1
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Palma JA, Bunyatov MI, Hulbert SW, Jewett MC, DeLisa MP. Bacterial glycoengineering: Cell-based and cell-free routes for producing biopharmaceuticals with customized glycosylation. Curr Opin Chem Biol 2024; 81:102500. [PMID: 38991462 DOI: 10.1016/j.cbpa.2024.102500] [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: 04/08/2024] [Revised: 06/17/2024] [Accepted: 06/18/2024] [Indexed: 07/13/2024]
Abstract
Glycosylation plays a pivotal role in tuning the folding and function of proteins. Because most human therapeutic proteins are glycosylated, understanding and controlling glycosylation is important for the design, optimization, and manufacture of biopharmaceuticals. Unfortunately, natural eukaryotic glycosylation pathways are complex and often produce heterogeneous glycan patterns, making the production of glycoproteins with chemically precise and homogeneous glycan structures difficult. To overcome these limitations, bacterial glycoengineering has emerged as a simple, cost-effective, and scalable approach to produce designer glycoprotein therapeutics and vaccines in which the glycan structures are engineered to reduce heterogeneity and improve biological and biophysical attributes of the protein. Here, we discuss recent advances in bacterial cell-based and cell-free glycoengineering that have enabled the production of biopharmaceutical glycoproteins with customized glycan structures.
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Affiliation(s)
- Jaymee A Palma
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Mehman I Bunyatov
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Sophia W Hulbert
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
| | - Michael C Jewett
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Matthew P DeLisa
- Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA; Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Cornell Institute of Biotechnology, Cornell University, Biotechnology Building, Ithaca, NY 14853, USA.
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2
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Makrydaki E, Donini R, Krueger A, Royle K, Moya Ramirez I, Kuntz DA, Rose DR, Haslam SM, Polizzi KM, Kontoravdi C. Immobilized enzyme cascade for targeted glycosylation. Nat Chem Biol 2024; 20:732-741. [PMID: 38321209 PMCID: PMC11142912 DOI: 10.1038/s41589-023-01539-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 12/21/2023] [Indexed: 02/08/2024]
Abstract
Glycosylation is a critical post-translational protein modification that affects folding, half-life and functionality. Glycosylation is a non-templated and heterogeneous process because of the promiscuity of the enzymes involved. We describe a platform for sequential glycosylation reactions for tailored sugar structures (SUGAR-TARGET) that allows bespoke, controlled N-linked glycosylation in vitro enabled by immobilized enzymes produced with a one-step immobilization/purification method. We reconstruct a reaction cascade mimicking a glycosylation pathway where promiscuity naturally exists to humanize a range of proteins derived from different cellular systems, yielding near-homogeneous glycoforms. Immobilized β-1,4-galactosyltransferase is used to enhance the galactosylation profile of three IgGs, yielding 80.2-96.3% terminal galactosylation. Enzyme recycling is demonstrated for a reaction time greater than 80 h. The platform is easy to implement, modular and reusable and can therefore produce homogeneous glycan structures derived from various hosts for functional and clinical evaluation.
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Affiliation(s)
- Elli Makrydaki
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Roberto Donini
- Department of Life Sciences, Imperial College London, London, UK
| | - Anja Krueger
- Department of Life Sciences, Imperial College London, London, UK
| | - Kate Royle
- Department of Chemical Engineering, Imperial College London, London, UK
| | - Ignacio Moya Ramirez
- Department of Chemical Engineering, Imperial College London, London, UK
- Departamento de Ingeniería Química, Universidad de Granada, Granada, Spain
| | - Douglas A Kuntz
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - David R Rose
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
- Department of Biology, University of Waterloo, Waterloo, Ontario, Canada
| | - Stuart M Haslam
- Department of Life Sciences, Imperial College London, London, UK
| | - Karen M Polizzi
- Department of Chemical Engineering, Imperial College London, London, UK.
| | - Cleo Kontoravdi
- Department of Chemical Engineering, Imperial College London, London, UK.
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3
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Su T, Chua WZ, Liu Y, Fan J, Tan SY, Yang DW, Sham LT. Rewiring the pneumococcal capsule pathway for investigating glycosyltransferase specificity and genetic glycoengineering. SCIENCE ADVANCES 2023; 9:eadi8157. [PMID: 37672581 PMCID: PMC10482335 DOI: 10.1126/sciadv.adi8157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 08/03/2023] [Indexed: 09/08/2023]
Abstract
Virtually all living cells are covered with glycans. Their structures are primarily controlled by the specificities of glycosyltransferases (GTs). GTs typically adopt one of the three folds, namely, GT-A, GT-B, and GT-C. However, what defines their specificities remain poorly understood. Here, we developed a genetic glycoengineering platform by reprogramming the capsular polysaccharide pathways in Streptococcus pneumoniae to interrogate GT specificity and manipulate glycan structures. Our findings suggest that the central cleft of GT-B enzymes is important for determining acceptor specificity. The constraint of the glycoengineering platform was partially alleviated when the specificity of the precursor transporter was reduced, indicating that the transporter contributes to the overall fidelity of glycan synthesis. We also modified the pneumococcal capsule to produce several medically important mammalian glycans, as well as demonstrated the importance of regiochemistry in a glycosidic linkage on binding lung epithelial cells. Our work provided mechanistic insights into GT specificity and an approach for investigating glycan functions.
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Affiliation(s)
- Tong Su
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Wan-Zhen Chua
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Yao Liu
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Jingsong Fan
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117545, Singapore
| | - Si-Yin Tan
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Dai-wen Yang
- Department of Biological Sciences, Faculty of Science, National University of Singapore, Singapore 117545, Singapore
| | - Lok-To Sham
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
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4
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Jaroentomeechai T, Kwon YH, Liu Y, Young O, Bhawal R, Wilson JD, Li M, Chapla DG, Moremen KW, Jewett MC, Mizrachi D, DeLisa MP. A universal glycoenzyme biosynthesis pipeline that enables efficient cell-free remodeling of glycans. Nat Commun 2022; 13:6325. [PMID: 36280670 PMCID: PMC9592599 DOI: 10.1038/s41467-022-34029-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 10/11/2022] [Indexed: 12/25/2022] Open
Abstract
The ability to reconstitute natural glycosylation pathways or prototype entirely new ones from scratch is hampered by the limited availability of functional glycoenzymes, many of which are membrane proteins that fail to express in heterologous hosts. Here, we describe a strategy for topologically converting membrane-bound glycosyltransferases (GTs) into water soluble biocatalysts, which are expressed at high levels in the cytoplasm of living cells with retention of biological activity. We demonstrate the universality of the approach through facile production of 98 difficult-to-express GTs, predominantly of human origin, across several commonly used expression platforms. Using a subset of these water-soluble enzymes, we perform structural remodeling of both free and protein-linked glycans including those found on the monoclonal antibody therapeutic trastuzumab. Overall, our strategy for rationally redesigning GTs provides an effective and versatile biosynthetic route to large quantities of diverse, enzymatically active GTs, which should find use in structure-function studies as well as in biochemical and biomedical applications involving complex glycomolecules.
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Affiliation(s)
- Thapakorn Jaroentomeechai
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY, 14853, USA
| | - Yong Hyun Kwon
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY, 14853, USA
| | - Yiwen Liu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY, 14853, USA
| | - Olivia Young
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY, 14853, USA
| | - Ruchika Bhawal
- Cornell Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA
| | - Joshua D Wilson
- Glycobia, Inc., 33 Thornwood Drive, Suite 104, Ithaca, NY, 14850, USA
| | - Mingji Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY, 14853, USA
| | - Digantkumar G Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Michael C Jewett
- Department of Chemical and Biological Engineering, Northwestern University, 2145 Sheridan Rd Technological Institute E136, Evanston, IL, 60208-3120, USA
| | - Dario Mizrachi
- Department of Physiology & Developmental Biology, Brigham Young University, Provo, UT, 84602, USA
| | - Matthew P DeLisa
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 120 Olin Hall, Ithaca, NY, 14853, USA.
- Cornell Institute of Biotechnology, Cornell University, Ithaca, NY, 14853, USA.
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5
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She YM, Klupt K, Hatfield G, Jia Z, Tam RY. Unusual β1-4-galactosidase activity of an α1-6-mannosidase from Xanthomonas manihotis in the processing of branched hybrid and complex glycans. J Biol Chem 2022; 298:102313. [PMID: 35921895 PMCID: PMC9425025 DOI: 10.1016/j.jbc.2022.102313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/22/2022] [Accepted: 07/23/2022] [Indexed: 11/05/2022] Open
Abstract
Mannosidases are a diverse group of glycoside hydrolases that play crucial roles in mannose trimming of oligomannose glycans, glycoconjugates, and glycoproteins involved in numerous cellular processes, such as glycan biosynthesis and metabolism, structure regulation, cellular recognition, and cell–pathogen interactions. Exomannosidases and endomannosidases cleave specific glycosidic bonds of mannoside linkages in glycans and can be used in enzyme-based methods for sequencing of isomeric glycan structures. α1-6-mannosidase from Xanthomonas manihotis is known as a highly specific exoglycosidase that removes unbranched α1-6 linked mannose residues from oligosaccharides. However, we discovered that this α1-6-mannosidase also possesses an unexpected β1-4-galactosidase activity in the processing of branched hybrid and complex glycans through our use of enzymatic reactions, high performance anion-exchange chromatography, and liquid chromatography mass spectrometric sequencing. Our docking simulation of the α1-6-mannosidase with glycan substrates reveals potential interacting residues in a relatively shallow pocket slightly differing from its homologous enzymes in the glycoside hydrolase 125 family, which may be responsible for the observed higher promiscuity in substrate binding and subsequent terminal glycan hydrolysis. This observation of novel β1-4-galactosidase activity of the α1-6-mannosidase provides unique insights into its bifunctional activity on the substrate structure-dependent processing of terminal α1-6-mannose of unbranched glycans and terminal β1-4-galactose of hybrid and complex glycans. The finding thus suggests the dual glycosidase specificity of this α1-6-mannosidase and the need for careful consideration when used for the structural elucidation of glycan isomers.
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6
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Zhao X, Huang Y, Zhou S, Ao J, Cai H, Tanaka K, Ito Y, Ishiwata A, Ding F. Recent Chemical and Chemoenzymatic Strategies to Complex-Type N-Glycans. Front Chem 2022; 10:880128. [PMID: 35720985 PMCID: PMC9204336 DOI: 10.3389/fchem.2022.880128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/12/2022] [Indexed: 12/01/2022] Open
Abstract
Glycosylation is one of the major forms of protein post-translational modification. N-glycans attached to proteins by covalent bonds play an indispensable role in intercellular interaction and immune function. In human bodies, most of the cell surface glycoproteins and secreted glycopeptides are modified with complex-type N-glycans. Thus, for analytical or medicinal purposes, efficient and universal methods to provide homogeneous complex-type N-glycans have been an urgent need. Despite the extremely complicated structures, tremendous progress in the synthesis of N-glycans has been achieved. On one hand, chemical strategies are shown to be effective to prepare core oligosaccharides of N-glycans by focusing on stereoselective glycosylations such as β-mannosylation and α-sialylation, as well as the methodology of the N-glycan assembly. On the other hand, chemoenzymatic strategies have also become increasingly powerful in recent years. This review attempts to highlight the very recent advancements in chemical and chemoenzymatic strategies for eukaryotic complex-type N-glycans.
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Affiliation(s)
- Xiaoya Zhao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Yan Huang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Siai Zhou
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Jiaming Ao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
| | - Hui Cai
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
- *Correspondence: Hui Cai, ; Akihiro Ishiwata, ; Feiqing Ding,
| | - Katsunori Tanaka
- RIKEN Cluster for Pioneering Research, Saitama, Japan
- School of Materials and Chemical Technology, Tokyo Institute of Technology, Tokyo, Japan
- Alexander Butlerov Institute of Chemistry, Kazan Federal University, Kazan, Russian Federation
| | - Yukishige Ito
- RIKEN Cluster for Pioneering Research, Saitama, Japan
- Graduate School of Science, Osaka University, Osaka, Japan
| | - Akihiro Ishiwata
- RIKEN Cluster for Pioneering Research, Saitama, Japan
- *Correspondence: Hui Cai, ; Akihiro Ishiwata, ; Feiqing Ding,
| | - Feiqing Ding
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen, China
- *Correspondence: Hui Cai, ; Akihiro Ishiwata, ; Feiqing Ding,
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7
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Hsu YP, Verma D, Sun S, McGregor C, Mangion I, Mann BF. Successive remodeling of IgG glycans using a solid-phase enzymatic platform. Commun Biol 2022; 5:328. [PMID: 35393560 PMCID: PMC8990068 DOI: 10.1038/s42003-022-03257-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 03/11/2022] [Indexed: 12/02/2022] Open
Abstract
The success of glycoprotein-based drugs in various disease treatments has become widespread. Frequently, therapeutic glycoproteins exhibit a heterogeneous array of glycans that are intended to mimic human glycopatterns. While immunogenic responses to biologic drugs are uncommon, enabling exquisite control of glycosylation with minimized microheterogeneity would improve their safety, efficacy and bioavailability. Therefore, close attention has been drawn to the development of glycoengineering strategies to control the glycan structures. With the accumulation of knowledge about the glycan biosynthesis enzymes, enzymatic glycan remodeling provides a potential strategy to construct highly ordered glycans with improved efficiency and biocompatibility. In this study, we quantitatively evaluate more than 30 enzymes for glycoengineering immobilized immunoglobulin G, an impactful glycoprotein class in the pharmaceutical field. We demonstrate successive glycan remodeling in a solid-phase platform, which enabled IgG glycan harmonization into a series of complex-type N-glycoforms with high yield and efficiency while retaining native IgG binding affinity. A solid-phase glycan remodeling (SPGR) platform is presented. Over thirty enzymes were evaluated for successive glycoengineering of immobilized antibodies with outstanding performance in several SPGR reactions.
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Affiliation(s)
- Yen-Pang Hsu
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, 07065, USA.,Exploratory Science Center, Merck & Co., Inc, Cambridge, MA, 02141, USA
| | - Deeptak Verma
- Computational and Structural Chemistry, Discovery Chemistry, Merck & Co., Inc, Rahway, NJ, 07065, USA
| | - Shuwen Sun
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, 07065, USA
| | - Caroline McGregor
- Process Research & Development, Merck & Co., Inc, Rahway, NJ, 07065, USA
| | - Ian Mangion
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, 07065, USA
| | - Benjamin F Mann
- Analytical Research and Development, Merck & Co., Inc, Rahway, NJ, 07065, USA.
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8
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Aquino AK, Manzer ZA, Daniel S, DeLisa MP. Glycosylation-on-a-Chip: A Flow-Based Microfluidic System for Cell-Free Glycoprotein Biosynthesis. Front Mol Biosci 2022; 8:782905. [PMID: 35004852 PMCID: PMC8733600 DOI: 10.3389/fmolb.2021.782905] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/06/2021] [Indexed: 12/25/2022] Open
Abstract
In recent years, cell-free synthetic glycobiology technologies have emerged that enable production and remodeling of glycoproteins outside the confines of the cell. However, many of these systems combine multiple synthesis steps into one pot where there can be competing reactions and side products that ultimately lead to low yield of the desired product. In this work, we describe a microfluidic platform that integrates cell-free protein synthesis, glycosylation, and purification of a model glycoprotein in separate compartments where each step can be individually optimized. Microfluidics offer advantages such as reaction compartmentalization, tunable residence time, the ability to tether enzymes for reuse, and the potential for continuous manufacturing. Moreover, it affords an opportunity for spatiotemporal control of glycosylation reactions that is difficult to achieve with existing cell-based and cell-free glycosylation systems. In this work, we demonstrate a flow-based glycoprotein synthesis system that promotes enhanced cell-free protein synthesis, efficient protein glycosylation with an immobilized oligosaccharyltransferase, and enrichment of the protein product from cell-free lysate. Overall, this work represents a first-in-kind glycosylation-on-a-chip prototype that could find use as a laboratory tool for mechanistic dissection of the protein glycosylation process as well as a biomanufacturing platform for small batch, decentralized glycoprotein production.
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Affiliation(s)
- Alicia K Aquino
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Zachary A Manzer
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Susan Daniel
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Matthew P DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States.,Cornell Institute of Biotechnology, Cornell University, Ithaca, NY, United States
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9
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Liu M, Qin X, Ye XS. Glycan Assembly Strategy: From Concept to Application. CHEM REC 2021; 21:3256-3277. [PMID: 34498347 DOI: 10.1002/tcr.202100183] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 08/30/2021] [Indexed: 12/11/2022]
Abstract
Glycans have been hot topics in recent years due to their exhibition of numerous biological activities. However, the heterogeneity of their natural source and the complexity of their chemical synthesis impede the progress in their biological research. Thus, the development of glycan assembly strategies to acquire plenty of structurally well-defined glycans is an important issue in carbohydrate chemistry. In this review, the latest advances in glycan assembly strategies from concepts to their applications in carbohydrate synthesis, including chemical and enzymatic/chemo-enzymatic approaches, as well as solution-phase and solid-phase/tag-assisted synthesis, are summarized. Furthermore, the automated glycan assembly techniques are also outlined.
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Affiliation(s)
- Mingli Liu
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road No. 38, Beijing, 100191, China
| | - Xianjin Qin
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road No. 38, Beijing, 100191, China
| | - Xin-Shan Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, Xue Yuan Road No. 38, Beijing, 100191, China
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10
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García-García A, Serna S, Yang Z, Delso I, Taleb V, Hicks T, Artschwager R, Vakhrushev SY, Clausen H, Angulo J, Corzana F, Reichardt NC, Hurtado-Guerrero R. FUT8-Directed Core Fucosylation of N-glycans Is Regulated by the Glycan Structure and Protein Environment. ACS Catal 2021; 11:9052-9065. [PMID: 35662980 PMCID: PMC9161449 DOI: 10.1021/acscatal.1c01698] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/24/2021] [Indexed: 12/17/2022]
Abstract
FUT8 is an essential α-1,6-fucosyltransferase that fucosylates the innermost GlcNAc of N-glycans, a process called core fucosylation. In vitro, FUT8 exhibits substrate preference for the biantennary complex N-glycan oligosaccharide (G0), but the role of the underlying protein/peptide to which N-glycans are attached remains unclear. Here, we explored the FUT8 enzyme with a series of N-glycan oligosaccharides, N-glycopeptides, and an Asn-linked oligosaccharide. We found that the underlying peptide plays a role in fucosylation of paucimannose (low mannose) and high-mannose N-glycans but not for complex-type N-glycans. Using saturation transfer difference (STD) NMR spectroscopy, we demonstrate that FUT8 recognizes all sugar units of the G0 N-glycan and most of the amino acid residues (Asn-X-Thr) that serve as a recognition sequon for the oligosaccharyltransferase (OST). The largest STD signals were observed in the presence of GDP, suggesting that prior FUT8 binding to GDP-β-l-fucose (GDP-Fuc) is required for an optimal recognition of N-glycans. We applied genetic engineering of glycosylation capacities in CHO cells to evaluate FUT8 core fucosylation of high-mannose and complex-type N-glycans in cells with a panel of well-characterized therapeutic N-glycoproteins. This confirmed that core fucosylation mainly occurs on complex-type N-glycans, although clearly only at selected glycosites. Eliminating the capacity for complex-type glycosylation in cells (KO mgat1) revealed that glycosites with complex-type N-glycans when converted to high mannose lost the core Fuc. Interestingly, however, for erythropoietin that is uncommon among the tested glycoproteins in efficiently acquiring tetra-antennary N-glycans, two out of three N-glycosites obtained Fuc on the high-mannose N-glycans. An examination of the N-glycosylation sites of several protein crystal structures indicates that core fucosylation is mostly affected by the accessibility and nature of the N-glycan and not by the nature of the underlying peptide sequence. These data have further elucidated the different FUT8 acceptor substrate specificities both in vitro and in vivo in cells, revealing different mechanisms for promoting core fucosylation.
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Affiliation(s)
- Ana García-García
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain
| | - Sonia Serna
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, Donostia San Sebastián 20014, Spain
| | - Zhang Yang
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Ignacio Delso
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Víctor Taleb
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain
| | - Thomas Hicks
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Raik Artschwager
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, Donostia San Sebastián 20014, Spain
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark
| | - Jesús Angulo
- School of Pharmacy, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK.,Departamento de Química Orgánica, Universidad de Sevilla, Sevilla 41012, Spain.,Instituto de Investigaciones Químicas (CSIC-US), Avda. Américo Vespucio, 49, Seville 41092, Spain
| | - Francisco Corzana
- Departamento de Química, Universidad de La Rioja, Centro de Investigación en Síntesis Química, Logroño E-26006, Spain
| | - Niels C Reichardt
- Center for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramón 182, Donostia San Sebastián 20014, Spain.,CIBER-BBN, Paseo Miramón 182, San Sebastian 20014, Spain
| | - Ramon Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI), University of Zaragoza, Mariano Esquillor s/n, Campus Rio Ebro, Edificio I+D, Zaragoza 50018, Spain.,Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen DK-2200, Denmark.,Fundación ARAID, Zaragoza 50018, Spain
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11
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Zhang R, Zhu J, Lubman DM, Mechref Y, Tang H. GlycoHybridSeq: Automated Identification of N-Linked Glycopeptides Using Electron Transfer/High-Energy Collision Dissociation (EThcD). J Proteome Res 2021; 20:3345-3352. [PMID: 34010560 PMCID: PMC8185882 DOI: 10.1021/acs.jproteome.1c00245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Glycosylation is
one of the most common post-translational modifications
(PTM) occurring in a large variety of proteins with important biological
functions in human and other higher organisms. Liquid chromatography
tandem mass spectrometry (LC-MS/MS) has been routinely used to characterize
site-specific protein glycosylation at high throughput in complex
glycoproteomic samples. Recently, electron transfer/high-energy collision
dissociation (EThcD) was introduced for glycopeptide identification,
which offers rich structural information on glycopepides with the
fragment ions from the cleavages of both the glycan and the peptide
backbone. Herein, we present the software GlycoHybridSeq for automated
interpretation of EThcD-MS/MS spectra from glycoproteomic data using
a customized scoring function, which enables the functionalities of
identifying glycopeptides, characterizing glycosylation sites, and
distinguishing some isomeric glycans. We evaluate GlycoHybridSeq on
glycoproteomic data collected for cancer biomarker discovery. The
results showed that it achieved comparable or better performance than
that of Byonic and MSFragger. GlycoHybridSeq is released as an open
source software and is ready to be used in large-scale glycoproteomic
data analyses.
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Affiliation(s)
- Rui Zhang
- Department of Computer Science, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana 47405, United States
| | - Jianhui Zhu
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - David M Lubman
- Department of Surgery, University of Michigan Medical Center, Ann Arbor, Michigan 48109, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Haixu Tang
- Department of Computer Science, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, Indiana 47405, United States
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12
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Li Y, Hintze KJ, Ward RE. Effect of supplemental prebiotics, probiotics and bioactive proteins on the microbiome composition and fecal calprotectin in C57BL6/j mice. Biochimie 2021; 185:43-52. [PMID: 33609630 DOI: 10.1016/j.biochi.2021.02.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 01/11/2021] [Accepted: 02/14/2021] [Indexed: 02/07/2023]
Abstract
The composition and metabolic activity of the microbiome affect many aspects of health, and there is current interest in dietary constituents that may affect this system. The purpose of this study was to evaluate the effects of a mix of probiotics, a mix of prebiotics and a bioactive protein fraction on the microbiome, when fed to mice alone and in combination at physiologically relevant doses. Mice were fed the total western diet (TWD) supplemented with prebiotics, probiotics, and bioactive proteins individually and in combination for four weeks. Subsequently, effects on the composition of the gut microbiome, gut short-chain fatty acids (SCFAs) concentration, and gut inflammation were measured. Ruminococcus gnavus was increased in mice gut microbiome after feeding prebiotics. Bifidobacterium longum was increased after feeding probiotics. The treatments significantly affected beta-diversity with minor treatment effects on cecal or fecal SCFAs levels, and the treatments did not affect gut inflammation as measured by fecal calprotectin.
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Affiliation(s)
- Ye Li
- Nutrition, Dietetics and Food Sciences, Utah State University, 8700 Old Main Hill, Logan, UT, 84322-8700, USA
| | - Korry J Hintze
- Nutrition, Dietetics and Food Sciences, Utah State University, 8700 Old Main Hill, Logan, UT, 84322-8700, USA
| | - Robert E Ward
- Nutrition, Dietetics and Food Sciences, Utah State University, 8700 Old Main Hill, Logan, UT, 84322-8700, USA.
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13
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Jaroentomeechai T, Taw MN, Li M, Aquino A, Agashe N, Chung S, Jewett MC, DeLisa MP. Cell-Free Synthetic Glycobiology: Designing and Engineering Glycomolecules Outside of Living Cells. Front Chem 2020; 8:645. [PMID: 32850660 PMCID: PMC7403607 DOI: 10.3389/fchem.2020.00645] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/22/2020] [Indexed: 12/12/2022] Open
Abstract
Glycans and glycosylated biomolecules are directly involved in almost every biological process as well as the etiology of most major diseases. Hence, glycoscience knowledge is essential to efforts aimed at addressing fundamental challenges in understanding and improving human health, protecting the environment and enhancing energy security, and developing renewable and sustainable resources that can serve as the source of next-generation materials. While much progress has been made, there remains an urgent need for new tools that can overexpress structurally uniform glycans and glycoconjugates in the quantities needed for characterization and that can be used to mechanistically dissect the enzymatic reactions and multi-enzyme assembly lines that promote their construction. To address this technology gap, cell-free synthetic glycobiology has emerged as a simplified and highly modular framework to investigate, prototype, and engineer pathways for glycan biosynthesis and biomolecule glycosylation outside the confines of living cells. From nucleotide sugars to complex glycoproteins, we summarize here recent efforts that harness the power of cell-free approaches to design, build, test, and utilize glyco-enzyme reaction networks that produce desired glycomolecules in a predictable and controllable manner. We also highlight novel cell-free methods for shedding light on poorly understood aspects of diverse glycosylation processes and engineering these processes toward desired outcomes. Taken together, cell-free synthetic glycobiology represents a promising set of tools and techniques for accelerating basic glycoscience research (e.g., deciphering the "glycan code") and its application (e.g., biomanufacturing high-value glycomolecules on demand).
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Affiliation(s)
- Thapakorn Jaroentomeechai
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - May N. Taw
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Mingji Li
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Alicia Aquino
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Ninad Agashe
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
| | - Sean Chung
- Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY, United States
| | - Michael C. Jewett
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, United States
- Center for Synthetic Biology, Northwestern University, Evanston, IL, United States
- Chemistry of Life Processes Institute, Northwestern University, Evanston, IL, United States
| | - Matthew P. DeLisa
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, United States
- Graduate Field of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY, United States
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14
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Chao Q, Ding Y, Chen ZH, Xiang MH, Wang N, Gao XD. Recent Progress in Chemo-Enzymatic Methods for the Synthesis of N-Glycans. Front Chem 2020; 8:513. [PMID: 32612979 PMCID: PMC7309569 DOI: 10.3389/fchem.2020.00513] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 05/18/2020] [Indexed: 01/06/2023] Open
Abstract
Asparagine (N)-linked glycosylation is one of the most common co- and post-translational modifications of both intra- and extracellularly distributing proteins, which directly affects their biological functions, such as protein folding, stability and intercellular traffic. Production of the structural well-defined homogeneous N-glycans contributes to comprehensive investigation of their biological roles and molecular basis. Among the various methods, chemo-enzymatic approach serves as an alternative to chemical synthesis, providing high stereoselectivity and economic efficiency. This review summarizes some recent advances in the chemo-enzymatic methods for the production of N-glycans, including the preparation of substrates and sugar donors, and the progress in the glycosyltransferases characterization which leads to the diversity of N-glycan synthesis. We discuss the bottle-neck and new opportunities in exploiting the chemo-enzymatic synthesis of N-glycans based on our research experiences. In addition, downstream applications of the constructed N-glycans, such as automation devices and homogeneous glycoproteins synthesis are also described.
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Affiliation(s)
| | | | | | | | - Ning Wang
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xiao-Dong Gao
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
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15
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McQuillan AM, Byrd-Leotis L, Heimburg-Molinaro J, Cummings RD. Natural and Synthetic Sialylated Glycan Microarrays and Their Applications. Front Mol Biosci 2019; 6:88. [PMID: 31572731 PMCID: PMC6753469 DOI: 10.3389/fmolb.2019.00088] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 08/28/2019] [Indexed: 12/28/2022] Open
Abstract
This focused chapter serves as a short survey of glycan microarrays that are available with sialylated glycans, including both defined and shotgun arrays, their generation, and their utility in studying differential binding interactions to sialylated compounds, highlighting N-glycolyl (Gc) modified sialylated compounds. A brief discussion of binding interactions by lectins, antibodies, and viruses, and their relevance that have been observed with sialylated glycan microarrays is presented, as well as a discussion of cross-comparisons of array platforms and efforts to centralize and standardize the glycan microarray data.
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Affiliation(s)
- Alyssa M. McQuillan
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, United States
| | - Lauren Byrd-Leotis
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, United States
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA, United States
| | - Jamie Heimburg-Molinaro
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, United States
| | - Richard D. Cummings
- Department of Surgery, Beth Israel Deaconess Medical Center, National Center for Functional Glycomics, Harvard Medical School, Boston, MA, United States
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16
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Abstract
The translation of biological glycosylation in humans to the clinical applications involves systematic studies using homogeneous samples of oligosaccharides and glycoconjugates, which could be accessed by chemical, enzymatic or other biological methods. However, the structural complexity and wide-range variations of glycans and their conjugates represent a major challenge in the synthesis of this class of biomolecules. To help navigate within many methods of oligosaccharide synthesis, this Perspective offers a critical assessment of the most promising synthetic strategies with an eye on the therapeutically relevant targets.
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Affiliation(s)
- Larissa Krasnova
- Department of Chemistry , The Scripps Research Institute , 10550 N. Torrey Pines Road , La Jolla , California 92037 , United States
| | - Chi-Huey Wong
- Department of Chemistry , The Scripps Research Institute , 10550 N. Torrey Pines Road , La Jolla , California 92037 , United States.,Genomics Research Center, Academia Sinica , Taipei 115 , Taiwan
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17
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Streamlining the chemoenzymatic synthesis of complex N-glycans by a stop and go strategy. Nat Chem 2018; 11:161-169. [PMID: 30532014 PMCID: PMC6347513 DOI: 10.1038/s41557-018-0188-3] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2018] [Accepted: 11/07/2018] [Indexed: 11/13/2022]
Abstract
Contemporary chemoenzymatic approaches can provide highly complex multi-antennary N-linked glycans. These procedures are, however, very demanding and typically involve as many as 100 chemical steps to prepare advanced intermediates that can be diversified by glycosyltransferases in a branch selective manner to give asymmetrical structures commonly found in Nature. Only highly specialized laboratories can perform such syntheses, which greatly hampers progress in glycoscience. Here we describe a biomimetic approach in which a readily available bi-antennary glycopeptide can be converted in 10 or fewer chemical and enzymatic steps into multi-antennary N-glycans that at each arm can be uniquely extended by glycosyltransferases to give access to highly complex asymmetrically branched N-glycans. A key feature of our approach is the installation of additional branching points using recombinant MGAT4 and MGAT5 in combination with unnatural sugar donors. At an appropriate point in the enzymatic synthesis, the unnatural monosaccharides can be converted into their natural counterpart allowing each arm to be elaborated into a unique appendage.
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18
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Glasscock CJ, Yates LE, Jaroentomeechai T, Wilson JD, Merritt JH, Lucks JB, DeLisa MP. A flow cytometric approach to engineering Escherichia coli for improved eukaryotic protein glycosylation. Metab Eng 2018; 47:488-495. [DOI: 10.1016/j.ymben.2018.04.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Revised: 04/17/2018] [Accepted: 04/19/2018] [Indexed: 12/31/2022]
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