at a higher sensitivity level, especially in a linear ion trap. Because it has been observed that there are instances when the electron transfer is efficient and still no significant fragmentation occurs, ETD is usually combined with supplementary (and gentle) CID activation (37). O-Glycosylation analysis using these new dissociative techniques has been investigated (38, 39). However, because of the complexity of extracellular O-glycosylation, analysis of complex mixtures is rarely attempted (18), and the above techniques are usually restricted to the analysis of purified proteins.In this study we present the analysis of secreted O-linked glycopeptides. Lectin (jacalin) affinity chromatography was used to achieve some enrichment of core-1 O-GalNAcα type carbohydrate-carrying glycopeptides from bovine serum. The glycopeptide fractions were subjected to CID and ETD analysis. These experiments were performed on a linear ion trap-Orbitrap hybrid mass spectrometer (40). The Orbitrap delivered high resolution, high mass accuracy for the precursor ions, whereas the linear trap provided high sensitivity MS/MS analyses. Some fractions were also subjected to sequential exoglycosidase digestions, and glycopeptides retaining only the proximal GalNAc residues were analyzed. ProteinProspector v5.2.1, developed to accommodate ETD product ion spectra, aided data interpretation (41). We identified 26 glycosylation sites from bovine serum unambiguously; 21 of these sites have never been reported by any other study. No other single study to date has yielded so much information about O-linked glycosylation sites.     

Human OS-9, a Lectin Required for Glycoprotein Endoplasmic Reticulum-associated Degradation, Recognizes Mannose-trimmed N-Glycans

In the endoplasmic reticulum (ER), lectins and processing enzymes are involved in quality control of newly synthesized proteins for productive folding as well as in the ER-associated degradation (ERAD) of misfolded proteins. ER quality control requires the recognition and modification of the N-linked oligosaccharides attached to glycoproteins. Mannose trimming from the N-glycans plays an important role in targeting of misfolded glycoproteins for ERAD. Recently, two mammalian lectins, OS-9 and XTP3-B, which contain mannose 6-phosphate receptor homology domains, were reported to be involved in ER quality control. Here, we examined the requirement for human OS-9 (hOS-9) lectin activity in degradation of the glycosylated ERAD substrate NHK, a genetic variant of α1-antitrypsin. Using frontal affinity chromatography, we demonstrated that the recombinant hOS-9 mannose 6-phosphate receptor homology domain specifically binds N-glycans lacking the terminal mannose from the C branch in vitro. To examine the specificity of OS-9 recognition of N-glycans in vivo, we modified the oligosaccharide structures on NHK by overexpressing ER α1,2-mannosidase I or EDEM3 and examined the effect of these modifications on NHK degradation in combination with small interfering RNA-mediated knockdown of hOS-9. The ability of hOS-9 to enhance glycoprotein ERAD depended on the N-glycan structures on NHK, consistent with the frontal affinity chromatography results. Thus, we propose a model for mannose trimming and the requirement for hOS-9 lectin activity in glycoprotein ERAD in which N-glycans lacking the terminal mannose from the C branch are recognized by hOS-9 and targeted for degradation.Recognition and sorting of improperly folded proteins is essential to cell survival, and hence, an elaborate quality control system is found in cells. ER⁴ quality control is well characterized with respect to the N-linked oligosaccharides regulating the folding and degradation of newly synthesized proteins in the ER (1). Immediately after polypeptides enter the ER, Glc₃Man₉GlcNAc₂ (G3M9) precursor oligosaccharides are covalently attached and subsequently processed. Terminally misfolded proteins are removed from the ER by the ERAD machinery (1–4). Aberrant conformers are recognized, retrotranslocated to the cytosol, and degraded by the ubiquitin-proteasome system (5, 6). Processing of mannose residues from the N-linked oligosaccharides acts as a timer for the recognition of misfolded glycoproteins in the ER lumen (1, 7). ER α1,2-mannosidase I (ER ManI) in mammals and ER α-mannosidase in yeast preferentially trim mannose residues from the middle branch of N-glycans, generating the Man₈GlcNAc₂ (M8) isomer B (M8B) (8). In mammals, further mannose processing is required as a signal for degradation (1, 9, 10), whereas the presence of M8B is sufficient to signal degradation in yeast (11). The postulated lectin EDEMs in mammals, their yeast homolog Htm1p/Mnl1p, and the yeast MRH domain-containing lectin Yos9p have all been proposed to recognize glycoproteins targeted for degradation (12).The role of Yos9p in glycoprotein ERAD was identified using a genetic screen in Saccharomyces cerevisiae (13). Yos9p, a homolog of hOS-9, contains an MRH domain (14) and functions as a lectin. Yos9p recognizes substrates of the ERAD-lumenal pathway (15–17), generating a large ER membrane complex containing the Hrd1p-Hrd3p ubiquitin ligase core complex (18–20). The M8B and Man₅GlcNAc₂ (M5) N-glycans are predicted to function as ligands for Yos9p (17). Bipartite recognition of both glycan and polypeptide by Yos9p has also been reported (15).Recent studies revealed that two mammalian MRH domain-containing lectins, OS-9 and XTP3-B, are ER luminal proteins involved in ER quality control and form a large complex containing the HRD1-SEL1L ubiquitin-ligase in the ER membrane (21–24). The components of the complex are similar to yeast, suggesting evolutionary conservation, although the molecular mechanisms underlying the role of OS-9 and XTP3-B remain elusive. Studies using lectin mutants have suggested that the MRH domains are required not for binding to ERAD substrates but for interactions with SEL1L (21), which has multiple N-glycans (25, 26). Additionally, lectin activity appears to be dispensable for hOS-9 binding to misfolded glycoproteins (21, 24). Thus, to understand the role of hOS-9 in the ER quality control pathway, the specific carbohydrate structures recognized by the hOS-9 MRH domain need to be identified, and the requirement of the lectin domain in substrate recognition needs to be determined.In the present study we demonstrate that the lectin activity of hOS-9 is required for enhancement of glycoprotein ERAD. We identified the N-glycan structures recognized by the recombinant hOS-9 MRH domain in vitro by frontal affinity chromatography (FAC). Using a model ERAD substrate, NHK (27), we show that the ability of hOS-9 to enhance ERAD in vivo depends on the oligosaccharides present on NHK, consistent with the FAC results.     

Core3 O-Glycan Synthase Suppresses Tumor Formation and Metastasis of Prostate Carcinoma PC3 and LNCaP Cells through Down-regulation of ��2��1 Integrin Complex

Although there are numerous reports of carbohydrates enriched in cancer cells, very few studies have addressed the functions of carbohydrates present in normal cells that decrease in cancer cells. It has been reported that core3 O-glycans are synthesized in normal gastrointestinal cells but are down-regulated in cancer cells. To determine the roles of core3 O-glycans, we transfected PC3 and LNCaP prostate cancer cells with β3-N-acetylglucosaminyltransferase-6 (core3 synthase) required to synthesize core3 O-glycans. Both engineered cell lines exhibited reduced migration and invasion through extracellular matrix components compared with mock-transfected cells. Moreover we found that α2β1 integrin acquired core3 O-glycans in cells expressing core3 synthase with decreased maturation of β1 integrin, leading to decreased levels of the α2β1 integrin complex, decreased activation of focal adhesion kinase, and reduced lamellipodia formation. Upon inoculation into the prostate of nude mice, PC3 cells expressing core3 O-glycans produced much smaller tumors without metastasis to the surrounding lymph nodes in contrast to robust tumor formation and metastasis seen in mock-transfected PC3 cells. Similarly LNCaP cells expressing core3 O-glycans barely produced subcutaneous tumors in contrast to robust tumor formation by mock-transfected LNCaP cells. These findings indicate that addition of core3 O-glycans to β1 and α2 integrin subunits in prostate cancer cells suppresses tumor formation and tumor metastasis.Cancer cells often express surface carbohydrates different from normal cells (1). One such change is expression of sialyl Lewis X and Lewis B blood group antigens in cancer cells (2, 3). These structural elements are seen as capping oligosaccharides attached to the underlying glycan backbone where they likely function as ligands for cell adhesion molecules.The structure of underlying glycans also changes during malignant transformation and differentiation. In particular, there are several reports that an increase in the β1,6-N-acetylglucosaminyl branch in N-glycans synthesized by β1,6-N-acetylglucosaminyltransferase-V is associated with oncogenic transformation (4–7). Similar structural changes are seen in mucin-type O-glycans, which have N-acetylgalactosamine at the reducing end linked to polypeptide threonine or serine residues. Addition of different carbohydrate residues to N-acetylgalactosamine confers a variety of backbone structures on mucin-type O-glycans; the most abundant of those are classified as core1, core2, core3, and core4 O-glycans (8) (Fig. 1). Among these O-glycans, the synthesis of the core2 branch has been extensively studied particularly because conversion of core1 to core2 O-glycans was observed in T cell activation (9). Expression of core2 branch apparently represents an oncodifferentiation antigen because core2 branched O-glycans are synthesized in early stages of T cell differentiation, down-regulated in mature T cells, and reappear in T cell leukemia and immune deficiencies such as AIDS and Wiskott-Aldrich syndrome (for a review, see Ref. 10). In addition, overexpression of core2 O-glycans is seen in many cancers, including lung and breast carcinoma cells (11, 12).Open in a separate windowFIGURE 1.Biosynthetic pathways of mucin-type O-glycans. N-Acetylgalactosamine is transferred to a serine or threonine residue in a polypeptide. Resultant GalNAcα1→Ser/Thr is converted by core3 synthase (β3GnT-6) to GlcNAcβ1→3GalNAcα1→Ser/Thr (core3). Core3 is then converted to core4 by C2GnT-2 (C2GnT-M). GalNAcα1→Ser/Thr is also converted to core1, Galβ1→3GalNAcα1→Ser/Thr, by core1 synthase. Core1 is then converted to core2 by C2GnT-1, C2GnT-2, and C2GnT-3.By contrast, core3 and core4 O-glycans are synthesized in normal cells but apparently down-regulated in gastric and colorectal carcinoma (13, 14). Core3 O-glycans are synthesized by core3 synthase (β3GnT-6),² which adds β1,3-linked N-acetylglucosamine to N-acetylgalactosamine at the reducing terminus (15) (Fig. 1). Iwai et al. (16) showed that forced expression of core3 synthase in human fibrosarcoma HT1080 FP-10 cells resulted in significant reduction in the formation of lung tumor foci in mice after intravenous injection of tumor cells through a tail vein. However, the same study did not address whether the expression of core3 influences tumor metastasis because the cancer cells were intravenously injected and no primary tumor was formed to spread into the lung as metastasis in contrast to the other studies (17, 18). Core4 O-glycan is synthesized by addition of β1,6-linked N-acetylglucosamine to a core3 acceptor by core2 β1,6-N-acetylglucosamine M type (C2GnT-M) or C2GnT-2 (19, 20) (Fig. 1). Huang et al. (21) reported that C2GnT-M is down-regulated in colonic carcinoma cells and that forced expression of C2GnT-M in HCT116 colonic carcinoma cells significantly decreased cell invasion and subcutaneous tumor formation. How up-regulation of core3 and core4 O-glycans influences the pathophysiology of cells expressing core3 and core4 O-glycans has not been addressed.Cell-extracellular matrix interaction plays an essential role during acquisition of migration and invasive behavior of cancer cells. For example, α2β1 integrin is the major receptor for collagen (22) and most abundantly expressed in prostate cancer cells (23). Glycosylation on integrin is one of the important modulators of integrin functions, and many glycan structures, mainly N-glycans, have been studied. An increase of bisecting GlcNAc structure on α5β1 integrin inhibits the cell spreading and migration (24), and induced β1,6-GlcNAc sugar chains on N-glycans of β1 integrin result in stimulation of cell migration (25). However, it has not been addressed whether changes in O-glycans affect integrin maturation and functions.To determine the role of core3 O-glycans in tumor formation and metastasis, we analyzed PC3 and LNCaP human prostate cancer cells. We found that these cell lines express only small amounts of detectable core3 synthase; thus we transfected the cell lines with core3 synthase. Core3 synthase-transfected PC3 and LNCaP cells expressed increased amounts of core3 O-glycans in α2β1 integrin, showed the reduced maturation of β1 integrin and low levels of α2β1 integrin formation, migrated less efficiently through collagen and other extracellular matrix components, and were less invasive than mock-transfected cells. Moreover those cells exhibited decreased activation of focal adhesion kinase (FAK) compared with mock-transfected cells. Significantly PC3 cells expressing core3 O-glycans produced almost no primary tumors in the prostate and formed much fewer metastases in the draining lymph nodes than mock-transfected cells. Similarly LNCaP cells expressing core3 O-glycans produced much smaller subcutaneous tumors than mock-transfected LNCaP cells. These findings indicate that addition of core3 O-glycans to the α2β1 integrin leads to decreased cell migration and invasion, resulting in decreased prostate tumor formation and metastasis.     

The O-glycomap of Lubricin,a Novel Mucin Responsible for Joint Lubrication,Identified by Site-specific Glycopeptide Analysis

The lubricative, heavily glycosylated mucin-like synovial glycoprotein lubricin has previously been observed to contain glycosylation changes related to rheumatoid and osteoarthritis. Thus, a site-specific investigation of the glycosylation of lubricin was undertaken, in order to further understand the pathological mechanisms involved in these diseases. Lubricin contains an serine/threonine/proline (STP)-rich domain composed of imperfect tandem repeats (EPAPTTPK), the target for O-glycosylation. In this study, using a liquid chromatography–tandem mass spectrometry approach, employing both collision-induced and electron-transfer dissociation fragmentation methods, we identified 185 O-glycopeptides within the STP-rich domain of human synovial lubricin. This showed that adjacent threonine residues within the central STP-rich region could be simultaneously and/or individually glycosylated. In addition to core 1 structures responsible for biolubrication, core 2 O-glycopeptides were also identified, indicating that lubricin glycosylation may have other roles. Investigation of the expression of polypeptide N-acetylgalactosaminyltransferase genes was carried out using cultured primary fibroblast-like synoviocytes, a cell type that expresses lubricin in vivo. This analysis showed high mRNA expression levels of the less understood polypeptide N-acetylgalactosaminyltransferase 15 and 5 in addition to the ubiquitously expressed polypeptide N-acetylgalactosaminyltransferase 1 and 2 genes. This suggests that there is a unique combination of transferase genes important for the O-glycosylation of lubricin. The site-specific glycopeptide analysis covered 82% of the protein sequence and showed that lubricin glycosylation displays both micro- and macroheterogeneity. The density of glycosylation was shown to be high: 168 sites of O-glycosylation, predominately sialylated, were identified. These glycosylation sites were focused in the central STP-rich region, giving the domain a negative charge. The more positively charged lysine and arginine residues in the N and C termini suggest that synovial lubricin exists as an amphoteric molecule. The identification of these unique properties of lubricin may provide insight into the important low-friction lubricating functions of lubricin during natural joint movement.Human diarthrodial joints are surrounded by synovial fluid (SF),¹ a dense extracellular matrix fluid composed of proteins, glycoproteins, hyaluronic acid, proteoglycans, and phospholipids (1). During movement, the cartilage surfaces of the articulating joints slide over each other with an extremely low coefficient of friction that ranges from 0.0005 to 0.04 (2) and handle pressures up to ∼200 atm (3). In a healthy state, the joint surface and SF constitute a system of reduced friction that results in lifelong lubrication and wear resistance, primarily due to biolubricating molecules such as hyaluronic acid and lubricin (4). Human synovial lubricin is encoded by the proteoglycan 4 (Prg4) gene (5, 6) and is synthesized by fibroblast-like synoviocytes (FLSs) and superficial zone chondrocytes. Its 1404-amino-acid sequence contains a central mucin-like domain consisting of 59 imperfectly repeated sequences of EPAPTTPK. The O-glycosylation (in particular core 1 and sialylated core 1) of lubricin is suggested to be responsible for its lubricating properties (7), as the removal of these residues results in the loss of boundary lubrication. The molecule has also been suggested to play a key role in protecting the cartilage surface from excessive adsorption of proteins and cells (8).Arthritis results in the loss of this joint surface, leading to severe pain and a restricted range of motion. The two most common arthritic diseases, osteoarthritis (OA) and rheumatoid arthritis (RA), have different mechanisms of degradation. RA is an autoimmune systemic high inflammatory disease that increases the friction between articulating cartilage surfaces, resulting in degradation of the joint (9), whereas OA is a result of mechanical stress (10). Degeneration of the cartilage can be detected from proteoglycan fragments in the SF (11, 12). Because of the limited efficacy of available treatments, particularly for OA, understanding the biological factors related to arthritis is essential.The joints of arthritis patients, both RA and OA, have shown a down-regulation of expression and changes in glycosylation of lubricin (13). Studies using OA animal models suggest that there is a relationship between pathogenesis and the down-regulation of lubricin (9, 14, 15). This decrease in lubricin expression exacerbates the disease by accelerating the joint destruction, suggesting that certain characteristics of lubricin may be indicators of disease progression in RA and OA. Given the critical nature of lubricin glycosylation, we initiated a site-specific glycopeptide characterization of the lubricin mucin-like domain using liquid chromatography–tandem mass spectrometry with both collision-induced and electron-transfer dissociation fragmentation methods (LC-CID/ETD-MS²) after tryptic digestion of both intact and partly de-glycosylated lubricin.Collision-induced dissociation–tandem mass spectrometry (CID-MSⁿ) of O-linked (and N-linked) glycopeptides is capable of generating sequence information both for the attached glycan (in MS²) and for the de-glycosylated peptide (in MS³), but it lacks the site-specific information of the modified amino acids (16). This is due to extensive glycosidic bond cleavage of the precursor ion in MS² producing B/C and Y/Z ions (Domon and Costello carbohydrate fragmentation nomenclature (17)). In addition, the identification of the modified amino acids is even more difficult for peptides containing several Ser/Thr residues because of the lack of a consensus sequence for mucin-type O-glycosylation. Electron-capture dissociation and ETD are fragmentation techniques used for the site-specific characterization of protein post-translational modifications including phosphorylation (18) and glycosylation (19). Both techniques induce cleavage of the N-Cα bonds of the peptide backbone, producing c- and z-type fragment ions, while leaving the post-translational modification unaffected.In order to understand the biosynthesis of O-linked glycoproteins, one needs to link site localization of glycosylation to the expression of enzymes responsible for GalNAc-type (or mucin-type) O-glycosylation. This is necessary because the prediction of the site of GalNAc-type O-glycosylation is difficult. One reason for this is the large, redundant UDP-GalNAc:polypeptide α-N-acetylgalactosaminyltransferase (ppGalNAc T) gene family containing 20 gene-encoded isoenzymes, all possessing unique and/or overlapping substrate specificities (20, 21). These ppGalNAc Ts transfer GalNAc from the sugar nucleotide donor UDP-GalNAc to the hydroxyl groups of Ser and Thr residues in the proteins traversing the Golgi/endoplasmic reticulum. Altered protein O-glycosylation, suggested to be due to changes in the expression of distinct ppGalNAc Ts, has been reported in various disease states, including ulcerative colitis and cancer (21, 22). Thus, the connection of site-specific O-glycosylation with the responsible ppGalNAc Ts is important for understanding the functions of lubricin, as site-specific O-glycosylation has been shown to regulate the functions of proteins (23, 24) and may be involved in the pathological transformation of the joint in arthritis diseases.Although the type of glycosylation present on lubricin has been investigated previously, the site-specific glycopeptide characterization, including the analysis of the glycan types at these locations, was investigated for the first time in this study. In order to understand the nature of glycoproteins, it is essential to not only define the protein component or the glycan characteristics, but also understand how these two essential components interact. The macro- (different site occupation) and micro-heterogeneity (different glycan structure at each site) provided a heterogeneous mixture of lubricin O-linked glycopeptides that might help to explain the extraordinary properties of lubricin and how it can function as a lubricating agent in a demanding environment.     

Splitting the BLOSUM Score into Numbers of Biological Significance

Mathematical tools developed in the context of Shannon information theory were used to analyze the meaning of the BLOSUM score, which was split into three components termed as the BLOSUM spectrum (or BLOSpectrum). These relate respectively to the sequence convergence (the stochastic similarity of the two protein sequences), to the background frequency divergence (typicality of the amino acid probability distribution in each sequence), and to the target frequency divergence (compliance of the amino acid variations between the two sequences to the protein model implicit in the BLOCKS database). This treatment sharpens the protein sequence comparison, providing a rationale for the biological significance of the obtained score, and helps to identify weakly related sequences. Moreover, the BLOSpectrum can guide the choice of the most appropriate scoring matrix, tailoring it to the evolutionary divergence associated with the two sequences, or indicate if a compositionally adjusted matrix could perform better.[1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29]