Name: analysis of n-glycans from raphanus sativus cultivars using pngase h+
Uploaded: 2018-06-25T15:00:00.000+00:00
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Description: Watch this Scientific Journal Video about Analysis of N-glycans from Raphanus sativus Cultivars Using PNGase H+ at JoVE.com

This work was supported in part by the Natural Science Foundation of China (grant numbers 31471703, A0201300537 and 31671854 to J.V. and L.L., grant number 31470435 to G.Y.), and the 100 Foreign Talents Plan (grant number JSB2014012 to J.V.).

1. Sample collection
<ol>
	<li>Purchase different cultivars of fresh radish (Raphanus sativus L.).</li>
</ol>
2. Isolation of Protein from Radish
<ol>
	<li>Homogenize approximately 100 g of fresh radish with a kitchen blender for 10 min.</li>
	<li>Transfer the slurry to a 50 mL centrifuge tube and centrifuge at 14,000 &#215; g at 4 &#176;C for 20 min to remove the insoluble material.</li>
	<li>Transfer the supernatant carefully into a new 50 mL centrifuge tube and add an equal volume of 2 M trichloroacetic acid (TCA) solution. 
	NOTE: Adding TCA will precipitate soluble (glyco)proteins.</li>
	<li>Centrifuge at 14,000 &#215; g at 4 &#176;C for 30 min and remove the supernatant from the pelleted (glyco) proteins.</li>
	<li>Wash the pellet with 20 mL of deionized water and centrifuge at 14,000 &#215; g at 4 &#176;C for 5 min to remove soluble oligosaccharides and polysaccharides.</li>
	<li>Repeat step 2.5. four times.</li>
	<li>Re-suspend the pellets in 1 mL of deionized water and transfer to a fresh 1.5 mL centrifuge tube.</li>
</ol>
3. Preparation of N-Glycans
<ol>
	<li>Mix 50 &#181;L of protein solution from step 2.7. (equal to 5 g of fresh radish) with 0.2 mU of recombinant PNGase H+ in 10 mM acetic acid.</li>
	<li>Incubate the reaction mixture at 37 &#176;C for 12 h. After the incubation, centrifuge at 14,000 &#215; g for 5 min to remove the extra protein and enzyme.</li>
	<li>Transfer the supernatant to a fresh 1.5 mL centrifuge tube.</li>
</ol>
4. Purification of N-Glycans
<ol>
	<li>Prepare the solid-phase extraction (SPE) column to enrich the N-glycans and remove salts and other impurities from the reaction mixture, increasing the selectivity of the fluorogenic 2-aminobenzamide (2-AB) labeling agent for N-glycan derivatization.
	<ol>
		<li>Add 3 mL of deionized water to wash the column.</li>
		<li>Add 3 mL of 80% acetonitrile solution containing trifluoroacetic acid (TFA, 0.1% v/v) to active the SPE-column.</li>
		<li>Add 3 mL of deionized water to equilibrate the SPE-column.</li>
	</ol>
	</li>
	<li>Transfer the sample from step 3.3 onto the column and discard the flow-through.</li>
	<li>Add 1.5 mL of deionized water to wash the column and discard the flow-through.</li>
	<li>Elute the released N-glycans from the column using 1.5 mL of aqueous 20% acetonitrile solution, containing 0.1% TFA (v/v) into a 2 mL centrifuge tube.</li>
	<li>Remove the solvent by centrifugal evaporation at room temperature. Evaporate until the sample is completely dry.</li>
</ol>
5. Fluorescence Derivatization of N-Glycans
<ol>
	<li>Prepare 1 mL of 2-AB solution, consisting of 35 mM 2-AB and 0.1 M sodium cyanoborohydride in dimethyl sulfoxide/acetic acid solution (7:3, v/v).</li>
	<li>Add 5 &#181;L of 2-AB solution to the dried samples (step 4.5.) derived from six different radishes. Vortex each sample until completely dissolved.</li>
	<li>Incubate the mixture for 2 h at 65 &#176;C.</li>
	<li>Let the sample cool down to room temperature for 5 min, and add 5 &#181;L of deionized water and 40 &#181;L of acetonitrile. Centrifuge the tubes at 14,000 x g for 3 min.</li>
	<li>Transfer 48 &#181;L from the supernatant into a 300 &#181;L high-recovery HPLC vial. Store the derivatized N-glycan samples at -20 &#176;C for up to one month.</li>
</ol>
6. HILIC-UPLC profiling of N-glycans
<ol>
	<li>Analyze the samples using a standard UPLC system connected to an online fluorescence detectorset at the excitation/emission wavelengths of 330 nm/420 nm, respectively.</li>
	<li>Use a hydrophobic interaction liquid chromatography (HILIC)-UPLC glycan column at a column temperature of 60 &#176;C for the analysis.</li>
	<li>Prepare solvent A by diluting 50 mL of stock solution (1 M ammonium formate solution, pH 4.5) with 950 mL of liquid chromatography-mass spectrometry (LCMS)-grade water. Prepare the stock solution as follows:
	<ol>
		<li>Add 43 mL of formic acid to 700 mL of LCMS-grade H2O.</li>
		<li>Adjust the pH to 4.5 by dropwise addition of aqueous ammonia solution (25% w/w).</li>
		<li>Transfer the solvent to a measuring cylinder and fill up to 1000 mL with LCMS-grade H2O. Store at 4-6 &#176;C for up to 3 months.</li>
	</ol>
	</li>
	<li>Use LCMS-grade acetonitrile as solvent B.</li>
	<li>Separate N-glycans with the following gradient elution:
	<ol>
		<li>Start by adding 95% of solvent B into solvent A. Set the flow rate at 0.5 mL/min from 0 to 44.5 min.</li>
		<li>From 0 min to 6 min, gradually decrease the proportion of solvent B with a linear gradient to78%.</li>
		<li>From 6 min to 44.5 min, gradually decrease the proportion of solvent B with a linear gradient to 55.9%.</li>
		<li>From 44.5 min to 46.5 min, rapidly decrease the proportion of solvent B with a linear gradient from 55.9% to 0% and hold at 0% for 2 min, and initiate washing of the column. Reduce the flow rate to 0.25 mL/min from 44.5 to 55 min.</li>
		<li>Wash the column further by increasing solvent B to 95% from 48.5 min to 50.5 min and hold at 95% for 4.5 min.</li>
		<li>Re-equilibrate the column to the starting conditions of 95% solvent B at 0.5 mL/min from 50.5 to 57 min.</li>
	</ol>
	</li>
	<li>Inject 45 &#181;L of the sample into the UPLC system.</li>
	<li>Elute the N-glycans by UPLC with retention times between 15 and 40 min.</li>
	<li>Collect each observed UPLC peak fraction using 2 mL centrifuge tubes and dry the samples by centrifugal evaporation.</li>
	<li>Inject approximately 1 pmol of 2-AB labeled dextran standard (2&#8722;20 glucose units) to calibrate the plant-N-glycan profiling, and to assign their elution times into standardized glucose units.</li>
</ol>
7. MALDI-TOF MS Analysis
<ol>
	<li>Dissolve the samples from step 6.8 in 5 &#181;L of LCMS -grade water. Mix 1 &#181;L of the sample solution and 1 &#181;L of 6-aza-2-thiothymine (ATT) solution (0.3% w/v in 70% v/v aqueous acetonitrile), and pipette the mixture onto the MALDI-TOF sample carrier.</li>
	<li>Analyze the samples using a MALDI-TOF mass spectrometer instrument in positive ion mode by pressing the Start button.</li>
	<li>Analyze the mass spectra by using the accompanying MALDI-TOF-MS analysis software.</li>
	<li>Interpret the spectra using an open source glycan interpretation software19. Set the search parameters for 2-AB labeling, [M+Na]+, and set the accuracy parameter to 2.0 Da.</li>
</ol>

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The authors have nothing to disclose.

The protocol we have presented here allows the comparison of the N-glycan profiles of various cultivars of radish. A significant advantage of this method compared to existing protocols is that no buffer changes between the enzymatic release of N-glycans and the derivatization reaction with 2-AB are required. The most critical step of this procedure is the purification of N-glycans using the SPE column, as failure to remove salts or other impurities in the reaction mixture may negatively impact ...

N-glycans in plants have drawn increased attention in recent years, as previous research has highlighted N-glycans as a potential source of immunological cross-reactions that may provoke allergic responses1,2. It has been demonstrated previously that N-glycans on plant glycoproteins can affect catalytic activity3,4, thermostability and folding5,6 or subcellular localization and secretion7. In order to correlate the glycan structures with their respective functions, N-glycans must first be released from glycoproteins either chemically or enzymatically. The classical chemical method for releasing both N- and O-glycans is &#946;-elimination, in which alkaline sample treatment is accompanied by reduction with borohydride to yield an alditol8. However, this procedure precludes labeling with a fluorophore and causes significant decay of monosaccharide units from the reducing end of the glycan structure. Chemical deglycosylation based on ammonium hydroxide/carbonate treatment is also a commonly used alternative method9. Neither of these chemical release methods degrades intact proteins, which allows mass spectrometric analysis of unlabeled glycan pools without the interference of peptide fragments in the same mass range. However, one drawback of these methods is the increased degradation rate of &#945;1,3-fucosylated N-glycans, a common carbohydrate structure found in plants10. Alternatively, enzymatic release methods using peptide:N-glycanases (PNGases, EC 3.5.1.52) are also widely applied. Recombinant PNGase F (from Flavobacterium meningosepticum) is the most common choice and permits the release of all types of N-glycans, except the structures bearing a core &#945;1,3 fucose11,12. Therefore, PNGase A (isolated from almond seeds) is usually used for the analysis of plant N-glycans13. However, this enzyme deglycosylates only proteolytically-derived glycopeptides, and is unable to deglycosylate native glycoproteins14. Hence, a multi-step sample workup is required before further analysis, which causes extensive loss of glycans, especially those of low abundance15.The overall goal of the method is to present an optimized workflow for N-glycan release and fluorescence labeling in a simple and robust manner. The underlying rationale is that PNGase H+, which was recently discovered in Terriglobus roseus and can be recombinantly expressed in E. coli, can hydrolyze N-glycans directly from the protein scaffold in acidic conditions16. A key advantage of using PNGase H+ over alternative methods is that fluorescent labeling reactions can be performed in the same reaction tube without changing the reaction buffers17,18. The simple preparation conditions and high recovery of low-abundance oligosaccharides make this method a valuable tool in the analysis of N-glycans. This protocol is suitable for the analysis of N-glycans from various plant species.

<table><tbody><tr><td>&lt;strong&gt;Chemicals:&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Trichloroacetic acid&amp;nbsp;</td><td>SCR, Shanghai</td><td>80132618</td><td></td></tr><tr><td>Acetic acid glacial</td><td>Huada, Guangzhou</td><td>64-19-7</td><td></td></tr><tr><td>Acetonitrile</td><td>General-reagent</td><td>G80988C</td><td></td></tr><tr><td>Trifluoroacetic acid</td><td>Energy chemical</td><td>W810031</td><td></td></tr><tr><td>2-aminobenzamide</td><td>Heowns, Tianjin</td><td>A41900</td><td></td></tr><tr><td>Sodium cyanoborohydride</td><td>J&amp;amp;K Scientific Ltd</td><td>314162</td><td></td></tr><tr><td>Dimethyl sulfoxide</td><td>Huada, Guangzhou</td><td>67-68-5</td><td></td></tr><tr><td>2AB-labeled dextran ladder, 200 pmol</td><td>Agilent Technologies</td><td>AT-5190-6998</td><td></td></tr><tr><td>6-Aza-2-thiothymine&amp;nbsp;</td><td>Sigma</td><td>275514</td><td></td></tr><tr><td>&lt;strong&gt;Tools/Materials:&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>Kitchen blender</td><td>Bear, Guangzhou</td><td>LLJ-A10T1</td><td></td></tr><tr><td>Centrifuge</td><td>Techcomp</td><td>CT15RT</td><td></td></tr><tr><td>Centrifugal Evaporator</td><td>Hualida, Taicang</td><td>LNG-T120</td><td></td></tr><tr><td>SPE column</td><td>Supelco</td><td>Supelclean ENVI Carb SPE column</td><td></td></tr><tr><td>MALDI-TOF mass spectrometer</td><td>Bruker</td><td>Autoflex</td><td></td></tr><tr><td>&lt;strong&gt;HPLC Analysis:&lt;/strong&gt;</td><td></td><td></td><td></td></tr><tr><td>High-recovery HPLC vial</td><td>Agilent Technologies</td><td>&amp;nbsp;# 5188-2788</td><td></td></tr><tr><td>HPLC System</td><td>Shimadzu</td><td>Nexera</td><td></td></tr><tr><td>Fluorescence Detector for HPLC</td><td>Shimadzu</td><td>RF-20Axs&amp;nbsp;</td><td></td></tr><tr><td>Column oven</td><td>Hengxin</td><td>CO-2000</td><td></td></tr><tr><td>HPLC Column</td><td>Waters</td><td>Acquity UPLC BEH glycan column</td><td>2.1 &amp;times; 150 mm, 1.7 &amp;mu;m particle size</td></tr><tr><td>LCMS-grade Water</td><td>Merck Millipore</td><td>#WX00011</td><td></td></tr><tr><td>LCMS-grade Acetonitrile</td><td>Merck Millipore</td><td># 100029</td><td></td></tr><tr><td>Formic acid</td><td>Aladdin</td><td>F112034</td><td></td></tr><tr><td>Ammonia solution</td><td>Aladdin</td><td>A112080</td><td></td></tr></tbody></table>

analysis of n-glycans from raphanus sativus cultivars using pngase h+

In recent years, the carbohydrate moieties of plants have received considerable attention, as they are a potential source of cross-reactive, allergy-provoking immune responses. In addition, carbohydrate structures also play a critical role in plant metabolism. Here, we present a simple and rapid method for preparing and analyzing N-glycans from different cultivars of radish (Raphanus sativus) using an N-glycanase specific for the release of plant-derived carbohydrate structures. To achieve this, crude trichloroacetic acid precipitates of radish homogenates were treated with PNGase H+, and labeled using 2-aminobenzamide as a fluorescent tag. The labeled N-glycan samples were subsequently analyzed by ultra performance liquid chromatography (UPLC) separation and matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry for a detailed structural evaluation and to quantify relative abundancies of the radish-derived N-glycan structures. This protocol can also be used for the analysis of N-glycans from various other plant species, and may be useful for further investigation of the function and effects of N-glycans on human health.

Figure 1 shows a schematic overview of the described protocol, including the isolation of (glyco-)proteins from radish, the preparation of N-glycans, the UPLC analysis, and the MALDI-TOF-MS analysis of these components. Figure 2 shows representative UPLC chromatograms of derivatized N-glycans of the analyzed radish cultivars. Figure 3 shows the obtained results of the 2AB-derivatize...

Watch this Scientific Journal Video about Analysis of N-glycans from Raphanus sativus Cultivars Using PNGase H+ at JoVE.com

Analysis of N-glycans from Raphanus sativus Cultivars Using PNGase H+

We describe a simple and rapid method for the preparation and analysis of N-glycans from different cultivars of radish (Raphanus sativus).

Analysis of N-glycans from Raphanus sativus Cultivars Using PNGase H+

In recent years, the carbohydrate moieties of plants have received considerable attention, as they are a potential source of cross-reactive, ...

analysis-of-n-glycans-from-raphanus-sativus-cultivars-using-pngase-h

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6.5K Views.  Nanjing Agricultural University. We describe a simple and rapid method for the preparation and analysis of N-glycans from different cultivars of radish (Raphanus sativus).

Video: Analysis of N-glycans from Raphanus sativus Cultivars Using PNGase H+

Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharide fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.

A protocol for the structural analysis of polysaccharides by gel electrophoresis (PACE), using mannan as an example, is described.

Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts ...

A Quantitative Glycomics and Proteomics Combined Purification Strategy

There is a growing desire in the biological and clinical sciences to integrate and correlate multiple classes of biomolecules to unravel biology, define pathways, improve treatment, understand disease, and aid biomarker discovery. N-linked glycosylation is one of the most important and robust post-translational modifications on proteins and regulates critical cell functions such as signaling, adhesion, and enzymatic function. Analytical techniques to purify and analyze N-glycans have remained relatively static over the last decade. While accurate and effective, they commonly require significant expertise and resources. Though some high-throughput purification schemes have been developed, they have yet to find widespread adoption and often rely on the enrichment of glycopeptides. One promising method, developed by Thomas-Oates et al., filter aided N-glycan separation (FANGS), was qualitatively demonstrated on tissues. Herein, we adapted FANGS to plasma and coupled it to the individuality normalization when labeling with glycan hydrazide tags strategy in order to achieve accurate relative quantification by liquid chromatography mass spectrometry and enhanced electrospray ionization. Furthermore, we designed new functionality to the protocol by achieving tandem, shotgun proteomics and glycosylation site analysis on hen plasma. We showed that N-glycans purified on filter and derivatized by hydrophobic hydrazide tags were comparable in terms of abundance and class to those by solid phase extraction (SPE); the latter is considered a gold standard in the field. Importantly, the variability in the two protocols was not statistically different. Proteomic data that was collected in-line with glycomic data had the same depth compared to a standard trypsin digest. Peptide deamidation is minimized in the protocol, limiting non-specific deamidation detected at glycosylation motifs. This allowed for direct glycosylation site analysis, though the protocol can accommodate 18O site labeling as well. Overall, we demonstrated a new in-line high-throughput, unbiased, filter based protocol for quantitative glycomics and proteomics analysis.

A high-throughput protocol was developed for combined proteomics and glycomics purification and LC-MS/MS quantification in plasma. Deamidation analysis of N-linked glycosylation motifs was specific to deglycosylated sites. Accurate quantitation of N-glycans was achieved by coupling filter aided N-glycan separation to the individuality normalization when labeling with glycan hydrazide tags strategy.

There is a growing desire in the biological and clinical sciences to integrate and correlate multiple classes of biomolecules to unravel biology, define ...

Chemistry

Chemo-enzymatic Synthesis of N-glycans for Array Development and HIV Antibody Profiling

We present a highly efficient way for the rapid preparation of a wide range of N-linked oligosaccharides (estimated to exceed 20,000 structures) that are commonly found on human glycoproteins. To achieve the desired structural diversity, the strategy began with the chemo-enzymatic synthesis of three kinds of oligosaccharyl fluoride modules, followed by their stepwise &#945;-selective glycosylations at the 3-O and 6-O positions of the mannose residue of the common core trisaccharide having a crucial &#946;-mannoside linkage. We further attached the N-glycans to the surface of an aluminum oxide-coated glass (ACG) slide to create a covalent mixed array for the analysis of hetero-ligand interaction with an HIV antibody. In particular, the binding behavior of a newly isolated HIV-1 broadly neutralizing antibody (bNAb), PG9, to the mixture of closely spaced Man5GlcNAc2 (Man5) and 2,6-di-sialylated bi-antennary complex type N-glycan (SCT) on an ACG array, opens a new avenue to guide the effective immunogen design for HIV vaccine development. In addition, our ACG array embodies a powerful tool to study other HIV antibodies for hetero-ligand binding behavior.

Chemo-enzymatic Synthesis of N-glycans for Array Development and HIV Antibody Profiling

A modular approach to the synthesis of N-glycans for attachment to an aluminum oxide-coated glass slide (ACG slide) as a glycan microarray has been developed and its use for the profiling of an HIV broadly neutralizing antibody has been demonstrated.

We present a highly efficient way for the rapid preparation of a wide range of N-linked oligosaccharides (estimated to exceed 20,000 structures) that are ...

N-glycan Profiling of Glycoproteins by Hydrophilic Interaction Liquid Chromatography with Fluorescence and Mass Spectrometric Detection

Glycosylation is a vital modification found in proteins. N-glycan profiling of glycoproteins is required to detect novel biomarker candidates and determine glycan alterations in diseases. Most commercially available biopharmaceutical proteins are glycoproteins. The efficacy of these drugs is affected by glycosylation patterns. Therefore, an in-depth characterization method for the N-glycans is necessary. Here, we present a comprehensive approach for qualitative and quantitative analysis of N-glycans using hydrophilic interaction liquid chromatography equipped with fluorescence detection and tandem mass spectrometry (HILIC-FLD-MS/MS). N-glycans were released from glycoproteins with a facile method and labeled by a procainamide fluorophore tag in the strategy. Subsequently, the procainamide labeled N-glycans were analyzed by a HILIC-FLD-MS/MS technique. In this approach, N-glycan structures were confirmed by the tandem mass spectrometric analysis, whereas fluorescence detection was used for the quantitative analysis. An application for data analysis of the detected N-glycan peaks is described in the study. This protocol can be applied to any glycoprotein extracted from various species.

N-glycan Profiling of Glycoproteins by Hydrophilic Interaction Liquid Chromatography with Fluorescence and Mass Spectrometric Detection

N-glycan profiling of glycoproteins is essential for discovering novel biomarkers and understanding glycan functions in cellular events. Additionally, N-glycan analysis of protein biopharmaceuticals is very important for human use. In this current article, a high-throughput strategy for identifying and quantifying N-glycan structures was presented using the HILIC-FLD-MS/MS technique.

Glycosylation is a vital modification found in proteins. N-glycan profiling of glycoproteins is required to detect novel biomarker candidates and ...

Pulse-chase Analysis of N-linked Sugar Chains from Glycoproteins in Mammalian Cells

Attachment of the Glc3Man9GlcNAc2 precursor oligosaccharide to nascent polypeptides in the ER is a common modification for secretory proteins. Although this modification was implicated in several biological processes, additional aspects of its function are emerging, with recent evidence of its role in the production of signals for glycoprotein quality control and trafficking. Thus, phenomena related to N-linked glycans and their processing are being intensively investigated. Methods that have been recently developed for proteomic analysis have greatly improved the characterization of glycoprotein N-linked glycans. Nevertheless, they do not provide insight into the dynamics of the sugar chain processing involved. For this, labeling and pulse-chase analysis protocols are used that are usually complex and give very low yields. We describe here a simple method for the isolation and analysis of metabolically labeled N-linked oligosaccharides. The protocol is based on labeling of cells with [2-3H] mannose, denaturing lysis and enzymatic release of the oligosaccharides from either a specifically immunoprecipitated protein of interest or from the general glycoprotein pool by sequential treatments with endo H and N-glycosidase F, followed by molecular filtration (Amicon). In this method the isolated oligosaccharides serve as an input for HPLC analysis, which allows discrimination between various glycan structures according to the number of monosaccharide units comprising them, with a resolution of a single monosaccharide. Using this method we were able to study high mannose N-linked oligosaccharide profiles of total cell glycoproteins after pulse-chase in normal conditions and under proteasome inhibition. These profiles were compared to those obtained from an immunoprecipitated ER-associated degradation (ERAD) substrate. Our results suggest that most NIH 3T3 cellular glycoproteins are relatively stable and that most of their oligosaccharides are trimmed to Man9-8GlcNAc2. In contrast, unstable ERAD substrates are trimmed to Man6-5GlcNAc2 and glycoproteins bearing these species accumulate upon inhibition of proteasomal degradation.

We describe a method for analysis of the alteration of N-linked glycans through the early life of glycoproteins after their biosynthesis in mammalian cells. This is achieved by pulse-chase analysis of metabolically labeled glycans, enzymatic release from glycoproteins and examination by HPLC.

Attachment of the Glc3Man9GlcNAc2 precursor oligosaccharide to nascent polypeptides in the ER is a common modification for secretory proteins. Although ...

Biology

Nonspecific Proteolysis-Based Glycomics Strategy for Bacterial Glycoproteins

Protein glycosylation is one of the most common and complex post-translational modifications. Many techniques have been developed to characterize the specific roles of glycans, the relationship between their structures and their impact on the functions of proteins. A common method for glycan analysis is to employ exoglycosidase cleavage to release N-linked glycans from glycoproteins or glycopeptides using Peptide-N-Glycosidase F (PNGase F). However, the glycan-protein linkages in bacteria are different and there is no enzyme available to release glycans from bacterial glycoproteins. In addition, free glycans have also been described in mammalian cells, bacteria, yeast, plants, and fish. In this article, we present a method that can characterize the N-linked glycosylation system in Campylobacter jejuni by detecting asparagine (Asn)-linked and free glycans that are not attached to their target proteins. In this method, total proteins from C. jejuni were digested by Pronase E with a higher enzyme to protein ratio (2:1&#8722;3:1) and a longer incubation time (48&#8722;72 h). The resulted Asn-glycans and free glycans were then purified using porous graphitic carbon cartridges, permethylated, and analyzed by mass spectrometry.

This study presents a method for glycomics analysis of glycoproteins by a combination of pronase E digestion, permethylation, and mass spectrometry analysis. This method is capable of analyzing all types of N-linked glycans, including bacterial N-glycans.

Protein glycosylation is one of the most common and complex post-translational modifications. Many techniques have been developed to characterize the ...

Profiling of Colorectal Cancer Tissues Using Glycomics-Guided Glycoproteomics

Glycomics-Guided Glycoproteomics Facilitates Comprehensive Profiling of the Glycoproteome in Complex Tumor Microenvironments

Glycosylation is a common and structurally diverse protein modification that impacts a wide range of tumorigenic processes. Mass spectrometry-driven glycomics and glycoproteomics have emerged as powerful approaches to analyze liberated glycans and intact glycopeptides, respectively, offering a deeper understanding of the heterogeneous glycoproteome in the tumor microenvironment (TME). This protocol details the glycomics-guided glycoproteomics method, an integrated omics technology, which firstly employs porous graphitized carbon-LC-MS/MS-based glycomics to elucidate the glycan structures and their quantitative distribution in the glycome of tumor tissues, cell populations, or bodily fluids being investigated. This allows for a comparative glycomics analysis to identify altered glycosylation across patient groups, disease stages, or conditions, and, importantly, serves to enhance the downstream glycoproteomics analysis of the same sample(s) by creating a library of known glycan structures, thus reducing the data search time and the glycoprotein misidentification rate. Focusing on N-glycoproteome profiling, the sample preparation steps for the glycomics-guided glycoproteomics method are detailed in this protocol, and key aspects of the data collection and analysis are discussed. The glycomics-guided glycoproteomics method provides quantitative information on the glycoproteins present in the TME and their glycosylation sites, site occupancy, and site-specific glycan structures. Representative results are presented from formalin-fixed paraffin-embedded tumor tissues from colorectal cancer patients, demonstrating that the method is sensitive and compatible with tissue sections commonly found in biobanks. Glycomics-guided glycoproteomics, therefore, offers a comprehensive view into the heterogeneity and dynamics of the glycoproteome in complex TMEs, generating robust biochemical data required to better understand the glycobiology of cancers.

This protocol details the glycomics-guided glycoproteomics method, an integrated omics technology that offers comprehensive insights into the heterogeneous glycoproteome in complex tumor microenvironments required to better understand the glycobiology of cancers.

Glycosylation is a common and structurally diverse protein modification that impacts a wide range of tumorigenic processes. Mass spectrometry-driven ...

Cancer Research

Identification and Characterization of Protein Glycosylation using Specific Endo- and Exoglycosidases

Glycosylation, the addition of covalently linked sugars, is a major post-translational modification of proteins that can significantly affect processes such as cell adhesion, molecular trafficking, clearance, and signal transduction1-4. In eukaryotes, the most common glycosylation modifications in the secretory pathway are additions at consensus asparagine residues (N-linked); or at serine or threonine residues (O-linked) (Figure 1). Initiation of N-glycan synthesis is highly conserved in eukaryotes, while the end products can vary greatly among different species, tissues, or proteins. Some glycans remain unmodified ("high mannose N-glycans") or are further processed in the Golgi ("complex N-glycans"). Greater diversity is found for O-glycans, which start with a common N-Acetylgalactosamine (GalNAc) residue in animal cells but differ in lower organisms1.
The detailed analysis of the glycosylation of proteins is a field unto itself and requires extensive resources and expertise to execute properly. However a variety of available enzymes that remove sugars (glycosidases) makes possible to have a general idea of the glycosylation status of a protein in a standard laboratory setting. Here we illustrate the use of glycosidases for the analysis of a model glycoprotein: recombinant human chorionic gonadotropin beta (hCG&beta;), which carries two N-glycans and four O-glycans 5. The technique requires only simple instrumentation and typical consumables, and it can be readily adapted to the analysis of multiple glycoprotein samples.
Several enzymes can be used in parallel to study a glycoprotein. PNGase F is able to remove almost all types of N-linked glycans6,7. For O-glycans, there is no available enzyme that can cleave an intact oligosaccharide from the protein backbone. Instead, O-glycans are trimmed by exoglycosidases to a short core, which is then easily removed by O-Glycosidase. The Protein Deglycosylation Mix contains PNGase F, O-Glycosidase, Neuraminidase (sialidase), &beta;1-4 Galactosidase, and &beta;-N-Acetylglucosaminidase. It is used to simultaneously remove N-glycans and some O-glycans8 . Finally, the Deglycosylation Mix was supplemented with a mixture of other exoglycosidases (&alpha;-N-Acetylgalactosaminidase, &alpha;1-2 Fucosidase, &alpha;1-3,6 Galactosidase, and &beta;1-3 Galactosidase ), which help remove otherwise resistant monosaccharides that could be present in certain O-glycans.
SDS-PAGE/Coomasie blue is used to visualize differences in protein migration before and after glycosidase treatment. In addition, a sugar-specific staining method, ProQ Emerald-300, shows diminished signal as glycans are successively removed. This protocol is designed for the analysis of small amounts of glycoprotein (0.5 to 2 &mu;g), although enzymatic deglycosylation can be scaled up to accommodate larger quantities of protein as needed.

Using specific glycosidases to remove sugars from glycoproteins followed by SDS-PAGE is a valuable method to detect glycan modifications on protein samples and is a good choice for initial glycobiology studies. Changes following deglycosylation can be detected as shifts in gel mobility or by staining with glycan sensitive reagents.

Glycosylation, the addition of covalently linked sugars, is a major post-translational modification of proteins that can significantly affect processes ...

Immunoglobulin G N-Glycan Analysis by Ultra-Performance Liquid Chromatography

Glycomics is a new subspecialty in omics system research that offers significant potential in discovering next-generation biomarkers for disease susceptibility, drug target discovery, and precision medicine. Alternative IgG N-glycans have been reported in several common chronic diseases and suggested to have great potential in clinical applications (i.e., biomarkers for diagnosis and prediction of diseases). IgG N-glycans are widely characterized using the method of hydrophilic interaction chromatography (HILIC) ultra-performance liquid chromatography (UPLC). UPLC is a stable detection technology with good reproducibility and high relative quantitative accuracy. In addition, the structure of IgG N-glycan is clearly separated, and glycan composition and relative abundance in plasma are characterized.

Immunoglobulin G (IgG) N-glycan is characterized using hydrophilic interaction chromatography UPLC. In addition, the structure of IgG N-glycan is clearly separated. Presented here is an introduction to this experimental method so that it can be widely used in research settings.

Glycomics is a new subspecialty in omics system research that offers significant potential in discovering next-generation biomarkers for disease ...

Medicine

Analysis of SCAP N-glycosylation and Trafficking in Human Cells

Elevated lipogenesis is a common characteristic of cancer and metabolic diseases. Sterol regulatory element-binding proteins (SREBPs), a family of membrane-bound transcription factors controlling the expression of genes important for the synthesis of cholesterol, fatty acids and phospholipids, are frequently upregulated in these diseases. In the process of SREBP nuclear translocation, SREBP-cleavage activating protein (SCAP) plays a central role in the trafficking of SREBP from the endoplasmic reticulum (ER) to the Golgi and in subsequent proteolysis activation. Recently, we uncovered that glucose-mediated N-glycosylation of SCAP is a prerequisite condition for the exit of SCAP/SREBP from the ER and movement to the Golgi. N-glycosylation stabilizes SCAP and directs SCAP/SREBP trafficking. Here, we describe a protocol for the isolation of membrane fractions in human cells and for the preparation of the samples for the detection of SCAP N-glycosylation and total protein by using western blot. We further provide a method to monitor SCAP trafficking by using confocal microscopy. This protocol is appropriate for the investigation of SCAP N-glycosylation and trafficking in mammalian cells.

Analysis of SCAP N-glycosylation and Trafficking in Human Cells

We describe a modified method for membrane fraction isolation from human cells and sample preparation for the detection of SCAP N-glycosylation and total protein by using western blot. We further introduce a GFP-labeling method to monitor SCAP trafficking using confocal microscopy. This protocol can be used in regular biology laboratories.

Analysis of N-glycans from Raphanus sativus Cultivars Using PNGase H⁺

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Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE

A Quantitative Glycomics and Proteomics Combined Purification Strategy

Chemo-enzymatic Synthesis of N-glycans for Array Development and HIV Antibody Profiling

N-glycan Profiling of Glycoproteins by Hydrophilic Interaction Liquid Chromatography with Fluorescence and Mass Spectrometric Detection

Pulse-chase Analysis of N-linked Sugar Chains from Glycoproteins in Mammalian Cells

Nonspecific Proteolysis-Based Glycomics Strategy for Bacterial Glycoproteins

Glycomics-Guided Glycoproteomics Facilitates Comprehensive Profiling of the Glycoproteome in Complex Tumor Microenvironments

Identification and Characterization of Protein Glycosylation using Specific Endo- and Exoglycosidases

Immunoglobulin G N-Glycan Analysis by Ultra-Performance Liquid Chromatography

Analysis of SCAP N-glycosylation and Trafficking in Human Cells