1
|
Lee S, Ono T, Masaaki S, Fujita A, Matsubara M, Zappa A, Yamada I, Aoki-Kinoshita KF. Updates implemented in version 4 of the GlyCosmos Glycoscience Portal. Anal Bioanal Chem 2024:10.1007/s00216-024-05692-0. [PMID: 39690313 DOI: 10.1007/s00216-024-05692-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2024] [Revised: 11/25/2024] [Accepted: 11/28/2024] [Indexed: 12/19/2024]
Abstract
Glycosylation, characterized by its complexity and diversity, is a common system across all domains of life. The glycosylation of proteins or lipids imparts them with structural and functional roles, ranging from development to infectious or Mendelian disease. The high-throughput-based omics data has revealed that glycans are involved in important cellular processes. Comprehensive knowledge of glycosylation has contributed not only to the fundamental concepts in glycoscience but also to its applications, including the development of molecular markers for diagnosis and therapeutic tools for treating diseases. The GlyCosmos Glycoscience Portal (GlyCosmos) has undergone significant updates to better support the scientific community in studying glycosylation-related phenomena. Key enhancements include the integration of expanded datasets linking glycans to other omics fields, improved tools for glycan structure prediction and analysis, and upgraded visualization capabilities to streamline data interpretation. A strengthened focus on data standardization has also been introduced, fostering interoperability between glycoscience resources and external databases. Since its release in 2019, the portal has seen a fivefold increase in user engagement, reflecting its growing relevance. These recent advancements aim to provide researchers with a more comprehensive and user-friendly platform, enabling deeper insights into glycan roles in cellular processes and disease mechanisms. GlyCosmos will continue to evolve, prioritizing community needs and advancing the integration of glycoscience with broader biological and biomedical research.
Collapse
Affiliation(s)
- Sunmyoung Lee
- Glycan and Life Systems Integration Center (GaLSIC), Soka University, Hachioji, Tokyo, Japan
| | - Tamiko Ono
- Glycan and Life Systems Integration Center (GaLSIC), Soka University, Hachioji, Tokyo, Japan
| | - Shiota Masaaki
- Glycan and Life Systems Integration Center (GaLSIC), Soka University, Hachioji, Tokyo, Japan
| | - Akihiro Fujita
- Institute for Glyco-Core Research, Nagoya University, Nagoya, Japan
| | | | - Achille Zappa
- Glycan and Life Systems Integration Center (GaLSIC), Soka University, Hachioji, Tokyo, Japan
| | | | - Kiyoko F Aoki-Kinoshita
- Glycan and Life Systems Integration Center (GaLSIC), Soka University, Hachioji, Tokyo, Japan.
- Graduate School of Science and Engineering, Soka University, Hachioji, Tokyo, Japan.
- Institute for Glyco-Core Research, Nagoya University, Nagoya, Japan.
| |
Collapse
|
2
|
Heimburg-Molinaro J, Mehta AY, Tilton CA, Cummings RD. Insights Into Glycobiology and the Protein-Glycan Interactome Using Glycan Microarray Technologies. Mol Cell Proteomics 2024; 23:100844. [PMID: 39307422 PMCID: PMC11585810 DOI: 10.1016/j.mcpro.2024.100844] [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: 06/13/2024] [Revised: 08/26/2024] [Accepted: 08/28/2024] [Indexed: 11/11/2024] Open
Abstract
Glycans linked to proteins and lipids and also occurring in free forms have many functions, and these are partly elicited through specific interactions with glycan-binding proteins (GBPs). These include lectins, adhesins, toxins, hemagglutinins, growth factors, and enzymes, but antibodies can also bind glycans. While humans and other animals generate a vast repertoire of GBPs and different glycans in their glycomes, other organisms, including phage, microbes, protozoans, fungi, and plants also express glycans and GBPs, and these can also interact with their host glycans. This can be termed the protein-glycan interactome, and in nature is likely to be vast, but is so far very poorly described. Understanding the breadth of the protein-glycan interactome is also a key to unlocking our understanding of infectious diseases involving glycans, and immunology associated with antibodies binding to glycans. A key technological advance in this area has been the development of glycan microarrays. This is a display technology in which minute quantities of glycans are attached to the surfaces of slides or beads. This allows the arrayed glycans to be interrogated by GBPs and antibodies in a relatively high throughput approach, in which a protein may bind to one or more distinct glycans. Such binding can lead to novel insights and hypotheses regarding both the function of the GBP, the specificity of an antibody and the function of the glycan within the context of the protein-glycan interactome. This article focuses on the types of glycan microarray technologies currently available to study animal glycobiology and examples of breakthroughs aided by these technologies.
Collapse
Affiliation(s)
- Jamie Heimburg-Molinaro
- Department of Surgery Beth Israel Deaconess Medical Center, National Center for Functional Glycomics (NCFG), Harvard Medical School, Boston, Massachusetts, USA
| | - Akul Y Mehta
- Department of Surgery Beth Israel Deaconess Medical Center, National Center for Functional Glycomics (NCFG), Harvard Medical School, Boston, Massachusetts, USA
| | - Catherine A Tilton
- Department of Surgery Beth Israel Deaconess Medical Center, National Center for Functional Glycomics (NCFG), Harvard Medical School, Boston, Massachusetts, USA
| | - Richard D Cummings
- Department of Surgery Beth Israel Deaconess Medical Center, National Center for Functional Glycomics (NCFG), Harvard Medical School, Boston, Massachusetts, USA.
| |
Collapse
|
3
|
Benjamin SV, Jégouzo SAF, Lieng C, Daniels C, Coispeau M, Lau RJ, Kim S, Metaxa Y, Philpott J, Li T, Dai C, Wang X, Newby ML, Pier GB, Crispin M, Clements A, Taylor ME, Drickamer K. A human lectin array for characterizing host-pathogen interactions. J Biol Chem 2024; 300:107869. [PMID: 39384043 PMCID: PMC11566865 DOI: 10.1016/j.jbc.2024.107869] [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: 07/16/2024] [Revised: 09/21/2024] [Accepted: 10/01/2024] [Indexed: 10/11/2024] Open
Abstract
A human lectin array has been developed to probe the interactions of innate immune receptors with pathogenic and commensal microorganisms. Following the successful introduction of a lectin array containing all of the cow C-type carbohydrate-recognition domains (CRDs), a human array described here contains the C-type CRDs as well as CRDs from other classes of sugar-binding receptors, including galectins, siglecs, R-type CRDs, ficolins, intelectins, and chitinase-like lectins. The array is constructed with CRDs modified with single-site biotin tags, ensuring that the sugar-binding sites in CRDs are displayed on a streptavidin-coated surface in a defined orientation and are accessible to the surfaces of microbes. A common approach used for expression and display of CRDs from all of the different structural categories of glycan-binding receptors allows comparisons across lectin families. In addition to previously documented protocols for binding of fluorescently labeled bacteria, methods have been developed for detecting unlabeled bacteria bound to the array by counter-staining with DNA-binding dye. Screening has also been undertaken with viral glycoproteins and bacterial and fungal polysaccharides. The array provides an unbiased screen for sugar ligands that interact with receptors and many show binding not anticipated from earlier studies. For example, some of the galectins bind with high affinity to bacterial glycans that lack lactose or N-acetyllactosamine. The results demonstrate the utility of the human lectin array for providing a unique overview of the interactions of multiple classes of glycan-binding proteins in the innate immune system with different types of microorganisms.
Collapse
Affiliation(s)
- Stefi V Benjamin
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Sabine A F Jégouzo
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Chloe Lieng
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Connor Daniels
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Marine Coispeau
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Rikin J Lau
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Suyeon Kim
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Yasmine Metaxa
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - James Philpott
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Tiannuo Li
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Chao Dai
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Xin Wang
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Maddy L Newby
- School of Biological Sciences, University of Southampton, United Kingdom
| | - Gerald B Pier
- Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Max Crispin
- School of Biological Sciences, University of Southampton, United Kingdom
| | - Abigail Clements
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Maureen E Taylor
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Kurt Drickamer
- Department of Life Sciences, Imperial College London, London, United Kingdom.
| |
Collapse
|
4
|
Wrage M, Holland T, Nüse B, Kaltwasser J, Fröhlich J, Arnold H, Gießler C, Flamann C, Bruns H, Berges J, Daniel C, Hoffmann MH, Anish C, Seeberger PH, Bogdan C, Dettmer K, Rauh M, Mattner J. Cell type-specific modulation of metabolic, immune-regulatory, and anti-microbial pathways by CD101. Mucosal Immunol 2024; 17:892-910. [PMID: 38901763 DOI: 10.1016/j.mucimm.2024.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 06/05/2024] [Accepted: 06/09/2024] [Indexed: 06/22/2024]
Abstract
T lymphocytes and myeloid cells express the immunoglobulin-like glycoprotein cluster of differentiation (CD)101, notably in the gut. Here, we investigated the cell-specific functions of CD101 during dextran sulfate sodium (DSS)-induced colitis and Salmonella enterica Typhimurium infection. Similar to conventional CD101-/- mice, animals with a regulatory T cell-specific Cd101 deletion developed more severe intestinal pathology than littermate controls in both models. While the accumulation of T helper 1 cytokines in a CD101-deficient environment entertained DSS-induced colitis, it impeded the replication of Salmonella as revealed by studying CD101-/- x interferon-g-/- mice. Moreover, CD101-expressing neutrophils were capable to restrain Salmonella infection in vitro and in vivo. Both cell-intrinsic and -extrinsic mechanisms of CD101 contributed to the control of bacterial growth and spreading. The CD101-dependent containment of Salmonella infection required the expression of Irg-1 and Nox2 and the production of itaconate and reactive oxygen species. The level of intestinal microbial antigens in the sera of inflammatory bowel disease patients correlated inversely with the expression of CD101 on myeloid cells, which is in line with the suppression of CD101 seen in mice following DSS application or Salmonella infection. Thus, depending on the experimental or clinical setting, CD101 helps to limit inflammatory insults or bacterial infections due to cell type-specific modulation of metabolic, immune-regulatory, and anti-microbial pathways.
Collapse
Affiliation(s)
- Marius Wrage
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitäts-klinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Tim Holland
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitäts-klinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Björn Nüse
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitäts-klinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Johanna Kaltwasser
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitäts-klinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Jessica Fröhlich
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitäts-klinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Harald Arnold
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitäts-klinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Claudia Gießler
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitäts-klinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Cindy Flamann
- Medizinische Klinik 5, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Heiko Bruns
- Medizinische Klinik 5, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Johannes Berges
- Medizinische Klinik 5, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Christoph Daniel
- Nephropathologische Abteilung, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Markus H Hoffmann
- Medizinische Klinik 3, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany; Klinik für Dermatologie, Allergologie und Venerologie, Universitätsklinikum Schleswig-Holstein, Universität zu Lübeck, Lübeck, Germany
| | - Chakkumkal Anish
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany; Bacterial Vaccines Discovery and Early Development, Janssen Pharmaceuticals (Johnson & Johnson), CK Leiden, The Netherlands
| | - Peter H Seeberger
- Max Planck Institute of Colloids and Interfaces, Potsdam, Germany; Freie Universität Berlin, Department of Chemistry and Biochemistry, Berlin, Germany
| | - Christian Bogdan
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitäts-klinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; FAU Profilzentrum Immunmedizin (FAU I-MED), FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Katja Dettmer
- Institut für Funktionelle Genomik, Universität Regensburg, Regensburg, Germany
| | - Manfred Rauh
- Kinder- und Jugendklinik, Universitätsklinikum Erlangen, FAU Erlangen-Nürnberg, Erlangen, Germany
| | - Jochen Mattner
- Mikrobiologisches Institut-Klinische Mikrobiologie, Immunologie und Hygiene, Universitäts-klinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany; FAU Profilzentrum Immunmedizin (FAU I-MED), FAU Erlangen-Nürnberg, Erlangen, Germany.
| |
Collapse
|
5
|
Kooner AS, Yu H, Leviatan Ben-Arye S, Padler-Karavani V, Chen X. Broad-Spectrum Legionaminic Acid-Specific Antibodies in Pooled Human IgGs Revealed by Glycan Microarrays with Chemoenzymatically Synthesized Nonulosonosides. Molecules 2024; 29:3980. [PMID: 39203058 PMCID: PMC11356810 DOI: 10.3390/molecules29163980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/10/2024] [Accepted: 08/14/2024] [Indexed: 09/03/2024] Open
Abstract
The presence and the level of antibodies in human sera against bacterial glycans are indications of prior encounters with similar antigens and/or the bacteria that express them by the immune system. An increasing number of pathogenic bacteria that cause human diseases have been shown to express polysaccharides containing a bacterial nonulosonic acid called 5,7-di-N-acetyllegionaminic acid (Leg5,7Ac2). To investigate the immune recognition of Leg5,7Ac2, which is critical for the fight against bacterial infections, a highly effective chemoenzymatic synthon strategy was applied to construct a library of α2-3/6-linked Leg5,7Ac2-glycans via their diazido-derivatives (Leg5,7diN3-glycans) formed by efficient one-pot three-enzyme (OP3E) synthetic systems from a diazido-derivative of a six-carbon monosaccharide precursor. Glycan microarray studies using this synthetic library of a Leg5,7Ac2-capped collection of diverse underlying glycan carriers and their matched sialoside counterparts revealed specific recognition of Leg5,7Ac2 by human IgG antibodies pooled from thousands of healthy donors (IVIG), suggesting prior human encounters with Leg5,7Ac2-expressing pathogenic bacteria at the population level. These biologically relevant Leg5,7Ac2-glycans and their immune recognition assays are important tools to begin elucidating their biological roles, particularly in the context of infection and host-pathogen interactions.
Collapse
Affiliation(s)
- Anoopjit Singh Kooner
- Department of Chemistry, University of California, Davis, CA 95616, USA; (A.S.K.); (H.Y.)
| | - Hai Yu
- Department of Chemistry, University of California, Davis, CA 95616, USA; (A.S.K.); (H.Y.)
| | - Shani Leviatan Ben-Arye
- Department of Cell Research and Immunology, The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel;
| | - Vered Padler-Karavani
- Department of Cell Research and Immunology, The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel;
| | - Xi Chen
- Department of Chemistry, University of California, Davis, CA 95616, USA; (A.S.K.); (H.Y.)
| |
Collapse
|
6
|
Crawford CJ, Schultz-Johansen M, Luong P, Vidal-Melgosa S, Hehemann JH, Seeberger PH. Automated Synthesis of Algal Fucoidan Oligosaccharides. J Am Chem Soc 2024; 146:18320-18330. [PMID: 38916244 PMCID: PMC11240576 DOI: 10.1021/jacs.4c02348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Fucoidan, a sulfated polysaccharide found in algae, plays a central role in marine carbon sequestration and exhibits a wide array of bioactivities. However, the molecular diversity and structural complexity of fucoidan hinder precise structure-function studies. To address this, we present an automated method for generating well-defined linear and branched α-fucan oligosaccharides. Our syntheses include oligosaccharides with up to 20 cis-glycosidic linkages, diverse branching patterns, and 11 sulfate monoesters. In this study, we demonstrate the utility of these oligosaccharides by (i) characterizing two endo-acting fucoidan glycoside hydrolases (GH107), (ii) utilizing them as standards for NMR studies to confirm suggested structures of algal fucoidans, and (iii) developing a fucoidan microarray. This microarray enabled the screening of the molecular specificity of four monoclonal antibodies (mAb) targeting fucoidan. It was found that mAb BAM4 has cross-reactivity to β-glucans, while mAb BAM2 has reactivity to fucoidans with 4-O-sulfate esters. Knowledge of the mAb BAM2 epitope specificity provided evidence that a globally abundant marine diatom, Thalassiosira weissflogii, synthesizes a fucoidan with structural homology to those found in brown algae. Automated glycan assembly provides access to fucoidan oligosaccharides. These oligosaccharides provide the basis for molecular level investigations into fucoidan's roles in medicine and carbon sequestration.
Collapse
Affiliation(s)
- Conor J Crawford
- Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Mikkel Schultz-Johansen
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Phuong Luong
- Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Silvia Vidal-Melgosa
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Jan-Hendrik Hehemann
- Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
- MARUM, Center for Marine Environmental Sciences, University of Bremen, 28359 Bremen, Germany
| | - Peter H Seeberger
- Max Planck Institute for Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Institute for Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| |
Collapse
|
7
|
Jordan C, Siebold K, Priegue P, Seeberger PH, Gilmour R. A Fluorinated Sialic Acid Vaccine Lead Against Meningitis B and C. J Am Chem Soc 2024; 146:15366-15375. [PMID: 38768956 PMCID: PMC11157539 DOI: 10.1021/jacs.4c03179] [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: 03/04/2024] [Revised: 04/22/2024] [Accepted: 04/23/2024] [Indexed: 05/22/2024]
Abstract
Inspired by the specificity of α-(2,9)-sialyl epitopes in bacterial capsular polysaccharides (CPS), a doubly fluorinated disaccharide has been validated as a vaccine lead against Neisseria meningitidis serogroups C and/or B. Emulating the importance of fluorine in drug discovery, this molecular editing approach serves a multitude of purposes, which range from controlling α-selective chemical sialylation to mitigating competing elimination. Conjugation of the disialoside with two carrier proteins (CRM197 and PorA) enabled a semisynthetic vaccine to be generated; this was then investigated in six groups of six mice. The individual levels of antibodies formed were compared and classified as highly glycan-specific and protective. All glycoconjugates induced a stable and long-term IgG response and binding to the native CPS epitope was achieved. The generated antibodies were protective against MenC and/or MenB; this was validated in vitro by SBA and OPKA assays. By merging the fluorinated glycan epitope of MenC with an outer cell membrane protein of MenB, a bivalent vaccine against both serogroups was created. It is envisaged that validation of this synthetic, fluorinated disialoside bioisostere as a potent antigen will open new therapeutic avenues.
Collapse
Affiliation(s)
- Christina Jordan
- Institute
for Organic Chemistry, University of Münster, Corrensstraße 36, Münster 48149, Germany
| | - Kathrin Siebold
- Institute
for Organic Chemistry, University of Münster, Corrensstraße 36, Münster 48149, Germany
| | - Patricia Priegue
- Department
of Biomolecular Systems, Max Planck Institute
for Colloids and Interfaces, Am Mühlenberg 1, Potsdam 14476, Germany
- Freie
Universität Berlin, Institute of
Chemistry and Biochemistry, Arnimallee 22, Berlin 14195, Germany
| | - Peter H. Seeberger
- Department
of Biomolecular Systems, Max Planck Institute
for Colloids and Interfaces, Am Mühlenberg 1, Potsdam 14476, Germany
- Freie
Universität Berlin, Institute of
Chemistry and Biochemistry, Arnimallee 22, Berlin 14195, Germany
| | - Ryan Gilmour
- Institute
for Organic Chemistry, University of Münster, Corrensstraße 36, Münster 48149, Germany
| |
Collapse
|
8
|
Marglous S, Brown CE, Padler-Karavani V, Cummings RD, Gildersleeve JC. Serum antibody screening using glycan arrays. Chem Soc Rev 2024; 53:2603-2642. [PMID: 38305761 PMCID: PMC7616341 DOI: 10.1039/d3cs00693j] [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: 02/03/2024]
Abstract
Humans and other animals produce a diverse collection of antibodies, many of which bind to carbohydrate chains, referred to as glycans. These anti-glycan antibodies are a critical part of our immune systems' defenses. Whether induced by vaccination or natural exposure to a pathogen, anti-glycan antibodies can provide protection against infections and cancers. Alternatively, when an immune response goes awry, antibodies that recognize self-glycans can mediate autoimmune diseases. In any case, serum anti-glycan antibodies provide a rich source of information about a patient's overall health, vaccination history, and disease status. Glycan microarrays provide a high-throughput platform to rapidly interrogate serum anti-glycan antibodies and identify new biomarkers for a variety of conditions. In addition, glycan microarrays enable detailed analysis of the immune system's response to vaccines and other treatments. Herein we review applications of glycan microarray technology for serum anti-glycan antibody profiling.
Collapse
Affiliation(s)
- Samantha Marglous
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Claire E Brown
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| | - Vered Padler-Karavani
- Department of Cell Research and Immunology, Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 69978, Israel.
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02115, USA.
| | - Jeffrey C Gildersleeve
- Chemical Biology Laboratory, Center for Cancer Research, National Cancer Institute, Frederick, MD, 21702, USA.
| |
Collapse
|
9
|
Artyszuk D, Jachymek W, Izdebski R, Gniadkowski M, Lukasiewicz J. The OL101 O antigen locus specifies a novel Klebsiella pneumoniae serotype O13 structure. Carbohydr Polym 2024; 326:121581. [PMID: 38142087 DOI: 10.1016/j.carbpol.2023.121581] [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: 10/27/2023] [Accepted: 11/09/2023] [Indexed: 12/25/2023]
Abstract
Klebsiella pneumoniae is one of the priority objects for the development of new therapies against infections. The species has been perceived as of limited variety of O antigens (11 O serotypes identified to date). That trait makes lipopolysaccharide an attractive target for protective antibodies. Nowadays, K. pneumoniae O antigens encoding genes are often analysed by bioinformatic tools, such as Kaptive, indicating higher actual diversity of the O antigen loci. One of the novel K. pneumoniae O loci for which the antigen structure has not been elucidated so far is OL101. In this study, four clinical isolates predicted as OL101 were characterized and found to have the O antigen structure composed of β-Kdop-[→3)-α-l-Rhap-(1→4)-α-d-Glcp-(1→]n, representing a novel serotype O13. Identification of the β-Kdop terminus was based on the analysis of the complete LPS molecule by the HR-MAS NMR spectroscopy. The bioinformatic analysis of 71,377 K. pneumoniae genomes from public databases (July 2023) revealed a notable OL101 prevalence of 6.55 %.
Collapse
Affiliation(s)
- Daria Artyszuk
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Laboratory of Microbial Immunochemistry and Vaccines, 53-114 Wroclaw, Poland
| | - Wojciech Jachymek
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Laboratory of Microbial Immunochemistry and Vaccines, 53-114 Wroclaw, Poland
| | - Radosław Izdebski
- National Medicines Institute, Department of Molecular Microbiology, 00-725 Warsaw, Poland
| | - Marek Gniadkowski
- National Medicines Institute, Department of Molecular Microbiology, 00-725 Warsaw, Poland
| | - Jolanta Lukasiewicz
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Laboratory of Microbial Immunochemistry and Vaccines, 53-114 Wroclaw, Poland.
| |
Collapse
|
10
|
Krylov VB, Gómez-Redondo M, Solovev AS, Yashunsky DV, Brown AJ, Stappers MH, Gow NA, Ardá A, Jiménez-Barbero J, Nifantiev NE. Identification of a new DC-SIGN binding pentamannoside epitope within the complex structure of Candida albicans mannan. Cell Surf 2023; 10:100109. [PMID: 37520856 PMCID: PMC10382935 DOI: 10.1016/j.tcsw.2023.100109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 07/11/2023] [Accepted: 07/12/2023] [Indexed: 08/01/2023] Open
Abstract
The dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin (DC-SIGN) is an innate immune C-type lectin receptor that recognizes carbohydrate-based pathogen associated with molecular patterns of various bacteria, fungi, viruses and protozoa. Although a range of highly mannosylated glycoproteins have been shown to induce signaling via DC-SIGN, precise structure of the recognized oligosaccharide epitope is still unclear. Using the array of oligosaccharides related to selected fragments of main fungal antigenic polysaccharides we revealed a highly specific pentamannoside ligand of DC-SIGN, consisting of α-(1 → 2)-linked mannose chains with one inner α-(1 → 3)-linked unit. This structural motif is present in Candida albicans cell wall mannan and corresponds to its antigenic factors 4 and 13b. This epitope is not ubiquitous in other yeast species and may account for the species-specific nature of fungal recognition via DC-SIGN. The discovered highly specific oligosaccharide ligands of DC-SIGN are tractable tools for interdisciplinary investigations of mechanisms of fungal innate immunity and anti-Candida defense. Ligand- and receptor-based NMR data demonstrated the pentasaccharide-to-DC-SIGN interaction in solution and enabled the deciphering of the interaction topology.
Collapse
Affiliation(s)
- Vadim B. Krylov
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Arsenii S. Solovev
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Dmitry V. Yashunsky
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alistair J.P. Brown
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Mark H.T. Stappers
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Neil A.R. Gow
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Ana Ardá
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, 48160 Derio, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Basque Research Technology Alliance, BRTA, 48160 Derio, Spain
- IKERBASQUE, Basque Foundation for Science and Technology, Euskadi Plaza 5, 48009 Bilbao, Spain
- Department of Organic & Inorganic Chemistry, Faculty of Science and Technology, University of the Basque Country, 48940 Leioa, Spain
- Centro de Investigacion Biomedica En Red de Enfermedades Respiratorias, Madrid, Spain
| | - Nikolay E. Nifantiev
- Laboratory of Glycoconjugate Chemistry, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| |
Collapse
|
11
|
Abbas M, Maalej M, Nieto-Fabregat F, Thépaut M, Kleman JP, Ayala I, Molinaro A, Simorre JP, Marchetti R, Fieschi F, Laguri C. The unique 3D arrangement of macrophage galactose lectin enables Escherichia coli lipopolysaccharide recognition through two distinct interfaces. PNAS NEXUS 2023; 2:pgad310. [PMID: 37780233 PMCID: PMC10538476 DOI: 10.1093/pnasnexus/pgad310] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 09/14/2023] [Indexed: 10/03/2023]
Abstract
Lipopolysaccharides are a hallmark of gram-negative bacteria, and their presence at the cell surface is key for bacterial integrity. As surface-exposed components, they are recognized by immunity C-type lectin receptors present on antigen-presenting cells. Human macrophage galactose lectin binds Escherichia coli surface that presents a specific glycan motif. Nevertheless, this high-affinity interaction occurs regardless of the integrity of its canonical calcium-dependent glycan-binding site. NMR of macrophage galactose-type lectin (MGL) carbohydrate recognition domain and complete extracellular domain revealed a glycan-binding site opposite to the canonical site. A model of trimeric macrophage galactose lectin was determined based on a combination of small-angle X-ray scattering and AlphaFold. A disulfide bond positions the carbohydrate recognition domain perpendicular to the coiled-coil domain. This unique configuration for a C-type lectin orients the six glycan sites of MGL in an ideal position to bind lipopolysaccharides at the bacterial surface with high avidity.
Collapse
Affiliation(s)
- Massilia Abbas
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble 38000, France
| | - Meriem Maalej
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble 38000, France
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Ferran Nieto-Fabregat
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Michel Thépaut
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble 38000, France
| | - Jean-Philippe Kleman
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble 38000, France
| | - Isabel Ayala
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble 38000, France
| | - Antonio Molinaro
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Jean-Pierre Simorre
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble 38000, France
| | - Roberta Marchetti
- Department of Chemical Sciences, University of Naples Federico II, Naples 80126, Italy
| | - Franck Fieschi
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble 38000, France
- Institut Universitaire de France (IUF), Paris, France
| | - Cedric Laguri
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale, Grenoble 38000, France
| |
Collapse
|
12
|
Abstract
It has been widely appreciated that numerous bacterial species express chitinases for the purpose of degrading environmental chitin. However, chitinases and chitin-binding proteins are also expressed by pathogenic bacterial species during infection even though mammals do not produce chitin. Alternative molecular targets are therefore likely present within the host. Here, we will describe our current understanding of chitinase/chitin-binding proteins as virulence factors that promote bacterial colonization and infection. The targets of these chitinases in the host have been shown to include immune system components, mucins, and surface glycans. Bacterial chitinases have also been shown to interact with other microorganisms, targeting the peptidoglycan or chitin in the bacterial and fungal cell wall, respectively. This review highlights that even though the name "chitinase" implies activity toward chitin, chitinases can have a wide diversity of targets, including ones relevant to host infection. Chitinases may therefore be useful as a target of future anti-infective therapeutics.
Collapse
Affiliation(s)
- Jason R. Devlin
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| | - Judith Behnsen
- Department of Microbiology and Immunology, University of Illinois Chicago, Chicago, Illinois, USA
| |
Collapse
|
13
|
Le HT, Liu M, Grimes CL. Application of bioanalytical and computational methods in decoding the roles of glycans in host-pathogen interactions. Curr Opin Chem Biol 2023; 74:102301. [PMID: 37080155 PMCID: PMC10296625 DOI: 10.1016/j.cbpa.2023.102301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 04/22/2023]
Abstract
Host-pathogen interactions (HPIs) are complex processes that require tight regulation. A common regulatory mechanism of HPIs is through glycans of either host cells or pathogens. Due to their diverse sequences, complex structures, and conformations, studies of glycans require highly sensitive and powerful tools. Recent improvements in technology have enabled the application of many bioanalytical techniques and modeling methods to investigate glycans and their mechanisms in HPIs. This mini-review highlights how these advances have been used to understand the role glycans play in HPIs in the past 2 years.
Collapse
Affiliation(s)
- Ha T Le
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Min Liu
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Catherine L Grimes
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA; Department of Biological Sciences, University of Delaware, Newark, DE, USA.
| |
Collapse
|
14
|
Chaurasia R, Vinetz JM. In silico prediction of molecular mechanisms of toxicity mediated by the leptospiral PF07598 gene family-encoded virulence-modifying proteins. Front Mol Biosci 2023; 9:1092197. [PMID: 36756251 PMCID: PMC9900628 DOI: 10.3389/fmolb.2022.1092197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/20/2022] [Indexed: 01/24/2023] Open
Abstract
Mechanisms of leptospirosis pathogenesis remain unclear despite the identification of a number of potential leptospiral virulence factors. We recently demonstrated potential mechanisms by which the virulence-modifying (VM) proteins-defined as containing a Domain of Unknown function (DUF1561), encoded by the PF07598 gene family-found only in group 1 pathogenic Leptospira-might mediate the clinical pathogenesis of leptospirosis. VM proteins belongs to classical AB toxin paradigm though have a unique AB domain architecture, unlike other AB toxins such as diphtheria toxin, pertussis toxin, shiga toxin, or ricin toxin which are typically encoded by two or more genes and self-assembled into a multi-domain holotoxin. Leptospiral VM proteins are secreted R-type lectin domain-containing exotoxins with discrete N-terminal ricin B-like domains involved in host cell surface binding, and a C-terminal DNase/toxin domain. Here we use the artificial intelligence-based AlphaFold algorithm and other computational tools to predict and elaborate on details of the VM protein structure-function relationship. Comparative AlphaFold and CD-spectroscopy defined the consistent secondary structure (Helix and ß-sheet) content, and the stability of the functional domains were further supported by molecular dynamics simulation. VM proteins comprises distinctive lectic family (QxW)3 motifs, the Mycoplasma CARDS toxin (D3 domain, aromatic patches), C-terminal similarity with mammalian DNase I. In-silico study proposed that Gln412, Gln523, His533, Thr59 are the high binding energy or ligand binding residues plausibly anticipates in the functional activities. Divalent cation (Mg+2-Gln412) and phosphate ion (PO4]-3-Arg615) interaction further supports the functional activities driven by C-terminal domain. Computation-driven structure-function studies of VM proteins will guide experimentation towards mechanistic understandings of leptospirosis pathogenesis, which underlie development of new therapeutic and preventive measures for this devastating disease.
Collapse
|
15
|
Reis SF, Martins VJ, Bastos R, Lima T, Correia VG, Pinheiro BA, Silva LM, Palma AS, Ferreira P, Vilanova M, Coimbra MA, Coelho E. Feasibility of Brewer's Spent Yeast Microcapsules as Targeted Oral Carriers. Foods 2023; 12:246. [PMID: 36673340 PMCID: PMC9857821 DOI: 10.3390/foods12020246] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/15/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
Brewer's spent yeast (BSY) microcapsules have a complex network of cell-wall polysaccharides that are induced by brewing when compared to the baker's yeast (Saccharomyces cerevisiae) microcapsules. These are rich in (β1→3)-glucans and covalently linked to (α1→4)- and (β1→4)-glucans in addition to residual mannoproteins. S. cerevisiae is often used as a drug delivery system due to its immunostimulatory potential conferred by the presence of (β1→3)-glucans. Similarly, BSY microcapsules could also be used in the encapsulation of compounds or drug delivery systems with the advantage of resisting digestion conferred by (β1→4)-glucans and promoting a broader immunomodulatory response. This work aims to study the feasibility of BSY microcapsules that are the result of alkali and subcritical water extraction processes, as oral carriers for food and biomedical applications by (1) evaluating the resistance of BSY microcapsules to in vitro digestion (IVD), (2) their recognition by the human Dectin-1 immune receptor after IVD, and (3) the recognition of IVD-solubilized material by different mammalian immune receptors. IVD digested 44-63% of the material, depending on the extraction process. The non-digested material, despite some visible agglutination and deformation of the microcapsules, preserved their spherical shape and was enriched in (β1→3)-glucans. These microcapsules were all recognized by the human Dectin-1 immune receptor. The digested material was differentially recognized by a variety of lectins of the immune system related to (β1→3)-glucans, glycogen, and mannans. These results show the potential of BSY microcapsules to be used as oral carriers for food and biomedical applications.
Collapse
Affiliation(s)
- Sofia F. Reis
- REQUIMTE-LAQV, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Vitor J. Martins
- REQUIMTE-LAQV, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rita Bastos
- REQUIMTE-LAQV, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Tânia Lima
- I3S, Institute for Research in Innovation in Health, University of Porto, 4200-135 Porto, Portugal
| | - Viviana G. Correia
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Benedita A. Pinheiro
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Lisete M. Silva
- REQUIMTE-LAQV, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Angelina S. Palma
- UCIBIO—Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
| | - Paula Ferreira
- CICECO, Department of Materials and Ceramic Engineering, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Manuel Vilanova
- I3S, Institute for Research in Innovation in Health, University of Porto, 4200-135 Porto, Portugal
- IBMC, Institute for Molecular and Cell Biology, University of Porto, 4200-135 Porto, Portugal
- ICBAS, School of Medicine and Biomedical Sciences, University of Porto, 4050-313 Porto, Portugal
| | - Manuel A. Coimbra
- REQUIMTE-LAQV, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Elisabete Coelho
- REQUIMTE-LAQV, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| |
Collapse
|
16
|
Echeverri D, Orozco J. Glycan-Based Electrochemical Biosensors: Promising Tools for the Detection of Infectious Diseases and Cancer Biomarkers. Molecules 2022; 27:8533. [PMID: 36500624 PMCID: PMC9736010 DOI: 10.3390/molecules27238533] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/20/2022] [Accepted: 11/24/2022] [Indexed: 12/12/2022] Open
Abstract
Glycan-based electrochemical biosensors are emerging as analytical tools for determining multiple molecular targets relevant to diagnosing infectious diseases and detecting cancer biomarkers. These biosensors allow for the detection of target analytes at ultra-low concentrations, which is mandatory for early disease diagnosis. Nanostructure-decorated platforms have been demonstrated to enhance the analytical performance of electrochemical biosensors. In addition, glycans anchored to electrode platforms as bioreceptors exhibit high specificity toward biomarker detection. Both attributes offer a synergy that allows ultrasensitive detection of molecular targets of clinical interest. In this context, we review recent advances in electrochemical glycobiosensors for detecting infectious diseases and cancer biomarkers focused on colorectal cancer. We also describe general aspects of structural glycobiology, definitions, and classification of electrochemical biosensors and discuss relevant works on electrochemical glycobiosensors in the last ten years. Finally, we summarize the advances in electrochemical glycobiosensors and comment on some challenges and limitations needed to advance toward real clinical applications of these devices.
Collapse
Affiliation(s)
| | - Jahir Orozco
- Max Planck Tandem Group in Nanobioengineering, Institute of Chemistry, Faculty of Natural and Exact Sciences, University of Antioquia, Complejo Ruta N, Calle 67 N°52–20, Medellin 050010, Colombia
| |
Collapse
|
17
|
Abstract
Through their specific interactions with proteins, cellular glycans play key roles in a wide range of physiological and pathological processes. One of the main goals of research in the areas of glycobiology and glycomedicine is to understand glycan-protein interactions at the molecular level. Over the past two decades, glycan microarrays have become powerful tools for the rapid evaluation of interactions between glycans and proteins. In this review, we briefly describe methods used for the preparation of glycan probes and the construction of glycan microarrays. Next, we highlight applications of glycan microarrays to rapid profiling of glycan-binding patterns of plant, animal and pathogenic lectins, as well as other proteins. Finally, we discuss other important uses of glycan microarrays, including the rapid analysis of substrate specificities of carbohydrate-active enzymes, the quantitative determination of glycan-protein interactions, discovering high-affinity or selective ligands for lectins, and identifying functional glycans within cells. We anticipate that this review will encourage researchers to employ glycan microarrays in diverse glycan-related studies.
Collapse
Affiliation(s)
- Yujun Kim
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| | - Ji Young Hyun
- Department of Drug Discovery, Data Convergence Drug Research Center, Korea Research Institute of Chemical Technology (KRICT), Daejeon 34114, Republic of Korea.
| | - Injae Shin
- Department of Chemistry, Yonsei University, 03722 Seoul, Republic of Korea.
| |
Collapse
|
18
|
Kaplonek P, Seeberger PH. Glycan Microarrays Containing Synthetic Streptococcus pneumoniae CPS Fragments and Their Application to Vaccine Development. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2460:193-206. [PMID: 34972938 DOI: 10.1007/978-1-0716-2148-6_12] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Streptococcus pneumoniae is the leading source of life-endangering diseases like pneumonia, septicemia, and meningitis, as well as a major cause of death in children under 5 years old in developing countries. At least 98 serotypes of S. pneumoniae can be distinguished based on their structurally distinct capsular polysaccharides (CPS). Currently available CPS-based pneumococcal vaccines contain serotypes most frequently associated with invasive pneumococcal diseases. The polysaccharides used in commercial conjugate-vaccines are isolated from bacteria cultures comprising many laborious and operationally challenging steps followed by depolymerization of long polysaccharides into small fragments and their conjugation to the carrier protein. The medicinal chemistry approach for glycoconjugate vaccine development offers an exciting alternative to CPS isolation for a broad range of different glycan antigens. Glycan arrays containing well-defined synthetic glycans of CPS fragments and repeating units are used as a platform for the high-throughput screening of various serum samples and identification of protective glycotopes for vaccine candidates.
Collapse
Affiliation(s)
- Paulina Kaplonek
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universitat Berlin, Berlin, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany.
- Institute of Chemistry and Biochemistry, Freie Universitat Berlin, Berlin, Germany.
| |
Collapse
|
19
|
Schön K, Lindenwald DL, Monteiro JT, Glanz J, Jung K, Becker SC, Lepenies B. Vector and Host C-Type Lectin Receptor (CLR)-Fc Fusion Proteins as a Cross-Species Comparative Approach to Screen for CLR-Rift Valley Fever Virus Interactions. Int J Mol Sci 2022; 23:ijms23063243. [PMID: 35328665 PMCID: PMC8954825 DOI: 10.3390/ijms23063243] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 12/25/2022] Open
Abstract
Rift Valley fever virus (RVFV) is a mosquito-borne bunyavirus endemic to Africa and the Arabian Peninsula, which causes diseases in humans and livestock. C-type lectin receptors (CLRs) represent a superfamily of pattern recognition receptors that were reported to interact with diverse viruses and contribute to antiviral immune responses but may also act as attachment factors or entry receptors in diverse species. Human DC-SIGN and L-SIGN are known to interact with RVFV and to facilitate viral host cell entry, but the roles of further host and vector CLRs are still unknown. In this study, we present a CLR–Fc fusion protein library to screen RVFV–CLR interaction in a cross-species approach and identified novel murine, ovine, and Aedes aegypti RVFV candidate receptors. Furthermore, cross-species CLR binding studies enabled observations of the differences and similarities in binding preferences of RVFV between mammalian CLR homologues, as well as more distant vector/host CLRs.
Collapse
Affiliation(s)
- Kathleen Schön
- Institute for Parasitology & Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hanover, Germany;
- Institute for Immunology & Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hanover, Germany; (D.L.L.); (J.T.M.)
| | - Dimitri L. Lindenwald
- Institute for Immunology & Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hanover, Germany; (D.L.L.); (J.T.M.)
| | - João T. Monteiro
- Institute for Immunology & Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hanover, Germany; (D.L.L.); (J.T.M.)
| | - Julien Glanz
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, 30559 Hanover, Germany; (J.G.); (K.J.)
| | - Klaus Jung
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, 30559 Hanover, Germany; (J.G.); (K.J.)
| | - Stefanie C. Becker
- Institute for Parasitology & Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hanover, Germany;
- Correspondence: (S.C.B.); (B.L.)
| | - Bernd Lepenies
- Institute for Immunology & Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, 30559 Hanover, Germany; (D.L.L.); (J.T.M.)
- Correspondence: (S.C.B.); (B.L.)
| |
Collapse
|
20
|
Glycan-mediated molecular interactions in bacterial pathogenesis. Trends Microbiol 2022; 30:254-267. [PMID: 34274195 PMCID: PMC8758796 DOI: 10.1016/j.tim.2021.06.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/10/2021] [Accepted: 06/22/2021] [Indexed: 02/06/2023]
Abstract
Glycans are expressed on the surface of nearly all host and bacterial cells. Not surprisingly, glycan-mediated molecular interactions play a vital role in bacterial pathogenesis and host responses against pathogens. Glycan-mediated host-pathogen interactions can benefit the pathogen, host, or both. Here, we discuss (i) bacterial glycans that play a critical role in bacterial colonization and/or immune evasion, (ii) host glycans that are utilized by bacteria for pathogenesis, and (iii) bacterial and host glycans involved in immune responses against pathogens. We further discuss (iv) opportunities and challenges for transforming these research findings into more effective antibacterial strategies, and (v) technological advances in glycoscience that have helped to accelerate progress in research. These studies collectively offer valuable insights into new perspectives on antibacterial strategies that may effectively tackle the drug-resistant pathogens that are rapidly spreading globally.
Collapse
|
21
|
Oinam L, Minoshima F, Tateno H. Glycan profiling of the gut microbiota by Glycan-seq. ISME COMMUNICATIONS 2022; 2:1. [PMID: 37938656 PMCID: PMC9723764 DOI: 10.1038/s43705-021-00084-2] [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: 08/05/2021] [Revised: 12/09/2021] [Accepted: 12/16/2021] [Indexed: 05/07/2023]
Abstract
Bacterial glycans modulate the cross talk between the gut microbiota and its host. However, little is known about these glycans because of the lack of appropriate technology to study them. In this study, we applied Glycan-seq technology for glycan profiling of the intact gut microbiota of mice. The evaluation of cultured gram-positive (Deinococcus radiodurans) and gram-negative (Escherichia coli) bacteria showed significantly distinct glycan profiles between these bacteria, which were selected and further analyzed by flow cytometry. The results of flow cytometry agreed well with those obtained by Glycan-seq, indicating that Glycan-seq can be used for bacterial glycan profiling. We thus applied Glycan-seq for comparative glycan profiling of pups and adult mice gut microbiotas. The glycans of the pups and adult microbiotas had significantly distinct glycan profiles, which reflect the different bacterial compositions of pups and adult gut microbiotas based on 16S rRNA gene sequencing.α2-6Sia-binders bound specifically to the pups microbiota. Lectin pull-down followed by 16S rRNA gene sequencing of the pups microbiota identified Lactobacillaceae as the most abundant bacterial family with glycans reacting with α2-6Sia-binders. The Glycan-seq system can reveal the glycan profile of the intact bacterial gut microbiota.
Collapse
Affiliation(s)
- Lalhaba Oinam
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Fumi Minoshima
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Hiroaki Tateno
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
- AMED-Prime, AMED, Tsukuba Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
| |
Collapse
|
22
|
Lundstrøm J, Korhonen E, Lisacek F, Bojar D. LectinOracle: A Generalizable Deep Learning Model for Lectin-Glycan Binding Prediction. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022; 9:e2103807. [PMID: 34862760 PMCID: PMC8728848 DOI: 10.1002/advs.202103807] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 11/03/2021] [Indexed: 05/07/2023]
Abstract
Ranging from bacterial cell adhesion over viral cell entry to human innate immunity, glycan-binding proteins or lectins are abound in nature. Widely used as staining and characterization reagents in cell biology and crucial for understanding the interactions in biological systems, lectins are a focal point of study in glycobiology. Yet the sheer breadth and depth of specificity for diverse oligosaccharide motifs has made studying lectins a largely piecemeal approach, with few options to generalize. Here, LectinOracle, a model combining transformer-based representations for proteins and graph convolutional neural networks for glycans to predict their interaction, is presented. Using a curated data set of 564,647 unique protein-glycan interactions, it is shown that LectinOracle predictions agree with literature-annotated specificities for a wide range of lectins. Using a range of specialized glycan arrays, it is shown that LectinOracle predictions generalize to new glycans and lectins, with qualitative and quantitative agreement with experimental data. It is further demonstrated that LectinOracle can be used to improve lectin classification, accelerate lectin directed evolution, predict epidemiological outcomes in the context of influenza virus, and analyze whole lectomes in host-microbe interactions. It is envisioned that the herein presented platform will advance both the study of lectins and their role in (glyco)biology.
Collapse
Affiliation(s)
- Jon Lundstrøm
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburg41390Sweden
- Wallenberg Centre for Molecular and Translational MedicineUniversity of GothenburgGothenburg41390Sweden
| | - Emma Korhonen
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburg41390Sweden
- Wallenberg Centre for Molecular and Translational MedicineUniversity of GothenburgGothenburg41390Sweden
| | - Frédérique Lisacek
- Swiss Institute of BioinformaticsGeneva1227Switzerland
- Computer Science DepartmentUniGeGeneva1227Switzerland
- Section of BiologyUniGeGeneva1205Switzerland
| | - Daniel Bojar
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburg41390Sweden
- Wallenberg Centre for Molecular and Translational MedicineUniversity of GothenburgGothenburg41390Sweden
| |
Collapse
|
23
|
Akune Y, Arpinar S, Silva LM, Palma AS, Tajadura-Ortega V, Aoki-Kinoshita KF, Ranzinger R, Liu Y, Feizi T. OUP accepted manuscript. Glycobiology 2022; 32:552-555. [PMID: 35352122 PMCID: PMC9191619 DOI: 10.1093/glycob/cwac018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 03/07/2022] [Accepted: 03/08/2022] [Indexed: 11/25/2022] Open
Abstract
Glycan microarrays are essential tools in glycobiology and are being widely used for assignment of glycan ligands in diverse glycan recognition systems. We have developed a new software, called Carbohydrate microArray Analysis and Reporting Tool (CarbArrayART), to address the need for a distributable application for glycan microarray data management. The main features of CarbArrayART include: (i) Storage of quantified array data from different array layouts with scan data and array-specific metadata, such as lists of arrayed glycans, array geometry, information on glycan-binding samples, and experimental protocols. (ii) Presentation of microarray data as charts, tables, and heatmaps derived from the average fluorescence intensity values that are calculated based on the imaging scan data and array geometry, as well as filtering and sorting functions according to monosaccharide content and glycan sequences. (iii) Data export for reporting in Word, PDF, and Excel formats, together with metadata that are compliant with the guidelines of MIRAGE (Minimum Information Required for A Glycomics Experiment). CarbArrayART is designed for routine use in recording, storage, and management of any slide-based glycan microarray experiment. In conjunction with the MIRAGE guidelines, CarbArrayART addresses issues that are critical for glycobiology, namely, clarity of data for evaluation of reproducibility and validity.
Collapse
Affiliation(s)
- Yukie Akune
- Corresponding author: The Glycosciences Laboratory, Burlington Danes Building Room 509, Du Cane Road, London W12 0NN, United Kingdom.
| | - Sena Arpinar
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States
| | - Lisete M Silva
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College, Du Cane Road, London W12 0NN, United Kingdom
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Angelina S Palma
- UCIBIO, Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University Lisbon, 2819-516 Caparica, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, School of Science and Technology, NOVA University Lisbon, Lisbon, 2819-516 Caparica, Portugal
| | - Virginia Tajadura-Ortega
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College, Du Cane Road, London W12 0NN, United Kingdom
| | - Kiyoko F Aoki-Kinoshita
- Glycan and Life Systems Integration Center (GaLSIC), Soka University, 1-236 Tangi-machi, Hachioji, Tokyo 192-8577, Japan
| | - René Ranzinger
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, United States
| | - Yan Liu
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College, Du Cane Road, London W12 0NN, United Kingdom
| | - Ten Feizi
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College, Du Cane Road, London W12 0NN, United Kingdom
| |
Collapse
|
24
|
Klamer ZL, Harris CM, Beirne JM, Kelly JE, Zhang J, Haab BB. OUP accepted manuscript. Glycobiology 2022; 32:679-690. [PMID: 35352123 PMCID: PMC9280547 DOI: 10.1093/glycob/cwac022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 11/12/2022] Open
Abstract
Glycan arrays continue to be the primary resource for determining the glycan-binding specificity of proteins. The volume and diversity of glycan-array data are increasing, but no common method and resource exist to analyze, integrate, and use the available data. To meet this need, we developed a resource of analyzed glycan-array data called CarboGrove. Using the ability to process and interpret data from any type of glycan array, we populated the database with the results from 35 types of glycan arrays, 13 glycan families, 5 experimental methods, and 19 laboratories or companies. In meta-analyses of glycan-binding proteins, we observed glycan-binding specificities that were not uncovered from single sources. In addition, we confirmed the ability to efficiently optimize selections of glycan-binding proteins to be used in experiments for discriminating between closely related motifs. Through descriptive reports and a programmatically accessible Application Programming Interface, CarboGrove yields unprecedented access to the wealth of glycan-array data being produced and powerful capabilities for both experimentalists and bioinformaticians.
Collapse
Affiliation(s)
- Zachary L Klamer
- Department of Cancer and Cell Biology, Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49503, United States
| | | | | | | | | | - Brian B Haab
- Corresponding author: Van Andel Institute, 333 Bostwick Ave NE, Grand Rapids, MI 49504, United States.
| |
Collapse
|
25
|
Fischer S, Stegmann F, Gnanapragassam VS, Lepenies B. From structure to function – Ligand recognition by myeloid C-type lectin receptors. Comput Struct Biotechnol J 2022; 20:5790-5812. [DOI: 10.1016/j.csbj.2022.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 10/14/2022] [Accepted: 10/14/2022] [Indexed: 11/29/2022] Open
|
26
|
Ruprecht C, Pfrengle F. Synthetic Plant Glycan Microarrays as Tools for Plant Biology. Methods Mol Biol 2022; 2460:115-125. [PMID: 34972933 DOI: 10.1007/978-1-0716-2148-6_7] [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: 06/14/2023]
Abstract
Chemically synthesized plant oligosaccharides have recently evolved as powerful molecular tools for plant cell wall biology. Synthetic plant glycan microarrays equipped with these oligosaccharides enable high-throughput analyses of glycan-binding proteins and carbohydrate-active enzymes. To produce these glycan microarrays, small amounts of glycan solution are printed on suitable surfaces for covalent or non-covalent immobilization. Synthetic plant glycan microarrays have been used for example to map the epitopes of plant cell wall-directed antibodies, to characterize glycosyl hydrolases and glycosyl transferases, and to analyze lectin binding. In this chapter, detailed experimental procedures for the production of synthetic glycan microarrays and their use for the characterization of cell wall glycan-directed antibodies are described.
Collapse
Affiliation(s)
- Colin Ruprecht
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Fabian Pfrengle
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.
| |
Collapse
|
27
|
Uzawa H, Kondo S, Nagatsuka T, Miyaguchi H, Seto Y, Oshita A, Dohi H, Nishida Y, Saito M, Tamiya E. Assembly of Glycochips with Mammalian GSLs Mimetics toward the On-site Detection of Biological Toxins. ACS OMEGA 2021; 6:32597-32606. [PMID: 34901608 PMCID: PMC8655786 DOI: 10.1021/acsomega.1c04154] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/01/2021] [Indexed: 05/09/2023]
Abstract
According to our previously proposed scheme, each of three kinds of glycosphingolipid (GSL) derivatives, that is, lactosyl ceramide [Lac-Cer (1)] and gangliosides [GM1-Cer (2) and GT1b-Cer (3)], was installed onto the glass surface modified with Au nanoparticles. In the present study, we tried to apply microwave irradiation to promote their installing reactions. Otherwise, this procedure takes a lot of time as long as a conventional self-assembled monolayer (SAM) technique is applied. Using an advanced microwave reactor capable of adjusting ambient temperatures within a desired range, various GSL glycochips were prepared from the derivatives (1)-(3) under different microwave irradiation conditions. The overall assembling process was programed with an IC controller to finish in 1 h, and the derived GSL glycochips were evaluated in the analysis of three kinds of biological toxins [a Ricinus agglutinin (RCA120), botulinum toxin (BTX), and cholera toxin (CTX)] using a localized surface plasmon resonance (LSPR) biosensor. In the LSPR analysis, most of the irradiated GSL chips showed an enhanced response to the targeting toxin when they were irradiated under optimal temperature conditions. Lac-Cer chips showed the highest response to RCA120 (an agglutinin with β-D-Gal specificity) when the microwave irradiation was conducted at 30-35 °C. Compared to our former Lac-Cer glycochips with the conventional SAM condition, their response was enhanced by 3.6 times. Analogously, GT1b chips gained an approximately 4.1 times enhancement in their response to botulinum type C toxin (BTX/C) when the irradiation was conducted around at 45-60 °C. In the LSPR evaluation of the GM1-Cer glycochips using CTX, an optimal condition also appeared at around 30-35 °C. On the other hand, the microwave irradiation did not lead to a notable increase compared to the former GM1-Cer chips derived with the SAM technique. Judging from these experimental results, the microwave irradiation effectively promotes the installing process for all the three kinds of the GSL derivatives, while the optimal thermal condition becomes different from each other. Many bacterial and botanic proteinous toxins are composed of such carbohydrate binding domains or subunits that can discriminate both the key epitope structure and the dimension of glycoconjugates on the host cell surface. It is assumed that the optimal irradiation and thermal conditions are required to array these semi-synthetic GSL derivatives on the Au nanoparticles in a proper density and geometry for tight adhesion with each of the biological toxins.
Collapse
Affiliation(s)
- Hirotaka Uzawa
- Nanomaterials
Research Institute, Tsukuba Center, Tsukuba Central, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba 305-8565, Japan
| | - Satoshi Kondo
- Nanomaterials
Research Institute, Tsukuba Center, Tsukuba Central, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba 305-8565, Japan
| | - Takehiro Nagatsuka
- Nanomaterials
Research Institute, Tsukuba Center, Tsukuba Central, National Institute of Advanced Industrial Science and Technology, 1-1-1 Higashi, Tsukuba 305-8565, Japan
| | - Hajime Miyaguchi
- National
Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Yasuo Seto
- National
Research Institute of Police Science, 6-3-1 Kashiwanoha, Kashiwa, Chiba 277-0882, Japan
| | - Aguri Oshita
- Graduate
School of Environmental Horticulture, Chiba
University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan
- Graduate
School of Advanced Integration Science, Chiba University, 1-33
Yayoi-cho, Inage-ku, Chiba, Chiba 263-8522, Japan
| | - Hirofumi Dohi
- Graduate
School of Environmental Horticulture, Chiba
University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan
- Graduate
School of Advanced Integration Science, Chiba University, 1-33
Yayoi-cho, Inage-ku, Chiba, Chiba 263-8522, Japan
| | - Yoshihiro Nishida
- Graduate
School of Environmental Horticulture, Chiba
University, 648 Matsudo, Matsudo, Chiba 271-8510, Japan
- Graduate
School of Advanced Integration Science, Chiba University, 1-33
Yayoi-cho, Inage-ku, Chiba, Chiba 263-8522, Japan
| | - Masato Saito
- Department
of Applied Physics, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Eiichi Tamiya
- Department
of Applied Physics, Graduate School of Engineering, Osaka University, 2-1
Yamadaoka, Suita, Osaka 565-0871, Japan
| |
Collapse
|
28
|
Subramani B, Chaudhary PM, Kikkeri R. A Cell-Culture Technique to Encode Glyco-Nanoparticles Selectivity. Chem Asian J 2021; 16:3900-3904. [PMID: 34619024 DOI: 10.1002/asia.202101015] [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: 08/30/2021] [Revised: 10/06/2021] [Indexed: 11/07/2022]
Abstract
Nanoparticles (NPs) embedded with bioactive ligands such as carbohydrates, peptides, and nucleic acid have emerged as a potential tool to target biological processes. Traditional in vitro assays performed under statistic conditions may result in non-specific outcome sometimes, mainly because of the sedimentation and self-assembly nature of NPs. Inverted cell-culture assay allows for flexible and accurate detection of the receptor-mediated uptake and cytotoxicity of NPs. By combining this technique with glyco-gold nanoparticles, cellular internalization and cytotoxicity were investigated. Regioselective glycosylation patterns and shapes of the NPs could tune the receptors' binding affinity, resulting in precise cellular uptake of gold nanoparticles (AuNPs). Two cell lines HepG2 and HeLa were probed with galactosamine-embedded fluorescent AuNPs, revealing significant differences in cytotoxicity and uptake mechanism in upright and invert in vitro cell-culture assay, high-specificity toward uptake, and allowing for a rapid screening and optimization technique.
Collapse
Affiliation(s)
- Balamurugan Subramani
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Preeti Madhukar Chaudhary
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| | - Raghavendra Kikkeri
- Department of Chemistry, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pune, 411008, India
| |
Collapse
|
29
|
Bennett A, Hull J, Jolinon N, Tordo J, Moss K, Binns E, Mietzsch M, Hagemann C, Linden RM, Serio A, Chipman P, Sousa D, Broecker F, Seeberger P, Henckaerts E, McKenna R, Agbandje-McKenna M. Comparative structural, biophysical, and receptor binding study of true type and wild type AAV2. J Struct Biol 2021; 213:107795. [PMID: 34509611 PMCID: PMC9918372 DOI: 10.1016/j.jsb.2021.107795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/27/2021] [Accepted: 09/05/2021] [Indexed: 01/25/2023]
Abstract
Adeno-associated viruses (AAV) are utilized as gene transfer vectors in the treatment of monogenic disorders. A variant, rationally engineered based on natural AAV2 isolates, designated AAV-True Type (AAV-TT), is highly neurotropic compared to wild type AAV2 in vivo, and vectors based on it, are currently being evaluated for central nervous system applications. AAV-TT differs from AAV2 by 14 amino acids, including R585S and R588T, two residues previously shown to be essential for heparan sulfate binding of AAV2. The capsid structures of AAV-TT and AAV2 visualized by cryo-electron microscopy at 3.4 and 3.0 Å resolution, respectively, highlighted structural perturbations at specific amino acid differences. Differential scanning fluorimetry (DSF) performed at different pH conditions demonstrated that the melting temperature (Tm) of AAV2 was consistently ∼5 °C lower than AAV-TT, but both showed maximal stability at pH 5.5, corresponding to the pH in the late endosome, proposed as required for VP1u externalization to facilitate endosomal escape. Reintroduction of arginines at positions 585 and 588 in AAV-TT caused a reduction in Tm, demonstrating that the lack of basic amino acids at these positions are associated with capsid stability. These results provide structural and thermal annotation of AAV2/AAV-TT residue differences, that account for divergent cell binding, transduction, antigenic reactivity, and transduction of permissive tissues between the two viruses. Specifically, these data indicate that AAV-TT may not utilize a glycan receptor mediated pathway to enter cells and may have lower antigenic properties as compared to AAV2.
Collapse
Affiliation(s)
- Antonette Bennett
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Joshua Hull
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Nelly Jolinon
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK
| | | | - Katie Moss
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Enswert Binns
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Mario Mietzsch
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Cathleen Hagemann
- Centre for Craniofacial & Regenerative Biology, King's College London, London SE19RT, UK; The Francis Crick Institute, London NW1 1AT, UK
| | | | - Andrea Serio
- Centre for Craniofacial & Regenerative Biology, King's College London, London SE19RT, UK; The Francis Crick Institute, London NW1 1AT, UK
| | - Paul Chipman
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Duncan Sousa
- Biological Science Imaging Resource, Department of Biological Sciences, Florida State University, 89 Chieftan Way Rm 119, Tallahassee, FL 32306, USA
| | - Felix Broecker
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, 14476 Potsdam, Germany
| | - Peter Seeberger
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, 14195 Berlin, Germany
| | - Els Henckaerts
- Department of Infectious Diseases, School of Immunology and Microbial Sciences, King's College London, London SE1 9RT, UK; Laboratory of Viral Cell Biology and Therapeutics, Department of Cellular and Molecular Medicine, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium.
| | - Robert McKenna
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA.
| | - Mavis Agbandje-McKenna
- Department of Biochemistry & Molecular Biology, Center for Structural Biology, The McKnight Brain Institute, College of Medicine, University of Florida, Gainesville, FL 32610, USA
| |
Collapse
|
30
|
Willment JA. Fc-conjugated C-type lectin receptors: Tools for understanding host-pathogen interactions. Mol Microbiol 2021; 117:632-660. [PMID: 34709692 DOI: 10.1111/mmi.14837] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 12/24/2022]
Abstract
The use of soluble fusion proteins of pattern recognition receptors (PRRs) used in the detection of exogenous and endogenous ligands has helped resolve the roles of PRRs in the innate immune response to pathogens, how they shape the adaptive immune response, and function in maintaining homeostasis. Using the immunoglobulin (Ig) crystallizable fragment (Fc) domain as a fusion partner, the PRR fusion proteins are soluble, stable, easily purified, have increased affinity due to the Fc homodimerization properties, and consequently have been used in a wide range of applications such as flow cytometry, screening of protein and glycan arrays, and immunofluorescent microscopy. This review will predominantly focus on the recognition of pathogens by the cell membrane-expressed glycan-binding proteins of the C-type lectin receptor (CLR) subgroup of PRRs. PRRs bind to conserved pathogen-associated molecular patterns (PAMPs), such as glycans, usually located within or on the outer surface of the pathogen. Significantly, many glycans structures are identical on both host and pathogen (e.g. the Lewis (Le) X glycan), allowing the use of Fc CLR fusion proteins with known endogenous and/or exogenous ligands as tools to identify pathogen structures that are able to interact with the immune system. Screens of highly purified pathogen-derived cell wall components have enabled identification of many unique PAMP structures recognized by CLRs. This review highlights studies using Fc CLR fusion proteins, with emphasis on the PAMPs found in fungi, bacteria, viruses, and parasites. The structure and unique features of the different CLR families is presented using examples from a broad range of microbes whenever possible.
Collapse
Affiliation(s)
- Janet A Willment
- Medical Research Council Centre for Medical Mycology, University of Exeter, Exeter, UK
| |
Collapse
|
31
|
Smorodin EP. Prospects and Challenges of the Study of Anti-Glycan Antibodies and Microbiota for the Monitoring of Gastrointestinal Cancer. Int J Mol Sci 2021; 22:ijms222111608. [PMID: 34769037 PMCID: PMC8584091 DOI: 10.3390/ijms222111608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 11/26/2022] Open
Abstract
Over the past decades, a large amount of data has been accumulated in various subfields of glycobiology. However, much clinically relevant data and many tools are still not widely used in medicine. Synthetic glycoconjugates with the known structure of glycans are an accurate tool for the study of glycan-binding proteins. We used polyacrylamide glycoconjugates (PGs) including PGs with tumour-associated glycans (TAGs) in immunoassays to assess the prognostic potential of the serum level of anti-glycan antibodies (AG Abs) in gastrointestinal cancer patients and found an association of AG Abs with survival. The specificity of affinity-isolated AG Abs was investigated using synthetic and natural glycoconjugates. AG Abs showed mainly a low specificity to tumour-associated and tumour-derived mucins; therefore, the protective role of the examined circulating AG Abs against cancer remains a challenge. In this review, our findings are analysed and discussed in the context of the contribution of bacteria to the AG Abs stimulus and cancer progression. Examples of the influence of pathogenic bacteria colonising tumours on cancer progression and patient survival through mechanisms of interaction with tumours and dysregulated immune response are considered. The possibilities and problems of the integrative study of AG Abs and the microbiome using high-performance technologies are discussed.
Collapse
Affiliation(s)
- Eugeniy P Smorodin
- Department of Virology and Immunology, National Institute for Health Development, 11619 Tallinn, Estonia
| |
Collapse
|
32
|
Tsouka A, Hoetzel K, Mende M, Heidepriem J, Paris G, Eickelmann S, Seeberger PH, Lepenies B, Loeffler FF. Probing Multivalent Carbohydrate-Protein Interactions With On-Chip Synthesized Glycopeptides Using Different Functionalized Surfaces. Front Chem 2021; 9:766932. [PMID: 34778215 PMCID: PMC8589469 DOI: 10.3389/fchem.2021.766932] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Accepted: 10/11/2021] [Indexed: 01/01/2023] Open
Abstract
Multivalent ligand-protein interactions are a commonly employed approach by nature in many biological processes. Single glycan-protein interactions are often weak, but their affinity and specificity can be drastically enhanced by engaging multiple binding sites. Microarray technology allows for quick, parallel screening of such interactions. Yet, current glycan microarray methodologies usually neglect defined multivalent presentation. Our laser-based array technology allows for a flexible, cost-efficient, and rapid in situ chemical synthesis of peptide scaffolds directly on functionalized glass slides. Using copper(I)-catalyzed azide-alkyne cycloaddition, different monomer sugar azides were attached to the scaffolds, resulting in spatially defined multivalent glycopeptides on the solid support. Studying their interaction with several different lectins showed that not only the spatially defined sugar presentation, but also the surface functionalization and wettability, as well as accessibility and flexibility, play an essential role in such interactions. Therefore, different commercially available functionalized glass slides were equipped with a polyethylene glycol (PEG) linker to demonstrate its effect on glycan-lectin interactions. Moreover, different monomer sugar azides with and without an additional PEG-spacer were attached to the peptide scaffold to increase flexibility and thereby improve binding affinity. A variety of fluorescently labeled lectins were probed, indicating that different lectin-glycan pairs require different surface functionalization and spacers for enhanced binding. This approach allows for rapid screening and evaluation of spacing-, density-, ligand and surface-dependent parameters, to find optimal lectin binders.
Collapse
Affiliation(s)
- Alexandra Tsouka
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Kassandra Hoetzel
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Marco Mende
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Jasmin Heidepriem
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Grigori Paris
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of System Dynamics and Friction Physics, Institute of Mechanics, Technical University of Berlin, Berlin, Germany
| | - Stephan Eickelmann
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| | - Peter H. Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Bernd Lepenies
- Institute for Immunology and Research Center for Emerging Infections and Zoonoses, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Felix F. Loeffler
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
| |
Collapse
|
33
|
Ward EM, Kizer ME, Imperiali B. Strategies and Tactics for the Development of Selective Glycan-Binding Proteins. ACS Chem Biol 2021; 16:1795-1813. [PMID: 33497192 PMCID: PMC9200409 DOI: 10.1021/acschembio.0c00880] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The influences of glycans impact all biological processes, disease states, and pathogenic interactions. Glycan-binding proteins (GBPs), such as lectins, are decisive tools for interrogating glycan structure and function because of their ease of use and ability to selectively bind defined carbohydrate epitopes and glycosidic linkages. GBP reagents are prominent tools for basic research, clinical diagnostics, therapeutics, and biotechnological applications. However, the study of glycans is hindered by the lack of specific and selective protein reagents to cover the massive diversity of carbohydrate structures that exist in nature. In addition, existing GBP reagents often suffer from low affinity or broad specificity, complicating data interpretation. There have been numerous efforts to expand the GBP toolkit beyond those identified from natural sources through protein engineering, to improve the properties of existing GBPs or to engineer novel specificities and potential applications. This review details the current scope of proteins that bind carbohydrates and the engineering methods that have been applied to enhance the affinity, selectivity, and specificity of binders.
Collapse
Affiliation(s)
- Elizabeth M. Ward
- Department of Biology, Massachusetts Institute of Technology, 31 Ames St, Cambridge, MA 02142, USA
- Microbiology Graduate Program, Massachusetts Institute of Technology, 31 Ames St, Cambridge, MA 02142, USA
| | - Megan E. Kizer
- Department of Biology, Massachusetts Institute of Technology, 31 Ames St, Cambridge, MA 02142, USA
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
| | - Barbara Imperiali
- Department of Biology, Massachusetts Institute of Technology, 31 Ames St, Cambridge, MA 02142, USA
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Ave, Cambridge, MA 02139, USA
| |
Collapse
|
34
|
Zheng M, Zheng M, Epstein S, Harnagel AP, Kim H, Lupoli TJ. Chemical Biology Tools for Modulating and Visualizing Gram-Negative Bacterial Surface Polysaccharides. ACS Chem Biol 2021; 16:1841-1865. [PMID: 34569792 DOI: 10.1021/acschembio.1c00341] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Bacterial cells present a wide diversity of saccharides that decorate the cell surface and help mediate interactions with the environment. Many Gram-negative cells express O-antigens, which are long sugar polymers that makeup the distal portion of lipopolysaccharide (LPS) that constitutes the surface of the outer membrane. This review highlights chemical biology tools that have been developed in recent years to facilitate the modulation of O-antigen synthesis and composition, as well as related bacterial polysaccharide pathways, and the detection of unique glycan sequences. Advances in the biochemistry and structural biology of O-antigen biosynthetic machinery are also described, which provide guidance for the design of novel chemical and biomolecular probes. Many of the tools noted here have not yet been utilized in biological systems and offer researchers the opportunity to investigate the complex sugar architecture of Gram-negative cells.
Collapse
Affiliation(s)
- Meng Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Maggie Zheng
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Samuel Epstein
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Alexa P. Harnagel
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Hanee Kim
- Department of Chemistry, New York University, New York, 10003 New York, United States
| | - Tania J. Lupoli
- Department of Chemistry, New York University, New York, 10003 New York, United States
| |
Collapse
|
35
|
Midha A, Goyette-Desjardins G, Goerdeler F, Moscovitz O, Seeberger PH, Tedin K, Bertzbach LD, Lepenies B, Hartmann S. Lectin-Mediated Bacterial Modulation by the Intestinal Nematode Ascaris suum. Int J Mol Sci 2021; 22:ijms22168739. [PMID: 34445445 PMCID: PMC8395819 DOI: 10.3390/ijms22168739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 08/05/2021] [Accepted: 08/11/2021] [Indexed: 11/16/2022] Open
Abstract
Ascariasis is a global health problem for humans and animals. Adult Ascaris nematodes are long-lived in the host intestine where they interact with host cells as well as members of the microbiota resulting in chronic infections. Nematode interactions with host cells and the microbial environment are prominently mediated by parasite-secreted proteins and peptides possessing immunomodulatory and antimicrobial activities. Previously, we discovered the C-type lectin protein AsCTL-42 in the secreted products of adult Ascaris worms. Here we tested recombinant AsCTL-42 for its ability to interact with bacterial and host cells. We found that AsCTL-42 lacks bactericidal activity but neutralized bacterial cells without killing them. Treatment of bacterial cells with AsCTL-42 reduced invasion of intestinal epithelial cells by Salmonella. Furthermore, AsCTL-42 interacted with host myeloid C-type lectin receptors. Thus, AsCTL-42 is a parasite protein involved in the triad relationship between Ascaris, host cells, and the microbiota.
Collapse
Affiliation(s)
- Ankur Midha
- Institute of Immunology, Freie Universität Berlin, 14163 Berlin, Germany;
| | - Guillaume Goyette-Desjardins
- Institute for Immunology & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (G.G.-D.); (B.L.)
| | - Felix Goerdeler
- Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany; (F.G.); (O.M.); (P.H.S.)
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Oren Moscovitz
- Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany; (F.G.); (O.M.); (P.H.S.)
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Peter H. Seeberger
- Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476 Potsdam, Germany; (F.G.); (O.M.); (P.H.S.)
- Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, 14195 Berlin, Germany
| | - Karsten Tedin
- Institute of Microbiology and Epizootics, Freie Universität Berlin, 14163 Berlin, Germany;
| | - Luca D. Bertzbach
- Institute of Virology, Freie Universität Berlin, 14163 Berlin, Germany;
- Department of Viral Transformation, Leibniz Institute for Experimental Virology (HPI), 20251 Hamburg, Germany
| | - Bernd Lepenies
- Institute for Immunology & Research Center for Emerging Infections and Zoonoses (RIZ), University of Veterinary Medicine Hannover, 30559 Hannover, Germany; (G.G.-D.); (B.L.)
| | - Susanne Hartmann
- Institute of Immunology, Freie Universität Berlin, 14163 Berlin, Germany;
- Correspondence:
| |
Collapse
|
36
|
Klamer Z, Haab B. Combined Analysis of Multiple Glycan-Array Datasets: New Explorations of Protein-Glycan Interactions. Anal Chem 2021; 93:10925-10933. [PMID: 34319080 DOI: 10.1021/acs.analchem.1c01739] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Glycan arrays are indispensable for learning about the specificities of glycan-binding proteins. Despite the abundance of available data, the current analysis methods do not have the ability to interpret and use the variety of data types and to integrate information across datasets. Here, we evaluated whether a novel, automated algorithm for glycan-array analysis could meet that need. We developed a regression-tree algorithm with simultaneous motif optimization and packaged it in software called MotifFinder. We applied the software to analyze data from eight different glycan-array platforms with widely divergent characteristics and observed an accurate analysis of each dataset. We then evaluated the feasibility and value of the combined analyses of multiple datasets. In an integrated analysis of datasets covering multiple lectin concentrations, the software determined approximate binding constants for distinct motifs and identified major differences between the motifs that were not apparent from single-concentration analyses. Furthermore, an integrated analysis of data sources with complementary sets of glycans produced broader views of lectin specificity than produced by the analysis of just one data source. MotifFinder, therefore, enables the optimal use of the expanding resource of the glycan-array data and promises to advance the studies of protein-glycan interactions.
Collapse
Affiliation(s)
- Zachary Klamer
- Van Andel Institute, 333 Bostwick NE, Grand Rapids, Michigan 49503, United States
| | - Brian Haab
- Van Andel Institute, 333 Bostwick NE, Grand Rapids, Michigan 49503, United States
| |
Collapse
|
37
|
Mathez G, Cagno V. Viruses Like Sugars: How to Assess Glycan Involvement in Viral Attachment. Microorganisms 2021; 9:1238. [PMID: 34200288 PMCID: PMC8230229 DOI: 10.3390/microorganisms9061238] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022] Open
Abstract
The first step of viral infection requires interaction with the host cell. Before finding the specific receptor that triggers entry, the majority of viruses interact with the glycocalyx. Identifying the carbohydrates that are specifically recognized by different viruses is important both for assessing the cellular tropism and for identifying new antiviral targets. Advances in the tools available for studying glycan-protein interactions have made it possible to identify them more rapidly; however, it is important to recognize the limitations of these methods in order to draw relevant conclusions. Here, we review different techniques: genetic screening, glycan arrays, enzymatic and pharmacological approaches, and surface plasmon resonance. We then detail the glycan interactions of enterovirus D68 and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), highlighting the aspects that need further clarification.
Collapse
Affiliation(s)
| | - Valeria Cagno
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland;
| |
Collapse
|
38
|
Kim D, Rahhal N, Rademacher C. Elucidating Carbohydrate-Protein Interactions Using Nanoparticle-Based Approaches. Front Chem 2021; 9:669969. [PMID: 34046397 PMCID: PMC8144316 DOI: 10.3389/fchem.2021.669969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 04/06/2021] [Indexed: 12/12/2022] Open
Abstract
Carbohydrates are present on every living cell and coordinate important processes such as self/non-self discrimination. They are amongst the first molecular determinants to be encountered when cellular interactions are initiated. In particular, they resemble essential molecular fingerprints such as pathogen-, danger-, and self-associated molecular patterns guiding key decision-making in cellular immunology. Therefore, a deeper understanding of how cellular receptors of the immune system recognize incoming particles, based on their carbohydrate signature and how this information is translated into a biological response, will enable us to surgically manipulate them and holds promise for novel therapies. One approach to elucidate these early recognition events of carbohydrate interactions at cellular surfaces is the use of nanoparticles coated with defined carbohydrate structures. These particles are captured by carbohydrate receptors and initiate a cellular cytokine response. In the case of endocytic receptors, the capturing enables the engulfment of exogenous particles. Thereafter, the particles are sorted and degraded during their passage in the endolysosomal pathway. Overall, these processes are dependent on the nature of the endocytic carbohydrate receptors and consequently reflect upon the carbohydrate patterns on the exogenous particle surface. This interplay is still an under-studied subject. In this review, we summarize the application of nanoparticles as a promising tool to monitor complex carbohydrate-protein interactions in a cellular context and their application in areas of biomedicine.
Collapse
Affiliation(s)
- Dongyoon Kim
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Nowras Rahhal
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, Vienna, Austria
| | - Christoph Rademacher
- Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
- Max F. Perutz Laboratories, Department of Microbiology and Immunobiology, Vienna, Austria
| |
Collapse
|
39
|
Li C, Palma AS, Zhang P, Zhang Y, Gao C, Silva LM, Li Z, Trovão F, Weishaupt M, Seeberger PH, Likhosherstov LM, Piskarev V, Yu J, Westerlind U, Chai W. Non-Covalent Microarrays from Synthetic Amino-Terminating Glycans-Implications in Expanding Glycan Microarray Diversity and Platform Comparison. Glycobiology 2021; 31:931-946. [PMID: 33978739 PMCID: PMC8434801 DOI: 10.1093/glycob/cwab037] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/20/2021] [Accepted: 04/21/2021] [Indexed: 01/23/2023] Open
Abstract
Glycan microarrays have played important roles in detection and specificity assignment of glycan-recognition by proteins. However, the size and diversity of glycan libraries in current microarray systems are small compared to estimated glycomes, and these may lead to missed detection or incomplete assignment. For microarray construction, covalent and non-covalent immobilization are the two types of methods used, but a direct comparison of results from the two platforms is required. Here we develop a chemical strategy to prepare lipid-linked probes from both naturally-derived aldehyde-terminating and synthetic amino-terminating glycans that addresses the two aspects: expansion of sequence-defined glycan libraries and comparison of the two platforms. We demonstrate the specific recognition by plant and mammalian lectins, carbohydrate-binding modules and antibodies, and the overall similarities from the two platforms. Our results provide new knowledge on unique glycan-binding specificities for the immune-receptor Dectin-1 towards β-glucans and the interaction of rotavirus P[19] adhesive protein with mucin O-glycan cores.
Collapse
Affiliation(s)
- Chunxia Li
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy and Shandong Provincial Key laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266237, China
| | - Angelina S Palma
- Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, Portugal
| | - Pengtao Zhang
- Key Laboratory of Marine Drugs, Ministry of Education, School of Medicine and Pharmacy and Shandong Provincial Key laboratory of Glycoscience and Glycoengineering, Ocean University of China, Qingdao, China
| | - Yibing Zhang
- Glycosciences Laboratory, Imperial College London, London W12 0NN, United Kingdom
| | - Chao Gao
- Glycosciences Laboratory, Imperial College London, London W12 0NN, United Kingdom
| | - Lisete M Silva
- Glycosciences Laboratory, Imperial College London, London W12 0NN, United Kingdom
| | - Zhen Li
- Glycosciences Laboratory, Imperial College London, London W12 0NN, United Kingdom
| | - Filipa Trovão
- Applied Molecular Biosciences Unit, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, Portugal
| | - Markus Weishaupt
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany
| | - Leonid M Likhosherstov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir Piskarev
- Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, Moscow, Russia
| | - Jin Yu
- Umeå University, Department of Chemistry, KBC-building, Linneaus väg 6, S-907 36 Umeå, Sweden
| | - Ulrika Westerlind
- Umeå University, Department of Chemistry, KBC-building, Linneaus väg 6, S-907 36 Umeå, Sweden
| | - Wengang Chai
- Glycosciences Laboratory, Imperial College London, London W12 0NN, United Kingdom
| |
Collapse
|
40
|
Li S, Song G, Bai Y, Song N, Zhao J, Liu J, Hu C. Applications of Protein Microarrays in Biomarker Discovery for Autoimmune Diseases. Front Immunol 2021; 12:645632. [PMID: 34012435 PMCID: PMC8126629 DOI: 10.3389/fimmu.2021.645632] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/13/2021] [Indexed: 01/18/2023] Open
Abstract
Dysregulated autoantibodies and cytokines were deemed to provide important cues for potential illnesses, such as various carcinomas and autoimmune diseases. Increasing biotechnological approaches have been applied to screen and identify the specific alterations of these biomolecules as distinctive biomarkers in diseases, especially autoimmune diseases. As a versatile and robust platform, protein microarray technology allows researchers to easily profile dysregulated autoantibodies and cytokines associated with autoimmune diseases using various biological specimens, mainly serum samples. Here, we summarize the applications of protein microarrays in biomarker discovery for autoimmune diseases. In addition, the key issues in the process of using this approach are presented for improving future studies.
Collapse
Affiliation(s)
- Siting Li
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Guang Song
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yina Bai
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Ning Song
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Jiuliang Zhao
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| | - Jian Liu
- Department of Rheumatology, Aerospace Center Hospital, Aerospace, Clinical Medical College, Peking University, Beijing, China
| | - Chaojun Hu
- Department of Rheumatology, Peking Union Medical College Hospital, Peking Union Medical College & Chinese Academy of Medical Sciences, Key Laboratory of Rheumatology & Clinical Immunology, Ministry of Education, Beijing, China.,Department of Rheumatology, National Clinical Research Center for Dermatologic and Immunologic Diseases (NCRC-DID), Beijing, China
| |
Collapse
|
41
|
Anti-glycan antibodies: roles in human disease. Biochem J 2021; 478:1485-1509. [PMID: 33881487 DOI: 10.1042/bcj20200610] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 03/23/2021] [Accepted: 03/26/2021] [Indexed: 02/07/2023]
Abstract
Carbohydrate-binding antibodies play diverse and critical roles in human health. Endogenous carbohydrate-binding antibodies that recognize bacterial, fungal, and other microbial carbohydrates prevent systemic infections and help maintain microbiome homeostasis. Anti-glycan antibodies can have both beneficial and detrimental effects. For example, alloantibodies to ABO blood group carbohydrates can help reduce the spread of some infectious diseases, but they also impose limitations for blood transfusions. Antibodies that recognize self-glycans can contribute to autoimmune diseases, such as Guillain-Barre syndrome. In addition to endogenous antibodies that arise through natural processes, a variety of vaccines induce anti-glycan antibodies as a primary mechanism of protection. Some examples of approved carbohydrate-based vaccines that have had a major impact on human health are against pneumococcus, Haemophilus influeanza type b, and Neisseria meningitidis. Monoclonal antibodies specifically targeting pathogen associated or tumor associated carbohydrate antigens (TACAs) are used clinically for both diagnostic and therapeutic purposes. This review aims to highlight some of the well-studied and critically important applications of anti-carbohydrate antibodies.
Collapse
|
42
|
Pimenta AI, Kilcoyne M, Bernardes N, Mil-Homens D, Joshi L, Fialho AM. Burkholderia cenocepacia BCAM2418-induced antibody inhibits bacterial adhesion, confers protection to infection and enables identification of host glycans as adhesin targets. Cell Microbiol 2021; 23:e13340. [PMID: 33822465 DOI: 10.1111/cmi.13340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 03/25/2021] [Accepted: 04/01/2021] [Indexed: 12/18/2022]
Abstract
Trimeric Autotransporter Adhesins (TAA) found in Gram-negative bacteria play a key role in virulence. This is the case of Burkholderia cepacia complex (Bcc), a group of related bacteria able to cause infections in patients with cystic fibrosis. These bacteria use TAAs, among other virulence factors, to bind to host protein receptors and their carbohydrate ligands. Blocking such contacts is an attractive approach to inhibit Bcc infections. In this study, using an antibody produced against the TAA BCAM2418 from the epidemic strain Burkholderia cenocepacia K56-2, we were able to uncover its roles as an adhesin and the type of host glycan structures that serve as recognition targets. The neutralisation of BCAM2418 was found to cause a reduction in the adhesion of the bacteria to bronchial cells and mucins. Moreover, in vivo studies have shown that the anti-BCAM2418 antibody exerted an inhibitory effect during infection in Galleria mellonella. Finally, inferred by glycan arrays, we were able to predict for the first time, host glycan epitopes for a TAA. We show that BCAM2418 favoured binding to 3'sialyl-3-fucosyllactose, histo-blood group A, α-(1,2)-linked Fuc-containing structures, Lewis structures and GM1 gangliosides. In addition, the glycan microarrays demonstrated similar specificities of Burkholderia species for their most intensely binding carbohydrates.
Collapse
Affiliation(s)
- Andreia I Pimenta
- iBB-Institute for Bioengineering and Biosciences, and Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Michelle Kilcoyne
- Carbohydrate Signalling Group, Microbiology, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Nuno Bernardes
- iBB-Institute for Bioengineering and Biosciences, and Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Dalila Mil-Homens
- iBB-Institute for Bioengineering and Biosciences, and Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| | - Lokesh Joshi
- Glycoscience Group, School of Natural Sciences, National University of Ireland Galway, Galway, Ireland
| | - Arsenio M Fialho
- iBB-Institute for Bioengineering and Biosciences, and Department of Bioengineering, Instituto Superior Técnico, University of Lisbon, Lisbon, Portugal
| |
Collapse
|
43
|
Kellman BP, Lewis NE. Big-Data Glycomics: Tools to Connect Glycan Biosynthesis to Extracellular Communication. Trends Biochem Sci 2021; 46:284-300. [PMID: 33349503 PMCID: PMC7954846 DOI: 10.1016/j.tibs.2020.10.004] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 10/05/2020] [Accepted: 10/22/2020] [Indexed: 12/12/2022]
Abstract
Characteristically, cells must sense and respond to environmental cues. Despite the importance of cell-cell communication, our understanding remains limited and often lacks glycans. Glycans decorate proteins and cell membranes at the cell-environment interface, and modulate intercellular communication, from development to pathogenesis. Providing further challenges, glycan biosynthesis and cellular behavior are co-regulating systems. Here, we discuss how glycosylation contributes to extracellular responses and signaling. We further organize approaches for disentangling the roles of glycans in multicellular interactions using newly available datasets and tools, including glycan biosynthesis models, omics datasets, and systems-level analyses. Thus, emerging tools in big data analytics and systems biology are facilitating novel insights on glycans and their relationship with multicellular behavior.
Collapse
Affiliation(s)
- Benjamin P Kellman
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA; Department of Bioengineering, University of California San Diego School of Medicine, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Nathan E Lewis
- Department of Pediatrics, University of California San Diego School of Medicine, La Jolla, CA, USA; Department of Bioengineering, University of California San Diego School of Medicine, La Jolla, CA, USA; Bioinformatics and Systems Biology Program, University of California San Diego School of Medicine, La Jolla, CA, USA; Novo Nordisk Foundation Center for Biosustainability at the University of California San Diego School of Medicine, La Jolla, CA, USA.
| |
Collapse
|
44
|
Pan L, Cai C, Liu C, Liu D, Li G, Linhardt RJ, Yu G. Recent progress and advanced technology in carbohydrate-based drug development. Curr Opin Biotechnol 2021; 69:191-198. [PMID: 33530023 DOI: 10.1016/j.copbio.2020.12.023] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 12/21/2020] [Accepted: 12/27/2020] [Indexed: 11/18/2022]
Abstract
Carbohydrates, one of the most abundant and widespread biomolecules in nature, play indispensable roles in diverse biological functions, and represent a treasure trove of untapped potential for pharmaceutical applications. Here, we provide a brief overview of carbohydrate-based drug development (CBDD) over the past two decades. More importantly, advanced techniques and methodologies related to CBDD are emerging, including enzymatic synthesis, metabolic engineering, site-specific glycoconjugation, carbohydrate libraries and microarrays as well as carbohydrate-gut microbiome evaluation. These technologies have dramatically accelerated the speed of CBDD. The recently approved drugs and emerging techniques summarized herein will inspire new sights into potential opportunities to discover novel carbohydrate drugs.
Collapse
Affiliation(s)
- Lin Pan
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Chao Cai
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Chanjuan Liu
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Di Liu
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China
| | - Guoyun Li
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, 12180, USA
| | - Guangli Yu
- Key Laboratory of Marine Drugs of Ministry of Education, Shandong Provincial Key Laboratory of Glycoscience and Glycotechnology, School of Medicine and Pharmacy, Ocean University of China, Qingdao, 266003, China; Laboratory for Marine Drugs and Bioproducts, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, 266237, China.
| |
Collapse
|
45
|
Silva LM, Correia VG, Moreira ASP, Domingues MRM, Ferreira RM, Figueiredo C, Azevedo NF, Marcos-Pinto R, Carneiro F, Magalhães A, Reis CA, Feizi T, Ferreira JA, Coimbra MA, Palma AS. Helicobacter pylori lipopolysaccharide structural domains and their recognition by immune proteins revealed with carbohydrate microarrays. Carbohydr Polym 2020; 253:117350. [PMID: 33278960 DOI: 10.1016/j.carbpol.2020.117350] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 10/16/2020] [Accepted: 10/29/2020] [Indexed: 01/04/2023]
Abstract
The structural diversity of the lipopolysaccharides (LPSs) from Helicobacter pylori poses a challenge to establish accurate and strain-specific structure-function relationships in interactions with the host. Here, LPS structural domains from five clinical isolates were obtained and compared with the reference strain 26695. This was achieved combining information from structural analysis (GC-MS and ESI-MSn) with binding data after interrogation of a LPS-derived carbohydrate microarray with sequence-specific proteins. All LPSs expressed Lewisx/y and N-acetyllactosamine determinants. Ribans were also detected in LPSs from all clinical isolates, allowing their distinction from the 26695 LPS. There was evidence for 1,3-d-galactans and blood group H-type 2 sequences in two of the clinical isolates, the latter not yet described for H. pylori LPS. Furthermore, carbohydrate microarray analyses showed a strain-associated LPS recognition by the immune lectins DC-SIGN and galectin-3 and revealed distinctive LPS binding patterns by IgG antibodies in the serum from H. pylori-infected patients.
Collapse
Affiliation(s)
- Lisete M Silva
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, W12 0NN, UK.
| | - Viviana G Correia
- UCIBIO, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Lisbon, Portugal
| | - Ana S P Moreira
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; CICECO - Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Maria Rosário M Domingues
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal; CESAM - Centre for Environmental and Marine Studies, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Rui M Ferreira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-465 Porto, Portugal
| | - Céu Figueiredo
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-465 Porto, Portugal; Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Nuno F Azevedo
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal
| | - Ricardo Marcos-Pinto
- ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal; Department of Gastroenterology, Centro Hospitalar do Porto, 4099-001 Porto, Portugal; Medical Faculty, Centre for Research in Health Technologies and Information Systems, 4200-450 Porto, Portugal
| | - Fátima Carneiro
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; Department of Pathology, Centro Hospitalar Universitário de São João (CHUSJ), 4200-319 Porto, Portugal
| | - Ana Magalhães
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-465 Porto, Portugal
| | - Celso A Reis
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; IPATIMUP - Institute of Molecular Pathology and Immunology of the University of Porto, 4200-465 Porto, Portugal; Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal; ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal
| | - Ten Feizi
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, W12 0NN, UK
| | - José A Ferreira
- ICBAS - Institute of Biomedical Sciences Abel Salazar, University of Porto, 4050-313 Porto, Portugal; Experimental Pathology and Therapeutics Group, Research Center (CI-IPOP), Portuguese Institute of Oncology, 4200-072 Porto, Portugal
| | - Manuel A Coimbra
- LAQV-REQUIMTE, Department of Chemistry, University of Aveiro, 3810-193 Aveiro, Portugal
| | - Angelina S Palma
- Glycosciences Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, W12 0NN, UK; UCIBIO, Department of Chemistry, School of Science and Technology, NOVA University of Lisbon, 2829-516 Lisbon, Portugal
| |
Collapse
|
46
|
Li R, Yu H, Chen X. Recent progress in chemical synthesis of bacterial surface glycans. Curr Opin Chem Biol 2020; 58:121-136. [PMID: 32920523 DOI: 10.1016/j.cbpa.2020.08.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 08/05/2020] [Accepted: 08/06/2020] [Indexed: 12/13/2022]
Abstract
With the continuing advancement of carbohydrate chemical synthesis, bacterial glycomes have become increasingly attractive and accessible synthetic targets. Although bacteria also produce carbohydrate-containing secondary metabolites, our review here will cover recent chemical synthetic efforts on bacterial surface glycans. The obtained compounds are excellent candidates for the development of improved structurally defined glycoconjugate vaccines to combat bacterial infections. They are also important probes for investigating glycan-protein interactions. Glycosylation strategies applied for the formation of some challenging glycosidic bonds of various uncommon sugars in a number of recently synthesized bacterial surface glycans are highlighted.
Collapse
Affiliation(s)
- Riyao Li
- Department of Chemistry, University of California Davis, Davis, CA, USA
| | - Hai Yu
- Department of Chemistry, University of California Davis, Davis, CA, USA
| | - Xi Chen
- Department of Chemistry, University of California Davis, Davis, CA, USA.
| |
Collapse
|
47
|
Mehta AY, Heimburg-Molinaro J, Cummings RD. Tools for generating and analyzing glycan microarray data. Beilstein J Org Chem 2020; 16:2260-2271. [PMID: 32983270 PMCID: PMC7492694 DOI: 10.3762/bjoc.16.187] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Accepted: 08/19/2020] [Indexed: 12/14/2022] Open
Abstract
Glycans are one of the major biological polymers found in the mammalian body. They play a vital role in a number of physiologic and pathologic conditions. Glycan microarrays allow a plethora of information to be obtained on protein–glycan binding interactions. In this review, we describe the intricacies of the generation of glycan microarray data and the experimental methods for studying binding. We highlight the importance of this knowledge before moving on to the data analysis. We then highlight a number of tools for the analysis of glycan microarray data such as data repositories, data visualization and manual analysis tools, automated analysis tools and structural informatics tools.
Collapse
Affiliation(s)
- Akul Y Mehta
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, 02215, USA
| | - Jamie Heimburg-Molinaro
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, 02215, USA
| | - Richard D Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, 02215, USA
| |
Collapse
|
48
|
Mnich ME, van Dalen R, van Sorge NM. C-Type Lectin Receptors in Host Defense Against Bacterial Pathogens. Front Cell Infect Microbiol 2020; 10:309. [PMID: 32733813 PMCID: PMC7358460 DOI: 10.3389/fcimb.2020.00309] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 05/22/2020] [Indexed: 12/11/2022] Open
Abstract
Antigen-presenting cells (APCs) are present throughout the human body—in tissues, at barrier sites and in the circulation. They are critical for processing external signals to instruct both local and systemic responses toward immune tolerance or immune defense. APCs express an extensive repertoire of pattern-recognition receptors (PRRs) to detect and transduce these signals. C-type lectin receptors (CLRs) comprise a subfamily of PRRs dedicated to sensing glycans, including those expressed by commensal and pathogenic bacteria. This review summarizes recent findings on the recognition of and responses to bacteria by membrane-expressed CLRs on different APC subsets, which are discussed according to the primary site of infection. Many CLR-bacterial interactions promote bacterial clearance, whereas other interactions are exploited by bacteria to enhance their pathogenic potential. The discrimination between protective and virulence-enhancing interactions is essential to understand which interactions to target with new prophylactic or treatment strategies. CLRs are also densely concentrated at APC dendrites that sample the environment across intact barrier sites. This suggests an–as yet–underappreciated role for CLR-mediated recognition of microbiota-produced glycans in maintaining tolerance at barrier sites. In addition to providing a concise overview of identified CLR-bacteria interactions, we discuss the main challenges and potential solutions for the identification of new CLR-bacterial interactions, including those with commensal bacteria, and for in-depth structure-function studies on CLR-bacterial glycan interactions. Finally, we highlight the necessity for more relevant tissue-specific in vitro, in vivo and ex vivo models to develop therapeutic applications in this area.
Collapse
Affiliation(s)
- Malgorzata E Mnich
- Medical Microbiology, UMC Utrecht, Utrecht University, Utrecht, Netherlands.,GSK, Siena, Italy
| | - Rob van Dalen
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Nina M van Sorge
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands.,Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam University Medical Center, Amsterdam, Netherlands
| |
Collapse
|
49
|
Roderer D, Bröcker F, Sitsel O, Kaplonek P, Leidreiter F, Seeberger PH, Raunser S. Glycan-dependent cell adhesion mechanism of Tc toxins. Nat Commun 2020; 11:2694. [PMID: 32483155 PMCID: PMC7264150 DOI: 10.1038/s41467-020-16536-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/11/2020] [Indexed: 01/19/2023] Open
Abstract
Toxin complex (Tc) toxins are virulence factors of pathogenic bacteria. Tcs are composed of three subunits: TcA, TcB and TcC. TcA facilitates receptor-toxin interaction and membrane permeation, TcB and TcC form a toxin-encapsulating cocoon. While the mechanisms of holotoxin assembly and pore formation have been described, little is known about receptor binding of TcAs. Here, we identify heparins/heparan sulfates and Lewis antigens as receptors for different TcAs from insect and human pathogens. Glycan array screening reveals that all tested TcAs bind negatively charged heparins. Cryo-EM structures of Morganella morganii TcdA4 and Xenorhabdus nematophila XptA1 reveal that heparins/heparan sulfates unexpectedly bind to different regions of the shell domain, including receptor-binding domains. In addition, Photorhabdus luminescens TcdA1 binds to Lewis antigens with micromolar affinity. Here, the glycan interacts with the receptor-binding domain D of the toxin. Our results suggest a glycan dependent association mechanism of Tc toxins on the host cell surface.
Collapse
Affiliation(s)
- Daniel Roderer
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Felix Bröcker
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
- Vaxxilon Deutschland GmbH, 12489, Berlin, Germany
| | - Oleg Sitsel
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
| | - Paulina Kaplonek
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, 02139, USA
| | - Franziska Leidreiter
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, 69120, Heidelberg, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14476, Potsdam, Germany
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, 44227, Dortmund, Germany.
| |
Collapse
|
50
|
Jégouzo SAF, Nelson C, Hardwick T, Wong STA, Lau NKK, Neoh GKE, Castellanos-Rueda R, Huang Z, Mignot B, Hirdaramani A, Howitt A, Frewin K, Shen Z, Fox RJ, Wong R, Ando M, Emony L, Zhu H, Holder A, Werling D, Krishnan N, Robertson BD, Clements A, Taylor ME, Drickamer K. Mammalian lectin arrays for screening host-microbe interactions. J Biol Chem 2020; 295:4541-4555. [PMID: 32094229 PMCID: PMC7135977 DOI: 10.1074/jbc.ra120.012783] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 02/14/2020] [Indexed: 12/22/2022] Open
Abstract
Many members of the C-type lectin family of glycan-binding receptors have been ascribed roles in the recognition of microorganisms and serve as key receptors in the innate immune response to pathogens. Other mammalian receptors have become targets through which pathogens enter target cells. These receptor roles have often been documented with binding studies involving individual pairs of receptors and microorganisms. To provide a systematic overview of interactions between microbes and the large complement of C-type lectins, here we developed a lectin array and suitable protocols for labeling of microbes that could be used to probe this array. The array contains C-type lectins from cow, chosen as a model organism of agricultural interest for which the relevant pathogen–receptor interactions have not been previously investigated in detail. Screening with yeast cells and various strains of both Gram-positive and -negative bacteria revealed distinct binding patterns, which in some cases could be explained by binding to lipopolysaccharides or capsular polysaccharides, but in other cases they suggested the presence of novel glycan targets on many of the microorganisms. These results are consistent with interactions previously ascribed to the receptors, but they also highlight binding to additional sugar targets that have not previously been recognized. Our findings indicate that mammalian lectin arrays represent unique discovery tools for identifying both novel ligands and new receptor functions.
Collapse
Affiliation(s)
- Sabine A F Jégouzo
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Conor Nelson
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Thomas Hardwick
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - S T Angel Wong
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Noel Kuan Kiat Lau
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Gaik Kin Emily Neoh
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Zhiyao Huang
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Benjamin Mignot
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Aanya Hirdaramani
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Annie Howitt
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Kathryn Frewin
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Zheng Shen
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rhys J Fox
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Rachel Wong
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Momoko Ando
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Lauren Emony
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Henderson Zhu
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Angela Holder
- Department of Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, Hatfield, Hertfordshire AL9 7TA, United Kingdom
| | - Dirk Werling
- Department of Pathobiology and Population Sciences, Royal Veterinary College, North Mymms, Hatfield, Hertfordshire AL9 7TA, United Kingdom
| | - Nitya Krishnan
- Department of Infectious Disease and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Brian D Robertson
- Department of Infectious Disease and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Abigail Clements
- Department of Life Sciences and MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Maureen E Taylor
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - Kurt Drickamer
- Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| |
Collapse
|