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Wang CY, Bergström E, Southgate J, Thomas-Oates J. Surface Shave: Revealing the Apical-Restricted Uroglycome. J Proteome Res 2022; 21:360-374. [PMID: 34985888 DOI: 10.1021/acs.jproteome.1c00714] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study aimed to investigate the highly differentiated urothelial apical surface glycome. The functions of the mammalian urothelium, lining the majority of the urinary tract and providing a barrier against toxins in urine, are dependent on the correct differentiation of urothelial cells, relying on protein expression, modification, and complex assembly to regulate the formation of multiple differentiated cell layers. Protein glycosylation, a poorly studied aspect of urothelial differentiation, contributes to the apical glycome and is implicated in the development of urothelial diseases. To enable surface glycome characterization, we developed a method to collect tissue apical surface N- and O-glycans. A simple, novel device using basic laboratory supplies was developed for enzymatic shaving of the luminal bladder urothelial surface, with subsequent release and mass spectrometric analysis of apical surface O- and N-glycans, the first normal mammalian urothelial N-glycome to be defined. Trypsinization of superficial glycoproteins was tracked using immunolabeling of the apically expressed uroplakin 3a protein to optimize enzymatic release, without compromising the integrity of the superficial urothelial layer. The approach developed for releasing apical tissue surface glycans allowed for comparison with the N-glycome of the total porcine bladder urothelial cells and thus identification of apical surface glycans as candidates implicated in the urothelial barrier function. Data are available in MassIve: MSV000087851.
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Affiliation(s)
- Chung-Yao Wang
- Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K
| | - Edmund Bergström
- Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K.,Centre of Excellence in Mass Spectrometry, University of York, Heslington, York YO10 5DD, U.K
| | - Jennifer Southgate
- Jack Birch Unit, Department of Biology, York Biomedical Research Institute; University of York, Heslington, York YO10 5DD, U.K
| | - Jane Thomas-Oates
- Department of Chemistry, University of York, Heslington, York YO10 5DD, U.K.,Centre of Excellence in Mass Spectrometry, University of York, Heslington, York YO10 5DD, U.K
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2
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In vitro synthesis of mucin-type O-glycans using saccharide primers comprising GalNAc-Ser and GalNAc-Thr residues. Carbohydr Res 2021; 511:108495. [PMID: 35026558 DOI: 10.1016/j.carres.2021.108495] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/13/2021] [Accepted: 12/27/2021] [Indexed: 11/22/2022]
Abstract
Mucin-type O-glycosylation of serine or threonine residue in proteins is known to be one of the major post-translational modifications. In this study, two novel alkyl glycosides, Nα-lauryl-O-(2-acetamido-2-deoxy-α-d-galactopyranosyl)-l-serineamide (GalNAc-Ser-C12) and Nα-lauryl-O-(2-acetamido-2-deoxy-α-d-galactopyranosyl)-l-threonineamide (GalNAc-Thr-C12) were synthesized as saccharide primers to prime mucin-type O-glycan biosynthesis in cells. Upon incubating human gastric cancer MKN45 cells with the saccharide primers, 22 glycosylated products were obtained, and their structures were analyzed using liquid chromatography-mass spectrometry and enzyme digestion. The amounts of glycosylated products were dependent on the amino acid residues in the saccharide primers. For example, in vitro synthesis of T antigen (Galβ1-3GalNAc), fucosyl-T (Fucα1-2Galβ1-3GalNAc), and sialyl-T (NeuAcα2-3Galβ1-3GalNAc) preferred a serine residue, whereas sialyl-Tn (NeuAcα2-6GalNAc) preferred a threonine residue. Furthermore, the glycosylated products derived from GalNAc-Ser/Thr-C12 and Gal-GalNAc-Ser/Thr-C12 using cell-free synthesis showed the same amino acid selectivity as those in the cell experiments. These results indicate that glycosyltransferases involved in the biosynthesis of mucin-type O-glycans distinguish amino acid residues conjugated to GalNAc. The saccharide primers developed in this study might be useful for comparing mucin-type oligosaccharides in cells and constructing oligosaccharide libraries to study cell function.
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3
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Hauser JR, Bergström ET, Kulak AN, Warriner SL, Thomas-Oates J, Bon RS. Pyrene Tags for the Detection of Carbohydrates by Label-Assisted Laser Desorption/Ionisation Mass Spectrometry*. Chembiochem 2021; 22:1430-1439. [PMID: 33296552 DOI: 10.1002/cbic.202000721] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 12/08/2020] [Indexed: 12/15/2022]
Abstract
Matrix-assisted laser desorption/ionisation mass spectrometry (MALDI-MS) is widely used for the analysis of biomolecules. Label-assisted laser desorption/ionisation mass spectrometry (LALDI-MS) is a matrix-free variant of MALDI-MS, in which only analytes covalently attached to a laser desorption/ionisation (LDI) enhancer are detected. LALDI-MS has shown promise in overcoming the limitations of MALDI-MS in terms of sample preparation and MS analysis. In this work, we have developed a series of pyrene-based LDI reagents (LALDI tags) that can be used for labelling and LALDI-MS analysis of reducing carbohydrates from complex (biological) samples without the need for additional chemical derivatisation or purification. We have systematically explored the suitability of four pyrene-based LDI enhancers and three aldehyde-reactive handles, optimised sample preparation, and demonstrated the use of LALDI tags for the detection of lactose. We have also exemplified the potential of LALDI tags for labelling carbohydrates in biological samples by direct detection of lactose in cow's milk. These results demonstrate that LALDI-MS is a promising technique for the analysis of reducing carbohydrates in biological samples, and pave the way for the development of LALDI-MS for glycomics and diagnostics.
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Affiliation(s)
- Jacob R Hauser
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Edmund T Bergström
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.,Centre of Excellence in Mass Spectrometry, University of York, Heslington, York, YO10 5DD, UK
| | - Alexander N Kulak
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Stuart L Warriner
- School of Chemistry, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.,Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK
| | - Jane Thomas-Oates
- Department of Chemistry, University of York, Heslington, York, YO10 5DD, UK.,Centre of Excellence in Mass Spectrometry, University of York, Heslington, York, YO10 5DD, UK
| | - Robin S Bon
- Astbury Centre for Structural Molecular Biology, University of Leeds, Woodhouse Lane, Leeds, LS2 9JT, UK.,Discovery and Translational Science Department, Leeds Institute of Cardiovascular and Metabolic Medicine, LIGHT Laboratories, University of Leeds, Leeds, LS2 9JT, UK
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4
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Petrović T, Trbojević-Akmačić I. Lectin and Liquid Chromatography-Based Methods for Immunoglobulin (G) Glycosylation Analysis. EXPERIENTIA SUPPLEMENTUM (2012) 2021; 112:29-72. [PMID: 34687007 DOI: 10.1007/978-3-030-76912-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Immunoglobulin (Ig) glycosylation has been shown to dramatically affect its structure and effector functions. Ig glycosylation changes have been associated with different diseases and show a promising biomarker potential for diagnosis and prognosis of disease advancement. On the other hand, therapeutic biomolecules based on structural and functional features of Igs demand stringent quality control during the production process to ensure their safety and efficacy. Liquid chromatography (LC) and lectin-based methods are routinely used in Ig glycosylation analysis complementary to other analytical methods, e.g., mass spectrometry and capillary electrophoresis. This chapter covers analytical approaches based on LC and lectins used in low- and high-throughput N- and O-glycosylation analysis of Igs, with the focus on immunoglobulin G (IgG) applications. General principles and practical examples of the most often used LC methods for Ig purification are described, together with typical workflows for N- and O-glycan analysis on the level of free glycans, glycopeptides, subunits, or intact Igs. Lectin chromatography is a historical approach for the analysis of lectin-carbohydrate interactions and glycoprotein purification but is still being used as a valuable tool in Igs purification and glycan analysis. On the other hand, lectin microarrays have found their application in the rapid screening of glycan profiles on intact proteins.
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Affiliation(s)
- Tea Petrović
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
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Evolutionary Overview of Molecular Interactions and Enzymatic Activities in the Yeast Cell Walls. Int J Mol Sci 2020; 21:ijms21238996. [PMID: 33256216 PMCID: PMC7730094 DOI: 10.3390/ijms21238996] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 11/25/2022] Open
Abstract
Fungal cell walls are composed of a polysaccharide network that serves as a scaffold in which different glycoproteins are embedded. Investigation of fungal cell walls, besides simple identification and characterization of the main cell wall building blocks, covers the pathways and regulations of synthesis of each individual component of the wall and biochemical reactions by which they are cross-linked and remodeled in response to different growth phase and environmental signals. In this review, a survey of composition and organization of so far identified and characterized cell wall components of different yeast genera including Saccharomyces, Candida, Kluyveromyces, Yarrowia, and Schizosaccharomyces are presented with the focus on their cell wall proteomes.
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Mehta AY, Veeraiah RKH, Dutta S, Goth CK, Hanes MS, Gao C, Stavenhagen K, Kardish R, Matsumoto Y, Heimburg-Molinaro J, Boyce M, Pohl NLB, Cummings RD. Parallel Glyco-SPOT Synthesis of Glycopeptide Libraries. Cell Chem Biol 2020; 27:1207-1219.e9. [PMID: 32610041 PMCID: PMC7556346 DOI: 10.1016/j.chembiol.2020.06.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/27/2020] [Accepted: 06/12/2020] [Indexed: 12/13/2022]
Abstract
Glycan recognition is typically studied using free glycans, but glycopeptide presentations represent more physiological conditions for glycoproteins. To facilitate studies of glycopeptide recognition, we developed Glyco-SPOT synthesis, which enables the parallel production of diverse glycopeptide libraries at microgram scales. The method uses a closed system for prolonged reactions required for coupling Fmoc-protected glycoamino acids, including O-, N-, and S-linked glycosides, and release conditions to prevent side reactions. To optimize reaction conditions and sample reaction progress, we devised a biopsy testing method. We demonstrate the efficient utilization of such microscale glycopeptide libraries to determine the specificity of glycan-recognizing antibodies (e.g., CTD110.6) using microarrays, enzyme specificity on-array and in-solution (e.g., ST6GalNAc1, GCNT1, and T-synthase), and binding kinetics using fluorescence polarization. We demonstrated that the glycosylation on these peptides can be expanded using glycosyltransferases both in-solution and on-array. This technology will promote the discovery of biological functions of peptide modifications by glycans.
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Affiliation(s)
- Akul Y Mehta
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - Ravi Kumar H Veeraiah
- Department of Chemistry, Indiana University, 120A Simon Hall, 212 South Hawthorne Drive, Bloomington, IN 47405, USA
| | - Sucharita Dutta
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - Christoffer K Goth
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - Melinda S Hanes
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - Chao Gao
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - Kathrin Stavenhagen
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - Robert Kardish
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - Yasuyuki Matsumoto
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - Jamie Heimburg-Molinaro
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA
| | - Michael Boyce
- Department of Biochemistry and Program in Cell and Molecular Biology, Duke University School of Medicine, Durham, NC 27710, USA
| | - Nicola L B Pohl
- Department of Chemistry, Indiana University, 120A Simon Hall, 212 South Hawthorne Drive, Bloomington, IN 47405, USA.
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, National Center for Functional Glycomics, CLS 11087 - 3 Blackfan Circle, Boston, MA 02115, USA.
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7
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Xiao H, Sun F, Suttapitugsakul S, Wu R. Global and site-specific analysis of protein glycosylation in complex biological systems with Mass Spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:356-379. [PMID: 30605224 PMCID: PMC6610820 DOI: 10.1002/mas.21586] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/27/2018] [Indexed: 05/16/2023]
Abstract
Protein glycosylation is ubiquitous in biological systems and plays essential roles in many cellular events. Global and site-specific analysis of glycoproteins in complex biological samples can advance our understanding of glycoprotein functions and cellular activities. However, it is extraordinarily challenging because of the low abundance of many glycoproteins and the heterogeneity of glycan structures. The emergence of mass spectrometry (MS)-based proteomics has provided us an excellent opportunity to comprehensively study proteins and their modifications, including glycosylation. In this review, we first summarize major methods for glycopeptide/glycoprotein enrichment, followed by the chemical and enzymatic methods to generate a mass tag for glycosylation site identification. We next discuss the systematic and quantitative analysis of glycoprotein dynamics. Reversible protein glycosylation is dynamic, and systematic study of glycoprotein dynamics helps us gain insight into glycoprotein functions. The last part of this review focuses on the applications of MS-based proteomics to study glycoproteins in different biological systems, including yeasts, plants, mice, human cells, and clinical samples. Intact glycopeptide analysis is also included in this section. Because of the importance of glycoproteins in complex biological systems, the field of glycoproteomics will continue to grow in the next decade. Innovative and effective MS-based methods will exponentially advance glycoscience, and enable us to identify glycoproteins as effective biomarkers for disease detection and drug targets for disease treatment. © 2019 Wiley Periodicals, Inc. Mass Spec Rev 9999: XX-XX, 2019.
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Affiliation(s)
- Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
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8
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Yang S, Onigman P, Wu WW, Sjogren J, Nyhlen H, Shen RF, Cipollo J. Deciphering Protein O-Glycosylation: Solid-Phase Chemoenzymatic Cleavage and Enrichment. Anal Chem 2018; 90:8261-8269. [DOI: 10.1021/acs.analchem.8b01834] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Shuang Yang
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - Philip Onigman
- Genovis Inc., Cambridge, Massachusetts 02142, United States
| | - Wells W. Wu
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | | | | | - Rong-Fong Shen
- Facility for Biotechnology Resources, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
| | - John Cipollo
- Laboratory of Bacterial Polysaccharides, Division of Bacterial, Parasitic and Allergenic Products, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, Maryland 20993, United States
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Affiliation(s)
- David J. Harvey
- Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Biological Sciences and the Institute for Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK
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Everest-Dass AV, Moh ESX, Ashwood C, Shathili AMM, Packer NH. Human disease glycomics: technology advances enabling protein glycosylation analysis - part 1. Expert Rev Proteomics 2018; 15:165-182. [PMID: 29285957 DOI: 10.1080/14789450.2018.1421946] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
INTRODUCTION Protein glycosylation is recognized as an important post-translational modification, with specific substructures having significant effects on protein folding, conformation, distribution, stability and activity. However, due to the structural complexity of glycans, elucidating glycan structure-function relationships is demanding. The fine detail of glycan structures attached to proteins (including sequence, branching, linkage and anomericity) is still best analysed after the glycans are released from the purified or mixture of glycoproteins (glycomics). The technologies currently available for glycomics are becoming streamlined and standardized and many features of protein glycosylation can now be determined using instruments available in most protein analytical laboratories. Areas covered: This review focuses on the current glycomics technologies being commonly used for the analysis of the microheterogeneity of monosaccharide composition, sequence, branching and linkage of released N- and O-linked glycans that enable the determination of precise glycan structural determinants presented on secreted proteins and on the surface of all cells. Expert commentary: Several emerging advances in these technologies enabling glycomics analysis are discussed. The technological and bioinformatics requirements to be able to accurately assign these precise glycan features at biological levels in a disease context are assessed.
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Affiliation(s)
- Arun V Everest-Dass
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,b Institute for Glycomics , Griffith University , Gold Coast , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
| | - Edward S X Moh
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
| | - Christopher Ashwood
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
| | - Abdulrahman M M Shathili
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
| | - Nicolle H Packer
- a Biomolecular Discovery and Design Research Centre, Faculty of Science and Engineering , Macquarie University , Sydney , Australia.,b Institute for Glycomics , Griffith University , Gold Coast , Australia.,c ARC Centre for Nanoscale BioPhotonics , Macquarie University , Sydney , Australia
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Ashwood C, Abrahams JL, Nevalainen H, Packer NH. Enhancing structural characterisation of glucuronidated O-linked glycans using negative mode ion trap higher energy collision-induced dissociation mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2017; 31:851-858. [PMID: 28277614 DOI: 10.1002/rcm.7851] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Revised: 02/20/2017] [Accepted: 03/04/2017] [Indexed: 06/06/2023]
Abstract
RATIONALE High protein production and secretion with eukaryotic glycosylation machinery make T. reesei RUT-C30 a suitable expression host for recombinant proteins. The N-glycosylation of secreted proteins of RUT-C30 is known to vary depending on culture nutrients but O-glycosylation has been less extensively studied. METHODS O-Glycans and glycopeptides from secreted proteins were separated by porous graphitised carbon and C-18 liquid chromatography, respectively. O-Glycans were analysed in negative ion mode by electrospray ionisation linear ion trap mass spectrometry and glycopeptides in positive ion mode by electrospray ionisation hybrid quadrupole-orbitrap mass spectrometry. Tandem mass spectrometry was used on O-glycans and glycopeptides including ion trap higher energy collision-induced dissociation (tHCD) to detect glycan fragments not detectable with standard ion trap fragmentation. tHCD allowed targeted MS3 experiments to be performed on structures containing hexuronic acid, which was not possible with ion trap CID, validating this novel O-glycan composition. Positive mode C18-LC/ESI-MS/MS was used to identify and characterise glycopeptides found to be modified with this class of O-glycans, identifying cellobiohydrolase I as a carrier of these novel O-glycans. RESULTS Negative mode ion trap higher energy collision-induced dissociation allowed detection and targeted MS3 experiments to be performed on the hexuronic acid substituent of O-glycan structures, which was not possible with ion trap CID, validating the novel O-glycan composition to include hexuronic acid. Using glycopeptide analysis, this novel O-glycan composition was found to be present on the catalytic domain of cellobiohydrolase I, the most abundant secreted protein by T. reesei. CONCLUSIONS These are the first reported O-glycans to contain acidic sugars in fungi and they could have significant implications for cellobiohydrolase I structure and activity as well as the activity of recombinant proteins expressed in this host system. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- Christopher Ashwood
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW, 2109, Australia
| | - Jodie L Abrahams
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Helena Nevalainen
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
| | - Nicolle H Packer
- Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, 2109, Australia
- ARC Centre of Excellence for Nanoscale BioPhotonics, Macquarie University, Sydney, NSW, 2109, Australia
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12
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Skeene K, Walker M, Clarke G, Bergström E, Genever P, Ungar D, Thomas-Oates J. One Filter, One Sample, and the N- and O-Glyco(proteo)me: Toward a System to Study Disorders of Protein Glycosylation. Anal Chem 2017; 89:5840-5849. [DOI: 10.1021/acs.analchem.7b00143] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
| | | | - Graham Clarke
- Bristol-Myers Squibb, Reeds Lane, Moreton, Wirral, CH46 1QW, United Kingdom
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13
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Abstract
Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.
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Affiliation(s)
- Krishnan K. Palaniappan
- Verily Life Sciences, 269 East Grand Ave., South San Francisco, California 94080, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
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14
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Bai X, Li D, Zhu J, Guan Y, Zhang Q, Chi L. From individual proteins to proteomic samples: characterization of O-glycosylation sites in human chorionic gonadotropin and human-plasma proteins. Anal Bioanal Chem 2015; 407:1857-69. [DOI: 10.1007/s00216-014-8439-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 12/19/2014] [Indexed: 12/27/2022]
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15
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Tatara Y, Kakizaki I, Suto S, Ishioka H, Negishi M, Endo M. Chondroitin sulfate cluster of epiphycan from salmon nasal cartilage defines binding specificity to collagens. Glycobiology 2014; 25:557-69. [PMID: 25533443 DOI: 10.1093/glycob/cwu186] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Epiphycan (EPY) from salmon nasal cartilage has a glycosaminoglycan (GAG) domain that is heavily modified by chondroitin 4-sulfate and chondroitin 6-sulfate. The functional role of the GAG domain has not been investigated. The interaction of EPY with collagen was examined in vitro using surface plasmon resonance analysis. EPY was found to bind to type I collagen via clustered chondroitin sulfate (CS), while a single chain of CS was unable to bind. Types I, III, VII, VIII and X collagen showed high binding affinity with EPY, whereas types II, IV, V, VI and IX showed low binding affinities. Chemical modification of lysine residues in collagen decreased the affinity with the clustered CS. These results suggest that lysine residues of collagen are involved in the interaction with the clustered CS, and the difference in lysine modification defines the binding affinity to EPY. The clustered CS was also involved in an inter-saccharide interaction, and formed self-associated EPY. CS of EPY promoted fibril formation of type I collagen.
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Affiliation(s)
- Yota Tatara
- Department of Glycotechnology, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan Department of Glycobiomedicine, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan
| | - Ikuko Kakizaki
- Department of Glycotechnology, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan Department of Glycobiomedicine, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan
| | - Shinichiro Suto
- Department of Glycotechnology, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan Department of Glycobiomedicine, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan
| | - Haruna Ishioka
- Department of Glycotechnology, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan Department of Glycobiomedicine, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan
| | - Mika Negishi
- Department of Glycotechnology, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan Department of Glycobiomedicine, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan
| | - Masahiko Endo
- Department of Glycobiomedicine, Hirosaki University Graduate School of Medicine, Hirosaki 036-8562, Japan
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Levery SB, Steentoft C, Halim A, Narimatsu Y, Clausen H, Vakhrushev SY. Advances in mass spectrometry driven O-glycoproteomics. Biochim Biophys Acta Gen Subj 2014; 1850:33-42. [PMID: 25284204 DOI: 10.1016/j.bbagen.2014.09.026] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Global analyses of proteins and their modifications by mass spectrometry are essential tools in cell biology and biomedical research. Analyses of glycoproteins represent particular challenges and we are only at the beginnings of the glycoproteomic era. Some of the challenges have been overcome with N-glycoproteins and proteome-wide analysis of N-glycosylation sites is accomplishable today but only by sacrificing information of structures at individual glycosites. More recently advances in analysis of O-glycoproteins have been made and proteome-wide analysis of O-glycosylation sites is becoming available as well. SCOPE OF REVIEW Here we discuss the challenges of analysis of O-glycans and new O-glycoproteomics strategies focusing on O-GalNAc and O-Man glycoproteomes. MAJOR CONCLUSIONS A variety of strategies are now available for proteome-wide analysis of O-glycosylation sites enabling functional studies. However, further developments are still needed for complete analysis of glycan structures at individual sites for both N- and O-glycoproteomics strategies. GENERAL SIGNIFICANCE The advances in O-glycoproteomics have led to identification of new biological functions of O-glycosylation and a new understanding of the importance of where O-glycans are positioned on proteins.
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Affiliation(s)
- Steven B Levery
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Catharina Steentoft
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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Yang S, Zhang H. Glycomic analysis of glycans released from glycoproteins using chemical immobilization and mass spectrometry. ACTA ACUST UNITED AC 2014; 6:191-208. [PMID: 25205566 DOI: 10.1002/9780470559277.ch140085] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Protein glycosylation is one of most common protein modifications and is involved in many biological activities. N-linked and O-linked glycosylation not only represent abundant glycan modifications, but also are structurally diverse. Mass spectrometry has emerged as a major method for glycomic analysis. However, glycan extraction from proteins and glycan modification are two critical steps in glycomic analysis of glycans using mass spectrometry. In this protocol, we describe a novel and high-throughput method for isolation and modification of glycans from glycoproteins using a chemoenzymatic approach on solid-phase. Proteins are first immobilized to a solid support and unconjugated molecules are washed away; glycans, while still linked to glycoproteins on the solid support, can be treated enzymatically or chemically on solid phase for glycan derivatization. Glycans are then released from the solid support for analysis by mass spectrometry. The procedures outlined are robust and useful for high-throughput glycomic analysis from complex biological or clinical samples.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland
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18
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Panin VM, Wells L. Protein O-mannosylation in metazoan organisms. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2014; 75:12.12.1-12.12.29. [PMID: 24510673 PMCID: PMC3984005 DOI: 10.1002/0471140864.ps1212s75] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Protein O-mannosylation is a special type of glycosylation that plays prominent roles in metazoans, affecting development and physiology of the nervous system and muscles. A major biological effect of O-mannosylation involves the regulation of α-dystroglycan, a membrane glycoprotein mediating cell-extracellular matrix interactions. Genetic defects of O-mannosylation result in the loss of ligand-binding activity of α-dystroglycan and cause congenital muscular dystrophies termed dystroglycanopathies. Recent progress in mass spectrometry and in vitro analyses has shed new light on the mechanism of α-dystroglycan glycosylation; however, this mechanism is underlain by complex genetic and molecular elements that remain poorly understood. Protein O-mannosylation is evolutionarily conserved in metazoans, yet the pathway is simplified and more amenable to genetic analyses in invertebrate organisms, indicating that genetically tractable in vivo models could facilitate research in this area. This unit describes recent methodological strategies for studying protein O-mannosylation using in vitro and in vivo approaches.
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Affiliation(s)
- Vladislav M. Panin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843; Tel. 979-458-4630, FAX 979-845-9274
| | - Lance Wells
- Complex Carbohydrate Research Center, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602; Tel 706-542-7806, FAX 706-542-4412
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19
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Turyan I, Hronowski X, Sosic Z, Lyubarskaya Y. Comparison of two approaches for quantitative O-linked glycan analysis used in characterization of recombinant proteins. Anal Biochem 2014; 446:28-36. [DOI: 10.1016/j.ab.2013.10.019] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 10/09/2013] [Accepted: 10/11/2013] [Indexed: 11/30/2022]
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20
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Bellwied P, Staubach S, Hanisch FG. Chemical in-gel deglycosylation ofO-glycoproteins improves their staining and mass spectrometric identification. Electrophoresis 2013; 34:2387-93. [DOI: 10.1002/elps.201200647] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Revised: 12/21/2012] [Accepted: 01/25/2013] [Indexed: 11/10/2022]
Affiliation(s)
- Petra Bellwied
- Medical Faculty, Institute of Biochemistry II; University of Cologne; Köln; Germany
| | - Simon Staubach
- Medical Faculty, Institute of Biochemistry II; University of Cologne; Köln; Germany
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21
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Tatara Y, Kakizaki I, Kuroda Y, Suto S, Ishioka H, Endo M. Epiphycan from salmon nasal cartilage is a novel type of large leucine-rich proteoglycan. Glycobiology 2013; 23:993-1003. [PMID: 23704297 DOI: 10.1093/glycob/cwt038] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chum salmon (Oncorhynchus keta) nasal cartilage was examined by next-generation DNA sequencing and mass spectrometric analyses, and 14 types of proteoglycans including epiphycan (EPY) were found. A cDNA encoding EPY was cloned and sequenced. The cDNA encoded 589 amino acids comprised a glycosaminoglycan (GAG) domain containing 55 potential GAG-modified sites (Ser-Gly and/or Gly-Ser), a cysteine cluster and 6 leucine-rich repeats. EPY was purified from salmon nasal cartilage and the structure of the GAG was characterized. As a result of unsaturated disaccharide analysis, GAG was found to be composed of chondroitin 6-sulfate (58.0%), chondroitin 4-sulfate (26.5%) and non-sulfated chondroitin (15.3%). The average molecular weight of GAG was estimated to be 3.0 × 10(4). Ser-100 and Ser-103 were identified as serine residues substituted by GAG chains by chemical modification and mass spectrometric analysis. More than 50 serine residues were assumed to be substituted by GAG chains. EPY is heavily substituted by chondroitin sulfate, giving an overall molecular weight of just under 2 × 10(6). EPY from salmon nasal cartilage is a novel type of large leucine-rich proteoglycan.
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Affiliation(s)
- Yota Tatara
- Department of Glycotechnology, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Japan.
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22
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Yang S, Li Y, Shah P, Zhang H. Glycomic analysis using glycoprotein immobilization for glycan extraction. Anal Chem 2013; 85:5555-61. [PMID: 23688297 DOI: 10.1021/ac400761e] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Glycosylation is one of the most common protein modifications and is involved in many functions of glycoproteins. Investigating aberrant protein glycosylation associated with diseases is useful in improving disease diagnostics. Due to the nontemplate nature of glycan biosynthesis, the glycans attached to glycoproteins are enormously complex; thus, a method for comprehensive analysis of glycans from biological or clinical samples is needed. Here, we describe a novel method for glycomic analysis using glycoprotein immobilization for glycan extraction (GIG). Proteins or peptides from complex samples were first immobilized on solid support, and other nonconjugated molecules were removed. Glycans were enzymatically or chemically modified on solid phase before releasing from glycoproteins/glycopeptides for mass spectrometry analysis. The method was applied to the glycomic analysis of both N- and O-glycans.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
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23
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Alley WR, Mann BF, Novotny MV. High-sensitivity analytical approaches for the structural characterization of glycoproteins. Chem Rev 2013; 113:2668-732. [PMID: 23531120 PMCID: PMC3992972 DOI: 10.1021/cr3003714] [Citation(s) in RCA: 239] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- William R. Alley
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
| | - Benjamin F. Mann
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
- Indiana University School of Medicine, Indiana University, Indianapolis, Indiana, United States
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Abstract
The composition and organization of the cell walls from Saccharomyces cerevisiae, Candida albicans, Aspergillus fumigatus, Schizosaccharomyces pombe, Neurospora crassa, and Cryptococcus neoformans are compared and contrasted. These cell walls contain chitin, chitosan, β-1,3-glucan, β-1,6-glucan, mixed β-1,3-/β-1,4-glucan, α-1,3-glucan, melanin, and glycoproteins as major constituents. A comparison of these cell walls shows that there is a great deal of variability in fungal cell wall composition and organization. However, in all cases, the cell wall components are cross-linked together to generate a cell wall matrix. The biosynthesis and properties of each of the major cell wall components are discussed. The chitin and glucans are synthesized and extruded into the cell wall space by plasma membrane-associated chitin synthases and glucan synthases. The glycoproteins are synthesized by ER-associated ribosomes and pass through the canonical secretory pathway. Over half of the major cell wall proteins are modified by the addition of a glycosylphosphatidylinositol anchor. The cell wall glycoproteins are also modified by the addition of O-linked oligosaccharides, and their N-linked oligosaccharides are extensively modified during their passage through the secretory pathway. These cell wall glycoprotein posttranslational modifications are essential for cross-linking the proteins into the cell wall matrix. Cross-linking the cell wall components together is essential for cell wall integrity. The activities of four groups of cross-linking enzymes are discussed. Cell wall proteins function as cross-linking enzymes, structural elements, adhesins, and environmental stress sensors and protect the cell from environmental changes.
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Affiliation(s)
- Stephen J Free
- Department of Biological Sciences, SUNY, University at Buffalo, Buffalo, New York, USA.
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25
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Valim CXR, Basso LR, dos Reis Almeida FB, Reis TF, Damásio ARL, Arruda LK, Martinez R, Roque-Barreira MC, Oliver C, Jamur MC, Coelho PSR. Characterization of PbPga1, an antigenic GPI-protein in the pathogenic fungus Paracoccidioides brasiliensis. PLoS One 2012; 7:e44792. [PMID: 23024763 PMCID: PMC3443090 DOI: 10.1371/journal.pone.0044792] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 08/14/2012] [Indexed: 12/21/2022] Open
Abstract
Paracoccidioides brasiliensis is the etiologic agent of paracoccidioidomycosis (PCM), one of the most prevalent mycosis in Latin America. P. brasiliensis cell wall components interact with host cells and influence the pathogenesis of PCM. Cell wall components, such as glycosylphosphatidylinositol (GPI)-proteins play a critical role in cell adhesion and host tissue invasion. Although the importance of GPI-proteins in the pathogenesis of other medically important fungi is recognized, little is known about their function in P. brasiliensis cells and PCM pathogenesis. We cloned the PbPga1 gene that codifies for a predicted GPI-anchored glycoprotein from the dimorphic pathogenic fungus P. brasiliensis. PbPga1 is conserved in Eurotiomycetes fungi and encodes for a protein with potential glycosylation sites in a serine/threonine-rich region, a signal peptide and a putative glycosylphosphatidylinositol attachment signal sequence. Specific chicken anti-rPbPga1 antibody localized PbPga1 on the yeast cell surface at the septum between the mother cell and the bud with stronger staining of the bud. The exposure of murine peritoneal macrophages to rPbPga1 induces TNF-α release and nitric oxide (NO) production by macrophages. Furthermore, the presence of O-glycosylation sites was demonstrated by β-elimination under ammonium hydroxide treatment of rPbPga1. Finally, sera from PCM patients recognized rPbPga1 by Western blotting indicating the presence of specific antibodies against rPbPga1. In conclusion, our findings suggest that the PbPga1gene codifies for a cell surface glycoprotein, probably attached to a GPI-anchor, which may play a role in P. brasiliensis cell wall morphogenesis and infection. The induction of inflammatory mediators released by rPbPga1 and the reactivity of PCM patient sera toward rPbPga1 imply that the protein favors the innate mechanisms of defense and induces humoral immunity during P. brasiliensis infection.
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Affiliation(s)
- Clarissa X. R. Valim
- Departamento de Biologia Celular e Molecular e Biagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, São Paulo, Brazil
| | - Luiz Roberto Basso
- Departamento de Biologia Celular e Molecular e Biagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, São Paulo, Brazil
| | - Fausto B. dos Reis Almeida
- Departamento de Biologia Celular e Molecular e Biagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, São Paulo, Brazil
| | - Thaila Fernanda Reis
- Departamento de Biologia Celular e Molecular e Biagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, São Paulo, Brazil
| | | | - Luisa Karla Arruda
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, São Paulo, Brazil
| | - Roberto Martinez
- Departamento de Clínica Médica, Faculdade de Medicina de Ribeirão Preto, São Paulo, Brazil
| | - Maria Cristina Roque-Barreira
- Departamento de Biologia Celular e Molecular e Biagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, São Paulo, Brazil
| | - Constance Oliver
- Departamento de Biologia Celular e Molecular e Biagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, São Paulo, Brazil
| | - Maria Célia Jamur
- Departamento de Biologia Celular e Molecular e Biagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, São Paulo, Brazil
| | - Paulo Sergio Rodrigues Coelho
- Departamento de Biologia Celular e Molecular e Biagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, São Paulo, Brazil
- * E-mail:
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26
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Kearney P, Thibault P. BIOINFORMATICS MEETS PROTEOMICS — BRIDGING THE GAP BETWEEN MASS SPECTROMETRY DATA ANALYSIS AND CELL BIOLOGY. J Bioinform Comput Biol 2012; 1:183-200. [PMID: 15290788 DOI: 10.1142/s021972000300023x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2003] [Revised: 04/11/2003] [Accepted: 04/11/2003] [Indexed: 11/18/2022]
Abstract
Proteomics research programs typically comprise the identification of protein content of any given cell, their isoforms, splice variants, post-translational modifications, interacting partners and higher-order complexes under different conditions. These studies present significant analytical challenges owing to the high proteome complexity and the low abundance of the corresponding proteins, which often requires highly sensitive and resolving techniques. Mass spectrometry plays an important role in proteomics and has become an indispensable tool for molecular and cellular biology. However, the analysis of mass spectrometry data can be a daunting task in view of the complexity of the information to decipher, the accuracy and dynamic range of quantitative analysis, the availability of appropriate bioinformatics software and the overwhelming size of data files. The past ten years have witnessed significant technological advances in mass spectrometry-based proteomics and synergy with bioinformatics is vital to fulfill the expectations of biological discovery programs. We present here the technological capabilities of mass spectrometry and bioinformatics for mining the cellular proteome in the context of discovery programs aimed at trace-level protein identification and expression from microgram amounts of protein extracts from human tissues.
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Affiliation(s)
- P Kearney
- Caprion Pharmaceuticals, 7150 Alexander Fleming, St-Laurent, Québec, H4S 2C8, Canada.
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27
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Hanisch FG. O-glycoproteomics: site-specific O-glycoprotein analysis by CID/ETD electrospray ionization tandem mass spectrometry and top-down glycoprotein sequencing by in-source decay MALDI mass spectrometry. Methods Mol Biol 2012; 842:179-189. [PMID: 22259136 DOI: 10.1007/978-1-61779-513-8_10] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
The sites of mucin-type O-glycosylation are difficult to predict, making structural analysis by mass spectrometry indispensible. This chapter refers to state-of-the-art techniques in the site localization of O-linked glycans and their structural characterization in situ using tandem ESI and MALDI mass spectrometry. Detailed protocols are provided that describe the application of nano-LC-ESI-MS/MS with alternative fragmentation modes (collision-induced dissociation vs. electron-transfer dissociation) for the analysis of O-glycopeptides. Moreover, a top-down sequencing approach by MALDI-MS is presented that is based on the in-source decay of intact glycoproteins or large glycopeptides and allows a ladder sequencing of up to 70 amino acid residues from both termini with unequivocal assignment of modified sites.
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Affiliation(s)
- Franz-Georg Hanisch
- Institute of Biochemistry II, Medical Faulty, and Center for Molecular Medicine Cologne, University of Cologne, Köln, Germany.
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28
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Halfinger B, Sarg B, Lindner HH. Evaluation of non-reductive β-elimination/Michael addition for glycosylation site determination in mucin-like O-glycopeptides. Electrophoresis 2011; 32:3546-53. [DOI: 10.1002/elps.201100393] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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29
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Hanisch FG. Chemical de-O-glycosylation of glycoproteins for applications in LC-based proteomics. Methods Mol Biol 2011; 753:323-33. [PMID: 21604133 DOI: 10.1007/978-1-61779-148-2_22] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
This paper describes a cyclic on-column procedure for the sequential degradation of complex O-glycans on proteins by periodate oxidation of sugars and cleavage of oxidation products by elimination. Glycoproteins are immobilized to alkali-stable, reversed-phase Poros 20 beads, desialylated by treatment with dilute trifluoroacetic acid, and de-O-glycosylated by two degradation cycles before the eluted apoproteins are digested with trypsin for analysis by liquid chromatography electrospray ionization-mass spectrometry. Even complex glycan moieties are removed under mild conditions with only minimal effects on structural integrity of the peptide core by fragmentation, dehydration, or racemization of lysine and arginine residues. The protocol is also applicable on gel-immobilized glycoproteins after 1D or 2D gel electrophoresis. Conversion of O-glycoproteins into their corresponding apoproteins results in facilitated accessibility of tryptic cleavage sites, increases the numbers of peptide fragments, and accordingly enhances protein coverage and identification rates within the subproteome of mucin-type O-glycoproteins. The protocol is suitable for automatization, but due to partial elution from the Poros 20 columns it is not recommended for applications on the glycopeptide level.
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Affiliation(s)
- Franz-Georg Hanisch
- Institute of Biochemistry II, Medical Faculty, Center for Molecular Medicine Cologne, University of Cologne, 50931, Köln, Germany.
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Abstract
In Francisella tularensis subsp. tularensis, DsbA has been shown to be an essential virulence factor and has been observed to migrate to multiple protein spots on two-dimensional electrophoresis gels. In this work, we show that the protein is modified with a 1,156-Da glycan moiety in O-linkage. The results of mass spectrometry studies suggest that the glycan is a hexasaccharide, comprised of N-acetylhexosamines, hexoses, and an unknown monosaccharide. Disruption of two genes within the FTT0789-FTT0800 putative polysaccharide locus, including a galE homologue (FTT0791) and a putative glycosyltransferase (FTT0798), resulted in loss of glycan modification of DsbA. The F. tularensis subsp. tularensis ΔFTT0798 and ΔFTT0791::Cm mutants remained virulent in the murine model of subcutaneous tularemia. This indicates that glycosylation of DsbA does not play a major role in virulence under these conditions. This is the first report of the detailed characterization of the DsbA glycan and putative role of the FTT0789-FTT0800 gene cluster in glycan biosynthesis.
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31
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Hanisch FG. Top-down sequencing of O-glycoproteins by in-source decay matrix-assisted laser desorption ionization mass spectrometry for glycosylation site analysis. Anal Chem 2011; 83:4829-37. [PMID: 21526855 DOI: 10.1021/ac200493c] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The sites of mucin-type O-glycosylation are largely unpredictable, making structural analysis by mass spectrometry (MS) indispensible. On the peptide level, a site localization and characterization of O-linked glycans in situ using tandem MS with electron-transfer dissociation or matrix-assisted laser desorption ionization (MALDI) MS with postsource decay have been reported. The top-down sequencing on the protein level by MALDI-MS is based on the in-source decay (ISD) of intact glycoproteins induced by hydrogen radical transfer from the matrix. It allows a ladder sequencing from both termini with assignment of O-glycosylation sites based on intense c-, y-, and z-type ions. The feasibility of ISD-MALDI-MS in the localization of O-glycosylation sites was demonstrated with synthetic O-glycopeptides, the tandem repeat domain of recombinant MUC1, and the natural bovine glycoproteins asialofetuin and desialylated κ-casein. Ladder sequencing of the 17-18.5 kD MUC1 hexarepeat domains revealed (1) cell-specific glycosylation site patterns on comparison of probes expressed in human HEK-293 or Drosophila S2 cells, and (2) a site-specific microheterogeneity at the Thr/Ser sites with variations of the glycan compositions from zero to four monosaccharides. Novel O-glycosylation sites in the C-terminal domains of fetuin (T334) and κ-caseinoglycopeptide (S154 and T156) were assigned, the former representing a sequence conflict with the published T154.
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Affiliation(s)
- Franz-Georg Hanisch
- Institute of Biochemistry II, Medical Faculty, University of Cologne, Joseph-Stelzmann-Strasse 52, 50931 Köln, Germany.
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Butterfield DA, Owen JB. Lectin-affinity chromatography brain glycoproteomics and Alzheimer disease: Insights into protein alterations consistent with the pathology and progression of this dementing disorder. Proteomics Clin Appl 2010; 5:50-6. [DOI: 10.1002/prca.201000070] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 08/04/2010] [Accepted: 08/10/2010] [Indexed: 11/05/2022]
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Kakizaki I, Tatara Y, Majima M, Kato Y, Endo M. Identification of proteoglycan from salmon nasal cartilage. Arch Biochem Biophys 2010; 506:58-65. [PMID: 21056541 DOI: 10.1016/j.abb.2010.10.025] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2010] [Revised: 10/29/2010] [Accepted: 10/31/2010] [Indexed: 11/28/2022]
Abstract
There has been no structural information about the core protein of salmon nasal cartilage proteoglycan although its physiological activities have been investigated. Internal amino acid sequencing using nano-LC/MS/MS revealed that the salmon proteoglycan was aggrecan. Primer walk sequencing based on the amino acid information determined that the salmon aggrecan cDNA is comprised of 4207bp nucleotides predicted to encode 1324 amino acids with a molecular mass of 143,276. It exhibited significant similarities to predicted pufferfish aggrecan, zebrafish similar to aggrecan, zebrafish aggrecan, bovine aggrecan and human aggrecan isoform 2 precursor; whose amino acid identities were 56%, 55%, 49%, 31% and 30%, respectively. Salmon cartilage aggrecan had globular domains G1, G2 and G3 as in mammalian aggrecans. Neither the putative keratan sulfate attachment domain enriched with serine, glutamic acid and proline, nor the putative chondroitin sulfate attachment domain with repeating amino acid sequence containing serine-glycine, found in mammalian aggrecans were observed in salmon, however, random serine-glycine (or glycine-serine) sequences predicted to the sugar chain attachment sites were observed. Based on cDNA analysis and amino acid analysis after β-elimination, the ratio of serine attached to sugar chains was calculated to be approximately 37.7% of total serine, that is, 46 of 123 serine residues.
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Affiliation(s)
- Ikuko Kakizaki
- Department of Glycotechnology, Center for Advanced Medical Research, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Japan.
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Yu G, Zhang Y, Zhang Z, Song L, Wang P, Chai W. Effect and Limitation of Excess Ammonium on the Release of O-Glycans in Reducing Forms from Glycoproteins under Mild Alkaline Conditions for Glycomic and Functional Analysis. Anal Chem 2010; 82:9534-42. [DOI: 10.1021/ac102300r] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Guangli Yu
- Key Laboratory of Glycoscience and Glycoengineering of Shandong Province, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong 266003, China, and Glycosciences Laboratory, Faculty of Medicine, Imperial College London, Northwick Park and St. Mark’s Campus, Harrow, Middlesex HA1 3UJ, United Kingdom
| | - Yibing Zhang
- Key Laboratory of Glycoscience and Glycoengineering of Shandong Province, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong 266003, China, and Glycosciences Laboratory, Faculty of Medicine, Imperial College London, Northwick Park and St. Mark’s Campus, Harrow, Middlesex HA1 3UJ, United Kingdom
| | - Zhenqing Zhang
- Key Laboratory of Glycoscience and Glycoengineering of Shandong Province, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong 266003, China, and Glycosciences Laboratory, Faculty of Medicine, Imperial College London, Northwick Park and St. Mark’s Campus, Harrow, Middlesex HA1 3UJ, United Kingdom
| | - Letian Song
- Key Laboratory of Glycoscience and Glycoengineering of Shandong Province, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong 266003, China, and Glycosciences Laboratory, Faculty of Medicine, Imperial College London, Northwick Park and St. Mark’s Campus, Harrow, Middlesex HA1 3UJ, United Kingdom
| | - Peipei Wang
- Key Laboratory of Glycoscience and Glycoengineering of Shandong Province, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong 266003, China, and Glycosciences Laboratory, Faculty of Medicine, Imperial College London, Northwick Park and St. Mark’s Campus, Harrow, Middlesex HA1 3UJ, United Kingdom
| | - Wengang Chai
- Key Laboratory of Glycoscience and Glycoengineering of Shandong Province, School of Medicine and Pharmacy, Ocean University of China, Qingdao, Shandong 266003, China, and Glycosciences Laboratory, Faculty of Medicine, Imperial College London, Northwick Park and St. Mark’s Campus, Harrow, Middlesex HA1 3UJ, United Kingdom
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Maniatis S, Zhou H, Reinhold V. Rapid de-O-glycosylation concomitant with peptide labeling using microwave radiation and an alkyl amine base. Anal Chem 2010; 82:2421-5. [PMID: 20178317 DOI: 10.1021/ac902734w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Procedures are detailed for a quantitative release of O-linked glycans from peptides that now provide a shorter reaction time, a possible identification of O-linked sites, and a quantification of all reaction products. The release was initiated by a mild base, dimethylamine, and accelerated by microwave radiation. Differential analysis using standard glycoproteins has shown improved release efficiency concurrent with facile incorporation of dimethylamine into the former O-linked sites. In situ glycan reduction insures protection against peeling and is synchronous with subsequent studies by high performance MS(n) sequencing. The protocols were established with a synthetic O-GlcNAc peptide that would mimic the linkage chemistry and applied to a well characterized glycoprotein bovine fetuin with both N- and O-linked glycans and a highly glycosylated swine mucin.
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Affiliation(s)
- Stephanie Maniatis
- Department of Chemistry, University of New Hampshire, Durham, New Hampshire 03824, USA
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Abstract
Increasing numbers of studies are reporting the modification of prokaryotic proteins with novel glycans. These proteins are often associated with virulence factors of medically important pathogens. Herein, we describe the steps required to characterize prokaryotic glycoproteins by mass spectrometry, using flagellin isolated from Clostridium botulinum strain Langeland as an example. Both "top-down" and "bottom-up" approaches will be described for characterizing the purified glycoprotein at the whole protein and peptide levels. The preliminary steps toward structural characterization of novel prokaryotic glycans by mass spectrometry and NMR are also described.
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Affiliation(s)
- Susan M Twine
- Institute for Biological Sciences, National Research Council Canada, Ottawa, Ontario, Canada
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Hwang H, Zhang J, Chung KA, Leverenz JB, Zabetian CP, Peskind ER, Jankovic J, Su Z, Hancock AM, Pan C, Montine TJ, Pan S, Nutt J, Albin R, Gearing M, Beyer RP, Shi M, Zhang J. Glycoproteomics in neurodegenerative diseases. MASS SPECTROMETRY REVIEWS 2010; 29:79-125. [PMID: 19358229 PMCID: PMC2799547 DOI: 10.1002/mas.20221] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protein glycosylation regulates protein function and cellular distribution. Additionally, aberrant protein glycosylations have been recognized to play major roles in human disorders, including neurodegenerative diseases. Glycoproteomics, a branch of proteomics that catalogs and quantifies glycoproteins, provides a powerful means to systematically profile the glycopeptides or glycoproteins of a complex mixture that are highly enriched in body fluids, and therefore, carry great potential to be diagnostic and/or prognostic markers. Application of this mass spectrometry-based technology to the study of neurodegenerative disorders (e.g., Alzheimer's disease and Parkinson's disease) is relatively new, and is expected to provide insight into the biochemical pathogenesis of neurodegeneration, as well as biomarker discovery. In this review, we have summarized the current understanding of glycoproteins in biology and neurodegenerative disease, and have discussed existing proteomic technologies that are utilized to characterize glycoproteins. Some of the ongoing studies, where glycoproteins isolated from cerebrospinal fluid and human brain are being characterized in Parkinson's disease at different stages versus controls, are presented, along with future applications of targeted validation of brain specific glycoproteins in body fluids.
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Affiliation(s)
- Hyejin Hwang
- Department of Pathology, University of Washington, Seattle, Washington
| | - Jianpeng Zhang
- Department of Pathology, University of Washington, Seattle, Washington
| | - Kathryn A. Chung
- Department of Neurology, Oregon Health and Science University, Portland, Oregon
| | - James B. Leverenz
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington
- Department of Neurology, University of Washington School of Medicine, Seattle, Washington
| | - Cyrus P. Zabetian
- Department of Neurology, University of Washington School of Medicine, Seattle, Washington
| | - Elaine R. Peskind
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington
- Department of Neurology, University of Washington School of Medicine, Seattle, Washington
| | - Joseph Jankovic
- Department of Neurology, Baylor College of Medicine, Houston, Texas
| | - Zhen Su
- Department of Pathology, University of Washington, Seattle, Washington
| | - Aneeka M. Hancock
- Department of Pathology, University of Washington, Seattle, Washington
| | - Catherine Pan
- Department of Pathology, University of Washington, Seattle, Washington
| | - Thomas J. Montine
- Department of Pathology, University of Washington, Seattle, Washington
| | - Sheng Pan
- Department of Pathology, University of Washington, Seattle, Washington
| | - John Nutt
- Department of Neurology, Oregon Health and Science University, Portland, Oregon
| | - Roger Albin
- Ann Arbor VAMC GRECC and Department of Neurology, University of Michigan, Ann Arbor, Michigan
| | - Marla Gearing
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia
| | - Richard P. Beyer
- Department of Environmental & Occupational Health Sciences, University of Washington School of Medicine, Seattle, Washington
| | - Min Shi
- Department of Pathology, University of Washington, Seattle, Washington
| | - Jing Zhang
- Department of Pathology, University of Washington, Seattle, Washington
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38
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Abstract
The O-glycosylation of Ser and Thr by N-acetylgalactosamine-linked (mucin-type) oligosaccharides is often overlooked in protein analysis. Three characteristics make O-linked glycosylation more difficult to analyse than N-linked glycosylation, namely: (a) no amino acid consensus sequence is known; (b) there is no universal enzyme for the release of O-glycans from the protein backbone; and (c) the density and number of occupied sites may be very high. For significant biological conclusions to be drawn, the complete picture of O-linked glycosylation on a protein needs to be determined. This review specifically addresses the analytical approaches that have been used, and the challenges remaining, in the characterization of both the composition and structure of mucin-type O-glycans, and the determination of the occupancy and heterogeneity at each amino acid attachment site.
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Affiliation(s)
- Pia H Jensen
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, Australia
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39
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Hanisch FG, Teitz S, Schwientek T, Müller S. Chemical de-O-glycosylation of glycoproteins for application in LC-based proteomics. Proteomics 2009; 9:710-9. [PMID: 19132687 DOI: 10.1002/pmic.200800492] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We describe a cyclic on-column procedure for the sequential degradation of complex O-glycans on proteins or peptides by periodate oxidation of sugars and cleavage of oxidation products by elimination. Desialylated glycoproteins were immobilized to alkali-stable, reversed-phase Poros 20 beads followed by two degradation cycles and the eluted apoproteins were either separated by SDS gel electrophoresis or digested with trypsin prior to LC/ESI-MS. We demonstrate on the peptide and protein level that even complex glycan moieties are removed under mild conditions with only minimal effects on structural integrity of the peptide core by fragmentation, dehydration or by racemization of the Lys/Arg residues. The protocol is applicable on gel-immobilized glycoproteins after SDS gel electrophoresis. Conversion of O-glycoproteins into their corresponding apoproteins should result in facilitated accessibility of tryptic cleavage sites, increase the numbers of peptide fragments, and accordingly enhance protein coverage and identification rates within the subproteome of mucin-type O-glycoproteins.
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Affiliation(s)
- Franz-Georg Hanisch
- Center of Biochemistry, Medical Faculty, University of Cologne, Köln, Germany.
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Chamot-Rooke J, Rousseau B, Lanternier F, Mikaty G, Mairey E, Malosse C, Bouchoux G, Pelicic V, Camoin L, Nassif X, Duménil G. Alternative Neisseria spp. type IV pilin glycosylation with a glyceramido acetamido trideoxyhexose residue. Proc Natl Acad Sci U S A 2007; 104:14783-8. [PMID: 17804791 PMCID: PMC1976187 DOI: 10.1073/pnas.0705335104] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The importance of protein glycosylation in the interaction of pathogenic bacteria with their host is becoming increasingly clear. Neisseria meningitidis, the etiological agent of cerebrospinal meningitis, crosses cellular barriers after adhering to host cells through type IV pili. Pilin glycosylation genes (pgl) are responsible for the glycosylation of PilE, the major subunit of type IV pili, with the 2,4-diacetamido-2,4,6-trideoxyhexose residue. Nearly half of the clinical isolates, however, display an insertion in the pglBCD operon, which is anticipated to lead to a different, unidentified glycosylation. Here the structure of pilin glycosylation was determined in such a strain by "top-down" MS approaches. MALDI-TOF, nanoelectrospray ionization Fourier transform ion cyclotron resonance, and nanoelectrospray ionization quadrupole TOF MS analysis of purified pili preparations originating from N. meningitidis strains, either wild type or deficient for pilin glycosylation, revealed a glycan mass inconsistent with 2,4-diacetamido-2,4,6-trideoxyhexose or any sugar in the databases. This unusual modification was determined by in-source dissociation of the sugar from the protein followed by tandem MS analysis with collision-induced fragmentation to be a hexose modified with a glyceramido and an acetamido group. We further show genetically that the nature of the sugar present on the pilin is determined by the carboxyl-terminal region of the pglB gene modified by the insertion in the pglBCD locus. We thus report a previously undiscovered monosaccharide involved in posttranslational modification of type IV pilin subunits by a MS-based approach and determine the molecular basis of its biosynthesis.
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Affiliation(s)
- Julia Chamot-Rooke
- *Ecole Polytechnique, Laboratoire des Mécanismes Réactionnels, Département de Chimie, F-91128 Palaiseau, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7651, F-91128 Paris, France
| | - Benoit Rousseau
- Institut National de la Santé et de la Recherche Médicale, Unité 570, F-75015 Paris, France
- Université René Descartes, Faculté de Médecine René Descartes, F-75006 Paris, France
| | - Fanny Lanternier
- Institut National de la Santé et de la Recherche Médicale, Unité 570, F-75015 Paris, France
- Université René Descartes, Faculté de Médecine René Descartes, F-75006 Paris, France
| | - Guillain Mikaty
- Institut National de la Santé et de la Recherche Médicale, Unité 570, F-75015 Paris, France
- Université René Descartes, Faculté de Médecine René Descartes, F-75006 Paris, France
| | - Emilie Mairey
- Institut National de la Santé et de la Recherche Médicale, Unité 570, F-75015 Paris, France
- Université René Descartes, Faculté de Médecine René Descartes, F-75006 Paris, France
| | - Christian Malosse
- *Ecole Polytechnique, Laboratoire des Mécanismes Réactionnels, Département de Chimie, F-91128 Palaiseau, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7651, F-91128 Paris, France
| | - Guy Bouchoux
- *Ecole Polytechnique, Laboratoire des Mécanismes Réactionnels, Département de Chimie, F-91128 Palaiseau, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 7651, F-91128 Paris, France
| | - Vladimir Pelicic
- Institut National de la Santé et de la Recherche Médicale, Unité 570, F-75015 Paris, France
- Université René Descartes, Faculté de Médecine René Descartes, F-75006 Paris, France
| | - Luc Camoin
- Université René Descartes, Faculté de Médecine René Descartes, F-75006 Paris, France
- Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8104, F-75014 Paris, France
- **Institut Cochin, Département de Biologie Cellulaire, F-75014 Paris, France
- Institut National de la Santé et de la Recherche Médicale, Unité 567, F-75014 Paris, France; and
| | - Xavier Nassif
- Institut National de la Santé et de la Recherche Médicale, Unité 570, F-75015 Paris, France
- Université René Descartes, Faculté de Médecine René Descartes, F-75006 Paris, France
- Assistance Publique–Hôpitaux de Paris, Hôpital Necker–Enfants Malades, F-75015 Paris, France
| | - Guillaume Duménil
- Institut National de la Santé et de la Recherche Médicale, Unité 570, F-75015 Paris, France
- Université René Descartes, Faculté de Médecine René Descartes, F-75006 Paris, France
- To whom correspondence should be addressed. E-mail:
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Chamot-Rooke J, van der Rest G, Dalleu A, Bay S, Lemoine J. The combination of electron capture dissociation and fixed charge derivatization increases sequence coverage for O-glycosylated and O-phosphorylated peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2007; 18:1405-13. [PMID: 17560119 DOI: 10.1016/j.jasms.2007.04.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2006] [Revised: 04/10/2007] [Accepted: 04/11/2007] [Indexed: 05/15/2023]
Abstract
Electron capture dissociation (ECD) has become an alternative method to collision-activated dissociation (CAD) to avoid gas-phase cleavage of post-translational modifications carried by side chains from the peptide backbone. Nonetheless, as illustrated herein by the study of O-glycosylated and O-phosphorylated peptides, the extent of ECD fragmentations may be insufficient to cover the entire peptide sequence and to localize accurately these modifications. The present work demonstrates that the derivatization of peptides at their N-terminus by a phosphonium group improves dramatically and systematically the sequence coverage deduced from the ECD spectrum for both O-glycosylated and O-phosphorylated peptides compared with their native counterparts. The exclusive presence of N-terminal fragments (c-type ions) in the ECD spectra of doubly charged molecular cations simplifies peptide sequence interpretation. Thus, the combination of ECD and fixed charge derivatization appears as an efficient analytical tool for the extensive sequencing of peptides bearing labile groups.
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Affiliation(s)
- Julia Chamot-Rooke
- Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, CNRS, Palaiseau, France.
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43
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Tarelli E. Resistance to deglycosylation by ammonia of IgA1 O-glycopeptides: implications for the beta-elimination of O-glycans linked to serine and threonine. Carbohydr Res 2007; 342:2322-5. [PMID: 17655836 DOI: 10.1016/j.carres.2007.06.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2007] [Revised: 06/11/2007] [Accepted: 06/20/2007] [Indexed: 10/23/2022]
Abstract
Pools of O-glycopeptides (and their deglycosylated analogues) derived from trypsin-digested normal human serum IgA1 have been treated with ammonia under conditions reported to result in complete liberation of O-glycans linked to serine and threonine residues in glycopeptides and glycoproteins. MALDI-TOF MS analysis has revealed that only one of the six glycosylated sites is susceptible to beta-elimination under these conditions. It is likely that resistance to beta-elimination is due to very close proximity of proline to the glycosylated serine or threonine residues. Preliminary results using 0.1M NaOH (instead of ammonia) to perform beta-elimination indicated that there was also selective de-O-glycosylation with this reagent, however, these results were complicated by the concomitant hydrolysis of the peptide bonds. These findings may have implications for similarly O-glycosylated peptides and proteins and possibly for other chemical methods that are used to carry out beta-eliminations of O-glycans.
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Affiliation(s)
- Edward Tarelli
- Medical Biomics Centre, St Georges University of London, Cranmer Terrace, London SW17 0RE, UK.
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44
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Zheng Y, Li H, Guo Z, Lin JM, Cai Z. Chip-based CE coupled to a quadrupole TOF mass spectrometer for the analysis of a glycopeptide. Electrophoresis 2007; 28:1305-11. [PMID: 17377943 DOI: 10.1002/elps.200600527] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
A novel approach using sheath flow chip-based CE coupled to a quadrupole TOF mass spectrometer was developed and applied to the analysis of an O-glycopeptide. The method provided good separation and sensitive analysis of the glycopeptide and its beta-elimination product. The beta-elimination reaction of the glycopeptide with ammonia or dimethylamine was adapted for changing the glycopeptide into deglycosylated form and for specifying the site of glycosylation. MS/MS analysis of the native peptide, glycopeptide and beta-elimination product enabled the identification of the glycosylation site through the comparison of the fragmentations and peptide sequence analysis.
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Affiliation(s)
- Yufang Zheng
- Department of Chemistry, Hong Kong Baptist University, Kowloon Tong, Kowloon, Hong Kong SAR, P. R. China
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45
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Hanna ES, Roque-Barreira MC, Bernardes ES, Panunto-Castelo A, Sousa MV, Almeida IC, Brocchi M. Evidence for glycosylation on a DNA-binding protein of Salmonella enterica. Microb Cell Fact 2007; 6:11. [PMID: 17407574 PMCID: PMC1855067 DOI: 10.1186/1475-2859-6-11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2007] [Accepted: 04/02/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND All organisms living under aerobic atmosphere have powerful mechanisms that confer their macromolecules protection against oxygen reactive species. Microorganisms have developed biomolecule-protecting systems in response to starvation and/or oxidative stress, such as DNA biocrystallization with Dps (DNA-binding protein from starved cells). Dps is a protein that is produced in large amounts when the bacterial cell faces harm, which results in DNA protection. In this work, we evaluated the glycosylation in the Dps extracted from Salmonella enterica serovar Typhimurium. This Dps was purified from the crude extract as an 18-kDa protein, by means of affinity chromatography on an immobilized jacalin column. RESULTS The N-terminal sequencing of the jacalin-bound protein revealed 100% identity with the Dps of S. enterica serovar Typhimurium. Methyl-alpha-galactopyranoside inhibited the binding of Dps to jacalin in an enzyme-linked lectin assay, suggesting that the carbohydrate recognition domain (CRD) of jacalin is involved in the interaction with Dps. Furthermore, monosaccharide compositional analysis showed that Dps contained mannose, glucose, and an unknown sugar residue. Finally, jacalin-binding Dps was detected in larger amounts during the bacterial earlier growth periods, whereas high detection of total Dps was verified throughout the bacterial growth period. CONCLUSION Taken together, these results indicate that Dps undergoes post-translational modifications in the pre- and early stationary phases of bacterial growth. There is also evidence that a small mannose-containing oligosaccharide is linked to this bacterial protein.
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Affiliation(s)
- Ebert S Hanna
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900, Brazil
| | - Maria-Cristina Roque-Barreira
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900, Brazil
| | - Emerson S Bernardes
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900, Brazil
| | - Ademilson Panunto-Castelo
- Departamento de Enfermagem Geral e Especializada, Escola de Enfermagem de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14040-902, Brazil
| | - Marcelo V Sousa
- Centro Brasileiro para Pesquisas e Serviços em Proteinas, Instituto de Biologia, Universidade de Brasília, Brasília, DF 70.910-900, Brazil
| | - Igor C Almeida
- Department of Biological Sciences, University of Texas at El Paso, TX 79968-0519, USA
| | - Marcelo Brocchi
- Departamento de Biologia Celular e Molecular e Bioagentes Patogênicos, Faculdade de Medicina de Ribeirão Preto, Universidade de São Paulo, Av. Bandeirantes 3900, Ribeirão Preto, SP 14049-900, Brazil
- Departmento de Microbiologia e Imunologia, Instituto de Biologia, Rua Charles Darwin s/n, UNICAMP, Campinas, SP 13083-862, Brazil
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47
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Kelley WP, Schulz JR, Jakubowski JA, Gilly WF, Sweedler JV. Two toxins from Conus striatus that individually induce tetanic paralysis. Biochemistry 2006; 45:14212-22. [PMID: 17115716 PMCID: PMC2530915 DOI: 10.1021/bi061485s] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe structural properties and biological activities of two related O-glycosylated peptide toxins isolated from injected (milked) venom of Conus striatus, a piscivorous snail that captures prey by injecting a venom that induces a violent, spastic paralysis. One 30 amino acid toxin is identified as kappaA-SIVA (termed s4a here), and another 37 amino acid toxin, s4b, corresponds to a putative peptide encoded by a previously reported cDNA. We confirm the amino acid sequences and carry out structural analyses of both mature toxins using multiple mass spectrometric techniques. These include electrospray ionization ion-trap mass spectrometry and nanoelectrospray techniques for small volume samples, as well as matrix-assisted laser desorption/ionization time of flight mass spectrometric analysis as a complementary method to assist in the determination of posttranslational modifications, including O-linked glycosylation. Physiological experiments indicate that both s4a and s4b induce intense repetitive firing of the frog neuromuscular junction, leading to a tetanic contracture in muscle fiber. These effects apparently involve modification of voltage-gated sodium channels in motor axons. Notably, application of either s4a or s4b alone mimics the biological effects of the whole injected venom on fish prey.
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Affiliation(s)
| | | | | | | | - Jonathan V. Sweedler
- To whom correspondence should be addressed. E-mail: . Tel: (217) 244-7359. Fax: (217) 244-8068
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48
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Geyer H, Geyer R. Strategies for analysis of glycoprotein glycosylation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2006; 1764:1853-69. [PMID: 17134948 DOI: 10.1016/j.bbapap.2006.10.007] [Citation(s) in RCA: 224] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2006] [Revised: 10/18/2006] [Accepted: 10/18/2006] [Indexed: 01/01/2023]
Abstract
Glycoproteins are known to exhibit multiple biological functions. In order to assign distinct functional properties to defined structural features, detailed information on the respective carbohydrate moieties is required. Chemical and biochemical analyses, however, are often impeded by the small amounts of sample available and the vast structural heterogeneity of these glycans, thus necessitating highly sensitive and efficient methods for detection, separation and structural investigation. The aim of this article is to briefly review suitable strategies for characterization of glycosylation at the levels of intact proteins, glycopeptides and free oligosaccharides. Furthermore, methods commonly used for isolation, fractionation and carbohydrate structure analysis of liberated glycoprotein glycans are discussed in the context of potential applications in glycoproteomics.
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Affiliation(s)
- Hildegard Geyer
- Institute of Biochemistry, Faculty of Medicine, University of Giessen, Friedrichstrasse 24, D-35392 Giessen, Germany
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49
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Steiner K, Pohlentz G, Dreisewerd K, Berkenkamp S, Messner P, Peter-Katalinić J, Schäffer C. New insights into the glycosylation of the surface layer protein SgsE from Geobacillus stearothermophilus NRS 2004/3a. J Bacteriol 2006; 188:7914-21. [PMID: 16963578 PMCID: PMC1636307 DOI: 10.1128/jb.00802-06] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The surface of Geobacillus stearothermophilus NRS 2004/3a cells is covered by an oblique surface layer (S-layer) composed of glycoprotein subunits. To this S-layer glycoprotein, elongated glycan chains are attached that are composed of [-->2)-alpha-l-Rhap-(1-->3)-beta-l-Rhap-(1-->2)-alpha-L-Rhap-(1-->] repeating units, with a 2-O-methyl modification of the terminal trisaccharide at the nonreducing end of the glycan chain and a core saccharide as linker to the S-layer protein. On sodium dodecyl sulfate-polyacrylamide gels, four bands appear, of which three represent glycosylated S-layer proteins. In the present study, nanoelectrospray ionization time-of-flight mass spectrometry (MS) and infrared matrix-assisted laser desorption/ionization orthogonal time-of-flight mass spectrometry were adapted for analysis of this high-molecular-mass and water-insoluble S-layer glycoprotein to refine insights into its glycosylation pattern. This is a prerequisite for artificial fine-tuning of S-layer glycans for nanobiotechnological applications. Optimized MS techniques allowed (i) determination of the average masses of three glycoprotein species to be 101.66 kDa, 108.68 kDa, and 115.73 kDa, (ii) assignment of nanoheterogeneity to the S-layer glycans, with the most prevalent variation between 12 and 18 trisaccharide repeating units, and the possibility of extension of the already-known -->3)-alpha-l-Rhap-(1-->3)-alpha-l-Rhap-(1--> core by one additional rhamnose residue, and (iii) identification of a third glycosylation site on the S-layer protein, at position threonine-590, in addition to the known sites threonine-620 and serine-794. The current interpretation of the S-layer glycoprotein banding pattern is that in the 101.66-kDa glycoprotein species only one glycosylation site is occupied, in the 108.68-kDa glycoprotein species two glycosylation sites are occupied, and in the 115.73-kDa glycoprotein species three glycosylation sites are occupied, while the 94.46-kDa band represents nonglycosylated S-layer protein.
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Affiliation(s)
- Kerstin Steiner
- Zentrum für NanoBiotechnologie, Universität für Bodenkultur Wien, A-1180 Vienna, Austria
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Verma A, Schirm M, Arora SK, Thibault P, Logan SM, Ramphal R. Glycosylation of b-Type flagellin of Pseudomonas aeruginosa: structural and genetic basis. J Bacteriol 2006; 188:4395-403. [PMID: 16740946 PMCID: PMC1482937 DOI: 10.1128/jb.01642-05] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The flagellin of Pseudomonas aeruginosa can be classified into two major types-a-type or b-type-which can be distinguished on the basis of molecular weight and reactivity with type-specific antisera. Flagellin from the a-type strain PAK was shown to be glycosylated with a heterogeneous O-linked glycan attached to Thr189 and Ser260. Here we show that b-type flagellin from strain PAO1 is also posttranslationally modified with an excess mass of up to 700 Da, which cannot be explained through phosphorylation. Two serine residues at positions 191 and 195 were found to be modified. Each site had a deoxyhexose to which is linked a unique modification of 209 Da containing a phosphate moiety. In comparison to strain PAK, which has an extensive flagellar glycosylation island of 14 genes in its genome, the equivalent locus in PAO1 comprises of only four genes. PCR analysis and sequence information suggested that there are few or no polymorphisms among the islands of the b-type strains. Mutations were made in each of the genes, PA1088 to PA1091, and the flagellin from these isogenic mutants was examined by mass spectrometry to determine whether they were involved in posttranslational modification of the type-b flagellin. While mutation of PA1088, PA1089, and PA1090 genes altered the composition of the flagellin glycan, only unmodified flagellin was produced by the PA1091 mutant strain. There were no changes in motility or lipopolysaccharide banding in the mutants, implying a role that is limited to glycosylation.
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Affiliation(s)
- Amrisha Verma
- Department of Medicine/Infectious Diseases, P.O. Box 100277, JHMHC, University of Florida, Gainesville, FL 32610, USA
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