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Mersha FB, McClung CM, Chen M, Ruse CI, Foster JM. Defining the filarial N-glycoproteome by glycosite mapping in the human parasitic nematode Brugia malayi. Sci Rep 2023; 13:7951. [PMID: 37193733 DOI: 10.1038/s41598-023-34936-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 05/10/2023] [Indexed: 05/18/2023] Open
Abstract
N-linked glycosylation is a critical post translational modification of eukaryotic proteins. N-linked glycans are present on surface and secreted filarial proteins that play a role in host parasite interactions. Examples of glycosylated Brugia malayi proteins have been previously identified but there has not been a systematic study of the N-linked glycoproteome of this or any other filarial parasite. In this study, we applied an enhanced N-glyco FASP protocol using an engineered carbohydrate-binding protein, Fbs1, to enrich N-glycosylated peptides for analysis by LC-MS/MS. We then mapped the N-glycosites on proteins from three host stages of the parasite: adult female, adult male and microfilariae. Fbs1 enrichment of N-glycosylated peptides enhanced the identification of N-glycosites. Our data identified 582 N-linked glycoproteins with 1273 N-glycosites. Gene ontology and cell localization prediction of the identified N-glycoproteins indicated that they were mostly membrane and extracellular proteins. Comparing results from adult female worms, adult male worms, and microfilariae, we find variability in N-glycosylation at the protein level as well as at the individual N-glycosite level. These variations are highlighted in cuticle N-glycoproteins and adult worm restricted N-glycoproteins as examples of proteins at the host parasite interface that are well positioned as potential therapeutic targets or biomarkers.
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2
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Chen M, Assis DM, Benet M, McClung CM, Gordon EA, Ghose S, Dupard SJ, Willetts M, Taron CH, Samuelson JC. Comparative site-specific N-glycoproteome analysis reveals aberrant N-glycosylation and gives insights into mannose-6-phosphate pathway in cancer. Commun Biol 2023; 6:48. [PMID: 36639722 PMCID: PMC9839730 DOI: 10.1038/s42003-023-04439-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Accepted: 01/06/2023] [Indexed: 01/15/2023] Open
Abstract
N-glycosylation is implicated in cancers and aberrant N-glycosylation is recognized as a hallmark of cancer. Here, we mapped and compared the site-specific N-glycoproteomes of colon cancer HCT116 cells and isogenic non-tumorigenic DNMT1/3b double knockout (DKO1) cells using Fbs1-GYR N-glycopeptide enrichment technology and trapped ion mobility spectrometry. Many significant changes in site-specific N-glycosylation were revealed, providing a molecular basis for further elucidation of the role of N-glycosylation in protein function. HCT116 cells display hypersialylation especially in cell surface membrane proteins. Both HCT116 and DKO1 show an abundance of paucimannose and 80% of paucimannose-rich proteins are annotated to reside in exosomes. The most striking N-glycosylation alteration was the degree of mannose-6-phosphate (M6P) modification. N-glycoproteomic analyses revealed that HCT116 displays hyper-M6P modification, which was orthogonally validated by M6P immunodetection. Significant observed differences in N-glycosylation patterns of the major M6P receptor, CI-MPR in HCT116 and DKO1 may contribute to the hyper-M6P phenotype of HCT116 cells. This comparative site-specific N-glycoproteome analysis provides a pool of potential N-glycosylation-related cancer biomarkers, but also gives insights into the M6P pathway in cancer.
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Affiliation(s)
- Minyong Chen
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - Diego M. Assis
- grid.423270.00000 0004 0491 2576Bruker, 40 Manning Road, Billerica, MA 01821 USA
| | - Matthieu Benet
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - Colleen M. McClung
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - Elizabeth A. Gordon
- grid.423270.00000 0004 0491 2576Bruker, 40 Manning Road, Billerica, MA 01821 USA
| | - Shourjo Ghose
- grid.423270.00000 0004 0491 2576Bruker, 40 Manning Road, Billerica, MA 01821 USA
| | - Steven J. Dupard
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - Matthew Willetts
- grid.423270.00000 0004 0491 2576Bruker, 40 Manning Road, Billerica, MA 01821 USA
| | - Christopher H. Taron
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
| | - James C. Samuelson
- grid.273406.40000 0004 0376 1796New England Biolabs, 240 County Road, Ipswich, MA 01938 USA
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Sellés Vidal L, Isalan M, Heap JT, Ledesma-Amaro R. A primer to directed evolution: current methodologies and future directions. RSC Chem Biol 2023; 4:271-291. [PMID: 37034405 PMCID: PMC10074555 DOI: 10.1039/d2cb00231k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/18/2023] [Indexed: 01/30/2023] Open
Abstract
This review summarises the methods available for directed evolution, including mutagenesis and variant selection techniques. The advantages and disadvantages of each technique are presented, and future challenges in the field are discussed.
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Affiliation(s)
- Lara Sellés Vidal
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
| | - Mark Isalan
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - John T. Heap
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
- School of Life Sciences, The University of Nottingham, University Park, Nottingham, NG7 2RD, UK
| | - Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
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4
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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5
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A novel graphene oxide/chitosan foam incorporated with metal–organic framework stationary phase for simultaneous enrichment of glycopeptide and phosphopeptide with high efficiency. Anal Bioanal Chem 2022; 414:2251-2263. [DOI: 10.1007/s00216-021-03861-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 12/07/2021] [Accepted: 12/20/2021] [Indexed: 01/07/2023]
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6
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Gao S, Guisán JM, Rocha-Martin J. Oriented immobilization of antibodies onto sensing platforms - A critical review. Anal Chim Acta 2022; 1189:338907. [PMID: 34815045 DOI: 10.1016/j.aca.2021.338907] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 07/08/2021] [Accepted: 07/31/2021] [Indexed: 12/26/2022]
Abstract
The immunosensor has been proven a versatile tool to detect various analytes, such as food contaminants, pathogenic bacteria, antibiotics and biomarkers related to cancer. To fabricate robust and reproducible immunosensors with high sensitivity, the covalent immobilization of immunoglobulins (IgGs) in a site-specific manner contributes to better performance. Instead of the random IgG orientations result from the direct yet non-selective immobilization techniques, this review for the first time introduces the advances of stepwise yet site-selective conjugation strategies to give better biosensing efficiency. Noncovalently adsorbing IgGs is the first but decisive step to interact specifically with the Fc fragment, then following covalent conjugate can fix this uniform and antigens-favorable orientation irreversibly. In this review, we first categorized this stepwise strategy into two parts based on the different noncovalent interactions, namely adhesive layer-mediated interaction onto homofunctional support and layer-free interaction onto heterofunctional support (which displays several different functionalities on its surface that are capable to interact with IgGs). Further, the influence of ligands characteristics (synthesis strategies, spacer requirements and matrices selection) on the heterofunctional support has also been discussed. Finally, conclusions and future perspectives for the real-world application of stepwise covalent conjugation are discussed. This review provides more insights into the fabrication of high-efficiency immunosensor, and special attention has been devoted to the well-orientation of full-length IgGs onto the sensing platform.
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Affiliation(s)
- Shipeng Gao
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP) CSIC, Campus UAM, Cantoblanco, 28049, Madrid, Spain
| | - José M Guisán
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP) CSIC, Campus UAM, Cantoblanco, 28049, Madrid, Spain.
| | - Javier Rocha-Martin
- Department of Biocatalysis, Institute of Catalysis and Petrochemistry (ICP) CSIC, Campus UAM, Cantoblanco, 28049, Madrid, Spain.
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8
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Chuzel L, Fossa SL, Boisvert ML, Cajic S, Hennig R, Ganatra MB, Reichl U, Rapp E, Taron CH. Combining functional metagenomics and glycoanalytics to identify enzymes that facilitate structural characterization of sulfated N-glycans. Microb Cell Fact 2021; 20:162. [PMID: 34419057 PMCID: PMC8379841 DOI: 10.1186/s12934-021-01652-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 08/06/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Sulfate modification of N-glycans is important for several biological functions such as clearance of pituitary hormones or immunoregulation. Yet, the prevalence of this N-glycan modification and its functions remain largely unexplored. Characterization of N-glycans bearing sulfate modifications is hampered in part by a lack of enzymes that enable site-specific detection of N-glycan sulfation. In this study, we used functional metagenomic screening to identify enzymes that act upon sulfated N-acetylglucosamine (GlcNAc). Using multiplexed capillary gel electrophoresis with laser-induced fluorescence detection (xCGE-LIF) -based glycoanalysis we proved their ability to act upon GlcNAc-6-SO4 on N-glycans. RESULTS Our screen identified a sugar-specific sulfatase that specifically removes sulfate from GlcNAc-6-SO4 when it is in a terminal position on an N-glycan. Additionally, in the absence of calcium, this sulfatase binds to the sulfated glycan but does not remove the sulfate group, suggesting it could be used for selective isolation of sulfated N-glycans. Further, we describe isolation of a sulfate-dependent hexosaminidase that removes intact GlcNAc-6-SO4 (but not asulfated GlcNAc) from a terminal position on N-glycans. Finally, the use of these enzymes to detect the presence of sulfated N-glycans by xCGE-LIF is demonstrated. CONCLUSION The present study demonstrates the feasibility of using functional metagenomic screening combined with glycoanalytics to discover enzymes that act upon chemical modifications of glycans. The discovered enzymes represent new specificities that can help resolve the presence of GlcNAc-6-SO4 in N-glycan structural analyses.
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Affiliation(s)
- Léa Chuzel
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
- New England Biolabs, Ipswich, MA, 01938, USA
| | | | | | - Samanta Cajic
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
| | | | | | - Udo Reichl
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
- Chair of Bioprocess Engineering, Otto-von-Guericke University, 39106, Magdeburg, Germany
| | - Erdmann Rapp
- Bioprocess Engineering, Max Planck Institute for Dynamics of Complex Technical Systems, 39106, Magdeburg, Germany
- glyXera GmbH, 39120, Magdeburg, Germany
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9
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Li Z, Bin Luo, Yu L, Lan F, Wu Y. Intermolecular B-N coordination and multi-interaction synergism induced selective glycoprotein adsorption by phenylboronic acid-functionalized magnetic composites under acidic and neutral conditions. J Mater Chem B 2021; 9:453-463. [PMID: 33289778 DOI: 10.1039/d0tb01901a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Abnormal protein glycosylation is associated with many diseases including cardiovascular disease, diabetes, and cancer. Therefore, selective capturing of glycoproteins under physiological or weak acid conditions (tumor microenvironment) is vital for disease diagnosis and further comprehensive analysis. Here, we propose a strategy of intermolecular B-N bond-based phenylboronic acid affinity to capture glycoproteins under neutral and slightly acidic conditions. Surprisingly, the captured glycoproteins were released in alkaline solution. This is contrary to the traditional phenylboric acid affinity, and we studied this from the perspective of materials, proteins, and incubation conditions. We identified the synergistic effect of intermolecular B-N bond-based phenylboronic acid affinity, electrostatic interaction, and polymer brush structure-based glycoprotein adsorption under slightly acidic conditions. The electrostatic repulsion between Fe3O4@SiO2@poly (2-aminoethyl methacrylate hydrochloride)-4-carboxyphenylboronic acid (Fe3O4@SiO2@PAMA-CPBA) nanoparticles and transferrin (TRF) was far greater than the specific binding between phenylboric acid of CPBA and glycosylation residues of TRF resulting in the release of the captured glycoproteins in alkaline solution. Fe3O4@SiO2@PAMA-CPBA nanoparticles exhibited different selectivity capabilities toward different glycoproteins in multiprotein solutions due to protein interactions. These results may pave a new way for the design of phenylboric acid-based materials towards glycoprotein adsorption in a physiological environment.
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Affiliation(s)
- Zhiyu Li
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Bin Luo
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Lingzhu Yu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Fang Lan
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
| | - Yao Wu
- National Engineering Research Center for Biomaterials, Sichuan University, Chengdu 610064, P. R. China.
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10
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Abstract
Folding of proteins is essential so that they can exert their functions. For proteins that transit the secretory pathway, folding occurs in the endoplasmic reticulum (ER) and various chaperone systems assist in acquiring their correct folding/subunit formation. N-glycosylation is one of the most conserved posttranslational modification for proteins, and in eukaryotes it occurs in the ER. Consequently, eukaryotic cells have developed various systems that utilize N-glycans to dictate and assist protein folding, or if they consistently fail to fold properly, to destroy proteins for quality control and the maintenance of homeostasis of proteins in the ER.
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11
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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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12
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Debets MF, Tastan OY, Wisnovsky SP, Malaker SA, Angelis N, Moeckl LKR, Choi J, Flynn H, Wagner LJS, Bineva-Todd G, Antonopoulos A, Cioce A, Browne WM, Li Z, Briggs DC, Douglas HL, Hess GT, Agbay AJ, Roustan C, Kjaer S, Haslam SM, Snijders AP, Bassik MC, Moerner WE, Li VSW, Bertozzi CR, Schumann B. Metabolic precision labeling enables selective probing of O-linked N-acetylgalactosamine glycosylation. Proc Natl Acad Sci U S A 2020; 117:25293-25301. [PMID: 32989128 DOI: 10.1101/2020.04.23.057208] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Protein glycosylation events that happen early in the secretory pathway are often dysregulated during tumorigenesis. These events can be probed, in principle, by monosaccharides with bioorthogonal tags that would ideally be specific for distinct glycan subtypes. However, metabolic interconversion into other monosaccharides drastically reduces such specificity in the living cell. Here, we use a structure-based design process to develop the monosaccharide probe N-(S)-azidopropionylgalactosamine (GalNAzMe) that is specific for cancer-relevant Ser/Thr(O)-linked N-acetylgalactosamine (GalNAc) glycosylation. By virtue of a branched N-acylamide side chain, GalNAzMe is not interconverted by epimerization to the corresponding N-acetylglucosamine analog by the epimerase N-acetylgalactosamine-4-epimerase (GALE) like conventional GalNAc-based probes. GalNAzMe enters O-GalNAc glycosylation but does not enter other major cell surface glycan types including Asn(N)-linked glycans. We transfect cells with the engineered pyrophosphorylase mut-AGX1 to biosynthesize the nucleotide-sugar donor uridine diphosphate (UDP)-GalNAzMe from a sugar-1-phosphate precursor. Tagged with a bioorthogonal azide group, GalNAzMe serves as an O-glycan-specific reporter in superresolution microscopy, chemical glycoproteomics, a genome-wide CRISPR-knockout (CRISPR-KO) screen, and imaging of intestinal organoids. Additional ectopic expression of an engineered glycosyltransferase, "bump-and-hole" (BH)-GalNAc-T2, boosts labeling in a programmable fashion by increasing incorporation of GalNAzMe into the cell surface glycoproteome. Alleviating the need for GALE-KO cells in metabolic labeling experiments, GalNAzMe is a precision tool that allows a detailed view into the biology of a major type of cancer-relevant protein glycosylation.
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Affiliation(s)
- Marjoke F Debets
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Omur Y Tastan
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Stacy A Malaker
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Nikolaos Angelis
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Junwon Choi
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Helen Flynn
- Proteomics Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Lauren J S Wagner
- Department of Chemistry, University of California, Berkeley, CA 94720
| | - Ganka Bineva-Todd
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Peptide Chemistry Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | | | - Anna Cioce
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - William M Browne
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Zhen Li
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - David C Briggs
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Holly L Douglas
- Mycobacterial Metabolism and Antibiotic Research Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Gaelen T Hess
- Department of Genetics, Stanford University, Stanford, CA 94305
- Program in Cancer Biology, Stanford University, Stanford, CA 94305
| | - Anthony J Agbay
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Chloe Roustan
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Svend Kjaer
- Structural Biology Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Stuart M Haslam
- Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Ambrosius P Snijders
- Proteomics Science Technology Platform, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Michael C Bassik
- Department of Genetics, Stanford University, Stanford, CA 94305
- Program in Cancer Biology, Stanford University, Stanford, CA 94305
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - Vivian S W Li
- Stem Cell and Cancer Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA 94305
- Howard Hughes Medical Institute, Stanford, CA 94305
| | - Benjamin Schumann
- The Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom;
- Signalling and Structural Biology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom
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13
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Metabolic precision labeling enables selective probing of O-linked N-acetylgalactosamine glycosylation. Proc Natl Acad Sci U S A 2020; 117:25293-25301. [PMID: 32989128 PMCID: PMC7568240 DOI: 10.1073/pnas.2007297117] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Protein glycosylation events that happen early in the secretory pathway are often dysregulated during tumorigenesis. These events can be probed, in principle, by monosaccharides with bioorthogonal tags that would ideally be specific for distinct glycan subtypes. However, metabolic interconversion into other monosaccharides drastically reduces such specificity in the living cell. Here, we use a structure-based design process to develop the monosaccharide probe N-(S)-azidopropionylgalactosamine (GalNAzMe) that is specific for cancer-relevant Ser/Thr(O)-linked N-acetylgalactosamine (GalNAc) glycosylation. By virtue of a branched N-acylamide side chain, GalNAzMe is not interconverted by epimerization to the corresponding N-acetylglucosamine analog by the epimerase N-acetylgalactosamine-4-epimerase (GALE) like conventional GalNAc-based probes. GalNAzMe enters O-GalNAc glycosylation but does not enter other major cell surface glycan types including Asn(N)-linked glycans. We transfect cells with the engineered pyrophosphorylase mut-AGX1 to biosynthesize the nucleotide-sugar donor uridine diphosphate (UDP)-GalNAzMe from a sugar-1-phosphate precursor. Tagged with a bioorthogonal azide group, GalNAzMe serves as an O-glycan-specific reporter in superresolution microscopy, chemical glycoproteomics, a genome-wide CRISPR-knockout (CRISPR-KO) screen, and imaging of intestinal organoids. Additional ectopic expression of an engineered glycosyltransferase, "bump-and-hole" (BH)-GalNAc-T2, boosts labeling in a programmable fashion by increasing incorporation of GalNAzMe into the cell surface glycoproteome. Alleviating the need for GALE-KO cells in metabolic labeling experiments, GalNAzMe is a precision tool that allows a detailed view into the biology of a major type of cancer-relevant protein glycosylation.
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14
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Saleem S, Sajid MS, Hussain D, Fatima B, Jabeen F, Najam-ul-Haq M, Saeed A. Highly porous terpolymer-ZIF8@BA MOF composite for identification of mono- and multi-glycosylated peptides/proteins using MS-based bottom-up approach. Mikrochim Acta 2020; 187:555. [DOI: 10.1007/s00604-020-04532-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 08/24/2020] [Indexed: 11/30/2022]
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15
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Kunstmann S, Engström O, Wehle M, Widmalm G, Santer M, Barbirz S. Increasing the Affinity of an O-Antigen Polysaccharide Binding Site in Shigella flexneri Bacteriophage Sf6 Tailspike Protein. Chemistry 2020; 26:7263-7273. [PMID: 32189378 PMCID: PMC7463171 DOI: 10.1002/chem.202000495] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/09/2020] [Indexed: 12/30/2022]
Abstract
Broad and unspecific use of antibiotics accelerates spread of resistances. Sensitive and robust pathogen detection is thus important for a more targeted application. Bacteriophages contain a large repertoire of pathogen-binding proteins. These tailspike proteins (TSP) often bind surface glycans and represent a promising design platform for specific pathogen sensors. We analysed bacteriophage Sf6 TSP that recognizes the O-polysaccharide of dysentery-causing Shigella flexneri to develop variants with increased sensitivity for sensor applications. Ligand polyrhamnose backbone conformations were obtained from 2D 1 H,1 H-trNOESY NMR utilizing methine-methine and methine-methyl correlations. They agreed well with conformations obtained from molecular dynamics (MD), validating the method for further predictions. In a set of mutants, MD predicted ligand flexibilities that were in good correlation with binding strength as confirmed on immobilized S. flexneri O-polysaccharide (PS) with surface plasmon resonance. In silico approaches combined with rapid screening on PS surfaces hence provide valuable strategies for TSP-based pathogen sensor design.
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Affiliation(s)
- Sonja Kunstmann
- Physikalische BiochemieUniversität PotsdamKarl-Liebknecht-Str. 24–2514476PotsdamGermany
- Theory and BiosystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Current address: Department of Biotechnology and BiomedicineTechnical University of DenmarkSøltofts Plads2800 Kgs.LyngbyDenmark
| | - Olof Engström
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Marko Wehle
- Theory and BiosystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Göran Widmalm
- Department of Organic ChemistryArrhenius LaboratoryStockholm University10691StockholmSweden
| | - Mark Santer
- Theory and BiosystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Stefanie Barbirz
- Physikalische BiochemieUniversität PotsdamKarl-Liebknecht-Str. 24–2514476PotsdamGermany
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16
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Schumann B, Malaker SA, Wisnovsky SP, Debets MF, Agbay AJ, Fernandez D, Wagner LJS, Lin L, Li Z, Choi J, Fox DM, Peh J, Gray MA, Pedram K, Kohler JJ, Mrksich M, Bertozzi CR. Bump-and-Hole Engineering Identifies Specific Substrates of Glycosyltransferases in Living Cells. Mol Cell 2020. [PMID: 32325029 DOI: 10.1016/jmolcel.2020.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2023]
Abstract
Studying posttranslational modifications classically relies on experimental strategies that oversimplify the complex biosynthetic machineries of living cells. Protein glycosylation contributes to essential biological processes, but correlating glycan structure, underlying protein, and disease-relevant biosynthetic regulation is currently elusive. Here, we engineer living cells to tag glycans with editable chemical functionalities while providing information on biosynthesis, physiological context, and glycan fine structure. We introduce a non-natural substrate biosynthetic pathway and use engineered glycosyltransferases to incorporate chemically tagged sugars into the cell surface glycome of the living cell. We apply the strategy to a particularly redundant yet disease-relevant human glycosyltransferase family, the polypeptide N-acetylgalactosaminyl transferases. This approach bestows a gain-of-chemical-functionality modification on cells, where the products of individual glycosyltransferases can be selectively characterized or manipulated to understand glycan contribution to major physiological processes.
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Affiliation(s)
- Benjamin Schumann
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom; Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom.
| | | | | | | | | | - Daniel Fernandez
- Stanford ChEM-H Macromolecular Structure Knowledge Center, Stanford, CA 94305, USA
| | | | - Liang Lin
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Zhen Li
- Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom; Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Junwon Choi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Jessie Peh
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Melissa Anne Gray
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Kayvon Pedram
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Jennifer Jean Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Milan Mrksich
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Carolyn Ruth Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA.
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17
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Schumann B, Malaker SA, Wisnovsky SP, Debets MF, Agbay AJ, Fernandez D, Wagner LJS, Lin L, Li Z, Choi J, Fox DM, Peh J, Gray MA, Pedram K, Kohler JJ, Mrksich M, Bertozzi CR. Bump-and-Hole Engineering Identifies Specific Substrates of Glycosyltransferases in Living Cells. Mol Cell 2020; 78:824-834.e15. [PMID: 32325029 PMCID: PMC7276986 DOI: 10.1016/j.molcel.2020.03.030] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 02/18/2020] [Accepted: 03/24/2020] [Indexed: 12/12/2022]
Abstract
Studying posttranslational modifications classically relies on experimental strategies that oversimplify the complex biosynthetic machineries of living cells. Protein glycosylation contributes to essential biological processes, but correlating glycan structure, underlying protein, and disease-relevant biosynthetic regulation is currently elusive. Here, we engineer living cells to tag glycans with editable chemical functionalities while providing information on biosynthesis, physiological context, and glycan fine structure. We introduce a non-natural substrate biosynthetic pathway and use engineered glycosyltransferases to incorporate chemically tagged sugars into the cell surface glycome of the living cell. We apply the strategy to a particularly redundant yet disease-relevant human glycosyltransferase family, the polypeptide N-acetylgalactosaminyl transferases. This approach bestows a gain-of-chemical-functionality modification on cells, where the products of individual glycosyltransferases can be selectively characterized or manipulated to understand glycan contribution to major physiological processes.
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Affiliation(s)
- Benjamin Schumann
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom; Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom.
| | | | | | | | | | - Daniel Fernandez
- Stanford ChEM-H Macromolecular Structure Knowledge Center, Stanford, CA 94305, USA
| | | | - Liang Lin
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Zhen Li
- Chemical Glycobiology Laboratory, The Francis Crick Institute, NW1 1AT London, United Kingdom; Department of Chemistry, Imperial College London, W12 0BZ London, United Kingdom
| | - Junwon Choi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | | | - Jessie Peh
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Melissa Anne Gray
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Kayvon Pedram
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Jennifer Jean Kohler
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Milan Mrksich
- Department of Biomedical Engineering, Northwestern University, Evanston, IL 60208, USA
| | - Carolyn Ruth Bertozzi
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford, CA 94305, USA.
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18
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Lectin-Type Ubiquitin Ligase Subunits: Fbs Proteins and Their Applications for Use. Methods Mol Biol 2020. [PMID: 32306330 DOI: 10.1007/978-1-0716-0430-4_22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Three lectin-type F-box proteins called Fbs (F-box protein-recognizing sugar chains) are found in mammals, and function as substrate-binding subunits in the SCF (Skp1/Cullin1/F-box protein) complex ubiquitin ligases. The SCFFbs recognizes cytosolic N-glycans as a signal for an adverse cellular state, and ubiquitinates glycoproteins which appear in the cytosol to remove them from cells. Although Fbs proteins recognize innermost Man3GlcNAc2 structure that is commonly found in most N-glycan structures, they preferentially bind high-mannose-type glycans. Recently, the recombinant Fbs1 derivative protein has been developed as a tool for comprehensive enrichment of N-glycopeptides. The labeled Fbs3 is also available as a tool for detecting organelle damage in cells as it has characteristic properties which cause it to quickly accumulate in damaged organelles. In this chapter, we introduce two applications of use for Fbs proteins: the unbiased N-glycopeptide capture method and the detection of damaged organelles in living cells.
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19
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Affiliation(s)
| | | | - Ronghu Wu
- School of Chemistry and Biochemistry and the Parker H. Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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20
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Luo B, He J, Li Z, Lan F, Wu Y. Glutathione-Functionalized Magnetic Covalent Organic Framework Microspheres with Size Exclusion for Endogenous Glycopeptide Recognition in Human Saliva. ACS APPLIED MATERIALS & INTERFACES 2019; 11:47218-47226. [PMID: 31750645 DOI: 10.1021/acsami.9b15905] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Endogenous glycopeptides have been confirmed to play a significant role in multifarious pathological and physiological processes. The low abundance of endogenous glycopeptides and abundant interferents (e.g., large-size proteins and heteropeptides) in complex biological matrices render the direct analysis of endogenous glycopeptides difficult. Reported here is a novel glutathione-functionalized magnetic covalent organic framework microsphere (denoted as MCNC@COF@GSH) endowed with size-exclusion effect and strong hydrophilicity for selective and efficient enrichment of N-linked glycopeptides. The as-prepared MCNC@COF@GSH microspheres possessed fast magnetic responsiveness, regular porosity, large surface areas, and good hydrophilicity, resulting in remarkable performances in N-linked glycopeptide enrichment with low detection limit (0.01 fmol μL-1), high selectivity (1:5000, human immunoglobulin G (IgG) digests to bovine serum albumin digests), excellent size-exclusion effect (IgG digests/IgG/bovine serum albumin (BSA), 1:500:500), and reusability (at least five times). More excitingly, 143 endogenous N-linked glycopeptides were clearly identified from 10 μL sample of human saliva treated with the MCNC@COF@GSH microspheres, which is the unprecedented high efficiency in endogenous N-linked glycopeptide enrichment from human saliva. In addition to providing a strategy for versatile functionalization of magnetic covalent organic frameworks (COFs), this study may be used to develop application of endogenous glycoproteome analysis.
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Affiliation(s)
- Bin Luo
- National Engineering Research Center for Biomaterials , Sichuan University , Chengdu 610064 , P. R. China
| | - Jia He
- National Engineering Research Center for Biomaterials , Sichuan University , Chengdu 610064 , P. R. China
| | - Zhiyu Li
- National Engineering Research Center for Biomaterials , Sichuan University , Chengdu 610064 , P. R. China
| | - Fang Lan
- National Engineering Research Center for Biomaterials , Sichuan University , Chengdu 610064 , P. R. China
| | - Yao Wu
- National Engineering Research Center for Biomaterials , Sichuan University , Chengdu 610064 , P. R. China
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21
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Huan W, Zhang J, Qin H, Huan F, Wang B, Wu M, Li J. A magnetic nanofiber-based zwitterionic hydrophilic material for the selective capture and identification of glycopeptides. NANOSCALE 2019; 11:10952-10960. [PMID: 31139800 DOI: 10.1039/c9nr01441a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
High-performance affinity materials are highly required in the sample preparation process in mass spectrometry-based glycoproteomics studies. In this research, a novel magnetic nanofiber-based zwitterionic hydrophilic material is prepared for glycopeptide enrichment and identification. The one-dimensional hydroxyapatite nanofiber (HN) acted as the supporting substance for immobilizing both Fe3O4 nanoparticles and Au nanoparticles, following the surface modification with a zwitterionic tripeptide l-glutathione (GSH) via the affinity interactions between the thiol group in GSH and both Au and Fe3O4 to form the magHN/Au-GSH nanofiber. Owing to the unique structural features, excellent hydrophilicity, abundant zwitterionic molecules, and strong magnetic responsiveness, the as-prepared magHN/Au-GSH nanofiber possesses satisfactory specificity for glycopeptide enrichment. As a result, the magHN/Au-GSH nanofiber demonstrated great detection sensitivity (2 fmol), satisfying enrichment recovery (89.65%), large binding capacity (100 mg g-1), and high enrichment selectivity (1 : 100) toward glycopeptides. Furthermore, 246 N-glycosylated peptides corresponding to 104 N-glycosylated proteins were identified from only 1 μL human serum, revealing the great potential of this affinity nanofiber for glycopeptide enrichment and glycoproteomics research.
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Affiliation(s)
- Weiwei Huan
- Zhejiang Provincial Key Laboratory of Chemical Utilization of Forestry Biomass, Zhejiang A & F University, Lin'an District, Hangzhou 311300, China.
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22
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Yu A, Zhao J, Peng W, Banazadeh A, Williamson SD, Goli M, Huang Y, Mechref Y. Advances in mass spectrometry-based glycoproteomics. Electrophoresis 2018; 39:3104-3122. [PMID: 30203847 PMCID: PMC6375712 DOI: 10.1002/elps.201800272] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 09/03/2018] [Accepted: 09/03/2018] [Indexed: 12/13/2022]
Abstract
Protein glycosylation, an important PTM, plays an essential role in a wide range of biological processes such as immune response, intercellular signaling, inflammation, and host-pathogen interaction. Aberrant glycosylation has been correlated with various diseases. However, studying protein glycosylation remains challenging because of low abundance, microheterogeneities of glycosylation sites, and poor ionization efficiency of glycopeptides. Therefore, the development of sensitive and accurate approaches to characterize protein glycosylation is crucial. The identification and characterization of protein glycosylation by MS is referred to as the field of glycoproteomics. Methods such as enrichment, metabolic labeling, and derivatization of glycopeptides in conjunction with different MS techniques and bioinformatics tools, have been developed to achieve an unequivocal quantitative and qualitative characterization of glycoproteins. This review summarizes the recent developments in the field of glycoproteomics over the past 6 years (2012 to 2018).
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Affiliation(s)
- Aiying Yu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Wenjing Peng
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Alireza Banazadeh
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Seth D. Williamson
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Mona Goli
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Yifan Huang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
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23
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Pu C, Zhao H, Hong Y, Zhan Q, Lan M. Elution-free ultra-sensitive enrichment for glycopeptides analyses: Using a degradable, post-modified Ce-metal-organic framework. Anal Chim Acta 2018; 1045:123-131. [PMID: 30454567 DOI: 10.1016/j.aca.2018.09.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/04/2018] [Accepted: 09/08/2018] [Indexed: 11/28/2022]
Abstract
In this work, we presented a facile elution-free method for ultrasensitive enrichment of glycopeptides using two kinds of novel Ce-metal-organic frameworks (Ce-MOF) post-modified with hyaluronic acid (Ce-MOF@HA) and glutamic acid (Ce-MOF@Glu). Both of the synthesized materials remained stable in the loading buffer to enrich glycopeptides selectively and degrade in the eluent to release captured glycopeptides. Due to the dissolution of materials, the elution step of the enrichment process is omitted, resulting in an extremely high sensitivity (detection limit, 0.5 fmol/μL). Meanwhile, Ce-MOF@HA and Ce-MOF@Glu also possessed excellent selectivity with molar ratios of IgG and BSA digests being 1:1000 and 1:500, respectively. Noticeably, the practical applicability of the obtained materials was inspected by analyzing the glycopeptides enriched from human serum (2 μL) by nano-LC-MS, in which 434 N-glycopeptides from 182 N-glycoproteins (by Ce-MOF@HA) and 328 N-glycopeptides from 135 N-glycoproteins (by Ce-MOF@Glu) were detected, respectively. This work provides a new method to simplify the process of glycopeptides enrichment and also paves a novel way for the enrichment of trace targets from complex matrices.
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Affiliation(s)
- Chenlu Pu
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Hongli Zhao
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China.
| | - Yayun Hong
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Qiliang Zhan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China
| | - Minbo Lan
- Shanghai Key Laboratory of Functional Materials Chemistry, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, 200237, PR China; State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, PR China.
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24
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Bai H, Pan Y, Qi L, Liu L, Zhao X, Dong H, Cheng X, Qin W, Wang X. Development a hydrazide-functionalized thermosensitive polymer based homogeneous system for highly efficient N-glycoprotein/glycopeptide enrichment from human plasma exosome. Talanta 2018; 186:513-520. [PMID: 29784395 DOI: 10.1016/j.talanta.2018.04.098] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/13/2018] [Accepted: 04/29/2018] [Indexed: 12/15/2022]
Abstract
As one of the most common post-translational modifications, protein N-glycosylation precipitates in many important biological processes and has closely correlations with the occurrence and progression of multiple diseases. Plasma exosomes secreted by cells contain various bioactive N-glycoproteins which may serve as potential biomarkers for early disease diagnosis and treatment. However, the protein N-glycosylation profile in human plasma exosome is largely unknown, due to the technical challenges in glycoprotein identification. Signals of the rare N-glycoproteins/N-glycopeptides are severely suppressed by the abundant coexisting non-glycosylated counterparts in mass spectrometry analysis. Therefore, specific enrichment of N-glycoprotein/glycopeptide is a prerequisite for large scale N-glycosylation profiling. In this work, we developed a hydrazide functionalized thermosensitive polymer for efficient enrichment and in-depth identification of protein N-glycosylation in human plasma exosome by mass spectrometry. The polymer chains completely dissolve in the enrichment system to form a homogeneous solution. Therefore, efficient covalent coupling between the N-glycoprotein/glycopeptide and the polymer chain is achieved, due to the reduced interfacial mass transfer resistance and the densely packed accessible functional groups on the polymer chains. Furthermore, the thermosensitive polymer can be easily precipitated and recovered by simply rising the system temperature to above 34 °C. As a result, 329 N-glycosylation sites corresponding to 180 N-glycoproteins were enriched and identified from plasma exosomes of glioma patients and healthy subjects using the thermosensitive polymer. By quantitative comparison, we found 26 N-glycoproteins significantly changed between the glioma patients and the healthy subjects, demonstrating the potential of this new strategy for N-glycoproteome research of plasma exosome and biomarker discovery.
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Affiliation(s)
- Haihong Bai
- Phase I Clinical Trial Center, Beijing Shijitan Hospital of Capital Medical University, Beijing 100038, PR China
| | - Yiting Pan
- Beijing Institute of Metrologe, Beijing 100022, PR China
| | - Lu Qi
- Phase I Clinical Trial Center, Beijing Shijitan Hospital of Capital Medical University, Beijing 100038, PR China
| | - Long Liu
- Phase I Clinical Trial Center, Beijing Shijitan Hospital of Capital Medical University, Beijing 100038, PR China
| | - Xinyuan Zhao
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, PR China
| | - Hangyan Dong
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, PR China
| | - Xiaoqiang Cheng
- Phase I Clinical Trial Center, Beijing Shijitan Hospital of Capital Medical University, Beijing 100038, PR China
| | - Weijie Qin
- State Key Laboratory of Proteomics, National Center for Protein Sciences Beijing, Beijing Institute of Lifeomics, Beijing Proteome Research Center, Beijing 102206, PR China.
| | - Xinghe Wang
- Phase I Clinical Trial Center, Beijing Shijitan Hospital of Capital Medical University, Beijing 100038, PR China.
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25
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Zhou T, Zheng A, Baxa U, Chuang GY, Georgiev IS, Kong R, O'Dell S, Shahzad-Ul-Hussan S, Shen CH, Tsybovsky Y, Bailer RT, Gift SK, Louder MK, McKee K, Rawi R, Stevenson CH, Stewart-Jones GBE, Taft JD, Waltari E, Yang Y, Zhang B, Shivatare SS, Shivatare VS, Lee CCD, Wu CY, Mullikin JC, Bewley CA, Burton DR, Polonis VR, Shapiro L, Wong CH, Mascola JR, Kwong PD, Wu X. A Neutralizing Antibody Recognizing Primarily N-Linked Glycan Targets the Silent Face of the HIV Envelope. Immunity 2018; 48:500-513.e6. [PMID: 29548671 PMCID: PMC6421865 DOI: 10.1016/j.immuni.2018.02.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2017] [Revised: 12/22/2017] [Accepted: 02/15/2018] [Indexed: 01/26/2023]
Abstract
Virtually the entire surface of the HIV-1-envelope trimer is recognized by neutralizing antibodies, except for a highly glycosylated region at the center of the "silent face" on the gp120 subunit. From an HIV-1-infected donor, #74, we identified antibody VRC-PG05, which neutralized 27% of HIV-1 strains. The crystal structure of the antigen-binding fragment of VRC-PG05 in complex with gp120 revealed an epitope comprised primarily of N-linked glycans from N262, N295, and N448 at the silent face center. Somatic hypermutation occurred preferentially at antibody residues that interacted with these glycans, suggesting somatic development of glycan recognition. Resistance to VRC-PG05 in donor #74 involved shifting of glycan-N448 to N446 or mutation of glycan-proximal residue E293. HIV-1 neutralization can thus be achieved at the silent face center by glycan-recognizing antibody; along with other known epitopes, the VRC-PG05 epitope completes coverage by neutralizing antibody of all major exposed regions of the prefusion closed trimer.
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Affiliation(s)
- Tongqing Zhou
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Anqi Zheng
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ulrich Baxa
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Gwo-Yu Chuang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Ivelin S Georgiev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Vanderbilt Vaccine Center, Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, and Department of Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN 37232, USA
| | - Rui Kong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Sijy O'Dell
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Syed Shahzad-Ul-Hussan
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Chen-Hsiang Shen
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Yaroslav Tsybovsky
- Electron Microscopy Laboratory, Cancer Research Technology Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Robert T Bailer
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Syna K Gift
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; Henry M. Jackson Foundation for the Advancement of Military Medicine, Bethesda, MD 20817, USA
| | - Mark K Louder
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Krisha McKee
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Catherine H Stevenson
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Guillaume B E Stewart-Jones
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Justin D Taft
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Eric Waltari
- Aaron Diamond AIDS Research Center, Affiliate of the Rockefeller University, New York, NY 10016, USA
| | - Yongping Yang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Baoshan Zhang
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA
| | - Sachin S Shivatare
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Vidya S Shivatare
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Chang-Chun D Lee
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - Chung-Yi Wu
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan
| | - James C Mullikin
- NIH Intramural Sequencing Center (NISC), National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Carole A Bewley
- Laboratory of Bioorganic Chemistry, National Institute of Diabetes and Digestive and Kidney Diseases, NIH, Bethesda, MD 20892, USA
| | - Dennis R Burton
- Department of Immunology and Microbiology, IAVI Neutralizing Antibody Center, Center for HIV/AIDS Vaccine Immunology and Immunogen Discovery, The Scripps Research Institute, La Jolla, CA 92037, USA; Ragon Institute of MGH, MIT, and Harvard, Cambridge, MA 02139, USA
| | - Victoria R Polonis
- U.S. Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA
| | - Lawrence Shapiro
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA
| | - Chi-Huey Wong
- Genomics Research Center, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 115, Taiwan; Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - John R Mascola
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA.
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY 10032, USA.
| | - Xueling Wu
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, MD 20892, USA; Aaron Diamond AIDS Research Center, Affiliate of the Rockefeller University, New York, NY 10016, USA.
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Yoshida Y, Tanaka K. Cytosolic N-Glycans: Triggers for Ubiquitination Directing Proteasomal and Autophagic Degradation: Molecular Systems for Monitoring Cytosolic N-Glycans as Signals for Unwanted Proteins and Organelles. Bioessays 2018; 40. [PMID: 29436721 DOI: 10.1002/bies.201700215] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 01/11/2018] [Indexed: 11/07/2022]
Abstract
Proteins on the cell surface and secreted proteins are modified with sugar chains that generate and modulate biological complexity and diversity. Sugar chains not only contribute physically to the conformation and solubility of proteins, but also exert various functions via sugar-binding proteins (lectins) that reside on the cell surface or in organelles of the secretory pathway. However, some glycosidases and lectins are found in the cytosol or nucleus. Recent studies of cytosolic sugar-related molecules have revealed that sugar chains on proteins in the cytosol act as signals of adverse cellular conditions. In this review, we summarize recent reports that cytosolic sugar chains can trigger ubiquitination, followed by proteasomal and autophagic degradation to maintain cellular homeostasis. In addition, we discuss the functions of sugar-binding proteins revealed to date, along with possibilities not yet explored.
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Affiliation(s)
- Yukiko Yoshida
- Ubiquitin Project Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
| | - Keiji Tanaka
- Laboratory of Protein Metabolism, Tokyo Metropolitan Institute of Medical Science, 2-1-6, Kamikitazawa, Setagaya-ku, Tokyo, 156-8506, Japan
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Zhang B, Yu RZ, Yu YH, Peng C, Xie R, Zhang Y, Chen JY. Lectin inspired polymers based on the dipeptide Ser-Asp for glycopeptide enrichment. Analyst 2018; 143:5090-5093. [DOI: 10.1039/c8an01258j] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Lectin inspired polymers polySD-SiO2were prepared and applied to the high-efficiency enrichment of glycopeptides.
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Affiliation(s)
- B. Zhang
- Department of Gastrointestinal Surgery
- Union Hospital
- Tongji Medical College
- Huazhong University of Science and Technology
- Wuhan 430022
| | - R. Z. Yu
- Medical Department, Chinese People's Liberation Army 210 Hospital
- Dalian, Liaoning 116015
- China
| | - Y. H. Yu
- Department of Gastrointestinal Surgery
- Union Hospital
- Tongji Medical College
- Huazhong University of Science and Technology
- Wuhan 430022
| | - C. Peng
- Department of Gastrointestinal Surgery
- Union Hospital
- Tongji Medical College
- Huazhong University of Science and Technology
- Wuhan 430022
| | - R. Xie
- Department of Gastrointestinal Surgery
- Union Hospital
- Tongji Medical College
- Huazhong University of Science and Technology
- Wuhan 430022
| | - Y. Zhang
- Department of Gastrointestinal Surgery
- Union Hospital
- Tongji Medical College
- Huazhong University of Science and Technology
- Wuhan 430022
| | - J. Y. Chen
- Department of Gastrointestinal Surgery
- Union Hospital
- Tongji Medical College
- Huazhong University of Science and Technology
- Wuhan 430022
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