Simultaneous Glycan-Peptide Characterization Using Hydrophilic Interaction Chromatography and Parallel Fragmentation by CID,Higher Energy Collisional Dissociation,and Electron Transfer Dissociation MS Applied to the N-Linked Glycoproteome of Campylobacter jejuni

Campylobacter jejuni is a gastrointestinal pathogen that is able to modify membrane and periplasmic proteins by the N-linked addition of a 7-residue glycan at the strict attachment motif (D/E)XNX(S/T). Strategies for a comprehensive analysis of the targets of glycosylation, however, are hampered by the resistance of the glycan-peptide bond to enzymatic digestion or β-elimination and have previously concentrated on soluble glycoproteins compatible with lectin affinity and gel-based approaches. We developed strategies for enriching C. jejuni HB93-13 glycopeptides using zwitterionic hydrophilic interaction chromatography and examined novel fragmentation, including collision-induced dissociation (CID) and higher energy collisional (C-trap) dissociation (HCD) as well as CID/electron transfer dissociation (ETD) mass spectrometry. CID/HCD enabled the identification of glycan structure and peptide backbone, allowing glycopeptide identification, whereas CID/ETD enabled the elucidation of glycosylation sites by maintaining the glycan-peptide linkage. A total of 130 glycopeptides, representing 75 glycosylation sites, were identified from LC-MS/MS using zwitterionic hydrophilic interaction chromatography coupled to CID/HCD and CID/ETD. CID/HCD provided the majority of the identifications (73 sites) compared with ETD (26 sites). We also examined soluble glycoproteins by soybean agglutinin affinity and two-dimensional electrophoresis and identified a further six glycosylation sites. This study more than doubles the number of confirmed N-linked glycosylation sites in C. jejuni and is the first to utilize HCD fragmentation for glycopeptide identification with intact glycan. We also show that hydrophobic integral membrane proteins are significant targets of glycosylation in this organism. Our data demonstrate that peptide-centric approaches coupled to novel mass spectrometric fragmentation techniques may be suitable for application to eukaryotic glycoproteins for simultaneous elucidation of glycan structures and peptide sequence.Campylobacter jejuni is a Gram-negative, microaerophilic, spiral-shaped, motile bacterium that is the most common cause of food- and water-borne diarrheal illness worldwide (1). Typical infections are acquired via the consumption of undercooked poultry where C. jejuni is found commensally (2). Symptoms in humans range from mild, non-inflammatory diarrhea to severe abdominal cramps, vomiting, and inflammation (3). Prior infection with C. jejuni is a common antecedent of two chronic immune-mediated disorders: Guillain-Barré syndrome (4) and immunoproliferative small intestine disease (5). A unique molecular trait of C. jejuni is the ability to post-translationally modify proteins by the N-linked addition of a 7-residue glycan (GalNAc-α1,4-GalNAc-α1,4-(Glcβ1,3)- GalNAc-α1,4-GalNAc-α1,4-GalNAc-α1,3-Bac-β1 where Bac is bacillosamine (2,4-diacetamido-2,4,6-trideoxyglucopyranose)) (6) at the consensus sequon (D/E)XNX(S/T) where X is any amino acid except proline (7).The N-linked C. jejuni heptasaccharide is encoded by the pgl (protein glycosylation) gene cluster (8–10), and the glycan is transferred to proteins by the PglB oligosaccharyltransferase (11) at the periplasmic face of the inner membrane (12). Removal of the N-glycosylation gene cluster (or indeed pglB alone) results in C. jejuni that displays poor adherence to and invasion of epithelial cell lines (13) and reduced colonization of the chicken gastrointestinal tract (14). Although this demonstrates a requirement for glycosylation in virulence, the proteins that mediate this are still unknown, and the overall role of glycan attachment remains to be elucidated. Our current understanding of the structural context of glycosylation in C. jejuni suggests that it does not play a role in steric stabilization by conferring structural rigidity as seen in eukaryotes (15) but occurs preferably on flexible loops and unordered regions of proteins (16–18). To investigate the role of glycosylation in protein function, recent studies have utilized mutagenesis to remove the N-linked sequon from three glycoproteins: Cj1496c (19), Cj0143c (20), and VirB10 (21). Removal of glycosylation from Cj1496c and Cj0143c had little effect on protein function; however, glycan attachment was required for correct localization of VirB10. Although the exact role of the glycan remains largely unknown, it appears to be site-specific with a single site, Asn⁹⁷, influencing localization of VirB10, whereas a second site, Asn³², is dispensable (21). It is clear that a more comprehensive analysis of the C. jejuni glycoproteome is required. A further complication in the elucidation of N-linked glycosylation is the use of the NCTC 11168 strain, which because of laboratory passage (22, 23) may not be the most appropriate model in which to study the virulence properties of glycan attachment. For example, we have recently shown that a surface-exposed virulence factor, JlpA, is glycosylated at two sites (Asn¹⁴⁶ and Asn¹⁰⁷) in all sequenced C. jejuni strains except NCTC 11168, which contains only Asn¹⁴⁶ (24).Glycoproteomics in C. jejuni is also a major technical challenge. Unlike eukaryotic N-linked glycans, the C. jejuni glycan is resistant to removal by protein N-glycosidase F (24) and chemical liberation via β-elimination (6) possibly because of the structure of the unique linking sugar, bacillosamine (25). Analysis therefore requires complementary methodology to elucidate the sites of glycosylation in the presence of the glycan. Preferential fragmentation of the glycan itself during collision-induced dissociation (CID) generally results in poor recovery of peptide fragment ions, and thus identification of the underlying protein and site of attachment remains problematic. MS³ has been attempted for site identification (6, 26); however, the data are limited by the requirement for sufficient ions for two rounds of tandem MS. We have also shown previously that C. jejuni encodes several hydrophobic integral membrane and outer membrane proteins possessing multiple transmembrane-spanning regions that are not amenable to gel-based approaches (27), particularly those using lectins for glycoprotein purification (28). We hypothesize that N-linked glycosylation is more widespread than previously demonstrated (6, 7, 26) because these studies examined only soluble proteins (6, 26) or used lectin affinity (6, 7), which limits the amount and type of detergents that can be used. Recent work (26) has demonstrated the potential of exploiting the hydrophilic nature of the C. jejuni glycan to enable glycopeptide enrichment.The ability to generate product ions useful for the identification of a glycosylated peptide is governed by three factors: the peptide backbone, the glycan, and the fragmentation approach. Multiple strategies exist to separately exploit the first two of these parameters (29, 30), but it is only recently that selective fragmentation of modified peptides has been available through electron transfer dissociation (ETD)¹ and electron capture dissociation (31, 32). ETD/electron capture dissociation enable the selective cleavage of the peptide while maintaining the carbohydrate structure, and this has been demonstrated using eukaryotic glycopeptides (33, 34) and more recently glycopeptides isolated from the pathogen Neisseria gonorrhoeae (35). A more recent fragmentation approach is higher energy collisional (C-trap) dissociation (HCD), which uses higher fragmentation energies than standard CID and enables identification of modifications, such as phosphotyrosine (36), via diagnostic immonium ions and high mass accuracy over the full mass range in MS/MS. HCD has not previously been applied to glycopeptides.We applied several enrichment and MS fragmentation approaches to the characterization of the glycoproteome of C. jejuni HB93-13. Sequence analysis determined that the HB93-13 genome contains 510 N-linked sequons ((D/E)XNX(S/T)) in 382 proteins of which 261 (with 371 potential N-linked sites) are predicted to pass through the inner membrane and are therefore the subset that may be glycosylated. We examined trypsin digests of whole cell and membrane protein preparations using zwitterionic hydrophilic interaction chromatography (ZIC-HILIC) and graphite enrichment of gel-separated proteins using several mass spectrometric techniques (CID, HCD, and ETD). This is the first study to demonstrate the potential of using the high energy fragmentation of HCD to overcome the signal disruption caused by labile glycan fragmentation and to provide peptide sequencing within a single step. Manual data analysis was also simplified as the GalNAc fragment ion (204.086 Da) provides a signature that can be used to highlight glycopeptides within a complex mixture. We identified 81 glycosylation sites, including 47 not described previously in the literature and a single site that cannot be unambiguously assigned. The majority of these are present on proteins not amenable to traditional gel-based analyses, such as hydrophobic transmembrane proteins. Our work more than doubles the previously known N-linked C. jejuni glycoproteome and provides a clear rationale for other studies where the peptide and glycan need to remain associated.