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Schaus SR, Vasconcelos Pereira G, Luis AS, Madlambayan E, Terrapon N, Ostrowski MP, Jin C, Henrissat B, Hansson GC, Martens EC. Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron. mBio 2024:e0003924. [PMID: 38975756 DOI: 10.1128/mbio.00039-24] [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: 01/10/2024] [Accepted: 05/23/2024] [Indexed: 07/09/2024] Open
Abstract
Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques-a known mucin degrader that has been implicated in inflammatory bowel diseases (IBDs)-degrades mucin glycoproteins or their component O-linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. We found that R. torques utilizes both mucin glycoproteins and released oligosaccharides from gastric and colonic mucins, degrading these substrates with a panoply of mostly constitutively expressed, secreted enzymes. Investigation of mucin oligosaccharide degradation by R. torques revealed strong α-L-fucosidase, sialidase and β1,4-galactosidase activities. There was a lack of detectable sulfatase and weak β1,3-galactosidase degradation, resulting in accumulation of glycans containing these structures on mucin polypeptides. While the Gram-negative symbiont, Bacteroides thetaiotaomicron grows poorly on mucin glycoproteins, we demonstrate a clear ability of R. torques to liberate products from mucins, making them accessible to B. thetaiotaomicron. This work underscores the diversity of mucin-degrading mechanisms in different bacterial species and the probability that some species are contingent on others for the ability to more fully access mucin-derived nutrients. The ability of R. torques to directly degrade a variety of mucin and mucin glycan structures and unlock released glycans for other species suggests that it is a keystone mucin degrader, which might contribute to its association with IBD.IMPORTANCEAn important facet of maintaining healthy symbiosis between host and intestinal microbes is the mucus layer, the first defense protecting the epithelium from lumenal bacteria. Some gut bacteria degrade the various components of intestinal mucins, but detailed mechanisms used by different species are still emerging. It is imperative to understand these mechanisms as they likely dictate interspecies interactions and may illuminate species associated with bacterial mucus damage and subsequent disease susceptibility. Ruminococcus torques is positively associated with IBD in multiple studies. We identified mucin glycan-degrading enzymes in R. torques and found that it shares mucin degradation products with another species of gut bacteria, Bacteroides thetaiotaomicron. Our findings underscore the importance of understanding mucin degradation mechanisms in different gut bacteria and their consequences on interspecies interactions, which may identify keystone bacteria that disproportionately affect mucus damage and could therefore be key players in effects that result from reductions in mucus integrity.
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Affiliation(s)
- Sadie R Schaus
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | | | - Ana S Luis
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Emily Madlambayan
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Nicolas Terrapon
- Centre National de la Recherche Scientifique, Aix-Marseille University, Marseille, France
- Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Marseille, France
| | - Matthew P Ostrowski
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
| | - Chunsheng Jin
- Proteomics Core Facility at Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Bernard Henrissat
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Gunnar C Hansson
- Department of Medical Biochemistry and Cell Biology, University of Gothenburg, Gothenburg, Sweden
| | - Eric C Martens
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA
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2
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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: 12] [Impact Index Per Article: 12.0] [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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3
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Li S, Chen M, Wang Z, Abudourexiti W, Zhang L, Ding C, Ding L, Gong J. Ant may well destroy a whole dam: glycans of colonic mucus barrier disintegrated by gut bacteria. Microbiol Res 2024; 281:127599. [PMID: 38219635 DOI: 10.1016/j.micres.2023.127599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/16/2024]
Abstract
The colonic mucus layer plays a critical role in maintaining the integrity of the colonic mucosal barrier, serving as the primary defense against colonic microorganisms. Predominantly composed of mucin 2 (MUC2), a glycosylation-rich protein, the mucus layer forms a gel-like coating that covers the colonic epithelium surface. This layer provides a habitat for intestinal microorganisms, which can utilize mucin glycans present in the mucus layer as a sustainable source of nutrients. Additionally, metabolites produced by the microbiota during the metabolism of mucus glycans have a profound impact on host health. Under normal conditions, the production and consumption of mucus maintain a dynamic balance. However, several studies have demonstrated that certain factors, such as dietary fiber deficiency, can enhance the metabolism of mucus glycans by gut bacteria, thereby disturbing this balance and weakening the mucus barrier function of the mucus layer. To better understand the occurrence and development of colon-related diseases, it is crucial to investigate the complex metabolic patterns of mucus glycosylation by intestinal microorganisms. Our objective was to comprehensively review these patterns in order to clarify the effects of mucus layer glycan metabolism by intestinal microorganisms on the host.
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Affiliation(s)
- Song Li
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Mingfei Chen
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Zhongyuan Wang
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Waresi Abudourexiti
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China
| | - Liang Zhang
- Department of Gastrointestinal Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical College, Jiangsu, China
| | - Chao Ding
- Department of General Surgery, Affiliated Drum Tower Hospital, Medical School, Nanjing University, Nanjing, China.
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China; Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.
| | - Jianfeng Gong
- Department of General Surgery, Affiliated Jinling Hospital, Medical School, Nanjing University, Nanjing, China.
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Park DD, Xu G, Park SS, Haigh NE, Phoomak C, Wongkham S, Maverakis E, Lebrilla CB. Combined analysis of secreted proteins and glycosylation identifies prognostic features in cholangiocarcinoma. J Cell Physiol 2024; 239:e31147. [PMID: 37921263 PMCID: PMC10939962 DOI: 10.1002/jcp.31147] [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: 05/07/2023] [Revised: 09/05/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
Secreted proteins are overexpressed in cholangiocarcinoma (CCA) and actively involved in promoting metastatic spread. Many of these proteins possess one or more sites of glycosylation and their various glycoforms have potential utility as prognostic or diagnostic biomarkers. To evaluate the effects of secretome glycosylation on patient outcome, we elucidated the glycosylation patterns of proteins secreted by parental and metastatic CCA cells using liquid chromatography-mass spectrometry. Our analysis showed that the secretome of CCA cells was dominated by fucosylated and fucosialylated glycoforms. Based on the glycan and protein profiles, we evaluated the combined prognostic significance of glycosyltransferases and secretory proteins. Significantly, genes encoding fucosyltransferases and sialyltransferases showed favorable prognostic effects when combined with secretory protein-coding gene expression, particularly thrombospondin-1. Combining these measures may provide improved risk assessment for CCA and be used to indicate stages of disease progression.
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Affiliation(s)
| | - Gege Xu
- Department of Chemistry, University of California, Davis, CA, 95616 USA
| | - Simon S. Park
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215 USA
| | - Nathan E. Haigh
- Department of Dermatology, University of California, Davis School of Medicine, Sacramento, CA, 95817 USA
| | - Chatchai Phoomak
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Thailand
| | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Thailand
| | - Emanual Maverakis
- Department of Dermatology, University of California, Davis School of Medicine, Sacramento, CA, 95817 USA
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5
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Schaus SR, Vasconcelos Periera G, Luis AS, Madlambayan E, Terrapon N, Ostrowski MP, Jin C, Hansson GC, Martens EC. Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.15.575725. [PMID: 38293123 PMCID: PMC10827045 DOI: 10.1101/2024.01.15.575725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques- a known mucin-degrader that remains poorly studied despite its implication in inflammatory bowel diseases (IBDs)- degrades mucin glycoproteins or their component O -linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. We found that R. torques utilizes both mucin glycoproteins and released oligosaccharides from gastric and colonic mucins, degrading these substrates with a panoply of mostly constitutively expressed, secreted enzymes. Investigation of mucin oligosaccharide degradation by R. torques revealed strong fucosidase, sialidase and β1,4-galactosidase activities. There was a lack of detectable sulfatase and weak β1,3-galactosidase degradation, resulting in accumulation of glycans containing these structures on mucin polypeptides. While the Gram-negative symbiont, Bacteroides thetaiotaomicron grows poorly on mucin glycoproteins, we demonstrate a clear ability of R. torques to liberate products from mucins, making them accessible to B. thetaiotaomicron . This work underscores the diversity of mucin-degrading mechanisms in different bacterial species and the probability that some species are contingent on others for the ability to more fully access mucin-derived nutrients. The ability of R. torques to directly degrade a variety of mucin and mucin glycan structures and unlock released glycans for other species suggests that it is a keystone mucin degrader, which may contribute to its association with IBD. Importance An important facet of maintaining healthy symbiosis between host and intestinal microbes is the mucus layer, the first defense protecting the epithelium from lumenal bacteria. Some gut bacteria degrade different components of intestinal mucins, but detailed mechanisms used by different species are still emerging. It is imperative to understand these mechanisms as they likely dictate interspecies interactions and may illuminate particular species associated with bacterial mucus destruction and subsequent disease susceptibility. Ruminococcus torques is positively associated with IBD in multiple studies. We identified mucin glycan-degrading enzymes in R. torques and found that it shares mucin degradation products with another gut bacterium implicated in IBD, Bacteroides thetaiotaomicron . Our findings underscore the importance of understanding the mucin degradation mechanisms of different gut bacteria and their consequences on interspecies interactions, which may identify keystone bacteria that disproportionately contribute to defects in mucus protection and could therefore be targets to prevent or treat IBD.
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6
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Takada H, Katayama T, Katoh T. Cultivation of Microorganisms in Media Supplemented with Mucin Glycoproteins. Methods Mol Biol 2024; 2763:331-335. [PMID: 38347422 DOI: 10.1007/978-1-0716-3670-1_27] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2024]
Abstract
To examine the mucin-utilizing capacity of bacterial isolates from fecal samples, an in vitro cultivation method using mucins as a carbon source should be considered. This chapter describes a practical method for cultivating bacteria in media containing mucin glycoproteins; for this cultivation method, several factors are considered due to the physical nature of mucin glycoproteins.
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Affiliation(s)
- Hiromi Takada
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Takane Katayama
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Toshihiko Katoh
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan.
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7
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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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8
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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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9
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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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10
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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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11
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Yue S, Wang X, Ge W, Li J, Yang C, Zhou Z, Zhang P, Yang X, Xiao W, Yang S. Deciphering Protein O-GalNAcylation: Method Development and Disease Implication. ACS OMEGA 2023; 8:19223-19236. [PMID: 37305274 PMCID: PMC10249083 DOI: 10.1021/acsomega.3c01653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 04/20/2023] [Indexed: 06/13/2023]
Abstract
Mucin-type O-glycosylation is an important protein post-translational modification that is abundantly expressed on cell surface proteins. Protein O-glycosylation plays a variety of roles in cellular biological functions including protein structure and signal transduction to the immune response. Cell surface mucins are highly O-glycosylated and are the main substance of the mucosal barrier that protects the gastrointestinal or respiratory tract from infection by pathogens or microorganisms. Dysregulation of mucin O-glycosylation may impair mucosal protection against pathogens that can invade cells to trigger infection or immune evasion. Truncated O-glycosylation, also known as Tn antigen or O-GalNAcylation, is highly upregulated in diseases such cancer, autoimmune disorders, neurodegenerative diseases, and IgA nephropathy. Characterization of O-GalNAcylation helps decipher the role of Tn antigen in physiopathology and therapy. However, the analysis of O-glycosylation, specifically the Tn antigen, remains challenging due to the lack of reliable enrichment and identification assays compared to N-glycosylation. Here, we summarize recent advances in analytical methods for O-GalNAcylation enrichment and identification and highlight the biological role of the Tn antigen in various diseases and the clinical implications of identifying aberrant O-GalNAcylation.
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Affiliation(s)
- Shuang Yue
- Center
for Clinical Mass Spectrometry, Department of Pharmaceutical Analysis,
College of Pharmaceutical Sciences, Soochow
University, Suzhou, Jiangsu 215123, China
- Department
of Endocrinology, The Second Affiliated
Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Xiaotong Wang
- Department
of Hepatology and Gastroenterology, The
Affiliated Infectious Hospital of Soochow University, Suzhou, Jiangsu 215004, China
- Department
of Endocrinology, The Second Affiliated
Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Wei Ge
- Center
for Clinical Mass Spectrometry, Department of Pharmaceutical Analysis,
College of Pharmaceutical Sciences, Soochow
University, Suzhou, Jiangsu 215123, China
| | - Jiajia Li
- Center
for Clinical Mass Spectrometry, Department of Pharmaceutical Analysis,
College of Pharmaceutical Sciences, Soochow
University, Suzhou, Jiangsu 215123, China
| | - Chuanlai Yang
- Scientific
Research Department, The Second Affiliated
Hospital of Soochow University, Suzhou, Jiangsu 215006, China
| | - Zeyang Zhou
- Department
of General Surgery, The Second Affiliated
Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Peng Zhang
- Department
of Orthopedics, The Second Affiliated Hospital
of Soochow University, Suzhou, Jiangsu 215004, China
| | - Xiaodong Yang
- Department
of General Surgery, The Second Affiliated
Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Wenjin Xiao
- Department
of Endocrinology, The Second Affiliated
Hospital of Soochow University, Suzhou, Jiangsu 215004, China
| | - Shuang Yang
- Center
for Clinical Mass Spectrometry, Department of Pharmaceutical Analysis,
College of Pharmaceutical Sciences, Soochow
University, Suzhou, Jiangsu 215123, China
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12
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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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13
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Sanz-Martinez I, Pereira S, Merino P, Corzana F, Hurtado-Guerrero R. Molecular Recognition of GalNAc in Mucin-Type O-Glycosylation. Acc Chem Res 2023; 56:548-560. [PMID: 36815693 PMCID: PMC9996832 DOI: 10.1021/acs.accounts.2c00723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
ConspectusN-Acetylgalactosamine (GalNAc)-type O-glycosylation is an essential posttranslational modification (PTM) that plays fundamental roles in biology. Malfunction of this PTM is exemplified by the presence of truncated O-glycans in cancer. For instance, the glycoprotein MUC1 is overexpressed in many tumor tissues and tends to carry simple oligosaccharides that allow for the presentation of different tumor-associated antigens, such as the Tn or sTn antigens (GalNAc-α-1-O-Thr/Ser and Neu5Acα2-6GalNAcα1-O-Ser/Thr, respectively). In other cases, such as tumoral calcinosis associated with O-glycosylation of the fibroblast growth factor 23, O-glycans are absent or less abundant. Significant progress has been made in determining the three-dimensional structures of biomolecules that recognize GalNAc, such as antibodies, lectins, mucinases, GalNAc-transferases, and other glycosyltransferases. Analysis of the complexes between these entities and GalNAc-containing glycopeptides, in most cases derived from crystallographic or NMR analysis, provides an understanding of the key structural elements that control molecular recognition of these glycopeptides. Here, we describe and compare the binding sites of these proteins in detail, focusing on how the GalNAc moieties interact selectively with them. We also summarize the differences and similarities in GalNAc recognition. In general, the recognition of GalNAc-containing glycopeptides is determined by hydrogen bonds between hydroxyl groups and the N-acetyl group of GalNAc with proteins, as well as CH-π contacts in which the hydrophobic α-face of the sugar and the methyl group of NHAc can be involved. The latter interaction usually provides the basis for selectivity. It is worth noting that binding of these glycopeptides depends primarily on recognition of the sugar moiety, with some exceptions such as a few anti-MUC1 antibodies that primarily recognize the peptide backbone and use the sugar to facilitate shape complementarity or to establish a limited number of interactions with the protein. Focusing specifically on the GalNAc moiety, we can observe that there is some degeneracy of interactions within the same protein families, likely due to substrate flexibility. However, when all studied proteins are considered together, despite the commonalities within each protein family, no pattern can be discerned between the different families, apart from the presence of common residues such as Tyr, His, or Asp, which are responsible for hydrogen bonds. The lack of a pattern can be anticipated, given the diverse functions of mucinases, glycosyltransferases, antibodies, and lectins. Finally, it is important to point out that the conformational differences observed in solution in glycopeptides bearing GalNAc-α-1-O-Ser or GalNAc-α-1-O-Thr also can be found in the bound state. This unique characteristic is exploited, for instance, by the enzyme C1GalT1 to broadly glycosylate both acceptor substrates. The findings summarized in this review may contribute to the rational structure-guided development of therapeutic vaccines, novel diagnostic tools for early cancer detection, and new cancer treatments for cancer with tailored anti-Tn or anti-STn antibodies or new drugs to inhibit GalNAc-T isoenzymes.
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Affiliation(s)
- Ignacio Sanz-Martinez
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Glycobiology Unit, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain.,Department of Organic Chemistry, Faculty of Sciences, University of Zaragoza, Campus San Francisco, 50009 Zaragoza, Spain
| | - Sandra Pereira
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Glycobiology Unit, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain.,Department of Organic Chemistry, Faculty of Sciences, University of Zaragoza, Campus San Francisco, 50009 Zaragoza, Spain
| | - Pedro Merino
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Glycobiology Unit, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain.,Department of Organic Chemistry, Faculty of Sciences, University of Zaragoza, Campus San Francisco, 50009 Zaragoza, Spain
| | - Francisco Corzana
- Department of Chemistry, Centro de Investigación en Síntesis Química, University of La Rioja, Madre de Dios 53, 26006 Logroño, Spain
| | - Ramon Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), Glycobiology Unit, University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain.,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark.,Fundación ARAID, 50018 Zaragoza, Spain
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14
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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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15
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Abstract
Proteases are an evolutionarily conserved family of enzymes that degrade peptide bonds and have been implicated in several common gastrointestinal (GI) diseases. Although luminal proteolytic activity is important for maintenance of homeostasis and health, the current review describes recent advances in our understanding of how overactivity of luminal proteases contributes to the pathophysiology of celiac disease, irritable bowel syndrome, inflammatory bowel disease and GI infections. Luminal proteases, many of which are produced by the microbiota, can modulate the immunogenicity of dietary antigens, reduce mucosal barrier function and activate pro-inflammatory and pro-nociceptive host signaling. Increased proteolytic activity has been ascribed to both increases in protease production and decreases in inhibitors of luminal proteases. With the identification of strains of bacteria that are important sources of proteases and their inhibitors, the stage is set to develop drug or microbial therapies to restore protease balance and alleviate disease.
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Affiliation(s)
- Alberto Caminero
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Mabel Guzman
- Gastrointestinal Diseases Research Unit, Kingston General Hospital, Queen’s University, Kingston, Ontario, Canada
| | - Josie Libertucci
- Department of Medicine, Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada
| | - Alan E. Lomax
- Gastrointestinal Diseases Research Unit, Kingston General Hospital, Queen’s University, Kingston, Ontario, Canada,CONTACT Alan E. Lomax Gastrointestinal Diseases Research Unit, Kingston General Hospital, Kingston, ON, K7L 2V7, Canada
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16
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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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17
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Abstract
Mucins are functionally implicated in a range of human pathologies, including cystic fibrosis, influenza, bacterial endocarditis, gut dysbiosis, and cancer. These observations have motivated the study of mucin biosynthesis as well as the development of strategies for inhibition of mucin glycosylation. Mammalian pathways for mucin catabolism, however, have remained underexplored. The canonical view, derived from analysis of N-glycoproteins in human lysosomal storage disorders, is that glycan degradation and proteolysis occur sequentially. Here, we challenge this view by providing genetic and biochemical evidence supporting mammalian proteolysis of heavily O-glycosylated mucin domains without prior deglycosylation. Using activity screening coupled with mass spectrometry, we ascribed mucin-degrading activity in murine liver to the lysosomal protease cathepsin D. Glycoproteomics of substrates digested with purified human liver lysosomal cathepsin D provided direct evidence for proteolysis within densely O-glycosylated domains. Finally, knockout of cathepsin D in a murine model of the human lysosomal storage disorder neuronal ceroid lipofuscinosis 10 resulted in accumulation of mucins in liver-resident macrophages. Our findings imply that mucin-degrading activity is a component of endogenous pathways for glycoprotein catabolism in mammalian tissues.
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18
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Wendo WD, Tangkawattana S, Saichua P, Ta BTT, Candra ARK, Tangkawattana P, Suttiprapa S. Immunolocalization and functional analysis of Opisthorchis viverrini-M60-like-1 metallopeptidase in animal models. Parasitology 2022; 149:1356-1363. [PMID: 35445647 PMCID: PMC11010479 DOI: 10.1017/s0031182022000403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/22/2022] [Accepted: 03/22/2022] [Indexed: 11/06/2022]
Abstract
Host mucins have crucial physical roles in preventing the parasitic establishment and maturation, and also in expelling the invading parasites. However, some parasites utilize mucinase enzymes to facilitate the infection. Recently, we have identified a mucinase enzyme of the liver fluke Opisthorchis viverrini, Ov-M60-like-1, which exhibits metallopeptidase activity against bovine submaxillary mucin substrate. Here, we aimed to study the localization of this enzyme in O. viverrini and the bile duct of hamsters using immunohistochemistry and functional analysis by mucin digestion in hamsters and mice tissues. The results showed that Ov-M60-like-1 was detected strongly in the tegument, tegumental cells, vitelline glands and mature eggs with miracidium. Expression in the gut, ovary and testis of the parasite was moderate while parenchyma showed slight colour intensity. In addition, the mucinase was also detected in the host biliary epithelial cells and goblet cells surrounding the worm. The mucinase assay revealed that the Ov-M60-like-1 could digest neutral mucin in the parenchyma, testis and seminal receptacle, but not the mucin in the tegument, tegumental cells and vitelline glands of the worm. The enzyme can also digest mucin in the cholangiocytes and modified the mixture type in the bile duct goblet cells of the infected hamsters, a susceptible host. In contrast, the enzyme was unable to digest neutral, acid and mixture mucin in the bile duct of the mice, a non-susceptible host. These findings indicate that Ov-M60-like-1 may have functions in both housekeeping tasks and host–parasite interactions, especially in modification of host susceptibility.
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Affiliation(s)
- Woro D. Wendo
- Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Graduate School, Khon Kaen University, Khon Kaen 40002, Thailand
- Department of Anatomy, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Sirikachorn Tangkawattana
- Faculty of Veterinary Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
- Tropical Disease Research Center, WHO Collaborating Centre for Research and Control of Opisthorchiasis, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Prasert Saichua
- Tropical Disease Research Center, WHO Collaborating Centre for Research and Control of Opisthorchiasis, Khon Kaen University, Khon Kaen 40002, Thailand
- Tropical Medicine Graduate Program, Academic Affairs, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Binh T. T. Ta
- Tropical Medicine Graduate Program, Academic Affairs, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Agatha R. K. Candra
- Department of Biomedicine, School of Life Sciences, Indonesia International Institute for Life Sciences, Jakarta, Indonesia
| | | | - Sutas Suttiprapa
- Tropical Disease Research Center, WHO Collaborating Centre for Research and Control of Opisthorchiasis, Khon Kaen University, Khon Kaen 40002, Thailand
- Tropical Medicine Graduate Program, Academic Affairs, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
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19
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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: 4] [Impact Index Per Article: 2.0] [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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20
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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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21
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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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22
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Structure-Functional Characteristics of the Svx Protein—The Virulence Factor of the Phytopathogenic Bacterium Pectobacterium atrosepticum. Int J Mol Sci 2022; 23:ijms23136914. [PMID: 35805920 PMCID: PMC9266454 DOI: 10.3390/ijms23136914] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/17/2022] [Accepted: 06/20/2022] [Indexed: 11/17/2022] Open
Abstract
The Svx proteins are virulence factors of phytopathogenic bacteria of the Pectobacterium genus. The specific functions of these proteins are unknown. Here we show that most of the phytopathogenic species of Pectobacterium, Dickeya, and Xanthomonas genera have genes encoding Svx proteins, as well as some plant-non-associated species of different bacterial genera. As such, the Svx-like proteins of phytopathogenic species form a distinct clade, pointing to the directed evolution of these proteins to provide effective interactions with plants. To get a better insight into the structure and functions of the Svx proteins, we analyzed the Svx of Pectobacterium atrosepticum (Pba)—an extracellular virulence factor secreted into the host plant cell wall (PCW). Using in silico analyses and by obtaining and analyzing the recombinant Pba Svx and its mutant forms, we showed that this protein was a gluzincin metallopeptidase. The 3D structure model of the Pba Svx was built and benchmarked against the experimental overall secondary structure content. Structure-based substrate specificity analysis using molecular docking revealed that the Pba Svx substrate-binding pocket might accept α-glycosylated proteins represented in the PCW by extensins—proteins that strengthen the PCW. Thus, these results elucidate the way in which the Pba Svx may contribute to the Pba virulence.
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23
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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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24
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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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25
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Coelho H, Rivas MDL, Grosso AS, Diniz A, Soares CO, Francisco RA, Dias JS, Compañon I, Sun L, Narimatsu Y, Vakhrushev SY, Clausen H, Cabrita EJ, Jiménez-Barbero J, Corzana F, Hurtado-Guerrero R, Marcelo F. Atomic and Specificity Details of Mucin 1 O-Glycosylation Process by Multiple Polypeptide GalNAc-Transferase Isoforms Unveiled by NMR and Molecular Modeling. JACS AU 2022; 2:631-645. [PMID: 35373202 PMCID: PMC8969996 DOI: 10.1021/jacsau.1c00529] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Indexed: 05/10/2023]
Abstract
The large family of polypeptide GalNAc-transferases (GalNAc-Ts) controls with precision how GalNAc O-glycans are added in the tandem repeat regions of mucins (e.g., MUC1). However, the structural features behind the creation of well-defined and clustered patterns of O-glycans in mucins are poorly understood. In this context, herein, we disclose the full process of MUC1 O-glycosylation by GalNAc-T2/T3/T4 isoforms by NMR spectroscopy assisted by molecular modeling protocols. By using MUC1, with four tandem repeat domains as a substrate, we confirmed the glycosylation preferences of different GalNAc-Ts isoforms and highlighted the importance of the lectin domain in the glycosylation site selection after the addition of the first GalNAc residue. In a glycosylated substrate, with yet multiple acceptor sites, the lectin domain contributes to orientate acceptor sites to the catalytic domain. Our experiments suggest that during this process, neighboring tandem repeats are critical for further glycosylation of acceptor sites by GalNAc-T2/T4 in a lectin-assisted manner. Our studies also show local conformational changes in the peptide backbone during incorporation of GalNAc residues, which might explain GalNAc-T2/T3/T4 fine specificities toward the MUC1 substrate. Interestingly, we postulate that a specific salt-bridge and the inverse γ-turn conformation of the PDTRP sequence in MUC1 are the main structural motifs behind the GalNAc-T4 specificity toward this region. In addition, in-cell analysis shows that the GalNAc-T4 isoform is the only isoform glycosylating the Thr of the immunogenic epitope PDTRP in vivo, which highlights the relevance of GalNAc-T4 in the glycosylation of this epitope. Finally, the NMR methodology established herein can be extended to other glycosyltransferases, such as C1GalT1 and ST6GalNAc-I, to determine the specificity toward complex mucin acceptor substrates.
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Affiliation(s)
- Helena Coelho
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
- CIC
bioGUNE, Basque Research and Technology
Alliance (BRTA), Bizkaia
Technology Park, Building 801A, 48170 Derio, Spain
- Department
of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, Leioa 48940, Bizkaia, Spain
| | - Matilde de las Rivas
- Institute
for Biocomputation and Physics of Complex Systems (BIFI), Laboratorio
de Microscopias Avanzadas (LMA), University
of Zaragoza, Mariano
Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain
| | - Ana S. Grosso
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ana Diniz
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Cátia O. Soares
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Rodrigo A. Francisco
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Jorge S. Dias
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Ismael Compañon
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, E-26006 Logroño, Spain
| | - Lingbo Sun
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Yoshiki Narimatsu
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Sergey Y. Vakhrushev
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Henrik Clausen
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Eurico J. Cabrita
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
| | - Jesús Jiménez-Barbero
- CIC
bioGUNE, Basque Research and Technology
Alliance (BRTA), Bizkaia
Technology Park, Building 801A, 48170 Derio, Spain
- Department
of Organic Chemistry II, Faculty of Science & Technology, University of the Basque Country, Leioa 48940, Bizkaia, Spain
- Ikerbasque,
Basque Foundation for Science, Maria Diaz de Haro 13, 48009 Bilbao, Spain
- Centro de Investigacion
Biomedica En Red de Enfermedades Respiratorias, 28029 Madrid, Spain
| | - Francisco Corzana
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, E-26006 Logroño, Spain
| | - Ramon Hurtado-Guerrero
- Institute
for Biocomputation and Physics of Complex Systems (BIFI), Laboratorio
de Microscopias Avanzadas (LMA), University
of Zaragoza, Mariano
Esquillor s/n, Campus Rio Ebro, Edificio I+D, 50018 Zaragoza, Spain
- Copenhagen
Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
- Fundación
ARAID, 50018 Zaragoza, Spain
| | - Filipa Marcelo
- Associate
Laboratory i4HB—Institute for Health and Bioeconomy, NOVA School
of Science and Technology, Universidade
NOVA de Lisboa, 2829-516 Caparica, Portugal
- UCIBIO,
Department of Chemistry, Faculdade de Ciências e Tecnologia, Universidade NOVA de Lisboa, 2829-516 Caparica, Portugal
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26
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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] [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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27
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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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28
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Corsini PM, Wang S, Rehman S, Fenn K, Sagar A, Sirovica S, Cleaver L, Edwards-Gayle CJC, Mastroianni G, Dorgan B, Sewell LM, Lynham S, Iuga D, Franks WT, Jarvis J, Carpenter GH, Curtis MA, Bernadó P, Darbari VC, Garnett JA. Molecular and cellular insight into Escherichia coli SslE and its role during biofilm maturation. NPJ Biofilms Microbiomes 2022; 8:9. [PMID: 35217675 PMCID: PMC8881592 DOI: 10.1038/s41522-022-00272-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 01/31/2022] [Indexed: 11/10/2022] Open
Abstract
Escherichia coli is a Gram-negative bacterium that colonises the human intestine and virulent strains can cause severe diarrhoeal and extraintestinal diseases. The protein SslE is secreted by a range of pathogenic and commensal E. coli strains. It can degrade mucins in the intestine, promotes biofilm maturation and it is a major determinant of infection in virulent strains, although how it carries out these functions is not well understood. Here, we examine SslE from the commensal E. coli Waksman and BL21 (DE3) strains and the enterotoxigenic H10407 and enteropathogenic E2348/69 strains. We reveal that SslE has a unique and dynamic structure in solution and in response to acidification within mature biofilms it can form a unique aggregate with amyloid-like properties. Furthermore, we show that both SslE monomers and aggregates bind DNA in vitro and co-localise with extracellular DNA (eDNA) in mature biofilms, and SslE aggregates may also associate with cellulose under certain conditions. Our results suggest that interactions between SslE and eDNA are important for biofilm maturation in many E. coli strains and SslE may also be a factor that drives biofilm formation in other SslE-secreting bacteria.
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Affiliation(s)
- Paula M Corsini
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Sunjun Wang
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Saima Rehman
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Katherine Fenn
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Amin Sagar
- Centre de Biologie Structurale, Université de Montpellier, INSERM, CNRS, Montpellier, France
| | - Slobodan Sirovica
- Centre for Oral Bioengineering, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Leanne Cleaver
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | | | - Giulia Mastroianni
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ben Dorgan
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Lee M Sewell
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Steven Lynham
- Proteomics Facility, Centre of Excellence for Mass Spectrometry, King's College London, London, UK
| | - Dinu Iuga
- Department of Physics, University of Warwick, Coventry, UK
| | - W Trent Franks
- Department of Physics, University of Warwick, Coventry, UK
| | - James Jarvis
- Randall Division of Cell and Molecular Biophysics and Centre for Biomolecular Spectroscopy, King's College London, London, UK
| | - Guy H Carpenter
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Michael A Curtis
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK
| | - Pau Bernadó
- Centre de Biologie Structurale, Université de Montpellier, INSERM, CNRS, Montpellier, France
| | - Vidya C Darbari
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
| | - James A Garnett
- Centre for Host-Microbiome Interactions, Faculty of Dental, Oral & Craniofacial Sciences, King's College London, London, UK.
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK.
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29
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Prediction of Potential Drug Targets and Vaccine Candidates Against Antibiotic-Resistant Pseudomonas aeruginosa. Int J Pept Res Ther 2022; 28:160. [PMCID: PMC9640888 DOI: 10.1007/s10989-022-10463-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/20/2022] [Indexed: 11/09/2022]
Abstract
Pseudomonas aeruginosa is one of the leading causes of nosocomial infections, characterized by increasing antibiotic resistance, severity and mortality. Therefore, numerous efforts have been made nowadays to identify new therapeutic targets. This study aimed to find potential drug targets and vaccine candidates in drug-resistant strains of P. aeruginosa. Extensive antibiotic-resistant and carbapenem-resistant strains of P. aeruginosa with complete genome were selected and ten common hypothetical proteins (HPs) containing more than 200 amino acids were obtained. The structural, functional and immunological predictions of these HPs were performed with the utility of bioinformatics approaches. Two common HPs (Gene ID: 2877781645 and 2877781936) among other investigated proteins were revealed as potential candidates for pharmaceutical and vaccine purposes based on structural and physicochemical properties, functional domains, subcellular localizations, signal peptides, toxicity, virulence factor, antigenicity, allergenicity and immunoinformatic predictions. The consequence of this predictive study will assist in novel drug and vaccine design through experimental investigations.
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30
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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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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: 2] [Impact Index Per Article: 0.7] [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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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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Fang J, Wang H, Zhou Y, Zhang H, Zhou H, Zhang X. Slimy partners: the mucus barrier and gut microbiome in ulcerative colitis. Exp Mol Med 2021; 53:772-787. [PMID: 34002011 PMCID: PMC8178360 DOI: 10.1038/s12276-021-00617-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 01/14/2021] [Accepted: 01/31/2021] [Indexed: 02/08/2023] Open
Abstract
Ulcerative colitis (UC) is a chronic recurrent intestinal inflammatory disease characterized by high incidence and young onset age. Recently, there have been some interesting findings in the pathogenesis of UC. The mucus barrier, which is composed of a mucin complex rich in O-glycosylation, not only provides nutrients and habitat for intestinal microbes but also orchestrates the taming of germs. In turn, the gut microbiota modulates the production and secretion of mucins and stratification of the mucus layers. Active bidirectional communication between the microbiota and its 'slimy' partner, the mucus barrier, seems to be a continually performed concerto, maintaining homeostasis of the gut ecological microenvironment. Any abnormalities may induce a disorder in the gut community, thereby causing inflammatory damage. Our review mainly focuses on the complicated communication between the mucus barrier and gut microbiome to explore a promising new avenue for UC therapy.
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Affiliation(s)
- Jian Fang
- grid.203507.30000 0000 8950 5267Department of Preventive Medicine, Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang People’s Republic of China ,grid.412551.60000 0000 9055 7865College of Medicine, Shaoxing University, 508 Huancheng Road, Shaoxing, Zhejiang Province People’s Republic of China
| | - Hui Wang
- grid.415644.60000 0004 1798 6662Department of Colorectal Surgery, Shaoxing people’s Hospital, 568 North Zhongxing Road, Shaoxing, Zhejiang Province People’s Republic of China
| | - Yuping Zhou
- grid.203507.30000 0000 8950 5267The Affiliated Hospital of Medical School, Ningbo University, 247 Renmin Road, Ningbo, Zhejiang People’s Republic of China
| | - Hui Zhang
- grid.203507.30000 0000 8950 5267Department of Preventive Medicine, Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang People’s Republic of China
| | - Huiting Zhou
- grid.203507.30000 0000 8950 5267Department of Preventive Medicine, Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang People’s Republic of China
| | - Xiaohong Zhang
- grid.203507.30000 0000 8950 5267Department of Preventive Medicine, Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, 818 Fenghua Road, Ningbo, Zhejiang People’s Republic of China
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34
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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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Towards structure-focused glycoproteomics. Biochem Soc Trans 2021; 49:161-186. [PMID: 33439247 PMCID: PMC7925015 DOI: 10.1042/bst20200222] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023]
Abstract
Facilitated by advances in the separation sciences, mass spectrometry and informatics, glycoproteomics, the analysis of intact glycopeptides at scale, has recently matured enabling new insights into the complex glycoproteome. While diverse quantitative glycoproteomics strategies capable of mapping monosaccharide compositions of N- and O-linked glycans to discrete sites of proteins within complex biological mixtures with considerable sensitivity, quantitative accuracy and coverage have become available, developments supporting the advancement of structure-focused glycoproteomics, a recognised frontier in the field, have emerged. Technologies capable of providing site-specific information of the glycan fine structures in a glycoproteome-wide context are indeed necessary to address many pending questions in glycobiology. In this review, we firstly survey the latest glycoproteomics studies published in 2018–2020, their approaches and their findings, and then summarise important technological innovations in structure-focused glycoproteomics. Our review illustrates that while the O-glycoproteome remains comparably under-explored despite the emergence of new O-glycan-selective mucinases and other innovative tools aiding O-glycoproteome profiling, quantitative glycoproteomics is increasingly used to profile the N-glycoproteome to tackle diverse biological questions. Excitingly, new strategies compatible with structure-focused glycoproteomics including novel chemoenzymatic labelling, enrichment, separation, and mass spectrometry-based detection methods are rapidly emerging revealing glycan fine structural details including bisecting GlcNAcylation, core and antenna fucosylation, and sialyl-linkage information with protein site resolution. Glycoproteomics has clearly become a mainstay within the glycosciences that continues to reach a broader community. It transpires that structure-focused glycoproteomics holds a considerable potential to aid our understanding of systems glycobiology and unlock secrets of the glycoproteome in the immediate future.
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Takeuchi K, Tsuchiya W, Fujimoto Z, Yamada K, Someya N, Yamazaki T. Discovery of an Antibiotic-Related Small Protein of Biocontrol Strain Pseudomonas sp. Os17 by a Genome-Mining Strategy. Front Microbiol 2020; 11:605705. [PMID: 33324389 PMCID: PMC7726476 DOI: 10.3389/fmicb.2020.605705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 10/26/2020] [Indexed: 11/13/2022] Open
Abstract
Many root-colonizing Pseudomonas spp. exhibiting biocontrol activities produce a wide range of secondary metabolites that exert antibiotic effects against other microbes, nematodes, and insects in the rhizosphere. The expression of these secondary metabolites depends on the Gac/Rsm signal transduction pathway. Based on the findings of a previous genomic study on newly isolated biocontrol pseudomonad strains, we herein investigated the novel gene cluster OS3, which consists of four genes (Os1348–Os1351) that are located upstream of putative efflux transporter genes (Os1352–Os1355). Os1348 was predicted to encode an 85-aa small precursor protein, the expression of which was under the control of GacA, and an X-ray structural analysis suggested that the Os1348 protein formed a dimer. The mutational loss of the Os1348 gene decreased the antibiotic activity of Pseudomonas sp. Os17 without changing its growth rate. The Os1349–1351 genes were predicted to be involved in post-translational modifications. Intracellular levels of the Os1348 protein in the deficient mutant of each gene differed from that in wild-type cells. These results suggest that Os1348 is involved in antibiotic activity and that the structure or expression of this protein is under the control of downstream gene products.
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Affiliation(s)
- Kasumi Takeuchi
- Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Wataru Tsuchiya
- Structural Biology Team, Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Zui Fujimoto
- Structural Biology Team, Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Kosumi Yamada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Nobutaka Someya
- Division of Vegetable Production System, Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Toshimasa Yamazaki
- Structural Biology Team, Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Japan
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37
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Sjögren J, Lood R, Nägeli A. On enzymatic remodeling of IgG glycosylation; unique tools with broad applications. Glycobiology 2020; 30:254-267. [PMID: 31616919 PMCID: PMC7109354 DOI: 10.1093/glycob/cwz085] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 09/05/2019] [Accepted: 09/30/2019] [Indexed: 01/14/2023] Open
Abstract
The importance of IgG glycosylation has been known for many years not only by scientists in glycobiology but also by human pathogens that have evolved specific enzymes to modify these glycans with fundamental impact on IgG function. The rise of IgG as a major therapeutic scaffold for many cancer and immunological indications combined with the availability of unique enzymes acting specifically on IgG Fc-glycans have spurred a range of applications to study this important post-translational modification on IgG. This review article introduces why the IgG glycans are of distinguished interest, gives a background on the unique enzymatic tools available to study the IgG glycans and finally presents an overview of applications utilizing these enzymes for various modifications of the IgG glycans. The applications covered include site-specific glycan transglycosylation and conjugation, analytical workflows for monoclonal antibodies and serum diagnostics. Additionally, the review looks ahead and discusses the importance of O-glycosylation for IgG3, Fc-fusion proteins and other new formats of biopharmaceuticals.
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Affiliation(s)
| | - Rolf Lood
- Genovis AB, Scheelevägen 2, 223 63 Lund, Sweden
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38
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Tamura K, Brumer H. Glycan utilization systems in the human gut microbiota: a gold mine for structural discoveries. Curr Opin Struct Biol 2020; 68:26-40. [PMID: 33285501 DOI: 10.1016/j.sbi.2020.11.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 10/20/2020] [Accepted: 11/01/2020] [Indexed: 12/17/2022]
Abstract
The complex glycans comprising 'dietary fiber' evade the limited repertoire of human digestive enzymes and hence feed the vast community of microbes in the lower gastrointestinal tract. As such, complex glycans drive the composition of the human gut microbiota and, in turn, influence diverse facets of our nutrition and health. To access these otherwise recalcitrant carbohydrates, gut bacteria produce coordinated, substrate-specific arsenals of carbohydrate-active enzymes, glycan-binding proteins, oligosaccharide transporters, and transcriptional regulators. A recent explosion of biochemical and enzymological studies of these systems has led to the discovery of manifold new carbohydrate-active enzyme (CAZyme) families. Crucially underpinned by structural biology, these studies have also provided unprecedented molecular insight into the exquisite specificity of glycan recognition in the diverse CAZymes and non-catalytic proteins from the HGM. The revelation of a multitude of new three-dimensional structures and substrate complexes constitutes a 'gold rush' in the structural biology of the human gut microbiota.
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Affiliation(s)
- Kazune Tamura
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada
| | - Harry Brumer
- Michael Smith Laboratories, University of British Columbia, 2185 East Mall, Vancouver, BC, V6T 1Z4, Canada; Department of Biochemistry and Molecular Biology, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC, V6T 1Z3, Canada; Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC, V6T 1Z1, Canada.
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39
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Noach I, Boraston AB. Structural evidence for a proline-specific glycopeptide recognition domain in an O-glycopeptidase. Glycobiology 2020; 31:385-390. [PMID: 33030205 DOI: 10.1093/glycob/cwaa095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/21/2020] [Accepted: 10/02/2020] [Indexed: 12/12/2022] Open
Abstract
The glycosylation of proteins is typically considered as a stabilizing modification, including resistance to proteolysis. A class of peptidases, referred to as glycopeptidases or O-glycopeptidases, circumvent the protective effect of glycans against proteolysis by accommodating the glycans in their active sites as specific features of substrate recognition. IMPa from Pseudomonas aeruginosa is such an O-glycopeptidase that cleaves the peptide bond immediately preceding a site of O-glycosylation, and through this glycoprotein-degrading function contributes to the host-pathogen interaction. IMPa, however, is a relatively large multidomain protein and how its additional domains may contribute to its function remains unknown. Here, through the determination of a crystal structure of IMPa in complex with an O-glycopeptide, we reveal that the N-terminal domain of IMPa, which is classified in Pfam as IMPa_N_2, is a proline recognition domain that also shows the properties of recognizing an O-linked glycan on the serine/threonine residue following the proline. The proline is bound in the center of a bowl formed by four functionally conserved aromatic amino acid side chains while the glycan wraps around one of the tyrosine residues in the bowl to make classic aromatic ring-carbohydrate CH-π interactions. This structural evidence provides unprecedented insight into how the ancillary domains in glycoprotein-specific peptidases can noncatalytically recognize specific glycosylated motifs that are common in mucin and mucin-like molecules.
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Affiliation(s)
- Ilit Noach
- Biochemistry & Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC V8W 3P6, Canada
| | - Alisdair B Boraston
- Biochemistry & Microbiology, University of Victoria, PO Box 3055 STN CSC, Victoria, BC V8W 3P6, Canada
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40
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The Glycoprotease CpaA Secreted by Medically Relevant Acinetobacter Species Targets Multiple O-Linked Host Glycoproteins. mBio 2020; 11:mBio.02033-20. [PMID: 33024038 PMCID: PMC7542363 DOI: 10.1128/mbio.02033-20] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
CpaA is a glycoprotease expressed by members of the Acinetobacter baumannii-calcoaceticus complex, and it is the first bona fide secreted virulence factor identified in these species. Here, we show that CpaA cleaves multiple targets precisely at O-glycosylation sites preceded by a Pro residue. This feature, together with the observation that sialic acid does not impact CpaA activity, makes this enzyme an attractive tool for the analysis of O-linked human protein for biotechnical and diagnostic purposes. Previous work identified proteins involved in blood coagulation as targets of CpaA. Our work broadens the set of targets of CpaA, pointing toward additional roles in bacterium-host interactions. We propose that CpaA belongs to an expanding class of functionally defined glycoproteases that targets multiple O-linked host glycoproteins. Glycans decorate proteins and affect their biological function, including protection against proteolytic degradation. However, pathogenic, and commensal bacteria have evolved specific glycoproteases that overcome the steric impediment posed by carbohydrates, cleaving glycoproteins precisely at their glycosylation site(s). Medically relevant Acinetobacter strains employ their type II secretion system (T2SS) to secrete the glycoprotease CpaA, which contributes to virulence. Previously, CpaA was shown to cleave two O-linked glycoproteins, factors V and XII, leading to reduced blood coagulation. In this work, we show that CpaA cleaves a broader range of O-linked human glycoproteins, including several glycoproteins involved in complement activation, such as CD55 and CD46. However, only CD55 was removed from the cell surface, while CD46 remained unaltered during the Acinetobacter nosocomialis infection assay. We show that CpaA has a unique consensus target sequence that consists of a glycosylated serine or threonine residue after a proline residue (P-S/T), and its activity is not affected by sialic acids. Molecular modeling and mutagenesis analysis of CpaA suggest that the indole ring of Trp493 and the ring of the Pro residue in the substrate form a key interaction that contributes to CpaA sequence selectivity. Similar bacterial glycoproteases have recently gained attention as tools for proteomic analysis of human glycoproteins, and CpaA appears to be a robust and attractive new component of the glycoproteomics toolbox. Combined, our work provides insight into the function and possible application of CpaA, a member of a widespread class of broad-spectrum bacterial glycoproteases involved in host-pathogen interactions.
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Katalani C, Ahmadian G, Nematzadeh G, Amani J, Ehsani P, Razmyar J, Kiani G. Immunization with oral and parenteral subunit chimeric vaccine candidate confers protection against Necrotic Enteritis in chickens. Vaccine 2020; 38:7284-7291. [PMID: 33012608 DOI: 10.1016/j.vaccine.2020.09.047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 09/09/2020] [Accepted: 09/15/2020] [Indexed: 11/28/2022]
Abstract
Following the ban on the use of in-feed antimicrobials, necrotic enteritis (NE) NE is the most important clostridial disease. Vaccination has been considered as a possible approach to prevent NE. Our previous study showed that a chimeric protein product consisting of antigenic epitopes of NetB, Alpha-toxin and Zinc metallopeptidase (Zmp) triggered immune response against C. perfringens. In the current study we optimized the chimeric gene and constructed a fusion protein containing NetB, Alpha-toxin and Metallopeptidase (NAM) for expressing in tobacco plant to use as an edible vaccine for immunizing the chicken against NE. Simultaneously, we expressed and purified a His-tagged recombinant version of the NAM (rNAM) expressed in E. coli BL21 for subcutaneous immunization of chickens. Immunized birds produced strong humoral immune responses against both edible plant-based and parenteral purified rNAM. The responses were determined by the mean titer of antibody in blood samples to be around 9000 and 32,000, for edible and injected rNAM, respectively. Birds immunized subcutaneously showed the most striking responses. However the edible vaccine provided a more long lasting IgY response 14 days after the third vaccination compared to the injected birds. Chickens immunized with either lyophilized leaves expressing rNAM or purified rNAM, subsequently were subjected to the challenge with a virulent C. perfringens strain using an NE disease model. Our results showed that birds immunized both parenterally and orally with recombinant chimeric vaccine were significantly protected against the severity of lesion in the intestinal tract, but the protection provided with the injectable form of the antigen was greater than that of the oral form. Further analysis is needed to check whether these strategies can be used as the potential platform for developing an efficient vaccine against NE.
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Affiliation(s)
- Camellia Katalani
- Sari Agriculture Science and Natural Resource University (SANRU), Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari, Iran
| | - Gholamreza Ahmadian
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Pajoohesh BLVD, Tehran-Karaj HWY, km 15, Tehran 1497716316, Iran.
| | - Ghorbanali Nematzadeh
- Sari Agriculture Science and Natural Resource University (SANRU), Genetics and Agricultural Biotechnology Institute of Tabarestan (GABIT), Sari, Iran.
| | - Jafar Amani
- Applied Microbiology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Parastoo Ehsani
- Department of Molecular Biology, Pasteur Institute of Iran, Iran
| | - Jamshid Razmyar
- Department of Avian Diseases, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Ghaffar Kiani
- Sari Agriculture Science and Natural Resource University (SANRU), Sari, Iran
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Trastoy B, Naegeli A, Anso I, Sjögren J, Guerin ME. Structural basis of mammalian mucin processing by the human gut O-glycopeptidase OgpA from Akkermansia muciniphila. Nat Commun 2020; 11:4844. [PMID: 32973204 PMCID: PMC7518263 DOI: 10.1038/s41467-020-18696-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 09/04/2020] [Indexed: 12/21/2022] Open
Abstract
Akkermansia muciniphila is a mucin-degrading bacterium commonly found in the human gut that promotes a beneficial effect on health, likely based on the regulation of mucus thickness and gut barrier integrity, but also on the modulation of the immune system. In this work, we focus in OgpA from A. muciniphila, an O-glycopeptidase that exclusively hydrolyzes the peptide bond N-terminal to serine or threonine residues substituted with an O-glycan. We determine the high-resolution X-ray crystal structures of the unliganded form of OgpA, the complex with the glycodrosocin O-glycopeptide substrate and its product, providing a comprehensive set of snapshots of the enzyme along the catalytic cycle. In combination with O-glycopeptide chemistry, enzyme kinetics, and computational methods we unveil the molecular mechanism of O-glycan recognition and specificity for OgpA. The data also contribute to understanding how A. muciniphila processes mucins in the gut, as well as analysis of post-translational O-glycosylation events in proteins.
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Affiliation(s)
- Beatriz Trastoy
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | | | - Itxaso Anso
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
| | | | - Marcelo E Guerin
- Structural Biology Unit, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, 48013, Bilbao, Spain.
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43
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An enzymatic toolkit for selective proteolysis, detection, and visualization of mucin-domain glycoproteins. Proc Natl Acad Sci U S A 2020; 117:21299-21307. [PMID: 32817557 PMCID: PMC7474620 DOI: 10.1073/pnas.2012196117] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Densely O-glycosylated mucin domains are found in a broad range of cell surface and secreted proteins, where they play key physiological roles. In addition, alterations in mucin expression and glycosylation are common in a variety of human diseases, such as cancer, cystic fibrosis, and inflammatory bowel diseases. These correlations have been challenging to uncover and establish because tools that specifically probe mucin domains are lacking. Here, we present a panel of bacterial proteases that cleave mucin domains via distinct peptide- and glycan-based motifs, generating a diverse enzymatic toolkit for mucin-selective proteolysis. By mutating catalytic residues of two such enzymes, we engineered mucin-selective binding agents with retained glycoform preferences. StcEE447D is a pan-mucin stain derived from enterohemorrhagic Escherichia coli that is tolerant to a wide range of glycoforms. BT4244E575A derived from Bacteroides thetaiotaomicron is selective for truncated, asialylated core 1 structures commonly associated with malignant and premalignant tissues. We demonstrated that these catalytically inactive point mutants enable robust detection and visualization of mucin-domain glycoproteins by flow cytometry, Western blot, and immunohistochemistry. Application of our enzymatic toolkit to ascites fluid and tissue slices from patients with ovarian cancer facilitated characterization of patients based on differences in mucin cleavage and expression patterns.
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Prominent members of the human gut microbiota express endo-acting O-glycanases to initiate mucin breakdown. Nat Commun 2020; 11:4017. [PMID: 32782292 PMCID: PMC7419316 DOI: 10.1038/s41467-020-17847-5] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Accepted: 07/21/2020] [Indexed: 12/22/2022] Open
Abstract
The thick mucus layer of the gut provides a barrier to infiltration of the underlying epithelia by both the normal microbiota and enteric pathogens. Some members of the microbiota utilise mucin glycoproteins as a nutrient source, but a detailed understanding of the mechanisms used to breakdown these complex macromolecules is lacking. Here we describe the discovery and characterisation of endo-acting enzymes from prominent mucin-degrading bacteria that target the polyLacNAc structures within oligosaccharide side chains of both animal and human mucins. These O-glycanases are part of the large and diverse glycoside hydrolase 16 (GH16) family and are often lipoproteins, indicating that they are surface located and thus likely involved in the initial step in mucin breakdown. These data provide a significant advance in our knowledge of the mechanism of mucin breakdown by the normal microbiota. Furthermore, we also demonstrate the potential use of these enzymes as tools to explore changes in O-glycan structure in a number of intestinal disease states. Epithelial cells that line the gut secrete complex glycoproteins that form a mucus layer to protect the gut wall from enteric pathogens. Here, the authors provide a comprehensive characterisation of endo-acting glycoside hydrolases expressed by mucin-degrading members of the microbiome that are able to cleave the O-glycan chains of a range of different animal and human mucins.
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Brown HA, Koropatkin NM. Host glycan utilization within the Bacteroidetes Sus-like paradigm. Glycobiology 2020; 31:697-706. [PMID: 32518945 DOI: 10.1093/glycob/cwaa054] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/29/2020] [Accepted: 05/30/2020] [Indexed: 12/12/2022] Open
Abstract
The Bacteroidetes are numerically abundant Gram-negative organisms of the distal human gut with a greatly expanded capacity to degrade complex glycans. A subset of these are adept at scavenging host glycans within this environment, including mucin O-linked glycans, N-linked glycoproteins and highly sulfated glycosaminoglycans (GAGs) such as heparin (Hep) and chondroitin sulfate (CS). Several recent biochemical studies have revealed the specific polysaccharide utilization loci (PULs) within the model symbiont Bacteroides thetaiotaomicron for the deconstruction of these host glycans. Here we discuss the Sus-like paradigm that defines glycan uptake by the Bacteroidetes and the salient details of the PULs that target heparin/heparan sulfate (HS) and chondroitin sulfate/dermatan sulfate (DS)/hyaluronic acid (HA), respectively, in B. thetaiotaomicron. The ability of the Bacteroidetes to target highly sulfated host glycans is key to their success in the gut environment but can lead to inflammation in susceptible hosts. Therefore, our continued understanding of the molecular strategies employed by these bacteria to scavenge carbohydrate nutrition is likely to lead to novel ways to alter their metabolism to promote host health.
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Affiliation(s)
- Haley A Brown
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA
| | - Nicole M Koropatkin
- Department of Microbiology and Immunology, University of Michigan Medical School, 1150 West Medical Center Drive, Ann Arbor, MI 48109, USA
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46
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Low KE, Smith SP, Abbott DW, Boraston AB. The glycoconjugate-degrading enzymes of Clostridium perfringens: Tailored catalysts for breaching the intestinal mucus barrier. Glycobiology 2020; 31:681-690. [PMID: 32472136 DOI: 10.1093/glycob/cwaa050] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/21/2020] [Accepted: 06/01/2020] [Indexed: 01/07/2023] Open
Abstract
The gastrointestinal (GI) tract of humans and animals is lined with mucus that serves as a barrier between the gut microbiota and the epithelial layer of the intestine. As the proteins present in mucus are typically heavily glycosylated, such as the mucins, several enteric commensal and pathogenic bacterial species are well-adapted to this rich carbon source and their genomes are replete with carbohydrate-active enzymes targeted toward dismantling the glycans and proteins present in mucus. One such species is Clostridium perfringens, a Gram-positive opportunistic pathogen indigenous to the gut of humans and animals. The genome of C. perfringens encodes numerous carbohydrate-active enzymes that are predicted or known to target glycosidic linkages within or on the termini of mucus glycans. Through this enzymatic activity, the degradation of the mucosal layer by C. perfringens has been implicated in a number of GI diseases, the most severe of which is necrotic enteritis. In this review, we describe the wide array of extracellular glycoside hydrolases, and their accessory modules, that is possessed by C. perfringens, and examine the unique multimodularity of these proteins in the context of degrading the glycoconjugates in mucus as a potential component of disease.
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Affiliation(s)
- Kristin E Low
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1 Ave S, Lethbridge T1J 4B1, Canada
| | - Steven P Smith
- Department of Biomedical and Molecular Sciences, Queen's University, 99 University Ave, Kingston K7L 3N6, Canada
| | - D Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1 Ave S, Lethbridge T1J 4B1, Canada
| | - Alisdair B Boraston
- Faculty of Biochemistry and Microbiology, University of Victoria, Victoria V8P 5C2, Canada
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Rehman S, Grigoryeva LS, Richardson KH, Corsini P, White RC, Shaw R, Portlock TJ, Dorgan B, Zanjani ZS, Fornili A, Cianciotto NP, Garnett JA. Structure and functional analysis of the Legionella pneumophila chitinase ChiA reveals a novel mechanism of metal-dependent mucin degradation. PLoS Pathog 2020; 16:e1008342. [PMID: 32365117 PMCID: PMC7224574 DOI: 10.1371/journal.ppat.1008342] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 05/14/2020] [Accepted: 01/22/2020] [Indexed: 12/18/2022] Open
Abstract
Chitinases are important enzymes that contribute to the generation of carbon and nitrogen from chitin, a long chain polymer of N-acetylglucosamine that is abundant in insects, fungi, invertebrates and fish. Although mammals do not produce chitin, chitinases have been identified in bacteria that are key virulence factors in severe respiratory, gastrointestinal and urinary diseases. However, it is unclear how these enzymes are able to carry out this dual function. Legionella pneumophila is the causative agent of Legionnaires' disease, an often-fatal pneumonia and its chitinase ChiA is essential for the survival of L. pneumophila in the lung. Here we report the first atomic resolution insight into the pathogenic mechanism of a bacterial chitinase. We derive an experimental model of intact ChiA and show how its N-terminal region targets ChiA to the bacterial surface after its secretion. We provide the first evidence that L. pneumophila can bind mucins on its surface, but this is not dependent on ChiA. This demonstrates that additional peripheral mucin binding proteins are also expressed in L. pneumophila. We also show that the ChiA C-terminal chitinase domain has novel Zn2+-dependent peptidase activity against mammalian mucin-like proteins, namely MUC5AC and the C1-esterase inhibitor, and that ChiA promotes bacterial penetration of mucin gels. Our findings suggest that ChiA can facilitate passage of L. pneumophila through the alveolar mucosa, can modulate the host complement system and that ChiA may be a promising target for vaccine development.
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Affiliation(s)
- Saima Rehman
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
| | - Lubov S. Grigoryeva
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Katherine H. Richardson
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Paula Corsini
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Richard C. White
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - Rosie Shaw
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Theo J. Portlock
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Benjamin Dorgan
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Zeinab S. Zanjani
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Arianna Fornili
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
| | - Nicholas P. Cianciotto
- Department of Microbiology and Immunology, Feinberg School of Medicine, Northwestern University, Chicago, Illinois, United States of America
| | - James A. Garnett
- Centre for Host-Microbiome Interactions, Dental Institute, King’s College London, London, United Kingdom
- Chemistry and Biochemistry Department, School of Biological and Chemical Sciences, Queen Mary University of London, London, United Kingdom
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Kurogochi M, Matsuda A, Mizuno M. Preparation of O-Glycopeptides from commercial bovine whey proteins using offline liquid chromatography-Mass spectrometry. Carbohydr Res 2020; 491:107981. [PMID: 32217362 DOI: 10.1016/j.carres.2020.107981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 10/24/2022]
Abstract
O-Glycopeptides derived from natural bioresources are an attractive material for a variety of purposes. Whey protein products are used as a human dietary supplement and in animal feed and are a readily available resource for the preparation of O-glycopeptides. The protein composition of bovine milk is well-studied, and many glycoproteins carrying N-glycans and O-glycans have been found in commercial whey protein products. In particular, κ-casein glycomacropeptide and lactophorin, which have several O-glycans, are known to exist in whey protein. Here, we report an isolation method of O-glycopeptides bearing disialyl core 1 type and core 2 type glycan moieties from commercially available whey protein products using proteose peptone extraction, enzymatic digestion (with trypsin or thermolysin), and sequential high-performance liquid chromatography purification. We were able to isolate several kinds of O-glycopeptides from lactophorin and κ-casein: six peptide sequences and five kinds of O-glycans. The O-glycopeptides were detected and identified by flow injection analysis combined with electrospray ionization mass spectrometry and tandem mass spectrometry using collision-induced dissociation and electron transfer dissociation. O-Glycopeptides bearing a variety of O-glycans could be used as a substrate for endo-α-N-acetyl galactosaminidase, and their various O-glycan structures were useful for the investigation of enzyme activities.
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Affiliation(s)
- Masaki Kurogochi
- Laboratory of Glyco-Organic Chemistry, The Noguchi Institute, 1-9-7 Kaga, Itabashi-ku, Tokyo, Japan.
| | - Akio Matsuda
- Laboratory of Glyco-Organic Chemistry, The Noguchi Institute, 1-9-7 Kaga, Itabashi-ku, Tokyo, Japan
| | - Mamoru Mizuno
- Laboratory of Glyco-Organic Chemistry, The Noguchi Institute, 1-9-7 Kaga, Itabashi-ku, Tokyo, Japan
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49
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In silico design and in vitro analysis of a recombinant trivalent fusion protein candidate vaccine targeting virulence factor of Clostridium perfringens. Int J Biol Macromol 2020; 146:1015-1023. [DOI: 10.1016/j.ijbiomac.2019.09.227] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 09/21/2019] [Accepted: 09/23/2019] [Indexed: 11/23/2022]
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50
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Wade B, Keyburn AL, Haring V, Ford M, Rood JI, Moore RJ. Two putative zinc metalloproteases contribute to the virulence of Clostridium perfringens strains that cause avian necrotic enteritis. J Vet Diagn Invest 2020; 32:259-267. [PMID: 31924132 DOI: 10.1177/1040638719898689] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Two putative zinc metalloproteases encoded by Clostridium perfringens have been implicated in the pathogenesis of necrotic enteritis, an economically significant poultry disease that is caused by this anaerobic bacterium. These proteases have ~64% amino acid identity and are encoded by the zmpA and zmpB genes. We screened 83 C. perfringens isolates by PCR for the presence of these genes. The first gene, zmpB, is chromosomally located and was present in all screened strains of C. perfringens, regardless of their origin and virulence. The second gene, zmpA, is plasmid-borne and was only found in isolates derived from chickens with necrotic enteritis. We describe the generation of insertionally inactivated mutants of both zmpA and zmpB in a virulent C. perfringens isolate. For each mutant, a significant (p < 0.001) reduction in virulence was observed in a chicken necrotic enteritis disease model. Examples of each mutant strain were characterized by whole genome sequencing, which showed that there were a few off-site mutations with the potential to affect the virulence of these strains. To confirm the importance of these genes, independently derived zmpA and zmpB mutants were constructed in different virulent C. perfringens isolates and shown to have reduced virulence in the experimental disease induction model. A zmpA-zmpB double mutant also was generated and shown to have significantly reduced virulence, to the same extent as the respective single mutants. Our results provide evidence that both putative zinc metalloproteases play an important role in disease pathogenesis.
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Affiliation(s)
- Ben Wade
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, Victoria, Australia (Wade, Keyburn, Haring, Ford, Moore).,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia (Wade, Keyburn, Rood, Moore).,Poultry Cooperative Research Centre, Armidale, New South Wales, Australia (Keyburn, Rood, Moore); School of Science, RMIT University, Bundoora, Victoria, Australia (Moore)
| | - Anthony L Keyburn
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, Victoria, Australia (Wade, Keyburn, Haring, Ford, Moore).,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia (Wade, Keyburn, Rood, Moore).,Poultry Cooperative Research Centre, Armidale, New South Wales, Australia (Keyburn, Rood, Moore); School of Science, RMIT University, Bundoora, Victoria, Australia (Moore)
| | - Volker Haring
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, Victoria, Australia (Wade, Keyburn, Haring, Ford, Moore).,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia (Wade, Keyburn, Rood, Moore).,Poultry Cooperative Research Centre, Armidale, New South Wales, Australia (Keyburn, Rood, Moore); School of Science, RMIT University, Bundoora, Victoria, Australia (Moore)
| | - Mark Ford
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, Victoria, Australia (Wade, Keyburn, Haring, Ford, Moore).,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia (Wade, Keyburn, Rood, Moore).,Poultry Cooperative Research Centre, Armidale, New South Wales, Australia (Keyburn, Rood, Moore); School of Science, RMIT University, Bundoora, Victoria, Australia (Moore)
| | - Julian I Rood
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, Victoria, Australia (Wade, Keyburn, Haring, Ford, Moore).,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia (Wade, Keyburn, Rood, Moore).,Poultry Cooperative Research Centre, Armidale, New South Wales, Australia (Keyburn, Rood, Moore); School of Science, RMIT University, Bundoora, Victoria, Australia (Moore)
| | - Robert J Moore
- CSIRO Biosecurity Flagship, Australian Animal Health Laboratory, Geelong, Victoria, Australia (Wade, Keyburn, Haring, Ford, Moore).,Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia (Wade, Keyburn, Rood, Moore).,Poultry Cooperative Research Centre, Armidale, New South Wales, Australia (Keyburn, Rood, Moore); School of Science, RMIT University, Bundoora, Victoria, Australia (Moore)
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