1
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Mohideen FI, Mahal LK. Infection and the Glycome─New Insights into Host Response. ACS Infect Dis 2024; 10:2540-2550. [PMID: 38990078 PMCID: PMC11320568 DOI: 10.1021/acsinfecdis.4c00315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 06/20/2024] [Accepted: 06/25/2024] [Indexed: 07/12/2024]
Abstract
Glycans play critical roles in the host-pathogen interactions leading to infection. However, we still understand very little about the dynamic nature of glycosylation in response to infection and its function in modulating host immunity. Many of the host proteins involved in immune defense are glycoproteins. Furthermore, the innate immune system recognizes glycans. The glycoform of a protein can impact proteolytic stability, receptor interactions, serum half-life, and other aspects. New, cutting-edge chemical biology tools are shedding light on the interplay between infection and the host glycome. In this review, we highlight new work on the importance of dynamic glycosylation of host proteins in the innate and adaptive immune pathways in response to infection. These include recent findings on altered glycoprofiles of mucins, complement components, and antibodies.
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Affiliation(s)
- F. Ifthiha Mohideen
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive NW, Edmonton, Alberta T6G 2G2, Canada
| | - Lara K. Mahal
- Department
of Chemistry, University of Alberta, 11227 Saskatchewan Drive NW, Edmonton, Alberta T6G 2G2, Canada
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2
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Chongsaritsinsuk J, Rangel-Angarita V, Mahoney KE, Lucas TM, Enny OM, Katemauswa M, Malaker SA. Quantification and site-specific analysis of co-occupied N- and O-glycopeptides. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.06.602348. [PMID: 39005468 PMCID: PMC11245114 DOI: 10.1101/2024.07.06.602348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Protein glycosylation is a complex post-translational modification that is generally classified as N- or O-linked. Site-specific analysis of glycopeptides is accomplished with a variety of fragmentation methods, depending on the type of glycosylation being investigated and the instrumentation available. For instance, collisional dissociation methods are frequently used for N-glycoproteomic analysis with the assumption that one N-sequon exists per tryptic peptide. Alternatively, electron-based methods are indispensable for O-glycosite localization. However, the presence of simultaneously N- and O-glycosylated peptides could suggest the necessity of electron-based fragmentation methods for N-glycoproteomics, which is not commonly performed. Thus, we quantified the prevalence of N- and O-glycopeptides in mucins and other glycoproteins. A much higher frequency of co-occupancy within mucins was detected whereas only a negligible occurrence occurred within non-mucin glycoproteins. This was demonstrated from analyses of recombinant and/or purified proteins, as well as more complex samples. Where co-occupancy occurred, O-glycosites were frequently localized to the Ser/Thr within the N-sequon. Additionally, we found that O-glycans in close proximity to the occupied Asn were predominantly unelaborated core 1 structures, while those further away were more extended. Overall, we demonstrate electron-based methods are required for robust site-specific analysis of mucins, wherein co-occupancy is more prevalent. Conversely, collisional methods are generally sufficient for analyses of other types of glycoproteins.
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3
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Mahoney KE, Malaker SA. Analysis of Mucin-Domain Glycoproteins Using Mass Spectrometry. Curr Protoc 2024; 4:e1100. [PMID: 38984456 PMCID: PMC11239139 DOI: 10.1002/cpz1.1100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/11/2024]
Abstract
Mucin-domain glycoproteins are characterized by their high density of glycosylated serine and threonine residues, which complicates their analysis by mass spectrometry. The dense glycosylation renders the protein backbone inaccessible to workhorse proteases like trypsin, the vast heterogeneity of glycosylation often results in ion suppression from unmodified peptides, and search algorithms struggle to confidently analyze and site-localize O-glycosites. We have made a number of advances to address these challenges, rendering mucinomics possible for the first time. Here, we summarize these contributions and provide a detailed protocol for mass spectrometric analysis of mucin-domain glycoproteins. © 2024 Wiley Periodicals LLC. Basic Protocol 1: Enrichment of mucin-domain glycoproteins Basic Protocol 2: Enzymatic digestion of mucin-domain glycoprotein(s) Basic Protocol 3: Mass spectrometry data collection for O-glycopeptides Basic Protocol 4: Mass spectrometry data analysis of O-glycopeptides.
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4
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Raba G, Luis AS, Schneider H, Morell I, Jin C, Adamberg S, Hansson GC, Adamberg K, Arike L. Metaproteomics reveals parallel utilization of colonic mucin glycans and dietary fibers by the human gut microbiota. iScience 2024; 27:110093. [PMID: 38947523 PMCID: PMC11214529 DOI: 10.1016/j.isci.2024.110093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 02/29/2024] [Accepted: 05/21/2024] [Indexed: 07/02/2024] Open
Abstract
A diet lacking dietary fibers promotes the expansion of gut microbiota members that can degrade host glycans, such as those on mucins. The microbial foraging on mucin has been associated with disruptions of the gut-protective mucus layer and colonic inflammation. Yet, it remains unclear how the co-utilization of mucin and dietary fibers affects the microbiota composition and metabolic activity. Here, we used 14 dietary fibers and porcine colonic and gastric mucins to study the dynamics of mucin and dietary fiber utilization by the human fecal microbiota in vitro. Combining metaproteome and metabolites analyses revealed the central role of the Bacteroides genus in the utilization of complex fibers together with mucin while Akkermansia muciniphila was the main utilizer of sole porcine colonic mucin but not gastric mucin. This study gives a broad overview of the colonic environment in response to dietary and host glycan availability.
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Affiliation(s)
- Grete Raba
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Ana S. Luis
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
- SciLifeLab, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Hannah Schneider
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Indrek Morell
- Center of Food and Fermentation Technologies, 12618 Tallinn, Estonia
| | - Chunsheng Jin
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Signe Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Gunnar C. Hansson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Kaarel Adamberg
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
- Center of Food and Fermentation Technologies, 12618 Tallinn, Estonia
| | - Liisa Arike
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, 41390 Gothenburg, Sweden
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5
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Elzinga J, Narimatsu Y, de Haan N, Clausen H, de Vos WM, Tytgat HLP. Binding of Akkermansia muciniphila to mucin is O-glycan specific. Nat Commun 2024; 15:4582. [PMID: 38811534 PMCID: PMC11137150 DOI: 10.1038/s41467-024-48770-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Accepted: 05/09/2024] [Indexed: 05/31/2024] Open
Abstract
The intestinal anaerobic bacterium Akkermansia muciniphila is specialized in the degradation of mucins, which are heavily O-glycosylated proteins that constitute the major components of the mucus lining the intestine. Despite that adhesion to mucins is considered critical for the persistence of A. muciniphila in the human intestinal tract, our knowledge of how this intestinal symbiont recognizes and binds to mucins is still limited. Here, we first show that the mucin-binding properties of A. muciniphila are independent of environmental oxygen concentrations and not abolished by pasteurization. We then dissected the mucin-binding properties of pasteurized A. muciniphila by use of a recently developed cell-based mucin array that enables display of the tandem repeats of human mucins with distinct O-glycan patterns and structures. We found that A. muciniphila recognizes the unsialylated LacNAc (Galβ1-4GlcNAcβ1-R) disaccharide selectively on core2 and core3 O-glycans. This disaccharide epitope is abundantly found on human colonic mucins capped by sialic acids, and we demonstrated that endogenous A. muciniphila neuraminidase activity can uncover the epitope and promote binding. In summary, our study provides insights into the mucin-binding properties important for colonization of a key mucin-foraging bacterium.
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Affiliation(s)
- Janneke Elzinga
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- GlycoDisplay ApS, Copenhagen, Denmark
| | - Noortje de Haan
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Willem M de Vos
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands
- Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hanne L P Tytgat
- Laboratory of Microbiology, Wageningen University & Research, Wageningen, The Netherlands.
- Nestlé Institute of Health Sciences, Nestlé Research, Lausanne, Switzerland.
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6
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Goyette MA, Stevens LE, DePinho CR, Seehawer M, Nishida J, Li Z, Wilde CM, Li R, Qiu X, Pyke AL, Zhao S, Lim K, Tender GS, Northey JJ, Riley NM, Long HW, Bertozzi CR, Weaver VM, Polyak K. Cancer-stromal cell interactions in breast cancer brain metastases induce glycocalyx-mediated resistance to HER2-targeting therapies. Proc Natl Acad Sci U S A 2024; 121:e2322688121. [PMID: 38709925 PMCID: PMC11098130 DOI: 10.1073/pnas.2322688121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/27/2024] [Indexed: 05/08/2024] Open
Abstract
Brain metastatic breast cancer is particularly lethal largely due to therapeutic resistance. Almost half of the patients with metastatic HER2-positive breast cancer develop brain metastases, representing a major clinical challenge. We previously described that cancer-associated fibroblasts are an important source of resistance in primary tumors. Here, we report that breast cancer brain metastasis stromal cell interactions in 3D cocultures induce therapeutic resistance to HER2-targeting agents, particularly to the small molecule inhibitor of HER2/EGFR neratinib. We investigated the underlying mechanisms using a synthetic Notch reporter system enabling the sorting of cancer cells that directly interact with stromal cells. We identified mucins and bulky glycoprotein synthesis as top-up-regulated genes and pathways by comparing the gene expression and chromatin profiles of stroma-contact and no-contact cancer cells before and after neratinib treatment. Glycoprotein gene signatures were also enriched in human brain metastases compared to primary tumors. We confirmed increased glycocalyx surrounding cocultures by immunofluorescence and showed that mucinase treatment increased sensitivity to neratinib by enabling a more efficient inhibition of EGFR/HER2 signaling in cancer cells. Overexpression of truncated MUC1 lacking the intracellular domain as a model of increased glycocalyx-induced resistance to neratinib both in cell culture and in experimental brain metastases in immunodeficient mice. Our results highlight the importance of glycoproteins as a resistance mechanism to HER2-targeting therapies in breast cancer brain metastases.
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Affiliation(s)
- Marie-Anne Goyette
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA02115
| | - Laura E. Stevens
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA02115
| | - Carolyn R. DePinho
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
| | - Marco Seehawer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA02115
| | - Jun Nishida
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA02115
| | - Zheqi Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA02115
| | - Callahan M. Wilde
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
| | - Rong Li
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA02215
| | - Xintao Qiu
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA02215
| | - Alanna L. Pyke
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
| | - Stephanie Zhao
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
| | - Klothilda Lim
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA02215
| | | | - Jason J. Northey
- Center for Bioengineering and Tissue Regeneration, University of California San Francisco, San Francisco, CA94143
| | | | - Henry W. Long
- Center for Functional Cancer Epigenetics, Dana-Farber Cancer Institute, Boston, MA02215
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA94305
- HHMI, Stanford University, Stanford, CA94305
- Sarafan ChEM-H, Stanford University, Stanford, CA94305
| | - Valerie M. Weaver
- Center for Bioengineering and Tissue Regeneration, University of California San Francisco, San Francisco, CA94143
- Helen Diller Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA94143
- Department of Surgery, University of California San Francisco, San Francisco, CA94143
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA94143
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA94143
- Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California San Francisco, San Francisco, CA94143
| | - Kornelia Polyak
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA02215
- Department of Medicine, Harvard Medical School, Boston, MA02115
- Department of Medicine, Brigham and Women's Hospital, Boston, MA02115
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7
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Mahoney KE, Chang V, Lucas TM, Maruszko K, Malaker SA. Mass Spectrometry-Compatible Elution Technique Enables an Improved Mucin-Selective Enrichment Strategy to Probe the Mucinome. Anal Chem 2024; 96:5242-5250. [PMID: 38512228 DOI: 10.1021/acs.analchem.3c05762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of healthy and disease-driven biological functions. Previously, we developed a mucin-selective enrichment strategy by employing a catalytically inactive mucinase (StcE) conjugated to a solid support. While this method was effective, it suffered from low throughput and high sample requirements. Further, the elution step required boiling in SDS, thus necessitating an in-gel digest with trypsin. Here, we introduce innovative elution conditions amenable to mucinase digestion and downstream analysis using mass spectrometry. This increased throughput and lowered sample input while maintaining mucin selectivity and enhancing the glycopeptide signal. We then benchmarked this technique against different O-glycan binding moieties for their ability to enrich mucins from various cell lines and human serum. Overall, the new method outperformed our previous procedure and all of the other enrichment techniques tested. This allowed for the effective isolation of more mucin-domain glycoproteins, resulting in a high number of O-glycopeptides, thus enhancing our ability to analyze the mucinome.
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Affiliation(s)
- Keira E Mahoney
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Vincent Chang
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Taryn M Lucas
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Krystyna Maruszko
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Stacy A Malaker
- Department of Chemistry, Yale University, New Haven, Connecticut 06511, United States
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8
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Pedram K, Shon DJ, Tender GS, Mantuano NR, Northey JJ, Metcalf KJ, Wisnovsky SP, Riley NM, Forcina GC, Malaker SA, Kuo A, George BM, Miller CL, Casey KM, Vilches-Moure JG, Ferracane MJ, Weaver VM, Läubli H, Bertozzi CR. Design of a mucin-selective protease for targeted degradation of cancer-associated mucins. Nat Biotechnol 2024; 42:597-607. [PMID: 37537499 PMCID: PMC11018308 DOI: 10.1038/s41587-023-01840-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 05/22/2023] [Indexed: 08/05/2023]
Abstract
Targeted protein degradation is an emerging strategy for the elimination of classically undruggable proteins. Here, to expand the landscape of targetable substrates, we designed degraders that achieve substrate selectivity via recognition of a discrete peptide and glycan motif and achieve cell-type selectivity via antigen-driven cell-surface binding. We applied this approach to mucins, O-glycosylated proteins that drive cancer progression through biophysical and immunological mechanisms. Engineering of a bacterial mucin-selective protease yielded a variant for fusion to a cancer antigen-binding nanobody. The resulting conjugate selectively degraded mucins on cancer cells, promoted cell death in culture models of mucin-driven growth and survival, and reduced tumor growth in mouse models of breast cancer progression. This work establishes a blueprint for the development of biologics that degrade specific protein glycoforms on target cells.
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Affiliation(s)
- Kayvon Pedram
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA, USA
| | - D Judy Shon
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Gabrielle S Tender
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Natalia R Mantuano
- Cancer Immunotherapy Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Oncology, Department of Theragnostics, University Hospital, Basel, Switzerland
| | - Jason J Northey
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Kevin J Metcalf
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Simon P Wisnovsky
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Giovanni C Forcina
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Stacy A Malaker
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Angel Kuo
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Benson M George
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Caitlyn L Miller
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA
| | - Kerriann M Casey
- Department of Comparative Medicine, Stanford University, Stanford, CA, USA
| | | | | | - Valerie M Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
- Departments of Radiation Oncology and Bioengineering and Therapeutic Sciences, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, and Helen Diller Comprehensive Cancer Center, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Heinz Läubli
- Cancer Immunotherapy Laboratory, Department of Biomedicine, University of Basel, Basel, Switzerland
- Division of Oncology, Department of Theragnostics, University Hospital, Basel, Switzerland
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, USA.
- Howard Hughes Medical Institute, Stanford, CA, USA.
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9
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Helms A, Brodbelt JS. Mass Spectrometry Strategies for O-Glycoproteomics. Cells 2024; 13:394. [PMID: 38474358 PMCID: PMC10930906 DOI: 10.3390/cells13050394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/19/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Glycoproteomics has accelerated in recent decades owing to numerous innovations in the analytical workflow. In particular, new mass spectrometry strategies have contributed to inroads in O-glycoproteomics, a field that lags behind N-glycoproteomics due to several unique challenges associated with the complexity of O-glycosylation. This review will focus on progress in sample preparation, enrichment strategies, and MS/MS techniques for the identification and characterization of O-glycoproteins.
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Affiliation(s)
| | - Jennifer S. Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA;
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10
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Leo F, Lood R, Thomsson KA, Nilsson J, Svensäter G, Wickström C. Characterization of MdpS: an in-depth analysis of a MUC5B-degrading protease from Streptococcus oralis. Front Microbiol 2024; 15:1340109. [PMID: 38304711 PMCID: PMC10830703 DOI: 10.3389/fmicb.2024.1340109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Accepted: 01/08/2024] [Indexed: 02/03/2024] Open
Abstract
Oral biofilms, comprising hundreds of bacteria and other microorganisms on oral mucosal and dental surfaces, play a central role in oral health and disease dynamics. Streptococcus oralis, a key constituent of these biofilms, contributes significantly to the formation of which, serving as an early colonizer and microcolony scaffold. The interaction between S. oralis and the orally predominant mucin, MUC5B, is pivotal in biofilm development, yet the mechanism underlying MUC5B degradation remains poorly understood. This study introduces MdpS (Mucin Degrading Protease from Streptococcus oralis), a protease that extensively hydrolyses MUC5B and offers an insight into its evolutionary conservation, physicochemical properties, and substrate- and amino acid specificity. MdpS exhibits high sequence conservation within the species and also explicitly among early biofilm colonizing streptococci. It is a calcium or magnesium dependent serine protease with strict physicochemical preferences, including narrow pH and temperature tolerance, and high sensitivity to increasing concentrations of sodium chloride and reducing agents. Furthermore, MdpS primarily hydrolyzes proteins with O-glycans, but also shows activity toward immunoglobulins IgA1/2 and IgM, suggesting potential immunomodulatory effects. Significantly, MdpS extensively degrades MUC5B in the N- and C-terminal domains, emphasizing its role in mucin degradation, with implications for carbon and nitrogen sequestration for S. oralis or oral biofilm cross-feeding. Moreover, depending on substrate glycosylation, the amino acids serine, threonine or cysteine triggers the enzymatic action. Understanding the interplay between S. oralis and MUC5B, facilitated by MdpS, has significant implications for the management of a healthy eubiotic oral microenvironment, offering potential targets for interventions aimed at modulating oral biofilm composition and succession. Additionally, since MdpS does not rely on O-glycan removal prior to extensive peptide backbone hydrolysis, the MdpS data challenges the current model of MUC5B degradation. These findings emphasize the necessity for further research in this field.
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Affiliation(s)
- Fredrik Leo
- Department of Oral Biology and Pathology, Faculty of Odontology, Malmö University, Malmö, Sweden
- Genovis AB, Kävlinge, Sweden
| | - Rolf Lood
- Genovis AB, Kävlinge, Sweden
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden
| | - Kristina A. Thomsson
- Proteomics Core Facility, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Jonas Nilsson
- Proteomics Core Facility, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Gunnel Svensäter
- Department of Oral Biology and Pathology, Faculty of Odontology, Malmö University, Malmö, Sweden
| | - Claes Wickström
- Department of Oral Biology and Pathology, Faculty of Odontology, Malmö University, Malmö, Sweden
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11
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Liu Y, Lu X, Chen M, Wei Z, Peng G, Yang J, Tang C, Yu P. Advances in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. Biofactors 2024; 50:33-57. [PMID: 37646383 DOI: 10.1002/biof.2001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 08/04/2023] [Indexed: 09/01/2023]
Abstract
Peptides and peptide aptamers have emerged as promising molecules for a wide range of biomedical applications due to their unique properties and versatile functionalities. The screening strategies for identifying peptides and peptide aptamers with desired properties are discussed, including high-throughput screening, display screening technology, and in silico design approaches. The synthesis methods for the efficient production of peptides and peptide aptamers, such as solid-phase peptide synthesis and biosynthesis technology, are described, along with their advantages and limitations. Moreover, various modification techniques are explored to enhance the stability, specificity, and pharmacokinetic properties of peptides and peptide aptamers. This includes chemical modifications, enzymatic modifications, biomodifications, genetic engineering modifications, and physical modifications. Furthermore, the review highlights the diverse biomedical applications of peptides and peptide aptamers, including targeted drug delivery, diagnostics, and therapeutic. This review provides valuable insights into the advancements in screening, synthesis, modification, and biomedical applications of peptides and peptide aptamers. A comprehensive understanding of these aspects will aid researchers in the development of novel peptide-based therapeutics and diagnostic tools for various biomedical challenges.
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Affiliation(s)
- Yijie Liu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Xiaoling Lu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Meilun Chen
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Zheng Wei
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Guangnan Peng
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Jie Yang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Chunhua Tang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
| | - Peng Yu
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha, China
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12
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Mahoney KE, Chang V, Lucas TM, Maruszko K, Malaker SA. Optimized mucin-selective enrichment strategy to probe the mucinome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.572204. [PMID: 38187615 PMCID: PMC10769219 DOI: 10.1101/2023.12.18.572204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of healthy and disease-driven biological functions. Previously, we developed a mucin-selective enrichment strategy by employing a catalytically inactive mucinase (StcE) conjugated to solid support. While this method was effective, it suffered from low throughput and high sample requirements. Further, the elution step required boiling in SDS, thus necessitating an in-gel digest with trypsin. Here, we optimized our previous enrichment method to include elution conditions amenable to mucinase digestion and downstream analysis with mass spectrometry. This increased throughput and lowered sample input while maintaining mucin selectivity and enhancing glycopeptide signal. We then benchmarked this technique against different O-glycan binding moieties for their ability to enrich mucins from various cell lines and human serum. Overall, the new method outperformed our previous procedure and all other enrichment techniques tested. This allowed for effective isolation of more mucin-domain glycoproteins, resulting in a high number of O-glycopeptides, thus enhancing our ability to analyze the mucinome.
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Affiliation(s)
- Keira E. Mahoney
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Vincent Chang
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Taryn M. Lucas
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | | | - Stacy A. Malaker
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
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13
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Tender GS, Bertozzi CR. Bringing enzymes to the proximity party. RSC Chem Biol 2023; 4:986-1002. [PMID: 38033727 PMCID: PMC10685825 DOI: 10.1039/d3cb00084b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 09/16/2023] [Indexed: 12/02/2023] Open
Abstract
Enzymes are used to treat a wide variety of human diseases, including lysosomal storage disorders, clotting disorders, and cancers. While enzyme therapeutics catalyze highly specific reactions, they often suffer from a lack of cellular or tissue selectivity. Targeting an enzyme to specific disease-driving cells and tissues can mitigate off-target toxicities and provide novel therapeutic avenues to treat otherwise intractable diseases. Targeted enzymes have been used to treat cancer, in which the enzyme is either carefully selected or engineered to reduce on-target off-tumor toxicity, or to treat lysosomal storage disorders in cell types that are not addressed by standard enzyme replacement therapies. In this review, we discuss the different targeted enzyme modalities and comment on the future of these approaches.
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Affiliation(s)
- Gabrielle S Tender
- Stanford University, Department of Chemistry and Sarafan ChEM-H Stanford CA 94305 USA
| | - Carolyn R Bertozzi
- Stanford University, Department of Chemistry and Sarafan ChEM-H Stanford CA 94305 USA
- Howard Hughes Medical Institute Stanford CA 94305 USA
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14
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Yang W, Tian E, Chernish A, McCluggage P, Dalal K, Lara A, Ten Hagen KG, Tabak LA. Quantitative mapping of the in vivo O-GalNAc glycoproteome in mouse tissues identifies GalNAc-T2 O-glycosites in metabolic disorder. Proc Natl Acad Sci U S A 2023; 120:e2303703120. [PMID: 37862385 PMCID: PMC10614836 DOI: 10.1073/pnas.2303703120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 09/03/2023] [Indexed: 10/22/2023] Open
Abstract
The family of GalNAc-Ts (GalNAcpolypeptide:N-Acetylgalactosaminyl transferases) catalyzes the first committed step in the synthesis of O-glycans, which is an abundant and biologically important protein modification. Abnormalities in the activity of individual GalNAc-Ts can result in congenital disorders of O-glycosylation (CDG) and influence a broad array of biological functions. How site-specific O-glycans regulate biology is unclear. Compiling in vivo O-glycosites would be an invaluable step in determining the function of site-specific O-glycans. We integrated chemical and enzymatic conditions that cleave O-glycosites, a higher-energy dissociation product ions-triggered electron-transfer/higher-energy collision dissociation mass spectrometry (MS) workflow and software to study nine mouse tissues and whole blood. We identified 2,154 O-glycosites from 595 glycoproteins. The O-glycosites and glycoproteins displayed consensus motifs and shared functions as classified by Gene Ontology terms. Limited overlap of O-glycosites was observed with protein O-GlcNAcylation and phosphorylation sites. Quantitative glycoproteomics and proteomics revealed a tissue-specific regulation of O-glycosites that the differential expression of Galnt isoenzymes in tissues partly contributes to. We examined the Galnt2-null mouse model, which phenocopies congenital disorder of glycosylation involving GALNT2 and revealed a network of glycoproteins that lack GalNAc-T2-specific O-glycans. The known direct and indirect functions of these glycoproteins appear consistent with the complex metabolic phenotypes observed in the Galnt2-null animals. Through this study and interrogation of databases and the literature, we have compiled an atlas of experimentally identified mouse O-glycosites consisting of 2,925 O-glycosites from 758 glycoproteins.
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Affiliation(s)
- Weiming Yang
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
| | - E. Tian
- Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
| | - Aliona Chernish
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
| | - Peggy McCluggage
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
| | - Kruti Dalal
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
| | - Alexander Lara
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
| | - Kelly G. Ten Hagen
- Developmental Glycobiology Section, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
| | - Lawrence A. Tabak
- Section on Biological Chemistry, National Institute of Dental and Craniofacial Research (NIDCR), NIH, Bethesda, MD20892
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15
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Chongsaritsinsuk J, Steigmeyer AD, Mahoney KE, Rosenfeld MA, Lucas TM, Smith CM, Li A, Ince D, Kearns FL, Battison AS, Hollenhorst MA, Judy Shon D, Tiemeyer KH, Attah V, Kwon C, Bertozzi CR, Ferracane MJ, Lemmon MA, Amaro RE, Malaker SA. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. Nat Commun 2023; 14:6169. [PMID: 37794035 PMCID: PMC10550946 DOI: 10.1038/s41467-023-41756-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 09/11/2023] [Indexed: 10/06/2023] Open
Abstract
Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of biological functions. In particular, the T cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, -3, -4) decorate immune cells and act as key regulators in cellular immunity. However, their dense O-glycosylation remains enigmatic, primarily due to the challenges associated with studying mucin domains. Here, we demonstrate that the mucinase SmE has a unique ability to cleave at residues bearing very complex glycans. SmE enables improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we perform molecular dynamics (MD) simulations of TIM-3 and -4 to understand how glycosylation affects structural features of these proteins. Finally, we use these models to investigate the functional relevance of glycosylation for TIM-3 function and ligand binding. Overall, we present a powerful workflow to better understand the detailed molecular structures and functions of the mucinome.
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Affiliation(s)
| | | | - Keira E Mahoney
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| | - Mia A Rosenfeld
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Taryn M Lucas
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| | - Courtney M Smith
- Yale Cancer Biology Institute and Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Alice Li
- Yale Cancer Biology Institute and Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Deniz Ince
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| | - Fiona L Kearns
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
| | | | - Marie A Hollenhorst
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Department of Pathology, Stanford University, Stanford, CA, 94305, USA
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, 94305, USA
| | - D Judy Shon
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Katherine H Tiemeyer
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
| | - Victor Attah
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| | - Catherine Kwon
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, 94305, USA
| | | | - Mark A Lemmon
- Yale Cancer Biology Institute and Department of Pharmacology, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Rommie E Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA, 92093, USA
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Stacy A Malaker
- Department of Chemistry, Yale University, New Haven, CT, 06511, USA.
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16
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Wardman JF, Sim L, Liu J, Howard TA, Geissner A, Danby PM, Boraston AB, Wakarchuk WW, Withers SG. A high-throughput screening platform for enzymes active on mucin-type O-glycoproteins. Nat Chem Biol 2023; 19:1246-1255. [PMID: 37592157 DOI: 10.1038/s41589-023-01405-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/12/2023] [Indexed: 08/19/2023]
Abstract
Mucin-type O-glycosylation is a post-translational modification present at the interface between cells where it has important roles in cellular communication. However, deciphering the function of O-glycoproteins and O-glycans can be challenging, especially as few enzymes are available for their assembly or selective degradation. Here, to address this deficiency, we developed a genetically encoded screening methodology for the discovery and engineering of the diverse classes of enzymes that act on O-glycoproteins. The method uses Escherichia coli that have been engineered to produce an O-glycosylated fluorescence resonance energy transfer probe that can be used to screen for O-glycopeptidase activity. Subsequent cleavage of the substrate by O-glycopeptidases provides a read-out of the glycosylation state of the probe, allowing the method to also be used to assay glycosidases and glycosyltransferases. We further show the potential of this methodology in the first ultrahigh-throughput-directed evolution of an O-glycopeptidase.
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Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Lyann Sim
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jennifer Liu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Teresa A Howard
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andreas Geissner
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Phillip M Danby
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Warren W Wakarchuk
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
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17
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Rangel-Angarita V, Mahoney KE, Kwon C, Sarker R, Lucas TM, Malaker SA. False-Positive Glycopeptide Identification via In-FAIMS Fragmentation. JACS AU 2023; 3:2498-2509. [PMID: 37772174 PMCID: PMC10523363 DOI: 10.1021/jacsau.3c00264] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 08/24/2023] [Accepted: 09/01/2023] [Indexed: 09/30/2023]
Abstract
High-field asymmetric waveform ion mobility spectrometry (FAIMS) separates glycopeptides in the gas phase prior to mass spectrometry (MS) analysis, thus offering the potential to analyze glycopeptides without prior enrichment. Several studies have demonstrated the ability of FAIMS to enhance glycopeptide detection but have primarily focused on N-glycosylation. Here, we evaluated FAIMS for O-glycoprotein and mucin-domain glycoprotein analysis using samples of varying complexity. We demonstrated that FAIMS was useful in increasingly complex samples as it allowed for the identification of more glycosylated species. However, during our analyses, we observed a phenomenon called "in FAIMS fragmentation" (IFF) akin to in source fragmentation but occurring during FAIMS separation. FAIMS experiments showed a 2- to 5-fold increase in spectral matches from IFF compared with control experiments. These results were also replicated in previously published data, indicating that this is likely a systemic occurrence when using FAIMS. Our study highlights that although there are potential benefits to using FAIMS separation, caution must be exercised in data analysis because of prevalent IFF, which may limit its applicability in the broader field of O-glycoproteomics.
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Affiliation(s)
- Valentina Rangel-Angarita
- Department of Chemistry, Yale University, 275 Prospect Street, New
Haven, Connecticut 06511, United States
| | - Keira E. Mahoney
- Department of Chemistry, Yale University, 275 Prospect Street, New
Haven, Connecticut 06511, United States
| | - Catherine Kwon
- Department of Chemistry, Yale University, 275 Prospect Street, New
Haven, Connecticut 06511, United States
| | - Raibat Sarker
- Department of Chemistry, Yale University, 275 Prospect Street, New
Haven, Connecticut 06511, United States
| | - Taryn M. Lucas
- Department of Chemistry, Yale University, 275 Prospect Street, New
Haven, Connecticut 06511, United States
| | - Stacy A. Malaker
- Department of Chemistry, Yale University, 275 Prospect Street, New
Haven, Connecticut 06511, United States
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18
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Suttapitugsakul S, Matsumoto Y, Aryal RP, Cummings RD. Large-Scale and Site-Specific Mapping of the Murine Brain O-Glycoproteome with IMPa. Anal Chem 2023; 95:13423-13430. [PMID: 37624755 PMCID: PMC10501376 DOI: 10.1021/acs.analchem.3c00408] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/16/2023] [Indexed: 08/27/2023]
Abstract
Altered protein glycosylation is typically associated with cognitive defects and other phenotypes, but there is a lack of knowledge about the brain glycoproteome. Here, we used the newly available O-glycoprotease IMPa from Pseudomonas aeruginosa for comprehensive O-glycoproteomic analyses of the mouse brain. In this approach, total tryptic glycopeptides were prepared, extracted, purified, and conjugated to a solid support before an enzymatic cleavage by IMPa. O-glycopeptides were analyzed by electron-transfer/higher-energy collision dissociation (EThcD), which permits site-specific and global analysis of all types of O-glycans. We developed two complementary approaches for the analysis of the total O-glycoproteome using HEK293 cells and derivatives. The results demonstrated that IMPa and EThcD facilitate the confident localization of O-glycans on glycopeptides. We then applied these approaches to characterize the O-glycoproteome of the mouse brain, which revealed the high frequency of various sialylated O-glycans along with the unusual presence of the Tn antigen. Unexpectedly, the results demonstrated that glycoproteins in the brain O-glycoproteome only partly overlap with those reported for the brain N-glycoproteome. These approaches will aid in identifying the novel O-glycoproteomes of different cells and tissues and foster clinical and translational insights into the functions of protein O-glycosylation in the brain and other organs.
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Affiliation(s)
- Suttipong Suttapitugsakul
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts 02215, United States
| | | | - Rajindra P. Aryal
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts 02215, United States
| | - Richard D. Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical
School, Boston, Massachusetts 02215, United States
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19
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Chatterjee M, Huang LZX, Mykytyn AZ, Wang C, Lamers MM, Westendorp B, Wubbolts RW, van Putten JPM, Bosch BJ, Haagmans BL, Strijbis K. Glycosylated extracellular mucin domains protect against SARS-CoV-2 infection at the respiratory surface. PLoS Pathog 2023; 19:e1011571. [PMID: 37561789 PMCID: PMC10464970 DOI: 10.1371/journal.ppat.1011571] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 08/29/2023] [Accepted: 07/21/2023] [Indexed: 08/12/2023] Open
Abstract
Mucins play an essential role in protecting the respiratory tract against microbial infections while also acting as binding sites for bacterial and viral adhesins. The heavily O-glycosylated gel-forming mucins MUC5AC and MUC5B eliminate pathogens by mucociliary clearance. Transmembrane mucins MUC1, MUC4, and MUC16 can restrict microbial invasion at the apical surface of the epithelium. In this study, we determined the impact of host mucins and mucin glycans on epithelial entry of SARS-CoV-2. Human lung epithelial Calu-3 cells express the SARS-CoV-2 entry receptor ACE2 and high levels of glycosylated MUC1, but not MUC4 and MUC16, on their cell surface. The O-glycan-specific mucinase StcE specifically removed the glycosylated part of the MUC1 extracellular domain while leaving the underlying SEA domain and cytoplasmic tail intact. StcE treatment of Calu-3 cells significantly enhanced infection with SARS-CoV-2 pseudovirus and authentic virus, while removal of terminal mucin glycans sialic acid and fucose from the epithelial surface did not impact viral entry. In Calu-3 cells, the transmembrane mucin MUC1 and ACE2 are located to the apical surface in close proximity and StcE treatment results in enhanced binding of purified spike protein. Both MUC1 and MUC16 are expressed on the surface of human organoid-derived air-liquid interface (ALI) differentiated airway cultures and StcE treatment led to mucin removal and increased levels of SARS-CoV-2 replication. In these cultures, MUC1 was highly expressed in non-ciliated cells while MUC16 was enriched in goblet cells. In conclusion, the glycosylated extracellular domains of different transmembrane mucins might have similar protective functions in different respiratory cell types by restricting SARS-CoV-2 binding and entry.
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Affiliation(s)
- Maitrayee Chatterjee
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Liane Z. X. Huang
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Anna Z. Mykytyn
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Chunyan Wang
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Mart M. Lamers
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Bart Westendorp
- Department of Biomolecular Health Sciences, Division Cell Biology, Metabolism and Cancer, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | | | - Jos P. M. van Putten
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Berend-Jan Bosch
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Bart L. Haagmans
- Viroscience Department, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Karin Strijbis
- Department of Biomolecular Health Sciences, Division Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
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20
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Davey LE, Malkus PN, Villa M, Dolat L, Holmes ZC, Letourneau J, Ansaldo E, David LA, Barton GM, Valdivia RH. A genetic system for Akkermansia muciniphila reveals a role for mucin foraging in gut colonization and host sterol biosynthesis gene expression. Nat Microbiol 2023; 8:1450-1467. [PMID: 37337046 DOI: 10.1038/s41564-023-01407-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/10/2023] [Indexed: 06/21/2023]
Abstract
Akkermansia muciniphila, a mucophilic member of the gut microbiota, protects its host against metabolic disorders. Because it is genetically intractable, the mechanisms underlying mucin metabolism, gut colonization and its impact on host physiology are not well understood. Here we developed and applied transposon mutagenesis to identify genes important for intestinal colonization and for the use of mucin. An analysis of transposon mutants indicated that de novo biosynthesis of amino acids was required for A. muciniphila growth on mucin medium and that many glycoside hydrolases are redundant. We observed that mucin degradation products accumulate in internal compartments within bacteria in a process that requires genes encoding pili and a periplasmic protein complex, which we term mucin utilization locus (MUL) genes. We determined that MUL genes were required for intestinal colonization in mice but only when competing with other microbes. In germ-free mice, MUL genes were required for A. muciniphila to repress genes important for cholesterol biosynthesis in the colon. Our genetic system for A. muciniphila provides an important tool with which to uncover molecular links between the metabolism of mucins, regulation of lipid homeostasis and potential probiotic activities.
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Affiliation(s)
- Lauren E Davey
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
- Duke Microbiome Center, Duke University, Durham, NC, USA.
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada.
| | - Per N Malkus
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Max Villa
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Lee Dolat
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Zachary C Holmes
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Jeff Letourneau
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Eduard Ansaldo
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Lawrence A David
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA
- Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Gregory M Barton
- Division of Immunology and Pathogenesis, Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC, USA.
- Duke Microbiome Center, Duke University, Durham, NC, USA.
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21
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Helms A, Escobar EE, Vainauskas S, Taron CH, Brodbelt JS. Ultraviolet Photodissociation Permits Comprehensive Characterization of O-Glycopeptides Cleaved with O-Glycoprotease IMPa. Anal Chem 2023; 95:9280-9287. [PMID: 37290223 PMCID: PMC10587910 DOI: 10.1021/acs.analchem.3c01111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Complete O-glycosite characterization, including identification of the peptides, localization of the glycosites, and mapping of the glycans, has been a persistent challenge in O-glycoproteomics owing to the technical challenges surrounding O-glycan analysis. Multi-glycosylated peptides pose an even greater challenge owing to their potential heterogeneity. Ultraviolet photodissociation (UVPD) can localize multiple post-translational modifications and is well-suited for the characterization of glycans. Three glycoproteins were assessed based on a strategy combining the use of O-glycoprotease IMPa and HCD-triggered UVPD for the complete characterization of O-glycopeptides. This approach localized multiple adjacent or proximal O-glycosites on individual glycopeptides and identified a previously unknown glycosite on etanercept at S218. Nine different glycoforms were characterized as a multi-glycosylated peptide from etanercept. The performance of UVPD was compared to that of HCD and EThcD for the localization of O-glycosites and the characterization of the constituent peptides and glycans.
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Affiliation(s)
- Amanda Helms
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Edwin E Escobar
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
- New England Biolabs, Ipswich, Massachusetts 01938, United States
| | | | | | - Jennifer S Brodbelt
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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22
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Hollander MJ, Malaker SA, Riley NM, Perez I, Abney NM, Gray MA, Maxson JE, Cochran JR, Bertozzi CR. Mutational screens highlight glycosylation as a modulator of colony-stimulating factor 3 receptor (CSF3R) activity. J Biol Chem 2023; 299:104755. [PMID: 37116708 PMCID: PMC10245049 DOI: 10.1016/j.jbc.2023.104755] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 04/21/2023] [Accepted: 04/23/2023] [Indexed: 04/30/2023] Open
Abstract
The colony-stimulating factor 3 receptor (CSF3R) controls the growth of neutrophils, the most abundant type of white blood cell. In healthy neutrophils, signaling is dependent on CSF3R binding to its ligand, CSF3. A single amino acid mutation in CSF3R, T618I, instead allows for constitutive, ligand-independent cell growth and leads to a rare type of cancer called chronic neutrophilic leukemia. However, the disease mechanism is not well understood. Here, we investigated why this threonine to isoleucine substitution is the predominant mutation in chronic neutrophilic leukemia and how it leads to uncontrolled neutrophil growth. Using protein domain mapping, we demonstrated that the single CSF3R domain containing residue 618 is sufficient for ligand-independent activity. We then applied an unbiased mutational screening strategy focused on this domain and found that activating mutations are enriched at sites normally occupied by asparagine, threonine, and serine residues-the three amino acids which are commonly glycosylated. We confirmed glycosylation at multiple CSF3R residues by mass spectrometry, including the presence of GalNAc and Gal-GalNAc glycans at WT threonine 618. Using the same approach applied to other cell surface receptors, we identified an activating mutation, S489F, in the interleukin-31 receptor alpha chain. Combined, these results suggest a role for glycosylated hotspot residues in regulating receptor signaling, mutation of which can lead to ligand-independent, uncontrolled activity and human disease.
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Affiliation(s)
- Michael J Hollander
- Department of Bioengineering, Stanford University, Stanford, California, USA; Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, California, USA
| | - Stacy A Malaker
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, California, USA
| | - Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, California, USA
| | - Idalia Perez
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Nayla M Abney
- Department of Bioengineering, Stanford University, Stanford, California, USA
| | - Melissa A Gray
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, California, USA
| | - Julia E Maxson
- Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon, USA
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, California, USA; Department of Chemical Engineering, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA.
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23
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Li X, Du Y, Chen X, Liu C. Emerging roles of O-glycosylation in regulating protein aggregation, phase separation, and functions. Curr Opin Chem Biol 2023; 75:102314. [PMID: 37156204 DOI: 10.1016/j.cbpa.2023.102314] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/28/2023] [Accepted: 04/02/2023] [Indexed: 05/10/2023]
Abstract
Protein O-glycosylation is widely identified in various proteins involved in diverse biological processes. Recent studies have demonstrated that O-glycosylation plays crucial and multifaceted roles in modulating protein amyloid aggregation and liquid-liquid phase separation (LLPS) under physiological conditions. Dysregulation of these processes is closely associated with human diseases such as neurodegenerative diseases (NDs) and cancers. In this review, we first summarize the distinct roles of O-glycosylation in regulating pathological aggregation of different amyloid proteins related to NDs and elaborate the underlying mechanisms of how O-glycosylation modulates protein aggregation kinetics, induces new aggregated structures, and mediates the pathogenesis of amyloid aggregates under diseased conditions. Furthermore, we introduce recent discoveries on O-GlcNAc-mediated regulation of synaptic LLPS and phase separation potency of low-complexity domain-enriched proteins. Finally, we identify challenges in future research and highlight the potential for developing new therapeutic strategies of NDs by targeting protein O-glycosylation.
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Affiliation(s)
- Xiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Yifei Du
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China; Beijing National Laboratory for Molecular Sciences, Peking University, Beijing, China; Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Synthetic and Functional Biomolecules Center, Peking University, Beijing, China; Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, Peking University, Beijing, China.
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, China; State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.
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24
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Huang X, Nero T, Weerasekera R, Matej KH, Hinbest A, Jiang Z, Lee RF, Wu L, Chak C, Nijjer J, Gibaldi I, Yang H, Gamble N, Ng WL, Malaker SA, Sumigray K, Olson R, Yan J. Vibrio cholerae biofilms use modular adhesins with glycan-targeting and nonspecific surface binding domains for colonization. Nat Commun 2023; 14:2104. [PMID: 37055389 PMCID: PMC10102183 DOI: 10.1038/s41467-023-37660-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/24/2023] [Indexed: 04/15/2023] Open
Abstract
Bacterial biofilms are formed on environmental surfaces and host tissues, and facilitate host colonization and antibiotic resistance by human pathogens. Bacteria often express multiple adhesive proteins (adhesins), but it is often unclear whether adhesins have specialized or redundant roles. Here, we show how the model biofilm-forming organism Vibrio cholerae uses two adhesins with overlapping but distinct functions to achieve robust adhesion to diverse surfaces. Both biofilm-specific adhesins Bap1 and RbmC function as a "double-sided tape": they share a β-propeller domain that binds to the biofilm matrix exopolysaccharide, but have distinct environment-facing domains. Bap1 adheres to lipids and abiotic surfaces, while RbmC mainly mediates binding to host surfaces. Furthermore, both adhesins contribute to adhesion in an enteroid monolayer colonization model. We expect that similar modular domains may be utilized by other pathogens, and this line of research can potentially lead to new biofilm-removal strategies and biofilm-inspired adhesives.
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Affiliation(s)
- Xin Huang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Thomas Nero
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Ranjuna Weerasekera
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Katherine H Matej
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Alex Hinbest
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Zhaowei Jiang
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Rebecca F Lee
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
| | - Longjun Wu
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Department of Ocean Science and Hong Kong Branch of the Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), The Hong Kong University of Science and Technology, Hong Kong SAR, Guangzhou, Hong Kong SAR
| | - Cecilia Chak
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Japinder Nijjer
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA
| | - Isabella Gibaldi
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Hang Yang
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Nathan Gamble
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA
| | - Wai-Leung Ng
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA
| | - Stacy A Malaker
- Department of Chemistry, Yale University, New Haven, CT, USA
| | - Kaelyn Sumigray
- Department of Genetics, Yale School of Medicine, New Haven, CT, USA
- Yale Stem Cell Center, Yale School of Medicine, New Haven, CT, USA
- Yale Cancer Center, Yale School of Medicine, New Haven, CT, USA
| | - Rich Olson
- Department of Molecular Biology and Biochemistry, Molecular Biophysics Program, Wesleyan University, Middletown, CT, USA.
| | - Jing Yan
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA.
- Quantitative Biology Institute, Yale University, New Haven, CT, USA.
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25
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Shuoker B, Pichler MJ, Jin C, Sakanaka H, Wu H, Gascueña AM, Liu J, Nielsen TS, Holgersson J, Nordberg Karlsson E, Juge N, Meier S, Morth JP, Karlsson NG, Abou Hachem M. Sialidases and fucosidases of Akkermansia muciniphila are crucial for growth on mucin and nutrient sharing with mucus-associated gut bacteria. Nat Commun 2023; 14:1833. [PMID: 37005422 PMCID: PMC10067855 DOI: 10.1038/s41467-023-37533-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 03/21/2023] [Indexed: 04/04/2023] Open
Abstract
The mucolytic human gut microbiota specialist Akkermansia muciniphila is proposed to boost mucin-secretion by the host, thereby being a key player in mucus turnover. Mucin glycan utilization requires the removal of protective caps, notably fucose and sialic acid, but the enzymatic details of this process remain largely unknown. Here, we describe the specificities of ten A. muciniphila glycoside hydrolases, which collectively remove all known sialyl and fucosyl mucin caps including those on double-sulfated epitopes. Structural analyses revealed an unprecedented fucosidase modular arrangement and explained the sialyl T-antigen specificity of a sialidase of a previously unknown family. Cell-attached sialidases and fucosidases displayed mucin-binding and their inhibition abolished growth of A. muciniphila on mucin. Remarkably, neither the sialic acid nor fucose contributed to A. muciniphila growth, but instead promoted butyrate production by co-cultured Clostridia. This study brings unprecedented mechanistic insight into the initiation of mucin O-glycan degradation by A. muciniphila and nutrient sharing between mucus-associated bacteria.
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Affiliation(s)
- Bashar Shuoker
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark
- Biotechnology, Department of Chemistry, Lund University, Lund, Sweden
| | - Michael J Pichler
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Chunsheng Jin
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Hiroka Sakanaka
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Haiyang Wu
- Quadram Institute Bioscience, Norwich, UK
| | | | - Jining Liu
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Tine Sofie Nielsen
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark
| | - Jan Holgersson
- Department of Laboratory Medicine, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | | | | | - Sebastian Meier
- Department of Chemistry, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Jens Preben Morth
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark.
| | - Niclas G Karlsson
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Maher Abou Hachem
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, 2800, Denmark.
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26
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Chandler KB, Pavan CH, Cotto Aparicio HG, Sackstein R. Enrichment and nLC-MS/MS Analysis of Head and Neck Cancer Mucinome Glycoproteins. J Proteome Res 2023; 22:1231-1244. [PMID: 36971183 DOI: 10.1021/acs.jproteome.2c00746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
Mucin-domain glycoproteins expressed on cancer cell surfaces play central roles in cell adhesion, cancer progression, stem cell renewal, and immune evasion. Despite abundant evidence that mucin-domain glycoproteins are critical to the pathobiology of head and neck squamous cell carcinoma (HNSCC), our knowledge of the composition of that mucinome is grossly incomplete. Here, we utilized a catalytically inactive point mutant of the enzyme StcE (StcEE447D) to capture mucin-domain glycoproteins in head and neck cancer cell line lysates followed by their characterization using sodium dodecyl-sulfate polyacrylamide gel electrophoresis (SDS-PAGE), in-gel digestion, nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS), and enrichment analyses. We demonstrate the feasibility of this workflow for the study of mucin-domain glycoproteins in HNSCC, identify a set of mucin-domain glycoproteins common to multiple HNSCC cell lines, and report a subset of mucin-domain glycoproteins that are uniquely expressed in HSC-3 cells, a cell line derived from a highly aggressive metastatic tongue squamous cell carcinoma. This effort represents the first attempt to identify mucin-domain glycoproteins in HNSCC in an untargeted, unbiased analysis, paving the way for a more comprehensive characterization of the mucinome components that mediate aggressive tumor cell phenotypes. Data associated with this study have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the data set identifier PXD029420.
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27
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O-Mucin-degrading carbohydrate-active enzymes and their possible implication in inflammatory bowel diseases. Essays Biochem 2023; 67:331-344. [PMID: 36912232 PMCID: PMC10154620 DOI: 10.1042/ebc20220153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 03/14/2023]
Abstract
Inflammatory bowel diseases (IBD) are modern diseases, with incidence rising around the world. They are associated with perturbation of the intestinal microbiota, and with alteration and crossing of the mucus barrier by the commensal bacteria that feed on it. In the process of mucus catabolism and invasion by gut bacteria, carbohydrate-active enzymes (CAZymes) play a critical role since mucus is mainly made up by O- and N-glycans. Moreover, the occurrence of IBD seems to be associated with low-fiber diets. Conversely, supplementation with oligosaccharides, such as human milk oligosaccharides (HMOs), which are structurally similar to intestinal mucins and could thus compete with them towards bacterial mucus-degrading CAZymes, has been suggested to prevent inflammation. In this mini-review, we will establish the current state of knowledge regarding the identification and characterization of mucus-degrading enzymes from both cultured and uncultured species of gut commensals and enteropathogens, with a particular focus on the present technological opportunities available to further the discovery of mucus-degrading CAZymes within the entire gut microbiome, by coupling microfluidics with metagenomics and culturomics. Finally, we will discuss the challenges to overcome to better assess how CAZymes targeting specific functional oligosaccharides could be involved in the modulation of the mucus-driven cross-talk between gut bacteria and their host in the context of IBD.
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28
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Sun F, Suttapitugsakul S, Wu R. Systematic characterization of extracellular glycoproteins using mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:519-545. [PMID: 34047389 PMCID: PMC8627532 DOI: 10.1002/mas.21708] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 05/13/2023]
Abstract
Surface and secreted glycoproteins are essential to cells and regulate many extracellular events. Because of the diversity of glycans, the low abundance of many glycoproteins, and the complexity of biological samples, a system-wide investigation of extracellular glycoproteins is a daunting task. With the development of modern mass spectrometry (MS)-based proteomics, comprehensive analysis of different protein modifications including glycosylation has advanced dramatically. This review focuses on the investigation of extracellular glycoproteins using MS-based proteomics. We first discuss the methods for selectively enriching surface glycoproteins and investigating protein interactions on the cell surface, followed by the application of MS-based proteomics for surface glycoprotein dynamics analysis and biomarker discovery. We then summarize the methods to comprehensively study secreted glycoproteins by integrating various enrichment approaches with MS-based proteomics and their applications for global analysis of secreted glycoproteins in different biological samples. Collectively, MS significantly expands our knowledge of extracellular glycoproteins and enables us to identify extracellular glycoproteins as potential biomarkers for disease detection and drug targets for disease treatment.
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Affiliation(s)
| | | | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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29
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Chongsaritsinsuk J, Steigmeyer AD, Mahoney KE, Rosenfeld MA, Lucas TM, Ince D, Kearns FL, Battison AS, Hollenhorst MA, Shon DJ, Tiemeyer KH, Attah V, Kwon C, Bertozzi CR, Ferracane MJ, Amaro RE, Malaker SA. Glycoproteomic landscape and structural dynamics of TIM family immune checkpoints enabled by mucinase SmE. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.01.526488. [PMID: 36778266 PMCID: PMC9915616 DOI: 10.1101/2023.02.01.526488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Mucin-domain glycoproteins are densely O-glycosylated and play critical roles in a host of biological functions. In particular, the T cell immunoglobulin and mucin-domain containing family of proteins (TIM-1, -3, -4) decorate immune cells and act as key checkpoint inhibitors in cancer. However, their dense O-glycosylation remains enigmatic both in terms of glycoproteomic landscape and structural dynamics, primarily due to the challenges associated with studying mucin domains. Here, we present a mucinase (SmE) and demonstrate its ability to selectively cleave along the mucin glycoprotein backbone, similar to others of its kind. Unlike other mucinases, though, SmE harbors the unique ability to cleave at residues bearing extremely complex glycans which enabled improved mass spectrometric analysis of several mucins, including the entire TIM family. With this information in-hand, we performed molecular dynamics (MD) simulations of TIM-3 and -4 to demonstrate how glycosylation affects structural features of these proteins. Overall, we present a powerful workflow to better understand the detailed molecular structures of the mucinome.
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Affiliation(s)
| | | | - Keira E. Mahoney
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Mia A. Rosenfeld
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | - Taryn M. Lucas
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Deniz Ince
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Fiona L. Kearns
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
| | | | - Marie A. Hollenhorst
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA 94305, USA
| | - D. Judy Shon
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Katherine H. Tiemeyer
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Victor Attah
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Catherine Kwon
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
| | - Carolyn R. Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | | | - Rommie E. Amaro
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, CA 92093, USA
- Glycobiology Research and Training Center, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stacy A. Malaker
- Department of Chemistry, Yale University, New Haven, CT 06511, USA
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30
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Riley NM, Bertozzi CR. Deciphering O-glycoprotease substrate preferences with O-Pair Search. Mol Omics 2022; 18:908-922. [PMID: 36373229 PMCID: PMC10010678 DOI: 10.1039/d2mo00244b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
O-Glycoproteases are an emerging class of enzymes that selectively digest glycoproteins at positions decorated with specific O-linked glycans. O-Glycoprotease substrates range from any O-glycoprotein (albeit with specific O-glycan modifications) to only glycoproteins harboring specific O-glycosylated sequence motifs, such as those found in mucin domains. Their utility for multiple glycoproteomic applications is driving the search to both discover new O-glycoproteases and to understand how structural features of characterized O-glycoproteases influence their substrate specificities. One challenge of defining O-glycoprotease specificity restraints is the need to characterize O-glycopeptides with site-specific analysis of O-glycosites. Here, we demonstrate how O-Pair Search, a recently developed O-glycopeptide-centric identification platform that enables rapid searches and confident O-glycosite localization, can be used to determine substrate specificities of various O-glycoproteases de novo from LC-MS/MS data of O-glycopeptides. Using secreted protease of C1 esterase inhibitor (StcE) from enterohemorrhagic Escherichia coli and O-endoprotease OgpA from Akkermansia mucinophila, we explore numerous settings that effect O-glycopeptide identification and show how non-specific and semi-tryptic searches of O-glycopeptide data can produce candidate cleavage motifs. These putative motifs can be further used to define new protease cleavage settings that lower search times and improve O-glycopeptide identifications. We use this platform to generate a consensus motif for the recently characterized immunomodulating metalloprotease (IMPa) from Pseudomonas aeruginosa and show that IMPa is a favorable O-glycoprotease for characterizing densely O-glycosylated mucin-domain glycoproteins.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Sarafan ChEM-H, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Sarafan ChEM-H, Stanford University, Stanford, California, USA. .,Howard Hughes Medical Institute, Stanford, California, USA
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31
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Li J, Guo B, Zhang W, Yue S, Huang S, Gao S, Ma J, Cipollo JF, Yang S. Recent advances in demystifying O-glycosylation in health and disease. Proteomics 2022; 22:e2200156. [PMID: 36088641 DOI: 10.1002/pmic.202200156] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 08/30/2022] [Accepted: 09/02/2022] [Indexed: 11/09/2022]
Abstract
O-Glycosylation is one of the most common protein post-translational modifications (PTM) and plays an essential role in the pathophysiology of diseases. However, the complexity of O-glycosylation and the lack of specific enzymes for the processing of O-glycans and their O-glycopeptides make O-glycosylation analysis challenging. Recently, research on O-glycosylation has received attention owing to technological innovation and emerging O-glycoproteases. Several serine/threonine endoproteases have been found to specifically cleave O-glycosylated serine or threonine, allowing for the systematic analysis of O-glycoproteins. In this review, we first assessed the field of protein O-glycosylation over the past decade and used bibliometric analysis to identify keywords and emerging trends. We then summarized recent advances in O-glycosylation, covering several aspects: O-glycan release, site-specific elucidation of intact O-glycopeptides, identification of O-glycosites, characterization of different O-glycoproteases, mass spectrometry (MS) fragmentation methods for site-specific O-glycosylation assignment, and O-glycosylation data analysis. Finally, the role of O-glycosylation in health and disease was discussed.
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Affiliation(s)
- Jiajia Li
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Bo Guo
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Wenqi Zhang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Shuang Yue
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Shan Huang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
| | - Song Gao
- Jiangsu Key Laboratory of Marine Pharmaceutical Compound Screening, Jiangsu Key Laboratory of Marine Biological Resources and Environment, Co-Innovation Center of Jiangsu Marine Bio-industry Technology, School of Pharmacy, Jiangsu Ocean University, Lianyungang, China
| | - Junfeng Ma
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Georgetown University, Washington, DC, USA
| | - John F 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, USA
| | - Shuang Yang
- Center for Clinical Mass Spectrometry, College of Pharmaceutical Sciences, Soochow University, Suzhou, Jiangsu, China
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32
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Riley NM, Wen RM, Bertozzi CR, Brooks JD, Pitteri SJ. Measuring the multifaceted roles of mucin-domain glycoproteins in cancer. Adv Cancer Res 2022; 157:83-121. [PMID: 36725114 PMCID: PMC10582998 DOI: 10.1016/bs.acr.2022.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Mucin-domain glycoproteins are highly O-glycosylated cell surface and secreted proteins that serve as both biochemical and biophysical modulators. Aberrant expression and glycosylation of mucins are known hallmarks in numerous malignancies, yet mucin-domain glycoproteins remain enigmatic in the broad landscape of cancer glycobiology. Here we review the multifaceted roles of mucins in cancer through the lens of the analytical and biochemical methods used to study them. We also describe a collection of emerging tools that are specifically equipped to characterize mucin-domain glycoproteins in complex biological backgrounds. These approaches are poised to further elucidate how mucin biology can be understood and subsequently targeted for the next generation of cancer therapeutics.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States.
| | - Ru M Wen
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States
| | - Carolyn R Bertozzi
- Department of Chemistry and Sarafan ChEM-H, Stanford University, Stanford, CA, United States; Howard Hughes Medical Institute, Stanford, CA, United States
| | - James D Brooks
- Department of Urology, Stanford University School of Medicine, Stanford, CA, United States; Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, CA, United States.
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33
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Medley BJ, Leclaire L, Thompson N, Mahoney KE, Pluvinage B, Parson MAH, Burke JE, Malaker S, Wakarchuk W, Boraston AB. A previously uncharacterized O-glycopeptidase from Akkermansia muciniphila requires the Tn-antigen for cleavage of the peptide bond. J Biol Chem 2022; 298:102439. [PMID: 36049519 PMCID: PMC9513282 DOI: 10.1016/j.jbc.2022.102439] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 10/27/2022] Open
Abstract
Akkermansia muciniphila is key member of the human gut microbiota, impacting many features of host health. A major characteristic of this bacterium is its interaction with host mucin, which is abundant in the gut environment, and its ability to metabolize mucin as a nutrient source. The machinery deployed by A. muciniphila to enable this interaction appears to be extensive and sophisticated, yet it is incompletely defined. The uncharacterized protein AMUC_1438 is encoded by a gene that was previously shown to be upregulated when the bacterium is grown on mucin. This uncharacterized protein has features suggestive of carbohydrate-recognition and peptidase activity, which led us to hypothesize that it has a role in mucin depolymerization. Here we provide structural and functional support for the assignment of AMUC_1438 as a unique O-glycopeptidase with mucin degrading capacity. O-glycopeptidase enzymes recognize glycans but hydrolyze the peptide backbone and are common in host-adapted microbes that colonize or invade mucus layers. Structural, kinetic, and mutagenic analyses point to a metzincin metalloprotease catalytic motif but specific recognition of a GalNAc residue α-linked to serine or threonine (i.e. the Tn-antigen) within the AMUC_1438 active site. The enzyme catalyzes hydrolysis of the bond immediately N-terminal to the glycosylated residue. Additional modelling analyses suggest the presence of a carbohydrate-binding module that may assist in substrate recognition. We anticipate that these results will be fundamental to a wider understanding of the O-glycopeptidase class of enzymes and how they may contribute to host-adaptation.
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Affiliation(s)
- Brendon J Medley
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia, V8W 2Y2, Canada
| | - Leif Leclaire
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Nicole Thompson
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Keira E Mahoney
- Department of Chemistry, Yale University, 350 Edward St., New Haven CT, 06511
| | - Benjamin Pluvinage
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia, V8W 2Y2, Canada
| | - Matthew A H Parson
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia, V8W 2Y2, Canada
| | - John E Burke
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia, V8W 2Y2, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, V6T 1Z3, Canada
| | - Stacy Malaker
- Department of Chemistry, Yale University, 350 Edward St., New Haven CT, 06511
| | - Warren Wakarchuk
- Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
| | - Alisdair B Boraston
- Department of Biochemistry and Microbiology, University of Victoria, PO Box 1700 STN CSC, Victoria, British Columbia, V8W 2Y2, Canada.
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Taleb V, Liao Q, Narimatsu Y, García-García A, Compañón I, Borges RJ, González-Ramírez AM, Corzana F, Clausen H, Rovira C, Hurtado-Guerrero R. Structural and mechanistic insights into the cleavage of clustered O-glycan patches-containing glycoproteins by mucinases of the human gut. Nat Commun 2022; 13:4324. [PMID: 35882872 PMCID: PMC9325726 DOI: 10.1038/s41467-022-32021-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/13/2022] [Indexed: 11/09/2022] Open
Abstract
Mucinases of human gut bacteria cleave peptide bonds in mucins strictly depending on the presence of neighboring O-glycans. The Akkermansia muciniphila AM0627 mucinase cleaves specifically in between contiguous (bis) O-glycans of defined truncated structures, suggesting that this enzyme may recognize clustered O-glycan patches. Here, we report the structure and molecular mechanism of AM0627 in complex with a glycopeptide containing a bis-T (Galβ1-3GalNAcα1-O-Ser/Thr) O-glycan, revealing that AM0627 recognizes both the sugar moieties and the peptide sequence. AM0627 exhibits preference for bis-T over bis-Tn (GalNAcα1-O-Ser/Thr) O-glycopeptide substrates, with the first GalNAc residue being essential for cleavage. AM0627 follows a mechanism relying on a nucleophilic water molecule and a catalytic base Glu residue. Structural comparison among mucinases identifies a conserved Tyr engaged in sugar-π interactions in both AM0627 and the Bacteroides thetaiotaomicron BT4244 mucinase as responsible for the common activity of these two mucinases with bis-T/Tn substrates. Our work illustrates how mucinases through tremendous flexibility adapt to the diversity in distribution and patterns of O-glycans on mucins. AM0627 is a bis-O-glycan mucinase that might work in the final steps of mucus degradation, thereby providing a carbon and nitrogen source for Akkermansia muciniphila. Here, the authors provide molecular insights into AM0627 function from X-ray crystallography and computer simulations.
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Affiliation(s)
- Víctor Taleb
- Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | - Qinghua Liao
- Departament de Química Inorgánica i Orgánica (Secció de Química Orgánica) and Institut de Química Teorica i Computacional (IQTCUB), Universitat de Barcelona, 08028, Barcelona, Spain
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ana García-García
- Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | - Ismael Compañón
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006, Logroño, Spain
| | - Rafael Junqueira Borges
- Departamento de Biofísica e Farmacologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, Brazil
| | - Andrés Manuel González-Ramírez
- Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, E-26006, Logroño, Spain
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Carme Rovira
- Departament de Química Inorgánica i Orgánica (Secció de Química Orgánica) and Institut de Química Teorica i Computacional (IQTCUB), Universitat de Barcelona, 08028, Barcelona, Spain. .,Institució Catalana de Recerca i Estudis Avancats (ICREA), 08010, Barcelona, Spain.
| | - Ramon Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza, Spain. .,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark. .,Fundación ARAID, 50018, Zaragoza, Spain.
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35
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Ince D, Lucas TM, Malaker SA. Current strategies for characterization of mucin-domain glycoproteins. Curr Opin Chem Biol 2022; 69:102174. [PMID: 35752002 DOI: 10.1016/j.cbpa.2022.102174] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 05/02/2022] [Accepted: 05/19/2022] [Indexed: 11/18/2022]
Abstract
Glycosylation, and especially O-linked glycosylation, remains a critical blind spot in the understanding of post-translational modifications. Due to their nature as proteins defined by a large density and abundance of O-glycosylation, mucins present extra challenges in the analysis of their structure and function. However, recent breakthroughs in multiple areas of research have rendered mucin-domain glycoproteins more accessible to current characterization techniques. In particular, the adaptation of mucinases to glycoproteomic workflows, the manipulation of cellular glycosylation pathways, and the advances in synthetic methods to more closely mimic mucin domains have introduced new and exciting avenues to study mucin glycoproteins. Here, we summarize recent developments in understanding the structure and biological function of mucin domains and their associated glycans, from glycoproteomic tools and visualization methods to synthetic glycopeptide mimetics.
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Affiliation(s)
- Deniz Ince
- Department of Chemistry, Yale University, 275 Prospect St, New Haven, CT 06511, United States
| | - Taryn M Lucas
- Department of Chemistry, Yale University, 275 Prospect St, New Haven, CT 06511, United States
| | - Stacy A Malaker
- Department of Chemistry, Yale University, 275 Prospect St, New Haven, CT 06511, United States.
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36
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Abstract
Mucin domains are densely O-glycosylated modular protein domains found in various extracellular and transmembrane proteins. Mucin-domain glycoproteins play important roles in many human diseases, such as cancer and cystic fibrosis, but the scope of the mucinome remains poorly defined. Recently, we characterized a bacterial O-glycoprotease, StcE, and demonstrated that an inactive point mutant retains binding selectivity for mucin-domain glycoproteins. In this work, we leverage inactive StcE to selectively enrich and identify mucin-domain glycoproteins from complex samples like cell lysate and crude ovarian cancer patient ascites fluid. Our enrichment strategy is further aided by an algorithm to assign confidence to mucin-domain glycoprotein identifications. This mucinomics platform facilitates detection of hundreds of glycopeptides from mucin domains and highly overlapping populations of mucin-domain glycoproteins from ovarian cancer patients. Ultimately, we demonstrate our mucinomics approach can reveal key molecular signatures of cancer from in vitro and ex vivo sources. Mucin-domain glycoproteins are densely O-glycosylated proteins with unique secondary structure that imparts a large influence on cellular environments. Here, the authors develop a technique to selectively enrich and characterize mucin-domain glycoproteins from cell lysate and patient biofluids.
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37
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Purcell SC, Zhang MH, Honigfort DJ, Ng HJC, Michalak AL, Godula K. Cell surface photoengineering enables modeling of glycocalyx shedding dynamics. Chem Sci 2022; 13:6626-6635. [PMID: 35756522 PMCID: PMC9172368 DOI: 10.1039/d2sc00524g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 05/11/2022] [Indexed: 11/21/2022] Open
Abstract
The cellular glycocalyx, composed of membrane associated glycoproteins and glycolipids, is a complex and dynamic interface that facilitates interactions between cells and their environment. The glycocalyx composition is continuously changing through biosynthesis of new glycoconjugates and membrane turnover. Various glycocalyx components, such as mucins, can also be rapidly shed from the cell surface in response to acute events, such as pathogenic threat. Mucins, which are large extended glycoproteins, deliver important protective functions against infection by creating a physical barrier at the cell surface and by capturing and clearing pathogens through shedding. Evaluating these mucin functions may provide better understanding of early stages of pathogenesis; however, tools to tailor the composition and dynamics of the glycocalyx with precision are still limited. Here, we report a chemical cell surface engineering strategy to model the shedding behavior of mucins with spatial and temporal control. We generated synthetic mucin mimetic glycopolymers terminated with a photolabile membrane anchor, which could be introduced into the membranes of living cells and, subsequently, released upon exposure to UV light. By tuning the molecular density of the artificial glycocalyx we evaluated lectin crosslinking and its effect on shedding, showing that lectins can stabilize the glycocalyx and limit release of the mucin mimetics from the cell surface. Our findings indicate that endogenous and pathogen-associated lectins, which are known to interact with the host-cell glycocalyx, may alter mucin shedding dynamics and influence the protective properties of the mucosal barrier. More broadly, we present a method which enables photoengineering of the glycocalyx and can be used to facilitate the study of glycocalyx dynamics in other biological contexts.
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Affiliation(s)
- Sean C Purcell
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Michelle H Zhang
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Daniel J Honigfort
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Hans Jefferson C Ng
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Austen L Michalak
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
| | - Kamil Godula
- Department of Chemistry and Biochemistry, University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
- Glycobiology Research and Training Center, University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA
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38
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Konstantinidi A, Nason R, Čaval T, Sun L, Sørensen DM, Furukawa S, Ye Z, Vincentelli R, Narimatsu Y, Vakhrushev SY, Clausen H. Exploring the glycosylation of mucins by use of O-glycodomain reporters recombinantly expressed in glycoengineered HEK293 cells. J Biol Chem 2022; 298:101784. [PMID: 35247390 PMCID: PMC8980628 DOI: 10.1016/j.jbc.2022.101784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 02/25/2022] [Accepted: 02/27/2022] [Indexed: 12/18/2022] Open
Abstract
Mucins and glycoproteins with mucin-like regions contain densely O-glycosylated domains often found in tandem repeat (TR) sequences. These O-glycodomains have traditionally been difficult to characterize because of their resistance to proteolytic digestion, and knowledge of the precise positions of O-glycans is particularly limited for these regions. Here, we took advantage of a recently developed glycoengineered cell-based platform for the display and production of mucin TR reporters with custom-designed O-glycosylation to characterize O-glycodomains derived from mucins and mucin-like glycoproteins. We combined intact mass and bottom-up site-specific analysis for mapping O-glycosites in the mucins, MUC2, MUC20, MUC21, protein P-selectin-glycoprotein ligand 1, and proteoglycan syndecan-3. We found that all the potential Ser/Thr positions in these O-glycodomains were O-glycosylated when expressed in human embryonic kidney 293 SimpleCells (Tn-glycoform). Interestingly, we found that all potential Ser/Thr O-glycosites in TRs derived from secreted mucins and most glycosites from transmembrane mucins were almost fully occupied, whereas TRs from a subset of transmembrane mucins were less efficiently processed. We further used the mucin TR reporters to characterize cleavage sites of glycoproteases StcE (secreted protease of C1 esterase inhibitor from EHEC) and BT4244, revealing more restricted substrate specificities than previously reported. Finally, we conducted a bottom-up analysis of isolated ovine submaxillary mucin, which supported our findings that mucin TRs in general are efficiently O-glycosylated at all potential glycosites. This study provides insight into O-glycosylation of mucins and mucin-like domains, and the strategies developed open the field for wider analysis of native mucins.
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Affiliation(s)
- Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rebecca Nason
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tomislav Čaval
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lingbo Sun
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Daniel M Sørensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sanae Furukawa
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark; GlycoDisplay ApS, Copenhagen, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
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39
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Structure-guided mutagenesis of a mucin-selective metalloprotease from Akkermansia muciniphila alters substrate preferences. J Biol Chem 2022; 298:101917. [PMID: 35405095 PMCID: PMC9118916 DOI: 10.1016/j.jbc.2022.101917] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 02/07/2023] Open
Abstract
Akkermansia muciniphila, a mucin-degrading microbe found in the human gut, is often associated with positive health outcomes. The abundance of A. muciniphila is modulated by the presence and accessibility of nutrients, which can be derived from diet or host glycoproteins. In particular, the ability to degrade host mucins, a class of proteins carrying densely O-glycosylated domains, provides a competitive advantage in the sustained colonization of niche mucosal environments. Although A. muciniphila is known to rely on mucins as a carbon and nitrogen source, the enzymatic machinery used by this microbe to process mucins in the gut is not yet fully characterized. Here, we focus on the mucin-selective metalloprotease, Amuc_0627 (AM0627), which is known to cleave between adjacent residues carrying truncated core 1 O-glycans. We showed that this enzyme is capable of degrading purified mucin 2 (MUC2), the major protein component of mucus in the gut. An X-ray crystal structure of AM0627 (1.9 Å resolution) revealed O-glycan–binding residues that are conserved between structurally characterized enzymes from the same family. We further rationalized the substrate cleavage motif using molecular modeling to identify nonconserved glycan-interacting residues. We conclude that mutagenesis of these residues resulted in altered substrate preferences down to the glycan level, providing insight into the structural determinants of O-glycan recognition.
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40
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Wardman JF, Bains RK, Rahfeld P, Withers SG. Carbohydrate-active enzymes (CAZymes) in the gut microbiome. Nat Rev Microbiol 2022; 20:542-556. [PMID: 35347288 DOI: 10.1038/s41579-022-00712-1] [Citation(s) in RCA: 132] [Impact Index Per Article: 66.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/21/2022] [Indexed: 12/13/2022]
Abstract
The 1013-1014 microorganisms present in the human gut (collectively known as the human gut microbiota) dedicate substantial percentages of their genomes to the degradation and uptake of carbohydrates, indicating the importance of this class of molecules. Carbohydrates function not only as a carbon source for these bacteria but also as a means of attachment to the host, and a barrier to infection of the host. In this Review, we focus on the diversity of carbohydrate-active enzymes (CAZymes), how gut microorganisms use them for carbohydrate degradation, the different chemical mechanisms of these CAZymes and the roles that these microorganisms and their CAZymes have in human health and disease. We also highlight examples of how enzymes from this treasure trove have been used in manipulation of the microbiota for improved health and treatment of disease, in remodelling the glycans on biopharmaceuticals and in the potential production of universal O-type donor blood.
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Affiliation(s)
- Jacob F Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada.,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rajneesh K Bains
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Peter Rahfeld
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada. .,Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada. .,Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada.
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41
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Critcher M, Hassan AA, Huang ML. Seeing the forest through the trees: characterizing the glycoproteome. Trends Biochem Sci 2022; 47:492-505. [DOI: 10.1016/j.tibs.2022.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 12/14/2022]
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42
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Bouchard G, Garcia Marques FJ, Karacosta LG, Zhang W, Bermudez A, Riley NM, Varma S, Mehl LC, Benson JA, Shrager JB, Bertozzi CR, Pitteri S, Giaccia AJ, Plevritis SK. Multiomics Analysis of Spatially Distinct Stromal Cells Reveals Tumor-Induced O-Glycosylation of the CDK4-pRB Axis in Fibroblasts at the Invasive Tumor Edge. Cancer Res 2022; 82:648-664. [PMID: 34853070 PMCID: PMC9075699 DOI: 10.1158/0008-5472.can-21-1705] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/02/2021] [Accepted: 11/24/2021] [Indexed: 11/16/2022]
Abstract
The invasive leading edge represents a potential gateway for tumor metastasis. The role of fibroblasts from the tumor edge in promoting cancer invasion and metastasis has not been comprehensively elucidated. We hypothesize that cross-talk between tumor and stromal cells within the tumor microenvironment results in activation of key biological pathways depending on their position in the tumor (edge vs. core). Here we highlight phenotypic differences between tumor-adjacent-fibroblasts (TAF) from the invasive edge and tumor core fibroblasts from the tumor core, established from human lung adenocarcinomas. A multiomics approach that includes genomics, proteomics, and O-glycoproteomics was used to characterize cross-talk between TAFs and cancer cells. These analyses showed that O-glycosylation, an essential posttranslational modification resulting from sugar metabolism, alters key biological pathways including the cyclin-dependent kinase 4 (CDK4) and phosphorylated retinoblastoma protein axis in the stroma and indirectly modulates proinvasive features of cancer cells. In summary, the O-glycoproteome represents a new consideration for important biological processes involved in tumor-stroma cross-talk and a potential avenue to improve the anticancer efficacy of CDK4 inhibitors. SIGNIFICANCE A multiomics analysis of spatially distinct fibroblasts establishes the importance of the stromal O-glycoproteome in tumor-stroma interactions at the leading edge and provides potential strategies to improve cancer treatment. See related commentary by De Wever, p. 537.
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Affiliation(s)
- Gina Bouchard
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
- Department of Radiology, Canary Center for Cancer Early Detection, Palo Alto CA, 94304, USA
- Department of Radiation Oncology, Stanford, CA 94305, USA
| | | | | | - Weiruo Zhang
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - Abel Bermudez
- Department of Radiology, Canary Center for Cancer Early Detection, Palo Alto CA, 94304, USA
| | | | - Sushama Varma
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | | | - Jalen Anthony Benson
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | - Joseph B Shrager
- Department of Cardiothoracic Surgery, Stanford University, Stanford, CA 94305, USA
| | | | - Sharon Pitteri
- Department of Radiology, Canary Center for Cancer Early Detection, Palo Alto CA, 94304, USA
| | - Amato J Giaccia
- Department of Radiation Oncology, Stanford, CA 94305, USA
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Sylvia Katina Plevritis
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
- Department of Radiology, Canary Center for Cancer Early Detection, Palo Alto CA, 94304, USA
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43
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Genome-wide bidirectional CRISPR screens identify mucins as host factors modulating SARS-CoV-2 infection. Nat Genet 2022; 54:1078-1089. [PMID: 35879412 PMCID: PMC9355872 DOI: 10.1038/s41588-022-01131-x] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 06/10/2022] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causes a range of symptoms in infected individuals, from mild respiratory illness to acute respiratory distress syndrome. A systematic understanding of host factors influencing viral infection is critical to elucidate SARS-CoV-2-host interactions and the progression of Coronavirus disease 2019 (COVID-19). Here, we conducted genome-wide CRISPR knockout and activation screens in human lung epithelial cells with endogenous expression of the SARS-CoV-2 entry factors ACE2 and TMPRSS2. We uncovered proviral and antiviral factors across highly interconnected host pathways, including clathrin transport, inflammatory signaling, cell-cycle regulation, and transcriptional and epigenetic regulation. We further identified mucins, a family of high molecular weight glycoproteins, as a prominent viral restriction network that inhibits SARS-CoV-2 infection in vitro and in murine models. These mucins also inhibit infection of diverse respiratory viruses. This functional landscape of SARS-CoV-2 host factors provides a physiologically relevant starting point for new host-directed therapeutics and highlights airway mucins as a host defense mechanism.
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44
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Vainauskas S, Guntz H, McLeod E, McClung C, Ruse C, Shi X, Taron CH. A Broad-Specificity O-Glycoprotease That Enables Improved Analysis of Glycoproteins and Glycopeptides Containing Intact Complex O-Glycans. Anal Chem 2021; 94:1060-1069. [PMID: 34962767 DOI: 10.1021/acs.analchem.1c04055] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Characterization of mucin-type O-glycans linked to serine/threonine of glycoproteins is technically challenging, in part, due to a lack of effective enzymatic tools that enable their analysis. Recently, several O-glycan-specific endoproteases that can cleave the protein adjacent to the appended glycan have been described. Despite significant progress in understanding the biochemistry of these enzymes, known O-glycoproteases have specificity constraints, such as inefficient cleavage of glycoproteins bearing sialylated O-glycans, high selectivity for certain types of glycoproteins, or protein sequence bias. These factors limit their analytical application. In this study, we examined the capabilities of an immunomodulating metalloprotease (IMPa) from Pseudomonas aeruginosa. Peptide sequence selectivity and its impact on IMPa activity were interrogated using an array of synthetic peptides and their glycoforms. We show that IMPa has no specific P1 residue preference and can tolerate most amino acids at the P1 position, except aspartic acid. The enzyme does not cleave between two adjacent O-glycosites, indicating that O-glycosylated serine/threonine is not allowed at position P1. Glycopeptides with as few as two amino acids on either side of an O-glycosite were cleaved by IMPa. Finally, IMPa efficiently cleaved peptides and proteins carrying sialylated and asialylated O-glycans of varying complexity. We present the use of IMPa in a one-step O-glycoproteomic workflow for glycoprofiling of the purified glycoproteins granulocyte colony-stimulating factor and receptor-type tyrosine-protein phosphatase C without the need for glycopeptide enrichment. In these examples, IMPa enabled both the identification of O-glycosites and the range of complex O-glycan structures at each site.
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Affiliation(s)
- Saulius Vainauskas
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Hélène Guntz
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Elizabeth McLeod
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Colleen McClung
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Cristian Ruse
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Xiaofeng Shi
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, United States
| | - Christopher H Taron
- New England Biolabs, 240 County Road, Ipswich, Massachusetts 01938, United States
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45
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Burt RA, Dejanovic B, Peckham HJ, Lee KA, Li X, Ounadjela JR, Rao A, Malaker SA, Carr SA, Myers SA. Novel Antibodies for the Simple and Efficient Enrichment of Native O-GlcNAc Modified Peptides. Mol Cell Proteomics 2021; 20:100167. [PMID: 34678516 PMCID: PMC8605273 DOI: 10.1016/j.mcpro.2021.100167] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 09/26/2021] [Accepted: 10/18/2021] [Indexed: 01/03/2023] Open
Abstract
Antibodies against posttranslational modifications (PTMs) such as lysine acetylation, ubiquitin remnants, or phosphotyrosine have resulted in significant advances in our understanding of the fundamental roles of these PTMs in biology. However, the roles of a number of PTMs remain largely unexplored due to the lack of robust enrichment reagents. The addition of N-acetylglucosamine to serine and threonine residues (O-GlcNAc) by the O-GlcNAc transferase (OGT) is a PTM implicated in numerous biological processes and disease states but with limited techniques for its study. Here, we evaluate a new mixture of anti-O-GlcNAc monoclonal antibodies for the immunoprecipitation of native O-GlcNAcylated peptides from cells and tissues. The anti-O-GlcNAc antibodies display good sensitivity and high specificity toward O-GlcNAc-modified peptides and do not recognize O-GalNAc or GlcNAc in extended glycans. Applying this antibody-based enrichment strategy to synaptosomes from mouse brain tissue samples, we identified over 1300 unique O-GlcNAc-modified peptides and over 1000 sites using just a fraction of sample preparation and instrument time required in other landmark investigations of O-GlcNAcylation. Our rapid and robust method greatly simplifies the analysis of O-GlcNAc signaling and will help to elucidate the role of this challenging PTM in health and disease. Anti-O-GlcNAc antibodies are fast and simple enrichment reagents. Anti-O-GlcNAc antibodies are sensitive and achieve significant depth of coverage. Anti-O-GlcNAc antibodies are specific for singular O-GlcNAc modifications. Anti-O-GlcNAc antibody enrichment techniques can be applied to cells and tissues. HCD product-triggered EThcD data acquisition improves depth of coverage.
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Affiliation(s)
- Rajan A Burt
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Borislav Dejanovic
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | | | - Kimberly A Lee
- Cell Signaling Technology, Inc, Danvers, Massachusetts, USA
| | - Xiang Li
- La Jolla Institute for Immunology, La Jolla, California, USA
| | | | - Anjana Rao
- La Jolla Institute for Immunology, La Jolla, California, USA; Department of Pharmacology, University of California San Diego, La Jolla, California, USA; Moores Cancer Center, University of California San Diego, La Jolla, California, USA
| | - Stacy A Malaker
- Department of Chemistry, Yale University, New Haven, Connecticut, USA
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
| | - Samuel A Myers
- The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA; La Jolla Institute for Immunology, La Jolla, California, USA.
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46
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Wardman JF, Rahfeld P, Liu F, Morgan-Lang C, Sim L, Hallam SJ, Withers SG. Discovery and Development of Promiscuous O-Glycan Hydrolases for Removal of Intact Sialyl T-Antigen. ACS Chem Biol 2021; 16:2004-2015. [PMID: 34309358 DOI: 10.1021/acschembio.1c00316] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Mucin-type O-glycosylation (O-glycosylation) is a common post-translational modification that confers distinct biophysical properties to proteins and plays crucial roles in intercellular signaling. Yet, despite the importance of O-glycans, relatively few tools exist for their analysis and modification. In particular, there is a need for enzymes that can cleave the wide range of O-glycan structures found on protein surfaces, to facilitate glycan profiling and editing. Through functional metagenomic screening of the human gut microbiome, we discovered endo-O-glycan hydrolases from CAZy family GH101 that are capable of slowly cleaving the intact sialyl T-antigen trisaccharide (a ubiquitous O-glycan structure in humans) in addition to their primary activity against the T-antigen disaccharide. We then further explored this sequence space through phylogenetic profiling and analysis of representative enzymes, revealing large differences in the levels of this promiscuous activity between enzymes within the family. Through structural and sequence analysis, we identified active site residues that modulate specificity. Through subsequent rational protein engineering, we improved the activity of an enzyme identified by phylogenetic profiling sufficiently that substantial removal of the intact sialyl T-antigen from proteins could be readily achieved. Our best sialyl T-antigen hydrolase mutant, SpGH101 Q868G, is further shown to function on a number of proteins, tissues, and cells. Access to this enzyme opens up improved methodologies for unraveling the glycan code.
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Affiliation(s)
- Jacob F. Wardman
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Peter Rahfeld
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Feng Liu
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Connor Morgan-Lang
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
| | - Lyann Sim
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
| | - Steven J. Hallam
- Graduate Program in Bioinformatics, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Microbiology & Immunology, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
- Genome Science and Technology Program, University of British Columbia, 2329 West Mall, Vancouver, British Columbia V6T 1Z4, Canada
- Life Sciences Institute, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Stephen G. Withers
- Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia V6T 1Z4, Canada
- Department of Chemistry, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada
- Genome Science and Technology Program, University of British Columbia, 2329 West Mall, Vancouver, British Columbia V6T 1Z4, Canada
- ECOSCOPE Training Program, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
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47
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Abstract
Mucin-domain glycoproteins comprise a class of proteins whose densely O-glycosylated mucin domains adopt a secondary structure with unique biophysical and biochemical properties. The canonical family of mucins is well-known to be involved in various diseases, especially cancer. Despite this, very little is known about the site-specific molecular structures and biological activities of mucins, in part because they are extremely challenging to study by mass spectrometry (MS). Here, we summarize recent advancements toward this goal, with a particular focus on mucin-domain glycoproteins as opposed to general O-glycoproteins. We summarize proteolytic digestion techniques, enrichment strategies, MS fragmentation, and intact analysis, as well as new bioinformatic platforms. In particular, we highlight mucin directed technologies such as mucin-selective proteases, tunable mucin platforms, and a mucinomics strategy to enrich mucin-domain glycoproteins from complex samples. Finally, we provide examples of targeted mucin-domain glycoproteomics that combine these techniques in comprehensive site-specific analyses of proteins. Overall, this Review summarizes the methods, challenges, and new opportunities associated with studying enigmatic mucin domains.
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Affiliation(s)
- Valentina Rangel-Angarita
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States
| | - Stacy A. Malaker
- Department of Chemistry, Yale University, 275 Prospect Street, New Haven, Connecticut 06511, United States
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48
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Architecturally complex O-glycopeptidases are customized for mucin recognition and hydrolysis. Proc Natl Acad Sci U S A 2021; 118:2019220118. [PMID: 33658366 DOI: 10.1073/pnas.2019220118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
A challenge faced by peptidases is the recognition of highly diverse substrates. A feature of some peptidase families is the capacity to specifically use post-translationally added glycans present on their protein substrates as a recognition determinant. This is ultimately critical to enabling peptide bond hydrolysis. This class of enzyme is also frequently large and architecturally sophisticated. However, the molecular details underpinning glycan recognition by these O-glycopeptidases, the importance of these interactions, and the functional roles of their ancillary domains remain unclear. Here, using the Clostridium perfringens ZmpA, ZmpB, and ZmpC M60 peptidases as model proteins, we provide structural and functional insight into how these intricate proteins recognize glycans as part of catalytic and noncatalytic substrate recognition. Structural, kinetic, and mutagenic analyses support the key role of glycan recognition within the M60 domain catalytic site, though they point to ZmpA as an apparently inactive enzyme. Wider examination of the Zmp domain content reveals noncatalytic carbohydrate binding as a feature of these proteins. The complete three-dimensional structure of ZmpB provides rare insight into the overall molecular organization of a highly multimodular enzyme and reveals how the interplay of individual domain function may influence biological activity. O-glycopeptidases frequently occur in host-adapted microbes that inhabit or attack mucus layers. Therefore, we anticipate that these results will be fundamental to informing more detailed models of how the glycoproteins that are abundant in mucus are destroyed as part of pathogenic processes or liberated as energy sources during normal commensal lifestyles.
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49
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Nason R, Büll C, Konstantinidi A, Sun L, Ye Z, Halim A, Du W, Sørensen DM, Durbesson F, Furukawa S, Mandel U, Joshi HJ, Dworkin LA, Hansen L, David L, Iverson TM, Bensing BA, Sullam PM, Varki A, Vries ED, de Haan CAM, Vincentelli R, Henrissat B, Vakhrushev SY, Clausen H, Narimatsu Y. Display of the human mucinome with defined O-glycans by gene engineered cells. Nat Commun 2021; 12:4070. [PMID: 34210959 PMCID: PMC8249670 DOI: 10.1038/s41467-021-24366-4] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 06/08/2021] [Indexed: 02/08/2023] Open
Abstract
Mucins are a large family of heavily O-glycosylated proteins that cover all mucosal surfaces and constitute the major macromolecules in most body fluids. Mucins are primarily defined by their variable tandem repeat (TR) domains that are densely decorated with different O-glycan structures in distinct patterns, and these arguably convey much of the informational content of mucins. Here, we develop a cell-based platform for the display and production of human TR O-glycodomains (~200 amino acids) with tunable structures and patterns of O-glycans using membrane-bound and secreted reporters expressed in glycoengineered HEK293 cells. Availability of defined mucin TR O-glycodomains advances experimental studies into the versatile role of mucins at the interface with pathogenic microorganisms and the microbiome, and sparks new strategies for molecular dissection of specific roles of adhesins, glycoside hydrolases, glycopeptidases, viruses and other interactions with mucin TRs as highlighted by examples.
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Affiliation(s)
- Rebecca Nason
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Christian Büll
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andriana Konstantinidi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lingbo Sun
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Zilu Ye
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wenjuan Du
- Section Virology, Division of Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, CL, Utrecht, the Netherlands
| | - Daniel M Sørensen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Fabien Durbesson
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Sanae Furukawa
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulla Mandel
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Hiren J Joshi
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leo Alexander Dworkin
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Lars Hansen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Leonor David
- Institute of Molecular Pathology and Immunology of the University of Porto/I3S, Porto, Portugal.,Medical Faculty of the University of Porto, Porto, Portugal
| | - Tina M Iverson
- Departments of Pharmacology and Biochemistry, Vanderbilt University, Nashville, TN, USA
| | - Barbara A Bensing
- Department of Medicine, The San Francisco Veterans Affairs Medical Center, and the University of California, San Francisco, CA, USA
| | - Paul M Sullam
- Department of Medicine, The San Francisco Veterans Affairs Medical Center, and the University of California, San Francisco, CA, USA
| | - Ajit Varki
- The Glycobiology Research and Training Center, and the Department of Cellular and Molecular Medicine, University of California, San Diego, CA, USA
| | - Erik de Vries
- Section Virology, Division of Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, CL, Utrecht, the Netherlands
| | - Cornelis A M de Haan
- Section Virology, Division of Infectious Diseases and Immunology, Department Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, CL, Utrecht, the Netherlands
| | - Renaud Vincentelli
- Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France
| | - Bernard Henrissat
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.,Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, Marseille, France.,Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark.
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Departments of Cellular and Molecular Medicine and Odontology, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark. .,GlycoDisplay ApS, Copenhagen, Denmark.
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50
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Classification, structural biology, and applications of mucin domain-targeting proteases. Biochem J 2021; 478:1585-1603. [DOI: 10.1042/bcj20200607] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/14/2021] [Accepted: 03/17/2021] [Indexed: 12/11/2022]
Abstract
Epithelial surfaces throughout the body are coated by mucins, a class of proteins carrying domains characterized by a high density of O-glycosylated serine and threonine residues. The resulting mucosal layers form crucial host-microbe interfaces that prevent the translocation of microbes while also selecting for distinct bacteria via the presented glycan repertoire. The intricate interplay between mucus production and breakdown thus determines the composition of the microbiota maintained within these mucosal environments, which can have a large influence on the host during both homeostasis and disease. Most research to date on mucus breakdown has focused on glycosidases that trim glycan structures to release monosaccharides as a source of nutrients. More recent work has uncovered the existence of mucin-type O-glycosylation-dependent proteases that are secreted by pathogens, commensals, and mutualists to facilitate mucosal colonization and penetration. Additionally, immunoglobulin A (IgA) proteases promote bacterial colonization in the presence of neutralizing secretory IgA through selective cleavage of the heavily O-glycosylated hinge region. In this review, we summarize families of O-glycoproteases and IgA proteases, discuss known structural features, and review applications of these enzymes to glycobiology.
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