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 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 (2:1−3:1) and a longer incubation time (48−72 h). The resulted Asn-glycans and free glycans were then purified using porous graphitic carbon cartridges, permethylated, and analyzed by mass spectrometry.
Protein N-glycosylation is one of the most common and complex post-translational modifications in eukaryotes1. N-glycans play an essential role in protein folding and also have an impact on protein sorting in biosynthetic traffic2. Mass spectrometry has been widely used in the analysis of glycans released by exoglycosidase cleavage (glycomics). The remaining deglycosylated peptides (glycoproteomics) have been commonly used to identify the sequences of glycosylated peptides in eukaryotes3. The identification of N-linked glycans in Campylobacter jejuni suggested that N-glycosylation is not restricted to eukaryotes4,5,6,7,8. However, for bacteria, there is a lack of effective exoglycosidases or endoglycosidases to release oligosaccharides for glycan analysis.
An alternative approach has been developed to characterize glycosylation sites and glycan structures in glycoproteins, which is based on the use of nonspecific proteolysis to digest most peptides' backbone and generate pseudo-oligosaccharides that only contain a few amino acids. Various non-specific enzymes have been used to generate pseudo-oligosaccharides and it has been found that Pronase E offered the most efficient and reproducible digestion9. We have developed a glycomics strategy based on Pronase E to analyze C. jejuni N-glycans10,11. The pseudo-oligosaccharides were analyzed directly by capillary electrophoresis mass spectrometry (CE-MS) and/or by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) after permethylation.
Here, a universal method is described for glycomics analysis that uses nonspecific Pronase E digestion and permethylation to study glycosylation from mucosal pathogen C. jejuni. This method is capable of characterizing N-linked glycans expressed by both eukaryotic and bacterial systems and is also useful in identifying novel intermediates in N-linked glycosylation pathways.
1. Culture of C. jejuni 11168H and extraction of total proteins
NOTE: C. jejuni 11168H is a hypermotile clonal derivative of NCTC 1116812.
2. Purification using porous graphitic carbon (PGC)
3. Permethylation of Asn-glycans
4. Electrospray Ionization Mass Spectrometry (ESI-MS) and ESI-MS/MS analysis
5. Analysis of permethylated glycans by MALDI-TOF MS
The method based on the combination of pronase E digestion and permethylation was applied to N-glycan analysis from total protein extracts of C. jejuni 11168H. Figure 1 shows a flowchart of the experimental procedure. In typical digestion, the ratio of enzyme to glycoprotein was set between 1:100 to 1:20. Here, the ratio of Pronase E to protein was increased to 2:1-3:1 and longer digestion was employed to obtain exhaust digestion by incubation at 37 °C for 48 h. The Asn-glycans from exhaust digestion were then purified by PGC and permethylated with a routine DMSO-NaOH approach. The MALDI-MS analysis of the permethylated Pronase E digests is presented in Figure 2. Three permethylation reaction times, i.e., 5 min, 10 min, and 20 min, were investigated. The obtained MS spectra indicated that the combination of Protonase E digestion and permethylation is reproducible. While the ion at m/z 1755 corresponds to Glc1GalNAc5Bac, the ion at m/z 1866 was only 111 Da higher. To verify if this ion corresponds to the permethylated product of Glc1-GalNAc5Bac-Asn, the NMR analysis of the permethylated Glc-Asn standard was performed10. The results indicated that a double bond was formed to replace the NH2 group in Asn for Glc-Asn and Glc1GalNAc5Bac-Asn. Interestingly, the data reveals the presence of free N-glycan, i.e., m/z 1755, and its relative quantity is much higher than that of Asn-linked glycan, i.e., m/z 1866. Therefore, the combination of Pronase E digestion and permethylation is not only a universal glycomics technique, but it can also distinguish free glycans from amino acid-linked glycans.
The MS and MS/MS spectra of permethylated Glc1GalNAc5Bac and Glc1-GalNAc5Bac-Asn from ESI-MS and ESI-MS/MS analysis were shown in Figure 3. The ions at m/z 1755 and m/z 1866 correspond to Glc1GalNAc5Bac and Glc1GalNAc5Bac-Asn, respectively (Figure 3A). The Glc1GalNAc5Bac-Asn structure was confirmed by annotating the MS/MS experiment (Figure 3B). Free heptasaccharide structure was further confirmed from the fragment spectrum of m/z 1755 (Figure 3C). Moreover, one can easily distinguish free N-glycans from Asn-linked glycans by observing the mass interval of 111 Da.
Figure 1: Flowchart of the experimental procedure. Please click here to view a larger version of this figure.
Figure 2: MALDI-TOF analysis. Extracted spectra of permethylated glycans isolated from pronase E digested C. jejuni 11168H (1 mg) with different permethylation reaction times. (A) 5 min; (B) 10 min; and (C) 20 min. Abbreviations: Glc, glucose; GalNAc, N-acetylgalactosamine; Bac, bacillosamine; Asn, asparagine. Please click here to view a larger version of this figure.
Figure 3: ESI-MS analysis. Extracted spectra of N-linked glycans from C. jejuni after Pronase E digestion. (A) Extracted MS; (B) MS/MS of precursor ion at m/z 1866; (C) MS/MS of precursor ion at m/z 1755. Abbreviations: Glc, glucose; GalNAc, N-acetylgalactosamine; Bac, bacillosamine; Asn, asparagine. Please click here to view a larger version of this figure.
There are two critical steps in the protocol for the implementation of this universal glycomics strategy. The first critical step is the completion of exhaust digestion. This method strongly depends on the completion of Pronase E digestion. It is thus essential to use a long digestion time and a high enzyme-to-protein ratio. Typically, it is suggested to use a ratio of 2:1-3:1 for Pronase E/protein, and an incubation time of 48 h. It has been demonstrated that this proposed exhaust digestion produced the glycans with a single amino acid as the major component10. The products from exhaust digest need to be purified by a PGC cartridge. It did not only retain glycans but also the undigested enzymes. However, the enzyme proteins will not be eluted from the cartridge due to their high hydrophobicity.
The second critical step is the completion of methylation. Although MALDI-MS can be used to analyze glycans in their native forms, it is advantageous to convert glycans into their methylated derivatives. The analysis of permethylation glycans makes it feasible to determine branching and interglycosidic linkages. Permethylation can also help produce more predictable ion products during MS/MS fragmentation by stabilizing the sialic acid in oligosaccharides with terminal sialylation. It is worth mentioning that the molecular masses for permethylated Pronase E released Asn-glycans were only 111 Da higher compared to free oligosaccharides. This is due to molecular rearrangements. NMR spectroscopy of permethylated Asn-glycans confirmed that the NH2 group in Asn had been replaced with a double bond10.
A few experimental conditions can be modified when applied to different samples. Firstly, digestion time and enzyme-to-protein ratio can be optimized. Nonspecific proteolytic digestion of glycoproteins can be used in glycomics and glycoproteomics with different enzyme/protein ratios and digestion times, although it may result in producing Asn-glycans with different amino acid residues. For pronase E digestion, glycoproteins are digested to small Asn-glycans having one to six amino acid residues, which can also be analyzed using mass spectrometry. In addition, microwave irradiation can be employed to accelerate the proteolytic cleavage of glycoproteins mediated by Pronase E14. Secondly, different approaches can be used for the derivatization of glycans. In addition to the permethylation of glycans, a simple and rapid “one-pot” methylation method can be used to esterify sialic acids and construct a permanent charge for Asn-linked glycan analysis15. Briefly, the carboxylic acids of Asn and sialic acids were converted to Na+ form by passing through the cation exchange column. Converted Asn-glycans were then methylated with methyl iodide and the derivatized glycans can be purified with a hydrophilic interaction chromatography cartridge. Finally, other ESI mass spectrometers from different vendors can be used to analyze underivatized or permethylated glycans. MALDI-TOF/TOF can be used for analyzing permethylated glycans.
Unlike conventional glycomics strategy, this method is capable of differentiating free glycans and amino acid-linked glycans. For example, we characterized free glycans and N-linked glycans in C. jejuni. When glycans were directly isolated from C. jejuni 11168 whole-cell lysate, free glycans could be quantified in different culture conditions11. The results indicated that the quantity of free oligosaccharide (fOS) was inversely proportional to the solute concentration in the growth media. The higher salt and sucrose concentration resulted in lower quantity of fOS11.
There are also a few limitations of the method. The analytical throughput is limited by the long times for digestion (1-3 days) compared to routine digestion procedures (usually overnight). In addition, time-consuming permethylation can negatively impact the throughput.
The importance and potential of this method are the usefulness for screening N-linked glycans expressed by eukaryotes and bacteria and for detecting novel intermediates of N-linked glycosylation pathways.
The authors have nothing to disclose.
The authors thank Kenneth Chan, David J. McNally, Harald Nothaft, Christine M. Szymanski, Jean-Robert Brisson, and Eleonora Altman for assistance and helpful discussions.
2,5-dihydroxybenzoic acid (DHB), | Sigma-Aldrich (St. Louis, MO) | 149357 | |
2-Propanol | Fisher Scientific( Ottawa, Ontario,Canada) | AA22906K7 | |
4000 Q-Trap | AB Sciex (Concord, Canada) | Mass spectrometer | |
4800 MALDI-TOF/TOF | Applied Biosystems (Foster City, CA) | Mass spectrometer | |
acetonitrile (ACN) | Fisher Scientific( Ottawa, Ontario,Canada) | A996-4 | |
Brain Heart Infusion (BHI) broth | Sigma-Aldrich (St. Louis, MO) | 5121 | |
C18 Sep-Pak cartridges | Waters (Milford, MA). | WAT036945 | |
chloroform | Sigma-Aldrich (St. Louis, MO) | CX1054 | |
Difco | Fisher Science (Ottawa, Ontario,Canada) | DF0037-17-8 | Fisher Science |
dimethyl sulfoxide (DMSO) | Sigma-Aldrich (St. Louis, MO) | 276855 | |
Eppendorf tube | Diamed (Missisauga, Ontario,Canada) | SPE155-N | |
glacial acetic acid | Sigma-Aldrich (St. Louis, MO) | A6283 | |
methanol | Fisher Scientific, Ottawa, Ontario,Canada) | A544-4 | |
methyl iodide | Sigma-Aldrich (St. Louis, MO) | 289566 | |
PGC cartridge | Thermo Scientific(Waltham,MA) | 60106-303 | Porous graphitic carbon |
Pronase E | Sigma-Aldrich (St. Louis, MO) | 7433-2 | |
Protein Assay Kit | Bio-rad (Mississauga, Ontario, Canada) | 5000001 | |
Refrigerated vacuum concentrator | Thermo Scientific(Waltham,MA) | SRF110P2-230 | |
sodium hydroxide | Sigma-Aldrich (St. Louis, MO) | 367176 | |
Sonicator Ultrasonic Processor | Mandel Scientific (Guelph, Ontario,Canada) | XL 2020 | |
Trifluoacetic acid (TFA) | Fisher Scientific( Ottawa, Ontario,Canada) | A11650 | |
Tris-HCl | Sigma-Aldrich (St. Louis, MO) | T3253 |
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