1
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Tian Y, Ma S, Wen L. Towards chemoenzymatic labeling strategies for profiling protein glycosylation. Curr Opin Chem Biol 2024; 80:102460. [PMID: 38678979 DOI: 10.1016/j.cbpa.2024.102460] [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: 12/26/2023] [Revised: 03/31/2024] [Accepted: 04/07/2024] [Indexed: 05/01/2024]
Abstract
Protein glycosylation is one of the most common and important post-translational modifications of proteins involved in regulating glycoprotein functions. The chemoenzymatic glycan labeling strategy allows rapid, efficient, and selective interrogation of glycoproteins. Glycoproteomics identifies protein glycosylation events at a large scale, providing information such as peptide sequences, glycan structures, and glycosylated sites. This review discusses the recent development of chemoenzymatic labeling strategies for glycoprotein analysis, mainly including glycoprotein and glycosite profiling. Furthermore, we highlight the chemoenzymatic enrichment approaches in mass spectrometry analysis for three classes of glycan modifications, including N-glycosylation, O-GlcNAcylation, and mucin-type O-glycosylation. Finally, we highlight the emerging trends in new tools and cutting-edge technologies available for glycoproteomic research.
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Affiliation(s)
- Yinping Tian
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Shengzhou Ma
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Liuqing Wen
- State Key Laboratory of Drug Research and State Key Laboratory of Chemical Biology, Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China; University of Chinese Academy of Sciences, Beijing, China.
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2
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Li W, Guo J, Hobson EC, Xue X, Li Q, Fu J, Deng CX, Guo Z. Metabolic-Glycoengineering-Enabled Molecularly Specific Acoustic Tweezing Cytometry for Targeted Mechanical Stimulation of Cell Surface Sialoglycans. Angew Chem Int Ed Engl 2024; 63:e202401921. [PMID: 38498603 PMCID: PMC11073901 DOI: 10.1002/anie.202401921] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/14/2024] [Accepted: 03/18/2024] [Indexed: 03/20/2024]
Abstract
In this study, we developed a novel type of dibenzocyclooctyne (DBCO)-functionalized microbubbles (MBs) and validated their attachment to azide-labelled sialoglycans on human pluripotent stem cells (hPSCs) generated by metabolic glycoengineering (MGE). This enabled the application of mechanical forces to sialoglycans on hPSCs through molecularly specific acoustic tweezing cytometry (mATC), that is, displacing sialoglycan-anchored MBs using ultrasound (US). It was shown that subjected to the acoustic radiation forces of US pulses, sialoglycan-anchored MBs exhibited significantly larger displacements and faster, more complete recovery after each pulse than integrin-anchored MBs, indicating that sialoglycans are more stretchable and elastic than integrins on hPSCs in response to mechanical force. Furthermore, stimulating sialoglycans on hPSCs using mATC reduced stage-specific embryonic antigen-3 (SSEA-3) and GD3 expression but not OCT4 and SOX2 nuclear localization. Conversely, stimulating integrins decreased OCT4 nuclear localization but not SSEA-3 and GD3 expression, suggesting that mechanically stimulating sialoglycans and integrins initiated distinctive mechanoresponses during the early stages of hPSC differentiation. Taken together, these results demonstrated that MGE-enabled mATC uncovered not only different mechanical properties of sialoglycans on hPSCs and integrins but also their different mechanoregulatory impacts on hPSC differentiation, validating MGE-based mATC as a new, powerful tool for investigating the roles of glycans and other cell surface biomolecules in mechanotransduction.
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Affiliation(s)
- Weiping Li
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jiatong Guo
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
| | - Eric C. Hobson
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Xufeng Xue
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Qingjiang Li
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
- Department of Chemistry, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Jianping Fu
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Cheri X. Deng
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Mechanical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Zhongwu Guo
- Department of Chemistry, University of Florida, Gainesville, FL 32611, USA
- UF Health Cancer Center, University of Florida, Gainesville, FL 32611, USA
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3
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Fiore A, Yu G, Northey JJ, Patel R, Ravenscroft TA, Ikegami R, Kolkman W, Kumar P, Grimm JB, Dilan TL, Ruetten VM, Ahrens MB, Shroff H, Lavis LD, Wang S, Weaver VM, Pedram K. Imaging the extracellular matrix in live tissues and organisms with a glycan-binding fluorophore. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.09.593460. [PMID: 38766047 PMCID: PMC11100790 DOI: 10.1101/2024.05.09.593460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
All multicellular systems produce and dynamically regulate extracellular matrices (ECM) that play important roles in both biochemical and mechanical signaling. Though the spatial arrangement of these extracellular assemblies is critical to their biological functions, visualization of ECM structure is challenging, in part because the biomolecules that compose the ECM are difficult to fluorescently label individually and collectively. Here, we present a cell-impermeable small molecule fluorophore, termed Rhobo6, that turns on and red shifts upon reversible binding to glycans. Given that most ECM components are densely glycosylated, the dye enables wash-free visualization of ECM, in systems ranging from in vitro substrates to in vivo mouse mammary tumors. Relative to existing techniques, Rhobo6 provides a broad substrate profile, superior tissue penetration, nonperturbative labeling, and negligible photobleaching. This work establishes a straightforward method for imaging the distribution of ECM in live tissues and organisms, lowering barriers for investigation of extracellular biology.
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Affiliation(s)
- Antonio Fiore
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Guoqiang Yu
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Jason J. Northey
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Ronak Patel
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | | | - Richard Ikegami
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Wiert Kolkman
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Pratik Kumar
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Jonathan B. Grimm
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Tanya L. Dilan
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | | | - Misha B. Ahrens
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Hari Shroff
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Shaohe Wang
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Valerie M. Weaver
- Center for Bioengineering and Tissue Regeneration, Department of Surgery, University of California, San Francisco (UCSF), San Francisco, CA, USA
| | - Kayvon Pedram
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
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4
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Kumar BS. Recent Developments and Application of Mass Spectrometry Imaging in N-Glycosylation Studies: An Overview. Mass Spectrom (Tokyo) 2024; 13:A0142. [PMID: 38435075 PMCID: PMC10904931 DOI: 10.5702/massspectrometry.a0142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/06/2024] [Indexed: 03/05/2024] Open
Abstract
Among the most typical posttranslational modifications is glycosylation, which often involves the covalent binding of an oligosaccharide (glycan) to either an asparagine (N-linked) or a serine/threonine (O-linked) residue. Studies imply that the N-glycan portion of a glycoprotein could serve as a particular disease biomarker rather than the protein itself because N-linked glycans have been widely recognized to evolve with the advancement of tumors and other diseases. N-glycans found on protein asparagine sites have been especially significant. Since N-glycans play clearly defined functions in the folding of proteins, cellular transport, and transmission of signals, modifications to them have been linked to several illnesses. However, because these N-glycans' production is not template driven, they have a substantial morphological range, rendering it difficult to distinguish the species that are most relevant to biology and medicine using standard techniques. Mass spectrometry (MS) techniques have emerged as effective analytical tools for investigating the role of glycosylation in health and illness. This is due to developments in MS equipment, data collection, and sample handling techniques. By recording the spatial dimension of a glycan's distribution in situ, mass spectrometry imaging (MSI) builds atop existing methods while offering added knowledge concerning the structure and functionality of biomolecules. In this review article, we address the current development of glycan MSI, starting with the most used tissue imaging techniques and ionization sources before proceeding on to a discussion on applications and concluding with implications for clinical research.
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5
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Alghazali R, Nugud A, El-Serafi A. Glycan Modifications as Regulators of Stem Cell Fate. BIOLOGY 2024; 13:76. [PMID: 38392295 PMCID: PMC10886185 DOI: 10.3390/biology13020076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/21/2024] [Accepted: 01/24/2024] [Indexed: 02/24/2024]
Abstract
Glycosylation is a process where proteins or lipids are modified with glycans. The presence of glycans determines the structure, stability, and localization of glycoproteins, thereby impacting various biological processes, including embryogenesis, intercellular communication, and disease progression. Glycans can influence stem cell behavior by modulating signaling molecules that govern the critical aspects of self-renewal and differentiation. Furthermore, being located at the cell surface, glycans are utilized as markers for stem cell pluripotency and differentiation state determination. This review aims to provide a comprehensive overview of the current literature, focusing on the effect of glycans on stem cells with a reflection on the application of synthetic glycans in directing stem cell differentiation. Additionally, this review will serve as a primer for researchers seeking a deeper understanding of how synthetic glycans can be used to control stem cell differentiation, which may help establish new approaches to guide stem cell differentiation into specific lineages. Ultimately, this knowledge can facilitate the identification of efficient strategies for advancing stem cell-based therapeutic interventions.
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Affiliation(s)
- Raghad Alghazali
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, 58183 Linköping, Sweden
| | - Ahmed Nugud
- Clinical Sciences, University of Edinburgh, Edinburgh EH4 2XU, UK
- Gastroenterology, Hepatology & Nutrition, Sheikh Khalifa Medical City, Abu Dhabi 51900, United Arab Emirates
| | - Ahmed El-Serafi
- Department of Biomedical and Clinical Sciences (BKV), Linköping University, 58183 Linköping, Sweden
- Department of Hand Surgery, Plastic Surgery and Burns, Linköping University, 58185 Linköping, Sweden
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6
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Tian X, Zheng L, Wang C, Han Y, Li Y, Cui T, Liu J, Liu C, Jia G, Yang L, Hsu Y, Zeng C, Ding L, Wang C, Cheng B, Wang M, Xie R. Selenium-based metabolic oligosaccharide engineering strategy for quantitative glycan detection. Nat Commun 2023; 14:8281. [PMID: 38092825 PMCID: PMC10719347 DOI: 10.1038/s41467-023-44118-w] [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: 05/20/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023] Open
Abstract
Metabolic oligosaccharide engineering (MOE) is a classical chemical approach to perturb, profile and perceive glycans in physiological systems, but probes upon bioorthogonal reaction require accessibility and the background signal readout makes it challenging to achieve glycan quantification. Here we develop SeMOE, a selenium-based metabolic oligosaccharide engineering strategy that concisely combines elemental analysis and MOE,enabling the mass spectrometric imaging of glycome. We also demonstrate that the new-to-nature SeMOE probes allow for detection, quantitative measurement and visualization of glycans in diverse biological contexts. We also show that chemical reporters on conventional MOE can be integrated into a bifunctional SeMOE probe to provide multimodality signal readouts. SeMOE thus provides a convenient and simplified method to explore the glyco-world.
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Affiliation(s)
- Xiao Tian
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Lingna Zheng
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China
| | - Changjiang Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Yida Han
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Yujie Li
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Tongxiao Cui
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Jialin Liu
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Chuanming Liu
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Guogeng Jia
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Lujie Yang
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Yi Hsu
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China
| | - Chen Zeng
- Department of Pharmacology, School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Lijun Ding
- Center for Reproductive Medicine and Obstetrics and Gynecology, Nanjing Drum Tower Hospital, Nanjing University Medical School, Nanjing, China
| | - Chu Wang
- College of Chemistry and Molecular Engineering, Peking University, Beijing, China
| | - Bo Cheng
- School of Pharmaceutical Sciences, Peking University, Beijing, China
| | - Meng Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing, China.
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing, China.
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7
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Babulic JL, Kofsky JM, Boddington ME, Kim Y, Leblanc EV, Cook MG, Garnier CR, Emberley-Korkmaz S, Colpitts CC, Capicciotti CJ. One-Step Selective Labeling of Native Cell Surface Sialoglycans by Exogenous α2,8-Sialylation. ACS Chem Biol 2023; 18:2418-2429. [PMID: 37934063 DOI: 10.1021/acschembio.3c00475] [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: 11/08/2023]
Abstract
Exo-enzymatic glycan labeling strategies have emerged as versatile tools for efficient and selective installation of terminal glyco-motifs onto live cell surfaces. Through employing specific enzymes and nucleotide-sugar probes, cells can be equipped with defined glyco-epitopes for modulating cell function or selective visualization and enrichment of glycoconjugates. Here, we identifyCampylobacter jejunisialyltransferase Cst-II I53S as a tool for cell surface glycan modification, expanding the exo-enzymatic labeling toolkit to include installation of α2,8-disialyl epitopes. Labeling with Cst-II was achieved with biotin- and azide-tagged CMP-Neu5Ac derivatives on a model glycoprotein and native sialylated cell surface glycans across a panel of cell lines. The introduction of modified Neu5Ac derivatives onto cells by Cst-II was also retained on the surface for 6 h. By examining the specificity of Cst-II on cell surfaces, it was revealed that the α2,8-sialyltransferase primarily labeled N-glycans, with O-glycans labeled to a lesser extent, and there was an apparent preference for α2,3-linked sialosides on cells. This approach thus broadens the scope of tools for selective exo-enzymatic labeling of native sialylated glycans and is highly amenable for the construction of cell-based arrays.
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Affiliation(s)
- Jonathan L Babulic
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
| | - Joshua M Kofsky
- Department of Chemistry, Queen's University, Kingston K7L 3N6, Canada
| | - Marie E Boddington
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
| | - Youjin Kim
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
| | - Emmanuelle V Leblanc
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
| | - Madeleine G Cook
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
| | - Cole R Garnier
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
| | - Sophie Emberley-Korkmaz
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
| | - Che C Colpitts
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
| | - Chantelle J Capicciotti
- Department of Biomedical and Molecular Sciences, Queen's University, Kingston K7L 3N6, Canada
- Department of Chemistry, Queen's University, Kingston K7L 3N6, Canada
- Department of Surgery, Queen's University, Kingston K7L 3N6, Canada
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8
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Zheng X, Li Y, Cui T, Yang J, Meng X, Wang H, Chen L, He J, Chen N, Meng L, Ding L, Xie R. Traceless Protein-Selective Glycan Labeling and Chemical Modification. J Am Chem Soc 2023; 145:23670-23680. [PMID: 37857274 DOI: 10.1021/jacs.3c07889] [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: 10/21/2023]
Abstract
Executing glycan editing at a molecular level not only is pivotal for the elucidation of complicated mechanisms involved in glycan-relevant biological processes but also provides a promising solution to potentiate disease therapy. However, the precision control of glycan modification or glyco-editing on a selected glycoprotein is by far a grand challenge. Of note is to preserve the intact cellular glycan landscape, which is preserved after editing events are completed. We report herein a versatile, traceless glycan modification methodology for customizing the glycoforms of targeted proteins (subtypes), by orchestrating chemical- and photoregulation in a protein-selective glycoenzymatic system. This method relies on a three-module, ligand-photocleavable linker-glycoenzyme (L-P-G) conjugate. We demonstrated that RGD- or synthetic carbohydrate ligand-containing conjugates (RPG and SPG) would not activate until after the ligand-receptor interaction is accomplished (chemical regulation). RPG and SPG can both release the glycoenzyme upon photoillumination (photoregulation). The adjustable glycoenzyme activity, combined with ligand recognition selectivity, minimizes unnecessary glycan editing perturbation, and photolytic cleavage enables precise temporal control of editing events. An altered target protein turnover and dimerization were observed in our system, emphasizing the significance of preserving the native physiological niche of a particular protein when precise modification on the carbohydrate epitope occurs.
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Affiliation(s)
- Xiaocui Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yiran Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Tongxiao Cui
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jing Yang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xiangfeng Meng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Haiqi Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Liusheng Chen
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Jian He
- Department of Nuclear Medicine, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Nanjing 210008, China
| | - Nan Chen
- ChinaChomiX Biotech (Nanjing) Co., Ltd., Nanjing 210061, China
| | - Liying Meng
- Department of Medical Experimental Center, Qilu Hospital (Qingdao), Cheeloo College of Medicine, Shandong University, Qingdao 266035, China
| | - Lin Ding
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
- Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China
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9
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Yang Y, Chen M, Wu M, Hong S, Gao B, Liu Y, Yu C, Young TS, Chapla DG, Yang JY, Cappiello JR, Li JP, Sharpless KB, Moremen KW, Wu P. Chemoenzymatic Tagging of Tn/TF/STF Antigens in Living Systems. Isr J Chem 2023; 63:e202300081. [PMID: 38737670 PMCID: PMC11081099 DOI: 10.1002/ijch.202300081] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Indexed: 05/14/2024]
Abstract
Truncated mucin-type O-glycans, such as Tn-associated antigens, are aberrantly expressed biomarkers of cancer, but remain challenging to target. Reactive antibodies to these antigens either lack high-affinity or are prone to antigen escape. Here, we have developed a robust chemoenzymatic strategy for the global labeling of Tn-associated antigens, i.e. Tn (GalNAcα-O-Ser/Thr), Thomsen-Friedenreich (Galβ1-3GalNAcα-O-Ser/Thr, TF) and STF (Neu5Acα2-3Galβ1-3GalNAcα-O-Ser/Thr, STF) antigens, in human whole blood with high efficiency and selectivity. This method relies on the use of the O-glycan sialyltransferase ST6GalNAc1 to transfer a sialic acid-functionalized adaptor to the GalNAc residue of these antigens. By tagging, the adaptor functionalized antigens can be easily targeted by customized strategies such as, but not limited to, chimeric antigen receptor T-Cells (CAR-T). We expect this tagging system to find broad applications in cancer diagnostics and targeting in combination with established strategies.
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Affiliation(s)
- Yi Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mingkuan Chen
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Mengyao Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Senlian Hong
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Gao
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Yonghui Liu
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Chenhua Yu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Travis S. Young
- Department of Biology, California Institute for Biomedical Research (Calibr), The Scripps Research Institute, La Jolla, CA 92037, USA
| | | | - Jeong-Yeh Yang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
| | - John R. Cappiello
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Jie P. Li
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - K. Barry Sharpless
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602
| | - Peng Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037, USA
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10
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Wang M, Kejian S, Ye L, Chen J, Ma L. Transforms of Cell Surface Glycoproteins Charge Influences Tumor Cell Metastasis via Atypically Inhibiting Epithelial-Mesenchymal Transition Including Matrix Metalloproteinases and Cell Junctions. Bioconjug Chem 2023; 34:1498-1507. [PMID: 37498932 DOI: 10.1021/acs.bioconjchem.3c00303] [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: 07/29/2023]
Abstract
Cell communication and signal transduction rely heavily on the charge on the cell surface. The cell surface is negatively charged, with glycoproteins on the cell membrane providing a large percentage of the charge. Sialic acid is found on the outermost side of glycan chains and contributes to glycoprotein's negative charge. Sialic acid is highly expressed in tumor cells and plays an important role in tumor metastasis and immune escape by interacting with extracellular ligands. However, the specific effect of negative charge changes on glycoproteins is still poorly understood. In this study, we used 9-azido sialic acid (9Az-Sia) to create artificial epitopes on glycoproteins via metabolic glycan labeling, and we attached charged groups such as amino and carboxyl to 9Az-Sia via a click reaction with dibenzocyclooctyne (DBCO). The charge of glycoproteins was changed by metabolic glycan labeling and click modification. The results showed that the migration and invasion ability of the MDA-MB-231 cell labeled with 9Az-Sia was significantly reduced after the modification with amino groups rather than carboxyl groups. Epithelial-mesenchymal transition (EMT) is the biological process of metastatic tumor cells, with an increasing ability of tumor cells to migrate and invade. In particular, the expression of adhesion molecules increased in the amine-linked group, whereas the expression of matrix metalloproteinases (MMPs) increased significantly, which is not identical to EMT characteristics. In vivo experiments have demonstrated that the loss of negative charge on glycoproteins has an inhibitory effect on tumors. In conclusion, modifying the positive charge on the surface of glycoproteins can inhibit tumor cell metastasis and has great potential for tumor therapy.
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Affiliation(s)
- Mingzhe Wang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Shi Kejian
- Department of Thoracic Surgery, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
| | - Lei Ye
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jiaqi Chen
- School of Mechanical Engineering, Chengdu University, Chengdu 610000, China
| | - Lan Ma
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- School of Life Sciences, Tsinghua University, Beijing 100084, China
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Institute of Biomedical Health Technology and Engineering, Shenzhen 518055, China
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11
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Yu W, Zhao X, Jalloh AS, Li Y, Zhao Y, Dinner B, Yang Y, Ouyang S, Tian T, Zhao Z, Yang R, Chen M, Lauvau G, Guo Z, Wu P, Li JP. Chemoenzymatic Measurement of LacNAc in Single-Cell Multiomics Reveals It as a Cell-Surface Indicator of Glycolytic Activity of CD8 + T Cells. J Am Chem Soc 2023; 145:12701-12716. [PMID: 37276352 PMCID: PMC10733619 DOI: 10.1021/jacs.3c02602] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Despite the rich information about the physiological state of a cell encoded in the dynamic changes of cell-surface glycans, chemical methods to capture specific glycan epitopes at the single-cell level are quite limited. Here, we report a chemoenzymatic method for the single-cell detection of N-acetyllactosamine (LacNAc) by labeling LacNAc with a specific DNA barcode. The chemoenzymatic labeling does not alter the transcriptional status of immune cells and is compatible with multiple scRNA-seq platforms. Integrated analysis of LacNAc and the transcriptome of T cells at the single-cell level reveals that the amount of cell-surface LacNAc is significantly upregulated in activated CD8+ T cells but maintained at basal levels in resting CD8+ T cells (i.e., naive and central memory T cells). Further analysis confirms that LacNAc levels are positively correlated with the glycolytic activity of CD8+ T cells during differentiation. Taken together, our study demonstrates the feasibility of the chemoenzymatic detection of cell-surface glycan in single-cell RNA sequencing-based multiomics with TCR sequence and cell-surface epitope information (i.e., scTCR and CITE-seq), and provides a new way to characterize the biological role of glycan in diverse physiological states.
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Affiliation(s)
- Wenhao Yu
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xinlu Zhao
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Abubakar S Jalloh
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1301 Morris Park Avenue, Bronx, New York 10461, United States
| | - Yachao Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Yingying Zhao
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Brandon Dinner
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Yang Yang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shian Ouyang
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Tian Tian
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Zihan Zhao
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing 210008, China
| | - Rong Yang
- Department of Urology, Nanjing Drum Tower Hospital, The Affiliated Hospital of Nanjing University Medical School, Institute of Urology, Nanjing University, Nanjing 210008, China
| | - Mingkuan Chen
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Gregoire Lauvau
- Department of Microbiology & Immunology, Albert Einstein College of Medicine of Yeshiva University, 1301 Morris Park Avenue, Bronx, New York 10461, United States
| | - Zijian Guo
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Peng Wu
- Department of Biochemistry, Albert Einstein College of Medicine of Yeshiva University, 1301 Morris Park Avenue, Bronx, New York 10461, United States
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jie P Li
- State Key Laboratory of Coordination Chemistry, Chemistry and Biomedicine Innovation Center (ChemBIC), School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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12
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Lu X, McDowell CT, Blaschke CRK, Liu L, Grimsley G, Wisniewski L, Gao C, Mehta AS, Haab BB, Angel PM, Drake RR. Bioorthogonal Chemical Labeling Probes Targeting Sialic Acid Isomers for N-Glycan MALDI Imaging Mass Spectrometry of Tissues, Cells, and Biofluids. Anal Chem 2023; 95:7475-7486. [PMID: 37126482 PMCID: PMC10193362 DOI: 10.1021/acs.analchem.2c04882] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 04/04/2023] [Indexed: 05/02/2023]
Abstract
Sialic acid isomers attached in either α2,3 or α2,6 linkage to glycan termini confer distinct chemical, biological, and pathological properties, but they cannot be distinguished by mass differences in traditional mass spectrometry experiments. Multiple derivatization strategies have been developed to stabilize and facilitate the analysis of sialic acid isomers and their glycoconjugate carriers by high-performance liquid chromatography, capillary electrophoresis, and mass spectrometry workflows. Herein, a set of novel derivatization schemes are described that result in the introduction of bioorthogonal click chemistry alkyne or azide groups into α2,3- and α2,8-linked sialic acids. These chemical modifications were validated and structurally characterized using model isomeric sialic acid conjugates and model protein carriers. Use of an alkyne-amine, propargylamine, as the second amidation reagent effectively introduces an alkyne functional group into α2,3-linked sialic acid glycoproteins. In tissues, serum, and cultured cells, this allows for the detection and visualization of N-linked glycan sialic acid isomers by imaging mass spectrometry approaches. Formalin-fixed paraffin-embedded prostate cancer tissues and pancreatic cancer cell lines were used to characterize the numbers and distribution of alkyne-modified α2,3-linked sialic acid N-glycans. An azide-amine compound with a poly(ethylene glycol) linker was evaluated for use in histochemical staining. Formalin-fixed pancreatic cancer tissues were amidated with the azide amine, reacted with biotin-alkyne and copper catalyst, and sialic acid isomers detected by streptavidin-peroxidase staining. The direct chemical introduction of bioorthogonal click chemistry reagents into sialic acid-containing glycans and glycoproteins provides a new glycomic tool set to expand approaches for their detection, labeling, visualization, and enrichment.
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Affiliation(s)
- Xiaowei Lu
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
| | - Colin T. McDowell
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
| | - Calvin R. K. Blaschke
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
| | - Liping Liu
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
| | - Grace Grimsley
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
| | - Luke Wisniewski
- Department
of Cell Biology, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - ChongFeng Gao
- Department
of Cell Biology, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - Anand S. Mehta
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
| | - Brian B. Haab
- Department
of Cell Biology, Van Andel Institute, Grand Rapids, Michigan 49503, United States
| | - Peggi M. Angel
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
| | - Richard R. Drake
- Department
of Cellular and Molecular Pharmacology and Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina 29425-2503, United
States
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13
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Li Y, Wang M, Hong S. Live-Cell Glycocalyx Engineering. Chembiochem 2023; 24:e202200707. [PMID: 36642971 DOI: 10.1002/cbic.202200707] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/14/2023] [Accepted: 01/14/2023] [Indexed: 01/17/2023]
Abstract
A heavy layer of glycans forms a brush matrix bound to the outside of all the cells in our bodies; it is referred to as the "sugar forest" or glycocalyx. Beyond the increased appreciation of the glycocalyx over the past two decades, recent advances in engineering the glycocalyx on live cells have spurred the creation of cellular drugs and novel medical treatments. The development of new tools and techniques has empowered scientists to manipulate the structures and functions of cell-surface glycans on target cells and endow target cells with desired properties. Herein, we provide an overview of live-cell glycocalyx engineering strategies for controlling the cell-surface molecular repertory to suit therapeutic applications, even though the realm of this field remains young and largely unexplored.
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Affiliation(s)
- Yuxin Li
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, and School of Pharmaceutical Sciences, Peking University, Health Science Center, Beijing, 100191, China
| | - Mingzhen Wang
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, and School of Pharmaceutical Sciences, Peking University, Health Science Center, Beijing, 100191, China
| | - Senlian Hong
- State Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology Center, and School of Pharmaceutical Sciences, Peking University, Health Science Center, Beijing, 100191, China
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14
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Jaiswal M, Zhou M, Guo J, Tran TT, Kundu S, Jaufer AM, Fanucci GE, Guo Z. Different Biophysical Properties of Cell Surface α2,3- and α2,6-Sialoglycans Revealed by Electron Paramagnetic Resonance Spectroscopic Studies. J Phys Chem B 2023; 127:1749-1757. [PMID: 36808907 PMCID: PMC10116567 DOI: 10.1021/acs.jpcb.2c09048] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Sialoglycans on HeLa cells were labeled with a nitroxide spin radical through enzymatic glycoengineering (EGE)-mediated installation of azide-modified sialic acid (Neu5Ac9N3) and then click reaction-based attachment of a nitroxide spin radical. α2,6-Sialyltransferase (ST) Pd2,6ST and α2,3-ST CSTII were used for EGE to install α2,6- and α2,3-linked Neu5Ac9N3, respectively. The spin-labeled cells were analyzed by X-band continuous wave (CW) electron paramagnetic resonance (EPR) spectroscopy to gain insights into the dynamics and organizations of cell surface α2,6- and α2,3-sialoglycans. Simulations of the EPR spectra revealed average fast- and intermediate-motion components for the spin radicals in both sialoglycans. However, α2,6- and α2,3-sialoglycans in HeLa cells possess different distributions of the two components, e.g., a higher average population of the intermediate-motion component for α2,6-sialoglycans (78%) than that for α2,3-sialoglycans (53%). Thus, the average mobility of spin radicals in α2,3-sialoglycans was higher than that in α2,6-sialoglycans. Given the fact that a spin-labeled sialic acid residue attached to the 6-O-position of galactose/N-acetyl-galactosamine would experience less steric hindrance and show more flexibility than that attached to the 3-O-position, these results may reflect the differences in local crowding/packing that restrict the spin-label and sialic acid motion for α2,6-linked sialoglycans. The studies further suggest that Pd2,6ST and CSTII may have different preferences for glycan substrates in the complex environment of the extracellular matrix. The discoveries of this work are biologically important as they are useful for interpreting the different functions of α2,6- and α2,3-sialoglycans and indicate the possibility of using Pd2,6ST and CSTII to target different glycoconjugates on cells.
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Affiliation(s)
- Mohit Jaiswal
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, Florida 32611, United States
| | - Mingwei Zhou
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, Florida 32611, United States
| | - Jiatong Guo
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, Florida 32611, United States
| | - Trang T Tran
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, Florida 32611, United States
| | - Sayan Kundu
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, Florida 32611, United States
| | - Afnan M Jaufer
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, Florida 32611, United States
| | - Gail E Fanucci
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, Florida 32611, United States
| | - Zhongwu Guo
- Department of Chemistry, University of Florida, 214 Leigh Hall, Gainesville, Florida 32611, United States
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15
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Sun F, Suttapitugsakul S, Wu R. Systematic characterization of extracellular glycoproteins using mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:519-545. [PMID: 34047389 PMCID: PMC8627532 DOI: 10.1002/mas.21708] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 05/13/2023]
Abstract
Surface and secreted glycoproteins are essential to cells and regulate many extracellular events. Because of the diversity of glycans, the low abundance of many glycoproteins, and the complexity of biological samples, a system-wide investigation of extracellular glycoproteins is a daunting task. With the development of modern mass spectrometry (MS)-based proteomics, comprehensive analysis of different protein modifications including glycosylation has advanced dramatically. This review focuses on the investigation of extracellular glycoproteins using MS-based proteomics. We first discuss the methods for selectively enriching surface glycoproteins and investigating protein interactions on the cell surface, followed by the application of MS-based proteomics for surface glycoprotein dynamics analysis and biomarker discovery. We then summarize the methods to comprehensively study secreted glycoproteins by integrating various enrichment approaches with MS-based proteomics and their applications for global analysis of secreted glycoproteins in different biological samples. Collectively, MS significantly expands our knowledge of extracellular glycoproteins and enables us to identify extracellular glycoproteins as potential biomarkers for disease detection and drug targets for disease treatment.
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Affiliation(s)
| | | | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, USA
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16
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Cheng B, Wang C, Hao Y, Wang J, Xia X, Zhang H, He R, Zhang S, Dai P, Chen X. Facile Synthesis of Clickable Unnatural Sugars in the Unprotected and 1,6-Di-O-Acylated Forms for Metabolic Glycan Labeling. Chemistry 2023; 29:e202203054. [PMID: 36422057 DOI: 10.1002/chem.202203054] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/12/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022]
Abstract
Clickable unnatural sugars have been widely used in studying glycosylation in living systems via the metabolic glycan labelling (MGL) strategy. Partial protection of unnatural sugars by 1,6-di-O-acylation increases the labelling efficiency while avoiding the non-specific S-glyco-modification. Herein, we report the facile synthesis of a series of clickable unnatural sugars in both the unprotected and 1,6-di-O-acylated forms at the ten-gram scale. By evaluation of the labelling specificity, efficiency, and biocompatibility of various 1,6-di-O-acylated sugars for MGL in cell lines and living mice, we demonstrate that 1,6-di-O-propionylated unnatural sugars are optimal chemical reporters for glycan labelling. The synthetic routes developed in this work should facilitate the widespread use of MGL with no artificial S-glyco-modification for investigating the functional roles of glycans.
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Affiliation(s)
- Bo Cheng
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and, Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, P. R. China
| | - Chunting Wang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and, Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, P. R. China
| | - Yi Hao
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and, Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, P. R. China
| | - Jiankun Wang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and, Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, P. R. China
| | - Xiaoqian Xia
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and, Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, P. R. China
| | - Hao Zhang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and, Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, P. R. China
| | - Rundong He
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and, Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, P. R. China
| | - Shaoran Zhang
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and, Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, P. R. China
| | - Peng Dai
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and, Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, P. R. China
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Beijing National Laboratory for Molecular Sciences, Peking-Tsinghua Center for Life Sciences, Synthetic and Functional Biomolecules Center, Key Laboratory of Bioorganic Chemistry and, Molecular Engineering of Ministry of Education, Peking University, Beijing, 100871, P. R. China
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17
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Park S, Chin-Hun Kuo J, Reesink HL, Paszek MJ. Recombinant mucin biotechnology and engineering. Adv Drug Deliv Rev 2023; 193:114618. [PMID: 36375719 PMCID: PMC10253230 DOI: 10.1016/j.addr.2022.114618] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 10/14/2022] [Accepted: 11/04/2022] [Indexed: 11/13/2022]
Abstract
Mucins represent a largely untapped class of polymeric building block for biomaterials, therapeutics, and other biotechnology. Because the mucin polymer backbone is genetically encoded, sequence-specific mucins with defined physical and biochemical properties can be fabricated using recombinant technologies. The pendent O-glycans of mucins are increasingly implicated in immunomodulation, suppression of pathogen virulence, and other biochemical activities. Recent advances in engineered cell production systems are enabling the scalable synthesis of recombinant mucins with precisely tuned glycan side chains, offering exciting possibilities to tune the biological functionality of mucin-based products. New metabolic and chemoenzymatic strategies enable further tuning and functionalization of mucin O-glycans, opening new possibilities to expand the chemical diversity and functionality of mucin building blocks. In this review, we discuss these advances, and the opportunities for engineered mucins in biomedical applications ranging from in vitro models to therapeutics.
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Affiliation(s)
- Sangwoo Park
- Field of Biophysics, Cornell University, Ithaca, NY 14853, USA
| | - Joe Chin-Hun Kuo
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA
| | - Heidi L Reesink
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | - Matthew J Paszek
- Field of Biophysics, Cornell University, Ithaca, NY 14853, USA; Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY 14853, USA; Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY 14853, USA.
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18
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McLeish KR, Fernandes MJ. Understanding inhibitory receptor function in neutrophils through the lens of
CLEC12A. Immunol Rev 2022; 314:50-68. [PMID: 36424898 DOI: 10.1111/imr.13174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Neutrophils are the first leukocytes recruited from the circulation in response to invading pathogens or injured cells. To eradicate pathogens and contribute to tissue repair, recruited neutrophils generate and release a host of toxic chemicals that can also damage normal cells. To avoid collateral damage leading to tissue injury and organ dysfunction, molecular mechanisms evolved that tightly control neutrophil response threshold to activating signals, the strength and location of the response, and the timing of response termination. One mechanism of response control is interruption of activating intracellular signaling pathways by the 20 inhibitory receptors expressed by neutrophils. The two inhibitory C-type lectin receptors expressed by neutrophils, CLEC12A and DCIR, exhibit both common and distinct molecular and functional mechanisms, and they are associated with different diseases. In this review, we use studies on CLEC12A as a model of inhibitory receptor regulation of neutrophil function and participation in disease. Understanding the molecular mechanisms leading to inhibitory receptor specificity offers the possibility of using physiologic control of neutrophil functions as a pharmacologic tool to control inflammatory diseases.
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Affiliation(s)
- Kenneth R. McLeish
- Department of Medicine University of Louisville School of Medicine Louisville Kentucky USA
| | - Maria J. Fernandes
- Infectious and Immune Diseases Division CHU de Québec‐Laval University Research Center Québec Québec Canada
- Department of Microbiology‐Infectious Diseases and Immunology, Faculty of Medicine Laval University Québec Québec Canada
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19
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Scinto SL, Reagle TR, Fox JM. Affinity Bioorthogonal Chemistry (ABC) Tags for Site-Selective Conjugation, On-Resin Protein-Protein Coupling, and Purification of Protein Conjugates. Angew Chem Int Ed Engl 2022; 61:e202207661. [PMID: 36058881 PMCID: PMC10029600 DOI: 10.1002/anie.202207661] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Indexed: 11/12/2022]
Abstract
The site-selective functionalization of proteins has broad application in chemical biology, but can be limited when mixtures result from incomplete conversion or the formation of protein containing side products. It is shown here that when proteins are covalently tagged with pyridyl-tetrazines, the nickel-iminodiacetate (Ni-IDA) resins commonly used for His-tags can be directly used for protein affinity purification. These Affinity Bioorthogonal Chemistry (ABC) tags serve a dual role by enabling affinity-based protein purification while maintaining rapid kinetics in bioorthogonal reactions. ABC-tagging works with a range of site-selective bioconjugation methods with proteins tagged at the C-terminus, N-terminus or at internal positions. ABC-tagged proteins can also be purified from complex mixtures including cell lysate. The combination of site-selective conjugation and clean-up with ABC-tagged proteins also allows for facile on-resin reactions to provide protein-protein conjugates.
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Affiliation(s)
- Samuel L Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
| | - Tyler R Reagle
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
| | - Joseph M Fox
- Department of Chemistry and Biochemistry, University of Delaware, Ammon Pinizzotto Biopharmaceutical Innovation Center, Newark, DE 19713, USA
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20
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Zheng M, Lin Y, Wang W, Zhao Y, Bao X. Application of nucleoside or nucleotide analogues in RNA dynamics and RNA-binding protein analysis. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1722. [PMID: 35218164 DOI: 10.1002/wrna.1722] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 01/07/2022] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
Cellular RNAs undergo dynamic changes during RNA biological processes, which are tightly orchestrated by RNA-binding proteins (RBPs). Yet, the investigation of RNA dynamics is hurdled by highly abundant steady-state RNAs, which make the signals of dynamic RNAs less detectable. Notably, the exert of nucleoside or nucleotide analogue-based RNA technologies has provided a remarkable platform for RNA dynamics research, revealing diverse unnoticed features in RNA metabolism. In this review, we focus on the application of two types of analogue-based RNA sequencing, antigen-/antibody- and click chemistry-based methodologies, and summarize the RNA dynamics features revealed. Moreover, we discuss emerging single-cell newly transcribed RNA sequencing methodologies based on nucleoside analogue labeling, which provides novel insights into RNA dynamics regulation at single-cell resolution. On the other hand, we also emphasize the identification of RBPs that interact with polyA, non-polyA RNAs, or newly transcribed RNAs and also their associated RNA-binding domains at genomewide level through ultraviolet crosslinking and mass spectrometry in different contexts. We anticipated that further modification and development of these analogue-based RNA and RBP capture technologies will aid in obtaining an unprecedented understanding of RNA biology. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Methods > RNA Analyses in Cells.
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Affiliation(s)
- Meifeng Zheng
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yingying Lin
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- The Center for Infection and Immunity Study, School of Medicine, Sun Yat-sen University, Guangming Science City, Shenzhen, China
| | - Wei Wang
- Center for Biosafety, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
| | - Yu Zhao
- Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xichen Bao
- Center for Cell Lineage and Development, CAS Key Laboratory of Regenerative Biology, Guangdong Provincial Key Laboratory of Stem Cell and Regenerative Medicine, GIBH-HKU Guangdong-Hong Kong Stem Cell and Regenerative Medicine Research Centre, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Cell Lineage and Atlas, Bioland Laboratory (Guangzhou Regenerative Medicine and Health Guangdong Laboratory), Guangzhou, China
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21
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Li H, Chiang AWT, Lewis NE. Artificial intelligence in the analysis of glycosylation data. Biotechnol Adv 2022; 60:108008. [PMID: 35738510 PMCID: PMC11157671 DOI: 10.1016/j.biotechadv.2022.108008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Revised: 06/15/2022] [Accepted: 06/16/2022] [Indexed: 11/18/2022]
Abstract
Glycans are complex, yet ubiquitous across biological systems. They are involved in diverse essential organismal functions. Aberrant glycosylation may lead to disease development, such as cancer, autoimmune diseases, and inflammatory diseases. Glycans, both normal and aberrant, are synthesized using extensive glycosylation machinery, and understanding this machinery can provide invaluable insights for diagnosis, prognosis, and treatment of various diseases. Increasing amounts of glycomics data are being generated thanks to advances in glycoanalytics technologies, but to maximize the value of such data, innovations are needed for analyzing and interpreting large-scale glycomics data. Artificial intelligence (AI) provides a powerful analysis toolbox in many scientific fields, and here we review state-of-the-art AI approaches on glycosylation analysis. We further discuss how models can be analyzed to gain mechanistic insights into glycosylation machinery and how the machinery shapes glycans under different scenarios. Finally, we propose how to leverage the gained knowledge for developing predictive AI-based models of glycosylation. Thus, guiding future research of AI-based glycosylation model development will provide valuable insights into glycosylation and glycan machinery.
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Affiliation(s)
- Haining Li
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | - Austin W T Chiang
- Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Nathan E Lewis
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA 92093, USA.
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22
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Griffin ME, Hsieh-Wilson LC. Tools for mammalian glycoscience research. Cell 2022; 185:2657-2677. [PMID: 35809571 PMCID: PMC9339253 DOI: 10.1016/j.cell.2022.06.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 10/17/2022]
Abstract
Cellular carbohydrates or glycans are critical mediators of biological function. Their remarkably diverse structures and varied activities present exciting opportunities for understanding many areas of biology. In this primer, we discuss key methods and recent breakthrough technologies for identifying, monitoring, and manipulating glycans in mammalian systems.
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Affiliation(s)
- Matthew E. Griffin
- Department of Chemistry, University of California Irvine, Irvine, CA 92697, USA
| | - Linda C. Hsieh-Wilson
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 92115, USA,Correspondence: (L.C.H.W.)
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23
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Desrochers GF, Filip R, Bastianelli M, Stern T, Pezacki JP. microRNA-27b regulates hepatic lipase enzyme LIPC and reduces triglyceride degradation during hepatitis C virus infection. J Biol Chem 2022; 298:101983. [PMID: 35483451 PMCID: PMC9163519 DOI: 10.1016/j.jbc.2022.101983] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 03/24/2022] [Accepted: 03/26/2022] [Indexed: 11/26/2022] Open
Abstract
miRNAs are short, noncoding RNAs that negatively and specifically regulate protein expression, the cumulative effects of which can result in broad changes to cell systems and architecture. The miRNA miR-27b is known to regulate lipid regulatory pathways in the human liver and is also induced by the hepatitis C virus (HCV). However, the functional targets of miR-27b are not well established. Herein, an activity-based protein profiling method using a serine hydrolase probe, coupled with stable isotope labeling and mass spectrometry identified direct and indirect targets of miR-27b. The hepatic lipase C (LIPC) stood out as both highly dependent on miR-27b and as a major modulator of lipid pathway misregulation. Modulation of miR-27b using both exogenous miRNA mimics and inhibitors demonstrated that transcription factors Jun, PPARα, and HNF4α, all of which also influence LIPC levels and activity, are regulated by miR-27b. LIPC was furthermore shown to affect the progress of the life cycle of HCV and to decrease levels of intracellular triglycerides, upon which HCV is known to depend. In summary, this work has demonstrated that miR-27b mediates HCV infection by downregulating LIPC, thereby reducing triglyceride degradation, which in turn increases cellular lipid levels.
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Affiliation(s)
| | - Roxana Filip
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - Micheal Bastianelli
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada
| | - Tiffany Stern
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Canada; Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Canada.
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24
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Marando VM, Kim DE, Kiessling LL. Biosynthetic incorporation for visualizing bacterial glycans. Methods Enzymol 2022; 665:135-151. [PMID: 35379432 DOI: 10.1016/bs.mie.2021.12.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Cell-surface glycans are central to many biological processes, yet methods for their site-selective modification are limited. Strategies for interrogating the structure and function of proteins have been enabled by chemoselective reactions of sidechain functionality for covalent modification, capture, or imaging. However, unlike protein sidechains, glycan building blocks lack distinguishing reactivity. Moreover, glycans are not primary gene products, so encoding glycan variants through genetic manipulation is challenging. Reactive functional groups can be introduced into glycans through metabolic engineering, which involves the generation of modified nucleotide-sugar building blocks. Lipid-linked building blocks, which are also used in glycan biosynthesis, have the advantage that they can be delivered directly to glycosyltransferases to function as surrogate substrates. This process, termed "biosynthetic incorporation," takes advantage of the properties of bacterial glycosyltransferase: they are selective for the products they generate yet promiscuous in their donor preferences. We describe how this strategy can be implemented to label arabinofuranose-containing glycans on the surface of mycobacterial cells. We anticipate that this platform can be expanded to develop chemoselective labeling agents for other important bacterial monosaccharides.
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Affiliation(s)
- Victoria M Marando
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Daria E Kim
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA, United States.
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25
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Jemas A, Xie Y, Pigga JE, Caplan JL, am Ende CW, Fox JM. Catalytic Activation of Bioorthogonal Chemistry with Light (CABL) Enables Rapid, Spatiotemporally Controlled Labeling and No-Wash, Subcellular 3D-Patterning in Live Cells Using Long Wavelength Light. J Am Chem Soc 2022; 144:1647-1662. [PMID: 35072462 PMCID: PMC9364228 DOI: 10.1021/jacs.1c10390] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Described is the spatiotemporally controlled labeling and patterning of biomolecules in live cells through the catalytic activation of bioorthogonal chemistry with light, referred to as "CABL". Here, an unreactive dihydrotetrazine (DHTz) is photocatalytically oxidized in the intracellular environment by ambient O2 to produce a tetrazine that immediately reacts with a trans-cyclooctene (TCO) dienophile. 6-(2-Pyridyl)dihydrotetrazine-3-carboxamides were developed as stable, cell permeable DHTz reagents that upon oxidation produce the most reactive tetrazines ever used in live cells with Diels-Alder kinetics exceeding k2 of 106 M-1 s-1. CABL photocatalysts are based on fluorescein or silarhodamine dyes with activation at 470 or 660 nm. Strategies for limiting extracellular production of singlet oxygen are described that increase the cytocompatibility of photocatalysis. The HaloTag self-labeling platform was used to introduce DHTz tags to proteins localized in the nucleus, mitochondria, actin, or cytoplasm, and high-yielding subcellular activation and labeling with a TCO-fluorophore were demonstrated. CABL is light-dose dependent, and two-photon excitation promotes CABL at the suborganelle level to selectively pattern live cells under no-wash conditions. CABL was also applied to spatially resolved live-cell labeling of an endogenous protein target by using TIRF microscopy to selectively activate intracellular monoacylglycerol lipase tagged with DHTz-labeled small molecule covalent inhibitor. Beyond spatiotemporally controlled labeling, CABL also improves the efficiency of "ordinary" tetrazine ligations by rescuing the reactivity of commonly used 3-aryl-6-methyltetrazine reporters that become partially reduced to DHTzs inside cells. The spatiotemporal control and fast rates of photoactivation and labeling of CABL should enable a range of biomolecular labeling applications in living systems.
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Affiliation(s)
- Andrew Jemas
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Yixin Xie
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Jessica E. Pigga
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
| | - Jeffrey L. Caplan
- Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19716, USA
| | - Christopher W. am Ende
- Pfizer Worldwide Research and Development, Eastern Point Road, Groton, Connecticut 06340, United States
| | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, Delaware 19716, USA
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26
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Cui T, Man Y, Wang F, Bi S, Lin L, Xie R. Glycoenzyme Tool Development: Principles, Screening Methods, and Recent Advances
†. CHINESE J CHEM 2022. [DOI: 10.1002/cjoc.202100770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Tongxiao Cui
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University Nanjing, Jiagsu 210023 China
| | - Yi Man
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University Nanjing, Jiagsu 210023 China
| | - Feifei Wang
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University Nanjing, Jiagsu 210023 China
| | - Shuyang Bi
- State Key Laboratory of Bio‐organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry Shanghai 200032 China
| | - Liang Lin
- State Key Laboratory of Bio‐organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry Shanghai 200032 China
| | - Ran Xie
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Chemistry and Biomedicine Innovation Center (ChemBIC) Nanjing University Nanjing, Jiagsu 210023 China
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27
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Writing and erasing O-GlcNAc from target proteins in cells. Biochem Soc Trans 2021; 49:2891-2901. [PMID: 34783346 DOI: 10.1042/bst20210865] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/25/2021] [Accepted: 10/27/2021] [Indexed: 12/15/2022]
Abstract
O-linked N-acetylglucosamine (O-GlcNAc) is a widespread reversible modification on nucleocytoplasmic proteins that plays an important role in many biochemical processes and is highly relevant to numerous human diseases. The O-GlcNAc modification has diverse functional impacts on individual proteins and glycosites, and methods for editing this modification on substrates are essential to decipher these functions. Herein, we review recent progress in developing methods for O-GlcNAc regulation, with a focus on methods for editing O-GlcNAc with protein- and site-selectivity in cells. The applications, advantages, and limitations of currently available strategies for writing and erasing O-GlcNAc and future directions are also discussed. These emerging approaches to manipulate O-GlcNAc on a target protein in cells will greatly accelerate the development of functional studies and enable therapeutic interventions in the O-GlcNAc field.
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28
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Gong Y, Qin S, Dai L, Tian Z. The glycosylation in SARS-CoV-2 and its receptor ACE2. Signal Transduct Target Ther 2021; 6:396. [PMID: 34782609 PMCID: PMC8591162 DOI: 10.1038/s41392-021-00809-8] [Citation(s) in RCA: 102] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/24/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
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Affiliation(s)
- Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
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29
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Tian Y, Zhu Q, Sun Z, Geng D, Lin B, Su X, He J, Guo M, Xu H, Zhao Y, Qin W, Wang PG, Wen L, Yi W. One‐Step Enzymatic Labeling Reveals a Critical Role of O‐GlcNAcylation in Cell‐Cycle Progression and DNA Damage Response. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202110053] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Yinping Tian
- Department of Hepatobiliary and Pancreatic Surgery The First Affiliated Hospital Zhejiang Provincial Key Laboratory of Pancreatic Disease School of Medicine Zhejiang University Hangzhou China
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Qiang Zhu
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Zeyu Sun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious Diseases Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Didi Geng
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Bingyi Lin
- Department of Hepatobiliary and Pancreatic Surgery The First Affiliated Hospital Zhejiang Provincial Key Laboratory of Pancreatic Disease School of Medicine Zhejiang University Hangzhou China
| | - Xiaoling Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases National Clinical Research Center for Infectious Diseases Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease The First Affiliated Hospital School of Medicine Zhejiang University Hangzhou China
| | - Jiahui He
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Miao Guo
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
| | - Weijie Qin
- National Center for Protein Sciences Beijing State Key Laboratory of Proteomics, Beijing Proteome Research Center Beijing Institute of Lifeomics Beijing China
| | - Peng George Wang
- School of Medicine Southern University of Science and Technology Shenzhen China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center Shanghai Institute of Materia Medica Chinese Academy of Sciences Shanghai China
| | - Wen Yi
- Department of Hepatobiliary and Pancreatic Surgery The First Affiliated Hospital Zhejiang Provincial Key Laboratory of Pancreatic Disease School of Medicine Zhejiang University Hangzhou China
- MOE Key Laboratory of Biosystems Homeostasis & Protection College of Life Sciences Zhejiang University Hangzhou China
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30
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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.
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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
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31
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Jong H, Wösten MMSM, Wennekes T. Sweet impersonators: Molecular mimicry of host glycans by bacteria. Glycobiology 2021; 32:11-22. [PMID: 34939094 PMCID: PMC8881735 DOI: 10.1093/glycob/cwab104] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 09/03/2021] [Accepted: 09/28/2021] [Indexed: 12/02/2022] Open
Abstract
All bacteria display surface-exposed glycans that can play an important role in their interaction with the host and in select cases mimic the glycans found on host cells, an event called molecular or glycan mimicry. In this review, we highlight the key bacteria that display human glycan mimicry and provide an overview of the involved glycan structures. We also discuss the general trends and outstanding questions associated with human glycan mimicry by bacteria. Finally, we provide an overview of several techniques that have emerged from the discipline of chemical glycobiology, which can aid in the study of the composition, variability, interaction and functional role of these mimicking glycans.
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Affiliation(s)
- Hanna Jong
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomedical Research, Utrecht University, Utrecht, The Netherlands.,Department of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Marc M S M Wösten
- Department of Biomolecular Health Sciences, Utrecht University, Utrecht, The Netherlands
| | - Tom Wennekes
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences and Bijvoet Center for Biomedical Research, Utrecht University, Utrecht, The Netherlands
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32
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Tian Y, Zhu Q, Sun Z, Geng D, Lin B, Su X, He J, Guo M, Xu H, Zhao Y, Qin W, Wang PG, Wen L, Yi W. One-Step Enzymatic Labeling Reveals a Critical Role of O-GlcNAcylation in Cell-Cycle Progression and DNA Damage Response. Angew Chem Int Ed Engl 2021; 60:26128-26135. [PMID: 34590401 DOI: 10.1002/anie.202110053] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Indexed: 12/26/2022]
Abstract
O-linked N-acetylglucosamine (O-GlcNAcylation) is a ubiquitous post-translational modification of proteins that is essential for cell function. Perturbation of O-GlcNAcylation leads to altered cell-cycle progression and DNA damage response. However, the underlying mechanisms are poorly understood. Here, we develop a highly sensitive one-step enzymatic strategy for capture and profiling O-GlcNAcylated proteins in cells. Using this strategy, we discover that flap endonuclease 1 (FEN1), an essential enzyme in DNA synthesis, is a novel substrate for O-GlcNAcylation. FEN1 O-GlcNAcylation is dynamically regulated during the cell cycle. O-GlcNAcylation at the serine 352 of FEN1 disrupts its interaction with Proliferating Cell Nuclear Antigen (PCNA) at the replication foci, and leads to altered cell cycle, defects in DNA replication, accumulation of DNA damage, and enhanced sensitivity to DNA damage agents. Thus, our study provides a sensitive method for profiling O-GlcNAcylated proteins, and reveals an unknown mechanism of O-GlcNAcylation in regulating cell cycle progression and DNA damage response.
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Affiliation(s)
- Yinping Tian
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang Provincial Key Laboratory of Pancreatic Disease, School of Medicine, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Qiang Zhu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zeyu Sun
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Didi Geng
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Bingyi Lin
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang Provincial Key Laboratory of Pancreatic Disease, School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaoling Su
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Disease, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiahui He
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Miao Guo
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Hong Xu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Ye Zhao
- MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Weijie Qin
- National Center for Protein Sciences Beijing, State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, Beijing, China
| | - Peng George Wang
- School of Medicine, Southern University of Science and Technology, Shenzhen, China
| | - Liuqing Wen
- Carbohydrate-Based Drug Research Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Wen Yi
- Department of Hepatobiliary and Pancreatic Surgery, The First Affiliated Hospital, Zhejiang Provincial Key Laboratory of Pancreatic Disease, School of Medicine, Zhejiang University, Hangzhou, China.,MOE Key Laboratory of Biosystems Homeostasis & Protection, College of Life Sciences, Zhejiang University, Hangzhou, China
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33
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Hong S, Yu C, Rodrigues E, Shi Y, Chen H, Wang P, Chapla DG, Gao T, Zhuang R, Moremen KW, Paulson JC, Macauley MS, Wu P. Modulation of Siglec-7 Signaling Via In Situ-Created High-Affinity cis-Ligands. ACS CENTRAL SCIENCE 2021; 7:1338-1346. [PMID: 34471678 PMCID: PMC8393205 DOI: 10.1021/acscentsci.1c00064] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Indexed: 05/04/2023]
Abstract
Sialic acid-binding immunoglobulin-like lectins, also known as Siglecs, have recently been designated as glyco-immune checkpoints. Through their interactions with sialylated glycan ligands overexpressed on tumor cells, inhibitory Siglecs on innate and adaptive immune cells modulate signaling cascades to restrain anti-tumor immune responses. However, the elucidation of the mechanisms underlying these processes is just beginning. We find that when human natural killer (NK) cells attack tumor cells, glycan remodeling occurs on the target cells at the immunological synapse. This remodeling occurs through both the transfer of sialylated glycans from NK cells to target tumor cells and the accumulation of de novo synthesized sialosides on the tumor cells. The functionalization of NK cells with a high-affinity ligand of Siglec-7 leads to multifaceted consequences in modulating a Siglec-7-regulated NK-activation. At high levels of ligand, an enzymatically added Siglec-7 ligand suppresses NK cytotoxicity through the recruitment of Siglec-7 to an immune synapse, whereas at low levels of ligand an enzymatically added Siglec-7 ligand triggers the release of Siglec-7 from the cell surface into the culture medium, preventing a Siglec-7-mediated inhibition of NK cytotoxicity. These results suggest that a glycan engineering of NK cells may provide a means to boost NK effector functions for related applications.
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Affiliation(s)
- Senlian Hong
- State
Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology
Center, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Chenhua Yu
- Department of Molecular Medicine, Department of Immunology
and Microbiology, The Scripps Research Institute, La Jolla 92037, California, United States
- Tianjin
Medical University Cancer Institute and Hospital, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin 300060, China
| | - Emily Rodrigues
- Department of Chemistry, Department of Medical
Microbiology and Immunology, University
of Alberta, 11227 Saskatchewan Drive NW, Edmonton AB T6G 2G2, Alberta, Canada
| | - Yujie Shi
- Department of Molecular Medicine, Department of Immunology
and Microbiology, The Scripps Research Institute, La Jolla 92037, California, United States
| | - Hongmin Chen
- State
Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology
Center, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Peng Wang
- Department of Molecular Medicine, Department of Immunology
and Microbiology, The Scripps Research Institute, La Jolla 92037, California, United States
| | - Digantkumar G. Chapla
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - Tao Gao
- State
Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology
Center, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Ruoxuan Zhuang
- State
Key Laboratory of Natural and Biomimetic Drugs, Chemical Biology
Center, Department of Chemical Biology, School of Pharmaceutical Sciences, Peking University, Beijing 100191, China
| | - Kelley W. Moremen
- Complex
Carbohydrate Research Center, University
of Georgia, Athens, Georgia 30602, United States
| | - James C. Paulson
- Department of Molecular Medicine, Department of Immunology
and Microbiology, The Scripps Research Institute, La Jolla 92037, California, United States
| | - Matthew S. Macauley
- Department of Chemistry, Department of Medical
Microbiology and Immunology, University
of Alberta, 11227 Saskatchewan Drive NW, Edmonton AB T6G 2G2, Alberta, Canada
| | - Peng Wu
- Department of Molecular Medicine, Department of Immunology
and Microbiology, The Scripps Research Institute, La Jolla 92037, California, United States
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Nguyen K, Chakraborty S, Mansbach RA, Korber B, Gnanakaran S. Exploring the Role of Glycans in the Interaction of SARS-CoV-2 RBD and Human Receptor ACE2. Viruses 2021; 13:927. [PMID: 34067878 PMCID: PMC8156887 DOI: 10.3390/v13050927] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 05/03/2021] [Accepted: 05/07/2021] [Indexed: 01/01/2023] Open
Abstract
COVID-19 is a highly infectious respiratory disease caused by the novel coronavirus SARS-CoV-2. It has become a global pandemic and its frequent mutations may pose new challenges for vaccine design. During viral infection, the Spike RBD of SARS-CoV-2 binds the human host cell receptor ACE2, enabling the virus to enter the host cell. Both the Spike and ACE2 are densely glycosylated, and it is unclear how distinctive glycan types may modulate the interaction of RBD and ACE2. Detailed understanding of these determinants is key for the development of novel therapeutic strategies. To this end, we perform extensive all-atom simulations of the (i) RBD-ACE2 complex without glycans, (ii) RBD-ACE2 with oligomannose MAN9 glycans in ACE2, and (iii) RBD-ACE2 with complex FA2 glycans in ACE2. These simulations identify the key residues at the RBD-ACE2 interface that form contacts with higher probabilities, thus providing a quantitative evaluation that complements recent structural studies. Notably, we find that this RBD-ACE2 contact signature is not altered by the presence of different glycoforms, suggesting that RBD-ACE2 interaction is robust. Applying our simulated results, we illustrate how the recently prevalent N501Y mutation may alter specific interactions with host ACE2 that facilitate the virus-host binding. Furthermore, our simulations reveal how the glycan on Asn90 of ACE2 can play a distinct role in the binding and unbinding of RBD. Finally, an energetics analysis shows that MAN9 glycans on ACE2 decrease RBD-ACE2 affinity, while FA2 glycans lead to enhanced binding of the complex. Together, our results provide a more comprehensive picture of the detailed interplay between virus and human receptor, which is much needed for the discovery of effective treatments that aim at modulating the physical-chemical properties of this virus.
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Affiliation(s)
- Kien Nguyen
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
| | - Srirupa Chakraborty
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | | | - Bette Korber
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
| | - Sandrasegaram Gnanakaran
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, NM 87545, USA; (K.N.); (S.C.); (B.K.)
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35
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Huxley KE, Willems LI. Chemical reporters to study mammalian O-glycosylation. Biochem Soc Trans 2021; 49:903-913. [PMID: 33860782 PMCID: PMC8106504 DOI: 10.1042/bst20200839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Revised: 03/17/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022]
Abstract
Glycans play essential roles in a range of cellular processes and have been shown to contribute to various pathologies. The diversity and dynamic nature of glycan structures and the complexities of glycan biosynthetic pathways make it challenging to study the roles of specific glycans in normal cellular function and disease. Chemical reporters have emerged as powerful tools to characterise glycan structures and monitor dynamic changes in glycan levels in a native context. A variety of tags can be introduced onto specific monosaccharides via the chemical modification of endogenous glycan structures or by metabolic or enzymatic incorporation of unnatural monosaccharides into cellular glycans. These chemical reporter strategies offer unique opportunities to study and manipulate glycan functions in living cells or whole organisms. In this review, we discuss recent advances in metabolic oligosaccharide engineering and chemoenzymatic glycan labelling, focusing on their application to the study of mammalian O-linked glycans. We describe current barriers to achieving glycan labelling specificity and highlight innovations that have started to pave the way to overcome these challenges.
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Affiliation(s)
- Kathryn E. Huxley
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, U.K
| | - Lianne I. Willems
- York Structural Biology Laboratory, Department of Chemistry, The University of York, York YO10 5DD, U.K
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36
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Zhu Y, Liao JY, Qian L. Isocyanides: Promising Functionalities in Bioorthogonal Labeling of Biomolecules. Front Chem 2021; 9:670751. [PMID: 33996762 PMCID: PMC8117350 DOI: 10.3389/fchem.2021.670751] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 04/16/2021] [Indexed: 01/20/2023] Open
Abstract
Isocyanides have drawn increasing attention in biological applications due to their attractive properties and unique reactivities, which can undergo various reactions, such as multicomponent reactions, α-addition reactions, [4 + 1] cycloaddition reactions, and the reaction scope keeps expanding. In addition to acting as reactants for the preparation of structurally interesting and diverse N-heterocycles or peptidomimetics, this type of functionality may be a good choice in the labeling and modulation of biomolecules due to the high biocompatibility and small size to minimize modifications on the parent molecule. It has been demonstrated that isocyanides can participate in biomolecule labeling through three strategies, including the two-component bioorthogonal reaction, multicomponent reaction, and metal chelation. Among them, the isocyanide-tetrazine reaction has been better studied recently, augmenting the potency of isocyanide as a bioorthogonal handle. This review will focus on the recent progress in isocyanide chemistry for labeling of biomolecules. Meanwhile, methods to introduce isocyano groups into biomacromolecules are also described to facilitate wider applications of this unique functionality.
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Affiliation(s)
- Yuchen Zhu
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
| | - Jia-Yu Liao
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, China
| | - Linghui Qian
- College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
- Hangzhou Institute of Innovative Medicine, Zhejiang University, Hangzhou, China
- Cancer Center, Zhejiang University, Hangzhou, China
- Zhejiang Province Key Laboratory of Anti-Cancer Drug Research, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, China
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37
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Scinto SL, Bilodeau DA, Hincapie R, Lee W, Nguyen SS, Xu M, am Ende CW, Finn MG, Lang K, Lin Q, Pezacki JP, Prescher JA, Robillard MS, Fox JM. Bioorthogonal chemistry. NATURE REVIEWS. METHODS PRIMERS 2021; 1:30. [PMID: 34585143 PMCID: PMC8469592 DOI: 10.1038/s43586-021-00028-z] [Citation(s) in RCA: 159] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 03/05/2021] [Indexed: 12/11/2022]
Abstract
Bioorthogonal chemistry represents a class of high-yielding chemical reactions that proceed rapidly and selectively in biological environments without side reactions towards endogenous functional groups. Rooted in the principles of physical organic chemistry, bioorthogonal reactions are intrinsically selective transformations not commonly found in biology. Key reactions include native chemical ligation and the Staudinger ligation, copper-catalysed azide-alkyne cycloaddition, strain-promoted [3 + 2] reactions, tetrazine ligation, metal-catalysed coupling reactions, oxime and hydrazone ligations as well as photoinducible bioorthogonal reactions. Bioorthogonal chemistry has significant overlap with the broader field of 'click chemistry' - high-yielding reactions that are wide in scope and simple to perform, as recently exemplified by sulfuryl fluoride exchange chemistry. The underlying mechanisms of these transformations and their optimal conditions are described in this Primer, followed by discussion of how bioorthogonal chemistry has become essential to the fields of biomedical imaging, medicinal chemistry, protein synthesis, polymer science, materials science and surface science. The applications of bioorthogonal chemistry are diverse and include genetic code expansion and metabolic engineering, drug target identification, antibody-drug conjugation and drug delivery. This Primer describes standards for reproducibility and data deposition, outlines how current limitations are driving new research directions and discusses new opportunities for applying bioorthogonal chemistry to emerging problems in biology and biomedicine.
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Affiliation(s)
- Samuel L. Scinto
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
| | - Didier A. Bilodeau
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Robert Hincapie
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Wankyu Lee
- Pfizer Worldwide Research and Development, Cambridge, MA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Sean S. Nguyen
- Department of Chemistry, University of California, Irvine, CA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | - Minghao Xu
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
- These authors contributed equally: Didier A. Bilodeau, Robert Hincapie, Wankyu Lee, Sean S. Nguyen, Minghao Xu
| | | | - M. G. Finn
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kathrin Lang
- Department of Chemistry, Technical University of Munich, Garching, Germany
- Laboratory of Organic Chemistry, ETH Zurich, Zurich, Switzerland
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, USA
| | - John Paul Pezacki
- Department of Chemistry and Biomolecular Science, University of Ottawa, Ottawa, Ontario, Canada
| | - Jennifer A. Prescher
- Department of Chemistry, University of California, Irvine, CA, USA
- Molecular Biology & Biochemistry, University of California, Irvine, CA, USA
| | | | - Joseph M. Fox
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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Abstract
Systematically dissecting the molecular basis of the cell surface as well as its related biological activities is considered as one of the most cutting-edge fields in fundamental sciences. The advent of various advanced cell imaging techniques allows us to gain a glimpse of how the cell surface is structured and coordinated with other cellular components to respond to intracellular signals and environmental stimuli. Nowadays, cell surface-related studies have entered a new era featured by a redirected aim of not just understanding but artificially manipulating/remodeling the cell surface properties. To meet this goal, biologists and chemists are intensely engaged in developing more maneuverable cell surface labeling strategies by exploiting the cell's intrinsic biosynthetic machinery or direct chemical/physical binding methods for imaging, sensing, and biomedical applications. In this review, we summarize the recent advances that focus on the visualization of various cell surface structures/dynamics and accurate monitoring of the microenvironment of the cell surface. Future challenges and opportunities in these fields are discussed, and the importance of cell surface-based studies is highlighted.
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Affiliation(s)
- Hao-Ran Jia
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, 2 Sipailou Road, Nanjing 210096, P. R. China.
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39
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Hong S, Yu C, Wang P, Shi Y, Cao W, Cheng B, Chapla DG, Ma Y, Li J, Rodrigues E, Narimatsu Y, Yates JR, Chen X, Clausen H, Moremen KW, Macauley MS, Paulson JC, Wu P. Glycoengineering of NK Cells with Glycan Ligands of CD22 and Selectins for B‐Cell Lymphoma Therapy. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202005934] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Senlian Hong
- Department of Molecular Medicine The Scripps Research Institute La Jolla CA 92037 USA
| | - Chenhua Yu
- Department of Molecular Medicine The Scripps Research Institute La Jolla CA 92037 USA
- Tianjin Medical University Cancer Institute & Hospital Key laboratory of Breast Cancer Prevention and Therapy School of Medicine Nankai University Tianjin 300071 China
| | - Peng Wang
- Department of Molecular Medicine The Scripps Research Institute La Jolla CA 92037 USA
| | - Yujie Shi
- Department of Molecular Medicine The Scripps Research Institute La Jolla CA 92037 USA
| | - Weiqian Cao
- Department of Molecular Medicine The Scripps Research Institute La Jolla CA 92037 USA
- Department of Chemistry and Institutes of Biomedical Sciences The Fifth People's Hospital Fudan University Shanghai 200433 China
| | - Bo Cheng
- College of Chemistry and Molecular Engineering Beijing University Beijing 100871 China
| | | | - Yuanhui Ma
- Department of Molecular Medicine The Scripps Research Institute La Jolla CA 92037 USA
| | - Jie Li
- Department of Molecular Medicine The Scripps Research Institute La Jolla CA 92037 USA
| | - Emily Rodrigues
- Department of Chemistry University of Alberta 11227 Saskatchewan Dr NW Edmonton, AB T6G 2G2 Alberta Canada
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics Department of Cellular and Molecular Medicine University of Copenhagen Copenhagen Denmark
| | - John R. Yates
- Department of Molecular Medicine The Scripps Research Institute La Jolla CA 92037 USA
| | - Xing Chen
- College of Chemistry and Molecular Engineering Beijing University Beijing 100871 China
| | - Henrik Clausen
- Copenhagen Center for Glycomics Department of Cellular and Molecular Medicine University of Copenhagen Copenhagen Denmark
| | - Kelly W. Moremen
- Complex Carbohydrate Research Center University of Georgia Athens GA 30602 USA
| | - Matthew Scott Macauley
- Department of Chemistry University of Alberta 11227 Saskatchewan Dr NW Edmonton, AB T6G 2G2 Alberta Canada
| | - James C. Paulson
- Department of Molecular Medicine The Scripps Research Institute La Jolla CA 92037 USA
| | - Peng Wu
- Department of Molecular Medicine The Scripps Research Institute La Jolla CA 92037 USA
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40
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Hong S, Yu C, Wang P, Shi Y, Cao W, Cheng B, Chapla DG, Ma Y, Li J, Rodrigues E, Narimatsu Y, Yates JR, Chen X, Clausen H, Moremen KW, Macauley MS, Paulson JC, Wu P. Glycoengineering of NK Cells with Glycan Ligands of CD22 and Selectins for B-Cell Lymphoma Therapy. Angew Chem Int Ed Engl 2021; 60:3603-3610. [PMID: 33314603 PMCID: PMC7980786 DOI: 10.1002/anie.202005934] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 07/14/2020] [Indexed: 12/29/2022]
Abstract
CD22, a member of Siglec family of sialic acid binding proteins, has restricted expression on B cells. Antibody-based agents targeting CD22 or CD20 on B lymphoma and leukemia cells exhibit clinical efficacy for treating these malignancies, but also attack normal B cells leading to immune deficiency. Here, we report a chemoenzymatic glycocalyx editing strategy to introduce high-affinity and specific CD22 ligands onto NK-92MI and cytokine-induced natural killer cells to achieve tumor-specific CD22 targeting. These CD22-ligand modified cells exhibited significantly enhanced tumor cell binding and killing in vitro without harming healthy B cells. For effective lymphoma cell killing in vivo, we further functionalized CD22 ligand-modified NK-92MI cells with the E-selectin ligand sialyl Lewis X to promote trafficking to bone marrow. The dual-functionalized cells resulted in the efficient suppression of B lymphoma in a xenograft model. Our results suggest that natural killer cells modified with glycan ligands to CD22 and selectins promote both targeted killing of B lymphoma cells and improved trafficking to sites where the cancer cells reside, respectively.
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Affiliation(s)
- Senlian Hong
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Chenhua Yu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Tianjin Medical University Cancer Institute & Hospital, Key laboratory of Breast Cancer Prevention and Therapy, School of Medicine, Nankai University, Tianjin, 300071, China
| | - Peng Wang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Yujie Shi
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Weiqian Cao
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
- Department of Chemistry and Institutes of Biomedical Sciences, The Fifth People's Hospital, Fudan University, Shanghai, 200433, China
| | - Bo Cheng
- College of Chemistry and Molecular Engineering, Beijing University, Beijing, 100871, China
| | - Digantkumar G Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Yuanhui Ma
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jie Li
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Emily Rodrigues
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB, T6G 2G2, Alberta, Canada
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - John R Yates
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Xing Chen
- College of Chemistry and Molecular Engineering, Beijing University, Beijing, 100871, China
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kelly W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, 30602, USA
| | - Matthew Scott Macauley
- Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr NW, Edmonton, AB, T6G 2G2, Alberta, Canada
| | - James C Paulson
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Peng Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, 92037, USA
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41
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Towards structure-focused glycoproteomics. Biochem Soc Trans 2021; 49:161-186. [PMID: 33439247 PMCID: PMC7925015 DOI: 10.1042/bst20200222] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 02/06/2023]
Abstract
Facilitated by advances in the separation sciences, mass spectrometry and informatics, glycoproteomics, the analysis of intact glycopeptides at scale, has recently matured enabling new insights into the complex glycoproteome. While diverse quantitative glycoproteomics strategies capable of mapping monosaccharide compositions of N- and O-linked glycans to discrete sites of proteins within complex biological mixtures with considerable sensitivity, quantitative accuracy and coverage have become available, developments supporting the advancement of structure-focused glycoproteomics, a recognised frontier in the field, have emerged. Technologies capable of providing site-specific information of the glycan fine structures in a glycoproteome-wide context are indeed necessary to address many pending questions in glycobiology. In this review, we firstly survey the latest glycoproteomics studies published in 2018–2020, their approaches and their findings, and then summarise important technological innovations in structure-focused glycoproteomics. Our review illustrates that while the O-glycoproteome remains comparably under-explored despite the emergence of new O-glycan-selective mucinases and other innovative tools aiding O-glycoproteome profiling, quantitative glycoproteomics is increasingly used to profile the N-glycoproteome to tackle diverse biological questions. Excitingly, new strategies compatible with structure-focused glycoproteomics including novel chemoenzymatic labelling, enrichment, separation, and mass spectrometry-based detection methods are rapidly emerging revealing glycan fine structural details including bisecting GlcNAcylation, core and antenna fucosylation, and sialyl-linkage information with protein site resolution. Glycoproteomics has clearly become a mainstay within the glycosciences that continues to reach a broader community. It transpires that structure-focused glycoproteomics holds a considerable potential to aid our understanding of systems glycobiology and unlock secrets of the glycoproteome in the immediate future.
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42
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Riley NM, Bertozzi CR, Pitteri SJ. A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry-Based Glycoproteomics. Mol Cell Proteomics 2020; 20:100029. [PMID: 33583771 PMCID: PMC8724846 DOI: 10.1074/mcp.r120.002277] [Citation(s) in RCA: 103] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 09/14/2020] [Accepted: 09/16/2020] [Indexed: 12/26/2022] Open
Abstract
Glycosylation is a prevalent, yet heterogeneous modification with a broad range of implications in molecular biology. This heterogeneity precludes enrichment strategies that can be universally beneficial for all glycan classes. Thus, choice of enrichment strategy has profound implications on experimental outcomes. Here we review common enrichment strategies used in modern mass spectrometry-based glycoproteomic experiments, including lectins and other affinity chromatographies, hydrophilic interaction chromatography and its derivatives, porous graphitic carbon, reversible and irreversible chemical coupling strategies, and chemical biology tools that often leverage bioorthogonal handles. Interest in glycoproteomics continues to surge as mass spectrometry instrumentation and software improve, so this review aims to help equip researchers with the necessary information to choose appropriate enrichment strategies that best complement these efforts.
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Affiliation(s)
- Nicholas M Riley
- Department of Chemistry, Stanford University, Stanford, California, USA.
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California, USA; Howard Hughes Medical Institute, Stanford, California, USA
| | - Sharon J Pitteri
- Department of Radiology, Canary Center at Stanford for Cancer Early Detection, Stanford University School of Medicine, Palo Alto, California, USA.
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43
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Du JJ, Klontz EH, Guerin ME, Trastoy B, Sundberg EJ. Structural insights into the mechanisms and specificities of IgG-active endoglycosidases. Glycobiology 2020; 30:268-279. [PMID: 31172182 DOI: 10.1093/glycob/cwz042] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 05/22/2019] [Accepted: 06/02/2019] [Indexed: 11/12/2022] Open
Abstract
The conserved N-glycan on Asn297 of immunoglobulin G (IgG) has significant impacts on antibody effector functions, and is a frequent target for antibody engineering. Chemoenzymatic synthesis has emerged as a strategy for producing antibodies with homogenous glycosylation and improved effector functions. Central to this strategy is the use of enzymes with activity on the Asn297 glycan. EndoS and EndoS2, produced by Streptococcus pyogenes, are endoglycosidases with remarkable specificity for Asn297 glycosylation, making them ideal tools for chemoenzymatic synthesis. Although both enzymes are specific for IgG, EndoS2 recognizes a wider range of glycans than EndoS. Recent progress has been made in understanding the structural basis for their activities on antibodies. In this review, we examine the molecular mechanism of glycosidic bond cleavage by these enzymes and how specific point mutations convert them into glycosynthases. We also discuss the structural basis for differences in the glycan repertoire that IgG-active endoglycosidases recognize, which focuses on the structure of the loops within the glycoside hydrolase (GH) domain. Finally, we discuss the important contributions of carbohydrate binding modules (CBMs) to endoglycosidase activity, and how CBMs work in concert with GH domains to produce optimal activity on IgG.
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Affiliation(s)
- Jonathan J Du
- Institute of Human Virology 725 W Lombard Street, Baltimore, MD 21201, USA
| | - Erik H Klontz
- Institute of Human Virology 725 W Lombard Street, Baltimore, MD 21201, USA.,Department of Microbiology & Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 West Baltimore Street HSF-I Suite 380, Baltimore, MD 21201, USA.,Program in Molecular Microbiology & Immunology, University of Maryland School of Medicine, 685 West Baltimore Street, HSF-I Suite 380, Baltimore, MD 21201, USA
| | - Marcelo E Guerin
- Structural Biology Unit, CIC bioGUNE, Bizkaia Technology Park, 48160 Derio, Spain.,IKERBASQUE, Basque Foundation for Science, María Díaz Haroko Kalea, 3, 48013 Bilbo, Bizkaia, Spain
| | - Beatriz Trastoy
- Program in Molecular Microbiology & Immunology, University of Maryland School of Medicine, 685 West Baltimore Street, HSF-I Suite 380, Baltimore, MD 21201, USA
| | - Eric J Sundberg
- Institute of Human Virology 725 W Lombard Street, Baltimore, MD 21201, USA.,Department of Microbiology & Department of Microbiology and Immunology, University of Maryland School of Medicine, 685 West Baltimore Street HSF-I Suite 380, Baltimore, MD 21201, USA.,Department of Medicine, University of Maryland School of Medicine, 655 W Baltimore St, Baltimore, MD 21201, USA
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44
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George JT, Srivatsan SG. Bioorthogonal chemistry-based RNA labeling technologies: evolution and current state. Chem Commun (Camb) 2020; 56:12307-12318. [PMID: 33026365 PMCID: PMC7611129 DOI: 10.1039/d0cc05228k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
To understand the structure and ensuing function of RNA in various cellular processes, researchers greatly rely on traditional as well as contemporary labeling technologies to devise efficient biochemical and biophysical platforms. In this context, bioorthogonal chemistry based on chemoselective reactions that work under biologically benign conditions has emerged as a state-of-the-art labeling technology for functionalizing biopolymers. Implementation of this technology on sugar, protein, lipid and DNA is fairly well established. However, its use in labeling RNA has posed challenges due to the fragile nature of RNA. In this feature article, we provide an account of bioorthogonal chemistry-based RNA labeling techniques developed in our lab along with a detailed discussion on other technologies put forward recently. In particular, we focus on the development and applications of covalent methods to label RNA by transcription and posttranscription chemo-enzymatic approaches. It is expected that existing as well as new bioorthogonal functionalization methods will immensely advance our understanding of RNA and support the development of RNA-based diagnostic and therapeutic tools.
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Affiliation(s)
- Jerrin Thomas George
- Department of Chemistry, Indian Institute of Science Education and Research (IISER), Pune, Dr Homi Bhabha Road, Pune 411008, India.
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45
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Jaiswal M, Tran TT, Li Q, Yan X, Zhou M, Kundu K, Fanucci GE, Guo Z. A metabolically engineered spin-labeling approach for studying glycans on cells. Chem Sci 2020; 11:12522-12532. [PMID: 34094453 PMCID: PMC8162880 DOI: 10.1039/d0sc03874a] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Accepted: 10/14/2020] [Indexed: 11/30/2022] Open
Abstract
Metabolic glycan engineering (MGE) coupled with nitroxide spin-labeling (SL) was utilized to investigate the heterogeneous environment of cell surface glycans in select cancer and normal cells. This approach exploited the incorporation of azides into cell surface glycans followed by a click reaction with a new nitroxide spin label. Both sialic acid and N-acetylglucosamine (GlcNAc) were targeted for spin labelling. Although each of these moieties experiences a diverse and heterogeneous glycan environment, their EPR spectra and hence mobility are both characterized as a linear combination of two distinct spectra where one component reflects a highly mobile or uncrowded micro-environment with the second component reflecting more restricted motion, reflective of increased crowding and packing within the glycocalyx. What differs among the spectra of the targeted glycans is the relative percentage of each component, with sialic acid moieties experiencing on average an ∼80% less crowded environment, where conversely GlcNAc/GalNAz labeled sites reported on average a ∼50% more crowded environment. These distinct environments are consistent with the organization of sugar moieties within cellular glycans where some residues occur close to the cell membrane/protein backbone (i.e. more restricted) and others are more terminal in the glycan (i.e. more mobile). Strikingly, different cell lines displayed varied relative populations of these two components, suggesting distinctive glycan packing, organization, and composition of different cells. This work demonstrates the capability of SDSL EPR to be a broadly useful tool for studying glycans on cells, and interpretation of the results provides insights for distinguishing the differences and changes in the local organization and heterogeneity of the cellular glycocalyx.
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Affiliation(s)
- Mohit Jaiswal
- Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA
| | - Trang T Tran
- Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA
| | - Qingjiang Li
- Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA
| | - Xin Yan
- Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA
| | - Mingwei Zhou
- Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA
| | - Krishnendu Kundu
- National High Magnetic Field Laboratory, Florida State University Tallahassee Florida 32310 USA
| | - Gail E Fanucci
- Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA
| | - Zhongwu Guo
- Department of Chemistry, University of Florida 214 Leigh Hall Gainesville FL 32611 USA
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Khairnar A, Sunsunwal S, Babu P, Ramya TNC. Novel serine/threonine-O-glycosylation with N-acetylneuraminic acid and 3-deoxy-D-manno-octulosonic acid by bacterial flagellin glycosyltransferases. Glycobiology 2020; 31:288-306. [PMID: 32886756 DOI: 10.1093/glycob/cwaa084] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 08/05/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
Some bacterial flagellins are O-glycosylated on surface-exposed serine/threonine residues with nonulosonic acids such as pseudaminic acid, legionaminic acid and their derivatives by flagellin nonulosonic acid glycosyltransferases, also called motility-associated factors (Maf). We report here two new glycosidic linkages previously unknown in any organism, serine/threonine-O-linked N-acetylneuraminic acid (Ser/Thr-O-Neu5Ac) and serine/threonine-O-linked 3-deoxy-D-manno-octulosonic acid or keto-deoxyoctulosonate (Ser/Thr-O-KDO), both catalyzed by Geobacillus kaustophilus Maf and Clostridium botulinum Maf. We identified these novel glycosidic linkages in recombinant G. kaustophilus and C. botulinum flagellins that were coexpressed with their cognate recombinant Maf protein in Escherichia coli strains producing the appropriate nucleotide sugar glycosyl donor. Our finding that both G. kaustophilus Maf (putative flagellin sialyltransferase) and C. botulinum Maf (putative flagellin legionaminic acid transferase) catalyzed Neu5Ac and KDO transfer on to flagellin indicates that Maf glycosyltransferases display donor substrate promiscuity. Maf glycosyltransferases have the potential to radically expand the scope of neoglycopeptide synthesis and posttranslational protein engineering.
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Affiliation(s)
- Aasawari Khairnar
- Department of Protein Science and Engineering, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
| | - Sonali Sunsunwal
- Department of Protein Science and Engineering, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
| | - Ponnusamy Babu
- Glycomics and Glycoproteomics & Biologics Characterization Facility, Centre for Cellular and Molecular Platforms, National Centre for Biological Sciences-TIFR, Bengaluru, UAS-GKVK Campus, Bellary Road, 560065, India
| | - T N C Ramya
- Department of Protein Science and Engineering, CSIR-Institute of Microbial Technology, Sector 39-A, Chandigarh 160036, India
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Abstract
In this method paper, we describe the protocols for selective labeling of GCGR, a member of the class B GPCR family regulating glucose homeostasis, in live cells. A two-step procedure is presented in which a strained alkene chemical reporter is inserted into any desired location within the GPCR in the first step, followed by a robust bioorthogonal ligation reaction with a fluorophore-conjugated tetrazine or tetrazole reagent in the second step. The amber codon suppression strategy was adopted for site-specific incorporation of the strained alkene reporter, either spirohexene or trans-cyclooctene, in HEK293T cells. Subsequently, the inverse electron-demand Diels-Alder reaction with an AF647-conjugated 3,6-di (2-pyridyl)-S-tetrazine (DpTz) was performed with the alkene-encoded GCGR on live-cell surface. Alternatively, a photo-induced cycloaddition with a Cy5-conjugated, sterically shielded tetrazole was carried out, giving rise to faster fluorescent labeling along with excellent selectivity. Owing to their robust reaction kinetics and excellent chemoselectivity, the bioorthogonal labeling protocols described here could be readily adapted to labeling any accessible protein targets, e.g., membrane proteins, in live cells.
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Affiliation(s)
- Srikanth Kumar Gangam
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, United States
| | - Qing Lin
- Department of Chemistry, State University of New York at Buffalo, Buffalo, NY, United States.
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48
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Hong S, Grande G, Yu C, Chapla DG, Reigh N, Yang JY, Yang Y, Izumori K, Moremen KW, Xie J, Wu P. hFUT1-Based Live-Cell Assay To Profile α1-2-Fucoside-Enhanced Influenza Virus A Infection. ACS Chem Biol 2020; 15:819-823. [PMID: 32271008 PMCID: PMC7521629 DOI: 10.1021/acschembio.9b00869] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Host cell surface glycans play critical roles in influenza virus A (IVA) infection ranging from modulation of IVA attachment to membrane fusion and host tropism. Approaches for quick and sensitive profile of viral avidity toward a specific type of host cell glycan can contribute to the understanding of tropism switching among different IVA strains. Here, we developed a method based on chemoenzymatic glycan engineering to investigate the possible involvement of α1-2-fucosides in IVA infections. Using a truncated human fucosyltransferase 1 (hFUT1), we created α1-2-fucosides in situ on host cells to assess their influence on the host cell binding to IVA hemagglutinin and the susceptibility of host cells toward IVA-induced killing. We discovered that the newly created α1-2-fucosides on host cells enhanced the infection of several human pandemic IVA subtypes either directly or indirectly. These findings suggest that glycan epitopes other than sialic acid should also be considered for assessing the human pandemic risk of this viral pathogen.
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Affiliation(s)
- Senlian Hong
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Geramie Grande
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Chenhua Yu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
- School of Medicine, Nankai University, Tianjin 300071, China
| | - Digantkumar G Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Natalie Reigh
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Yi Yang
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Ken Izumori
- International Institute of Rare Sugar Research and Education, Kagawa University, Miki, Kagawa 761-0795, Japan
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602, United States
| | - Jia Xie
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Peng Wu
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, California 92037, United States
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49
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Gloster TM. Exploitation of carbohydrate processing enzymes in biocatalysis. Curr Opin Chem Biol 2020; 55:180-188. [PMID: 32203896 DOI: 10.1016/j.cbpa.2020.01.015] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 01/26/2020] [Accepted: 01/31/2020] [Indexed: 12/14/2022]
Abstract
Exploitation of enzymes in biocatalytic processes provides scope both in the synthesis and degradation of molecules. Enzymes have power not only in their catalytic efficiency, but their chemoselectivity, regioselectivity, and stereoselectivity means the reactions they catalyze are precise and reproducible. Focusing on carbohydrate processing enzymes, this review covers advances in biocatalysis involving carbohydrates over the last 2-3 years. Given the notorious difficulties in the chemical synthesis of carbohydrates, the use of enzymes for synthesis has potential for significant impact in the future. The use of catabolic enzymes in the degradation of biomass, which can be exploited in the production of biofuels to provide a sustainable and greener source of energy, and the synthesis of molecules that have a range of applications including in the pharmaceutical and food industries will be explored.
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Affiliation(s)
- Tracey M Gloster
- Biomedical Sciences Research Complex, University of St Andrews, North Haugh, St Andrews, Fife, KY16 9ST, UK.
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50
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de Haas P, Hendriks WJAJ, Lefeber DJ, Cambi A. Biological and Technical Challenges in Unraveling the Role of N-Glycans in Immune Receptor Regulation. Front Chem 2020; 8:55. [PMID: 32117881 PMCID: PMC7013033 DOI: 10.3389/fchem.2020.00055] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 01/17/2020] [Indexed: 12/15/2022] Open
Abstract
N-glycosylation of membrane receptors is important for a wide variety of cellular processes. In the immune system, loss or alteration of receptor glycosylation can affect pathogen recognition, cell-cell interaction, and activation as well as migration. This is not only due to aberrant folding of the receptor, but also to altered lateral mobility or aggregation capacity. Despite increasing evidence of their biological relevance, glycosylation-dependent mechanisms of receptor regulation are hard to dissect at the molecular level. This is due to the intrinsic complexity of the glycosylation process and high diversity of glycan structures combined with the technical limitations of the current experimental tools. It is still challenging to precisely determine the localization and site-occupancy of glycosylation sites, glycan micro- and macro-heterogeneity at the individual receptor level as well as the biological function and specific interactome of receptor glycoforms. In addition, the tools available to manipulate N-glycans of a specific receptor are limited. Significant progress has however been made thanks to innovative approaches such as glycoproteomics, metabolic engineering, or chemoenzymatic labeling. By discussing examples of immune receptors involved in pathogen recognition, migration, antigen presentation, and cell signaling, this Mini Review will focus on the biological importance of N-glycosylation for receptor functions and highlight the technical challenges for examination and manipulation of receptor N-glycans.
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Affiliation(s)
- Paola de Haas
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Wiljan J A J Hendriks
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Dirk J Lefeber
- Department of Laboratory Medicine, Translational Metabolic Laboratory, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands.,Department of Neurology, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Center, Nijmegen, Netherlands
| | - Alessandra Cambi
- Department of Cell Biology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, Netherlands
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