101
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Peña MJ, Kulkarni AR, Backe J, Boyd M, O'Neill MA, York WS. Structural diversity of xylans in the cell walls of monocots. PLANTA 2016; 244:589-606. [PMID: 27105886 DOI: 10.1007/s00425-016-2527-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/08/2016] [Indexed: 05/02/2023]
Abstract
Xylans in the cell walls of monocots are structurally diverse. Arabinofuranose-containing glucuronoxylans are characteristic of commelinids. However, other structural features are not correlated with the major transitions in monocot evolution. Most studies of xylan structure in monocot cell walls have emphasized members of the Poaceae (grasses). Thus, there is a paucity of information regarding xylan structure in other commelinid and in non-commelinid monocot walls. Here, we describe the major structural features of the xylans produced by plants selected from ten of the twelve monocot orders. Glucuronoxylans comparable to eudicot secondary wall glucuronoxylans are abundant in non-commelinid walls. However, the α-D-glucuronic acid/4-O-methyl-α-D-glucuronic acid is often substituted at O-2 by an α-L-arabinopyranose residue in Alismatales and Asparagales glucuronoxylans. Glucuronoarabinoxylans were the only xylans detected in the cell walls of five different members of the Poaceae family (grasses). By contrast, both glucuronoxylan and glucuronoarabinoxylan are formed by the Zingiberales and Commelinales (commelinids). At least one species of each monocot order, including the Poales, forms xylan with the reducing end sequence -4)-β-D-Xylp-(1,3)-α-L-Rhap-(1,2)-α-D-GalpA-(1,4)-D-Xyl first identified in eudicot and gymnosperm glucuronoxylans. This sequence was not discernible in the arabinopyranose-containing glucuronoxylans of the Alismatales and Asparagales or the glucuronoarabinoxylans of the Poaceae. Rather, our data provide additional evidence that in Poaceae glucuronoarabinoxylan, the reducing end xylose residue is often substituted at O-2 with 4-O-methyl glucuronic acid or at O-3 with arabinofuranose. The variations in xylan structure and their implications for the evolution and biosynthesis of monocot cell walls are discussed.
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Affiliation(s)
- Maria J Peña
- Complex Carbohydrate Research Center and US Department of Energy Bioenergy Science Center, University of Georgia, Athens, GA, 30602, USA
| | - Ameya R Kulkarni
- Complex Carbohydrate Research Center and US Department of Energy Bioenergy Science Center, University of Georgia, Athens, GA, 30602, USA
- Incyte Corporation, Wilmington, DE, 19803, USA
| | - Jason Backe
- Complex Carbohydrate Research Center and US Department of Energy Bioenergy Science Center, University of Georgia, Athens, GA, 30602, USA
| | - Michael Boyd
- Department of Plant Biology, University of Georgia, Athens, GA, 30602, USA
| | - Malcolm A O'Neill
- Complex Carbohydrate Research Center and US Department of Energy Bioenergy Science Center, University of Georgia, Athens, GA, 30602, USA
| | - William S York
- Complex Carbohydrate Research Center and US Department of Energy Bioenergy Science Center, University of Georgia, Athens, GA, 30602, USA.
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, 30602, USA.
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102
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Wang Y, Wang J, Gao M, Zhang X. A novel carbon material with nanopores prepared using a metal-organic framework as precursor for highly selective enrichment of N-linked glycans. Anal Bioanal Chem 2016; 409:431-438. [PMID: 27485625 DOI: 10.1007/s00216-016-9796-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/07/2016] [Accepted: 07/14/2016] [Indexed: 12/28/2022]
Abstract
Protein glycosylation plays a key role in many biological processes. In this study, a novel carbon material with nanopores was prepared by carbonization of metal-organic framework (MOF) Mil-101(Cr). The parent MOF assembled from metal ions with bridging organic linkers had many fascinating properties, such as ultrahigh surface area, suitable nanopore structure, and especially a large amount of carbon after being calcined. Due to the strong interactions between carbon and glycans as well as the size-exclusion effect of pore against protein, the N-linked glycans from standard glycoprotein or complex human serum proteins could be identified with high efficiency. The simple synthesis method as well as good enrichment efficiency made this novel carbon material a promising tool for glycosylation research.
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Affiliation(s)
- Yanan Wang
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Jiaxi Wang
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China
| | - Mingxia Gao
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
| | - Xiangmin Zhang
- Department of Chemistry and Institute of Biomedical Sciences, Fudan University, Shanghai, 200433, China
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103
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Szwengiel A, Stachowiak B. Deproteinization of water-soluble ß-glucan during acid extraction from fruiting bodies of Pleurotus ostreatus mushrooms. Carbohydr Polym 2016; 146:310-9. [DOI: 10.1016/j.carbpol.2016.03.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Revised: 02/24/2016] [Accepted: 03/05/2016] [Indexed: 01/02/2023]
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104
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Nanofiltration Enrichment of Milk Oligosaccharides (MOS) in Relation to Process Parameters. FOOD BIOPROCESS TECH 2016. [DOI: 10.1007/s11947-016-1763-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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105
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Andersen MCF, Kračun SK, Rydahl MG, Willats WGT, Clausen MH. Synthesis of β-1,4-Linked Galactan Side-Chains of Rhamnogalacturonan I. Chemistry 2016; 22:11543-8. [PMID: 27305141 DOI: 10.1002/chem.201602197] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Indexed: 11/05/2022]
Abstract
The synthesis of linear- and (1→6)-branched β-(1→4)-d-galactans, side-chains of the pectic polysaccharide rhamnogalacturonan I is described. The strategy relies on iterative couplings of n-pentenyl disaccharides followed by a late stage glycosylation of a common hexasaccharide core. Reaction with a covalent linker and immobilization on N-hydroxysuccinimide (NHS)-modified glass surfaces allows the generation of carbohydrate microarrays. The glycan arrays enable the study of protein-carbohydrate interactions in a high-throughput fashion, demonstrated herein with binding studies of mAbs and a CBM.
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Affiliation(s)
- Mathias C F Andersen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, 2800 Kgs., Lyngby, Denmark
| | - Stjepan K Kračun
- Department of Plant and Environmental Sciences, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - Maja G Rydahl
- Department of Plant and Environmental Sciences, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark
| | - William G T Willats
- Department of Plant and Environmental Sciences, Thorvaldsensvej 40, Frederiksberg C, 1871, Denmark.,School of Agriculture, Food and Rural Development, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Mads H Clausen
- Center for Nanomedicine and Theranostics, Department of Chemistry, Technical University of Denmark, Kemitorvet, Building 207, 2800 Kgs., Lyngby, Denmark.
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106
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Nagy G, Peng T, Pohl NLB. General Label-Free Mass Spectrometry-Based Assay To Identify Glycosidase Substrate Competence. Anal Chem 2016; 88:7183-90. [DOI: 10.1021/acs.analchem.6b01360] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Gabe Nagy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Tianyuan Peng
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Nicola L. B. Pohl
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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107
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Htm1p-Pdi1p is a folding-sensitive mannosidase that marks N-glycoproteins for ER-associated protein degradation. Proc Natl Acad Sci U S A 2016; 113:E4015-24. [PMID: 27357682 DOI: 10.1073/pnas.1608795113] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Our understanding of how the endoplasmic reticulum (ER)-associated protein degradation (ERAD) machinery efficiently targets terminally misfolded proteins while avoiding the misidentification of nascent polypeptides and correctly folded proteins is limited. For luminal N-glycoproteins, demannosylation of their N-glycan to expose a terminal α1,6-linked mannose is necessary for their degradation via ERAD, but whether this modification is specific to misfolded proteins is unknown. Here we report that the complex of the mannosidase Htm1p and the protein disulfide isomerase Pdi1p (Htm1p-Pdi1p) acts as a folding-sensitive mannosidase for catalyzing this first committed step in Saccharomyces cerevisiae We reconstitute this step in vitro with Htm1p-Pdi1p and model glycoprotein substrates whose structural states we can manipulate. We find that Htm1p-Pdi1p is a glycoprotein-specific mannosidase that preferentially targets nonnative glycoproteins trapped in partially structured states. As such, Htm1p-Pdi1p is suited to act as a licensing factor that monitors folding in the ER lumen and preferentially commits glycoproteins trapped in partially structured states for degradation.
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108
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Highly specific purification of N-glycans using phosphate-based derivatization as an affinity tag in combination with Ti(4+)-SPE enrichment for mass spectrometric analysis. Anal Chim Acta 2016; 934:145-51. [PMID: 27506354 DOI: 10.1016/j.aca.2016.05.042] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Revised: 05/12/2016] [Accepted: 05/22/2016] [Indexed: 11/22/2022]
Abstract
N-linked protein glycosylation is involved in regulation of a wide variety of cellular processes and associated with numerous diseases. Highly specific identification of N-glycome remains a challenge while its biological significance is acknowledged. The relatively low abundance of glycan in complex biological mixtures, lack of basic sites for protonation, and suppression by other highly abundant proteins/peptides lead to the particularly poor detection sensitivity of N-glycans in the MS analysis. Therefore, the highly specific purification procedure becomes a crucial step prior to MS analysis of the N-glycome. Herein, a novel N-glycans enrichment approach based on phosphate derivatization combined with Ti(4+)-SPE (solid phase extraction) was developed. Briefly, in this strategy, N-glycans were chemically labeled with a phospho-group at their reducing ends, such that the Ti(4+)-SPE microspheres were able to capture the phospho-containing glycans. The enrichment method was developed and optimized using model oligosaccharides (maltoheptaose DP7 and sialylated glycan A1) and also glycans from a standard glycoprotein (asialofetuin, ASF). This method experimentally showed high derivatization efficiency (almost 100%), excellent selectivity (analyzing DP7 in the digests of bovine serum albumin at a mass ratio of 1:100), high enriching recovery (90%), good reproducibility (CV<15%) as well as high sensitivity (LOD at fmol level). At last, the proposed method was successfully applied in the profiling of N-glycome in human serum, in which a total of 31 N-glycan masses were identified.
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109
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Hwang HS, Park H, Kim J, Choi JY, Lee YK, Park HY, Choi HD, Kim HH. Significant reduction in allergenicity of ovalbumin from chicken egg white following treatment with ascidian viscera N-acetylglucosaminidase. Biochem Biophys Res Commun 2016; 475:107-12. [DOI: 10.1016/j.bbrc.2016.05.047] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 05/09/2016] [Indexed: 11/26/2022]
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110
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Andrade-Eiroa A, Canle M, Leroy-Cancellieri V, Cerdà V. Solid-phase extraction of organic compounds: A critical review (Part I). Trends Analyt Chem 2016. [DOI: 10.1016/j.trac.2015.08.015] [Citation(s) in RCA: 265] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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111
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Production and characterization of recombinant human acid α-glucosidase in transgenic rice cell suspension culture. J Biotechnol 2016; 226:44-53. [DOI: 10.1016/j.jbiotec.2016.03.031] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 03/05/2016] [Accepted: 03/21/2016] [Indexed: 01/16/2023]
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112
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Pfeiffer A, Stephanowitz H, Krause E, Volkwein C, Hirsch C, Jarosch E, Sommer T. A Complex of Htm1 and the Oxidoreductase Pdi1 Accelerates Degradation of Misfolded Glycoproteins. J Biol Chem 2016; 291:12195-207. [PMID: 27053108 DOI: 10.1074/jbc.m115.703256] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Indexed: 11/06/2022] Open
Abstract
A quality control system in the endoplasmic reticulum (ER) efficiently discriminates polypeptides that are in the process of productive folding from conformers that are trapped in an aberrant state. Only the latter are transported into the cytoplasm and degraded in a process termed ER-associated protein degradation (ERAD). In the ER, an enzymatic cascade generates a specific N-glycan structure of seven mannosyl and two N-acetylglucosamine residues (Man7GlcNAc2) on misfolded glycoproteins to facilitate their disposal. We show that a complex encompassing the yeast lectin-like protein Htm1 and the oxidoreductase Pdi1 converts Man8GlcNAc2 on glycoproteins into the Man7GlcNAc2 signal. In vitro the Htm1-Pdi1 complex processes both unfolded and native proteins albeit with a preference for the former. In vivo, elevated expression of HTM1 causes glycan trimming on misfolded and folded proteins, but only degradation of the non-native species is accelerated. Thus, modification with a Man7GlcNAc2 structure does not inevitably commit a protein for ER-associated protein degradation. The function of Htm1 in ERAD relies on its association with Pdi1, which appears to regulate the access to substrates. Our data support a model in which the balanced activities of Pdi1 and Htm1 are crucial determinants for the efficient removal of misfolded secretory glycoproteins.
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Affiliation(s)
| | - Heike Stephanowitz
- the Leibniz Institute for Molecular Pharmacology, 13125 Berlin, Germany and
| | - Eberhard Krause
- the Leibniz Institute for Molecular Pharmacology, 13125 Berlin, Germany and
| | | | | | - Ernst Jarosch
- From the Max-Delbrück-Center for Molecular Medicine and
| | - Thomas Sommer
- From the Max-Delbrück-Center for Molecular Medicine and Humboldt University, Faculty of Life Science, Institute of Biology, 10099 Berlin, Germany
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113
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Yang Q, Wang LX. Mammalian α-1,6-Fucosyltransferase (FUT8) Is the Sole Enzyme Responsible for the N-Acetylglucosaminyltransferase I-independent Core Fucosylation of High-mannose N-Glycans. J Biol Chem 2016; 291:11064-71. [PMID: 27008861 DOI: 10.1074/jbc.m116.720789] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2016] [Indexed: 01/19/2023] Open
Abstract
Understanding the biosynthetic pathway of protein glycosylation in various expression cell lines is important for controlling and modulating the glycosylation profiles of recombinant glycoproteins. We found that expression of erythropoietin (EPO) in a HEK293S N-acetylglucosaminyltransferase I (GnT I)(-/-) cell line resulted in production of the Man5GlcNAc2 glycoforms, in which more than 50% were core-fucosylated, implicating a clear GnT I-independent core fucosylation pathway. Expression of GM-CSF and the ectodomain of FcγIIIA receptor led to ∼30% and 3% core fucosylation, suggesting that the level of core fucosylation also depends on the nature of the recombinant proteins. To elucidate the GnT I-independent core fucosylation pathway, we generated a stable HEK293S GnT I(-/-) cell line with either knockdown or overexpression of FUT8 by a highly efficient lentivirus-mediated gene transfer approach. We found that the EPO produced from the FUT8 knockdown cell line was the pure Man5GlcNAc2 glycoform, whereas that produced from the FUT8-overexpressing cell line was found to be fully core-fucosylated oligomannose glycan (Man5GlcNAc2Fuc). These results provide direct evidence that FUT8, the mammalian α1,6-fucosyltransferase, is the sole enzyme responsible for the GnT I-independent core fucosylation pathway. The production of the homogeneous core-fucosylated Man5GlcNAc2 glycoform of EPO in the FUT8-overexpressed HEK293S GnT I(-/-) cell line represents the first example of production of fully core-fucosylated high-mannose glycoforms.
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Affiliation(s)
- Qiang Yang
- From the Department of Chemistry and Biochemistry, University of Maryland College Park, College Park, Maryland 20742
| | - Lai-Xi Wang
- From the Department of Chemistry and Biochemistry, University of Maryland College Park, College Park, Maryland 20742
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114
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Analysis of zwitterionic and anionic N-linked glycans from invertebrates and protists by mass spectrometry. Glycoconj J 2016; 33:273-83. [PMID: 26899268 PMCID: PMC4891362 DOI: 10.1007/s10719-016-9650-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Revised: 12/11/2015] [Accepted: 01/18/2016] [Indexed: 11/04/2022]
Abstract
Glycomic analyses over the years have revealed that non-vertebrate eukaryotes express oligosaccharides with inorganic and zwitterionic modifications which are either occurring in different contexts as compared to, or are absent from, mammals. Examples of anionic N-glycans (carrying sulphate or phosphate) are known from amoebae, fungi, molluscs and insects, while zwitterionic modifications by phosphorylcholine, phosphoethanolamine and aminoethylphosphonate occur on N-, O- and lipid-linked glycans from trichomonads, annelids, fungi, molluscs, insects, cestodes and nematodes. For detection of zwitterionic and anionic glycans, mass spectrometry has been a key method, but their ionic character affects the preparation and purification; therefore, as part of a glycomic strategy, the possibility of their presence must be considered in advance. On the other hand, their ionisation and fragmentation in positive and negative ion mode mass spectrometry as well as specific chemical or enzymatic treatments can prove diagnostic to their analysis. In our laboratory, we combine solid-phase extraction, reversed and normal phase HPLC, MALDI-TOF MS, exoglycosidase digests and hydrofluoric acid treatment to reveal N-glycans modified with anionic and zwitterionic moieties in a wide range of organisms. It is to be anticipated that, as more species are glycomically analysed, zwitterionic and anionic modifications of N-glycans will prove rather widespread. This knowledge is - in the longer term - then the basis for understanding the function of this cornucopia of glycan modifications.
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115
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Sun N, Yao J, Deng C. Designed synthesis of carbon-functional magnetic graphene mesoporous silica materials using polydopamine as carbon precursor for the selective enrichment of N-linked glycan. Talanta 2016; 148:439-43. [DOI: 10.1016/j.talanta.2015.11.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Revised: 11/02/2015] [Accepted: 11/04/2015] [Indexed: 12/24/2022]
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116
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Lactose- and cellobiose-derived branched trisaccharides and a sucrose-containing trisaccharide produced by acceptor reactions of Weissella confusa dextransucrase. Food Chem 2016. [DOI: 10.1016/j.foodchem.2015.05.090] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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117
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Eckmair B, Jin C, Abed-Navandi D, Paschinger K. Multistep Fractionation and Mass Spectrometry Reveal Zwitterionic and Anionic Modifications of the N- and O-glycans of a Marine Snail. Mol Cell Proteomics 2015; 15:573-97. [PMID: 26598642 DOI: 10.1074/mcp.m115.051573] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 12/11/2022] Open
Abstract
Various studies in the past have revealed that molluscs can produce a wide range of rather complex N-glycan structures, which vary from those occurring in other invertebrate animals; particularly methylated glycans have been found in gastropods, and there are some reports of anionic glycans in bivalves. Due to the high variability in terms of previously described structures and methodologies, it is a major challenge to establish glycomic workflows that yield the maximum amount of detailed structural information from relatively low quantities of sample. In this study, we apply differential release with peptide:N-glycosidases F and A followed by solid-phase extraction on graphitized carbon and reversed-phase materials to examine the glycome of Volvarina rubella (C. B. Adams, 1845), a margin snail of the clade Neogastropoda. The resulting four pools of N-glycans were fractionated on a fused core RP-HPLC column and subject to MALDI-TOF MS and MS/MS in conjunction with chemical and enzymatic treatments. In addition, selected N-glycan fractions, as well as O-glycans released by β-elimination, were analyzed by porous graphitized carbon-LC-MS and MS(n). This comprehensive approach enabled us to determine a number of novel modifications of protein-linked glycans, including N-methyl-2-aminoethylphosphonate on mannose and N-acetylhexosamine residues, core β1,3-linked mannose, zwitterionic moieties on core Galβ1,4Fuc motifs, additional mannose residues on oligomannosidic glycans, and bisubstituted antennal fucose; furthermore, typical invertebrate N-glycans with sulfate and core fucose residues are present in this gastropod.
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Affiliation(s)
- Barbara Eckmair
- From the ‡Department für Chemie, Universität für Bodenkultur Wien, 1190 Wien, Austria
| | - Chunsheng Jin
- §Institutionen för Biomedicin, Göteborgs universitet, 405 30 Göteborg, Sweden
| | | | - Katharina Paschinger
- From the ‡Department für Chemie, Universität für Bodenkultur Wien, 1190 Wien, Austria;
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118
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Faid V, Denguir N, Chapuis V, Bihoreau N, Chevreux G. Site-specific N-glycosylation analysis of human factor XI: Identification of a noncanonical NXC glycosite. Proteomics 2015; 14:2460-70. [PMID: 25092234 DOI: 10.1002/pmic.201400038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2014] [Revised: 05/07/2014] [Accepted: 07/31/2014] [Indexed: 01/13/2023]
Abstract
Human factor XI (hFXI) is a 160-kDa disulphide-linked homodimer zymogen involved in the coagulation cascade. Its deficiency results in bleeding diathesis referred to as hemophilia C. hFXI bears five N-glycosylation consensus sites per monomer, N72 , N108 , N335 on the heavy chain and N432 , N473 on the light chain. This study reports the first in-depth glycosylation analysis of hFXI based on advanced MS approaches. Hydrophilic interaction LC and MS characterization and quantification of the N-glycans showed that the two major forms are complex biantennary mono-α2,6-sialylated (A2 S1 , 20%) and bis-α2,6-sialylated structures (A2 S2 , 66%). Minor triantennary structures (A3 S3 F, ∼1.5%; A3 S3 , ∼2%) were also identified. MS analyses of intact hFXI revealed full occupation of two of the three heavy-chain glycosites and almost full-site occupancy of the light chain. Analysis of hFXI glycopeptides by LC-MS/MS enabled site-specific glycan profiling and occupancy. It was evidenced that N335 was not glycosylated and that N72 and N108 were fully occupied, whereas N432 and N473 were occupied at about 92 and 95%, respectively. We also identified a new glycosite of the noncanonical format NXC at N145 , occupied at around 5%. These data provide valuable structural information useful to understand the potential roles of N-glycosylation on hFXI function and could serve as a structural reference.
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Affiliation(s)
- Valegh Faid
- Analytical Department, LFB Biotechnologies, Courtaboeuf, France
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119
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Microfluidic Chip-LC/MS-based Glycomic Analysis Revealed Distinct N-glycan Profile of Rat Serum. Sci Rep 2015; 5:12844. [PMID: 26248949 PMCID: PMC4650694 DOI: 10.1038/srep12844] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 07/03/2015] [Indexed: 12/30/2022] Open
Abstract
The rat is an important alternative for studying human pathology owing to certain similarities to humans. Glycomic studies on rat serum have revealed that variations in the N-glycans of glycoproteins correlated with disease progression, which is consistent with the findings in human serum. Therefore, we comprehensively characterized the rat serum N-glycome using microfluidic chip-LC-ESI-QTOF MS and MS/MS techniques. In total, 282 N-glycans, including isomers, were identified. This study is the first to present comprehensive profiling of N-glycans containing O-acetylated sialic acid, among which 27 N-glycans are novel. In addition, the co-existence of N-acetylneuraminic acid (NeuAc) and N-glycolylneuraminic acid (NeuGc) in a single N-glycan ('mixed' N-glycan) was detected and represents a new type of N-glycan in rat serum. The existence of O-acetylated sialic acid is the characteristic feature of rat serum that distinguishes it from mouse and human sera. Comparisons between the rat, mouse, and human serum glycomes revealed that the rat glycome is more similar to that of human sera than to that of mouse sera. Our findings highlight the similarities between the glycomic profile of rat and human sera and provided important selection criteria for choosing an appropriate animal model for pathological and pharmacological studies.
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120
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Stöckmann H, Duke RM, Millán Martín S, Rudd PM. Ultrahigh throughput, ultrafiltration-based n-glycomics platform for ultraperformance liquid chromatography (ULTRA(3)). Anal Chem 2015; 87:8316-22. [PMID: 26183862 DOI: 10.1021/acs.analchem.5b01463] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Accurate, reproducible, and fast quantification of N-glycans is crucial not only for the development and quality control of modern glycosylated biopharmaceuticals, but also in clinical biomarker discovery. Several methods exist for fluorescent labeling of N-glycans and subsequent chromatographic separation and quantification. However, the methods can be complex, lengthy, and expensive. Here we report an automated ultrafiltration-based N-glycoanalytical workflow combined with a glycan labeling strategy that is based on the reaction of glycosylamines with fluorescent carbamate. The entire protocol is quick, simple, and cost-effective and requires less than 1 μg of protein per sample. As many as 768 affinity purified IgG glycoprotein samples can be prepared in a single run with a liquid handling platform.
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Affiliation(s)
- Henning Stöckmann
- NIBRT GlycoScience Group, NIBRT - The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Rebecca M Duke
- NIBRT GlycoScience Group, NIBRT - The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Silvia Millán Martín
- NIBRT GlycoScience Group, NIBRT - The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
| | - Pauline M Rudd
- NIBRT GlycoScience Group, NIBRT - The National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Co. Dublin, Ireland
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121
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Altmann K, Wutkowski A, Kämpfer S, Klempt M, Lorenzen PC, Clawin-Rädecker I. Comparison of the efficiency of different NF membranes for the enrichment of milk oligosaccharides from bovine milk. Eur Food Res Technol 2015. [DOI: 10.1007/s00217-015-2505-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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122
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Lu H, Lü Y, Ren J, Wang Z, Wang Q, Luo Y, Han J, Xiang H, Du Y, Jin C. Identification of the S-layer glycoproteins and their covalently linked glycans in the halophilic archaeon Haloarcula hispanica. Glycobiology 2015; 25:1150-62. [PMID: 26170448 DOI: 10.1093/glycob/cwv050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/03/2015] [Indexed: 12/21/2022] Open
Abstract
Haloarcula hispanica is one of members of the Halobacteriaceae, which displays particularly low restriction activity and is therefore important as one of the most tractable haloarchaea for archaeal genetic research. Although the Har. hispanica S-layer protein has been reported glycosylated, the S-layer glycoprotein and its glycosylation have not been investigated yet. In this study, the S-layer proteins of Har. hispanica were extracted and characterized. The S-layer was found containing two different glycoproteins which shared highly similar amino acid sequences. The genes coding for these two S-layer glycoproteins were found next to each other in the genome. Moreover, the N- and O-linked glycans were released from these two S-layer glycoproteins for structural determination. Based on the mass spectrometry and nuclear magnetic resonance, the N-glycan was determined as a branched trisaccharide containing a 225 Da residue corresponded to a 2-amino-6-sulfo-2, 6-dideoxy-quinovose, which was the first time that a naturally occurring form of sulfoquinovosamine was identified. Besides, the O-glycan was characterized as a Glcα-1,4-Gal disaccharide by mass spectrometry combined with monosaccharide composition analysis and glycosidase treatment. The determination of the N- and O-glycan structure will be helpful for studying the diverse protein glycosylation pathways in archaea utilizing H. hispanica as a new model.
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Affiliation(s)
- Hua Lu
- State Key Laboratory of Mycology University of Chinese Academy of Sciences, Beijing 100101, China
| | - Yang Lü
- State Key Laboratory of Mycology
| | | | - Zhongfu Wang
- Educational Ministry Key Laboratory of Resource Biology and Biotechnology in Western China, Life Science College, Northwest University, Xi'an 710069, China
| | - Qian Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanming Luo
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jing Han
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hua Xiang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuguo Du
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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123
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Sun N, Zhang X, Deng C. Designed synthesis of MOF-derived magnetic nanoporous carbon materials for selective enrichment of glycans for glycomics analysis. NANOSCALE 2015; 7:6487-6491. [PMID: 25805188 DOI: 10.1039/c5nr00244c] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this work, magnetic nanoporous carbon (NPC) materials were synthesized by choosing a MOF as a sacrificial template and a carbon precursor. The obtained Co-ZIF-67 materials showed strong magnetic response, high surface area, a uniform size of mesopores and high carbon content. The Co-ZIF-67 materials were successfully applied to glycomics analysis by enriching N-linked glycans in bio-samples with high selectivity and efficiency.
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Affiliation(s)
- Nianrong Sun
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
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124
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Monosaccharide Identification as a First Step toward de Novo Carbohydrate Sequencing: Mass Spectrometry Strategy for the Identification and Differentiation of Diastereomeric and Enantiomeric Pentose Isomers. Anal Chem 2015; 87:4566-71. [DOI: 10.1021/acs.analchem.5b00760] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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125
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Nagy G, Pohl NLB. Complete hexose isomer identification with mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:677-685. [PMID: 25652933 DOI: 10.1007/s13361-014-1072-z] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2014] [Revised: 12/19/2014] [Accepted: 12/19/2014] [Indexed: 06/04/2023]
Abstract
The first analytical method is presented for the identification and absolute configuration determination of all 24 aldohexose and 2-ketohexose isomers, including the D and L enantiomers for allose, altrose, galactose, glucose, gulose, idose, mannose, talose, fructose, psicose, sorbose, and tagatose. Two unique fixed ligand kinetic method combinations were discovered to create significant enough energetic differences to achieve chiral discrimination among all 24 hexoses. Each of these 24 hexoses yields unique ratios of a specific pair of fragment ions that allows for simultaneous determination of identification and absolute configuration. This mass spectrometric-based methodology can be readily employed for accurate identification of any isolated monosaccharide from an unknown biological source. This work provides a key step towards the goal of complete de novo carbohydrate analysis.
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Affiliation(s)
- Gabe Nagy
- Department of Chemistry, Indiana University, Bloomington, IN, 47405, USA
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126
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Ruhaak LR, Barkauskas DA, Torres J, Cooke CL, Wu LD, Stroble C, Ozcan S, Williams CC, Camorlinga M, Rocke DM, Lebrilla CB, Solnick JV. The Serum Immunoglobulin G Glycosylation Signature of Gastric Cancer. EUPA OPEN PROTEOMICS 2015; 6:1-9. [PMID: 25685702 DOI: 10.1016/j.euprot.2014.11.002] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Biomarkers may facilitate detection of gastric cancer at an earlier stage and reduce mortality. Here we sought to determine if the glycosylation profile of serum immunoglobulin G (IgG) could distinguish patients with non-atrophic gastritis (NAG), duodenal ulcer (DU) and gastric cancer (GC). Serum IgG was released and analyzed using nano-LC-TOF mass spectrometry. Statistically significant false discovery rate (FDR)-adjusted p-values were observed for 18 glycans, eight that differed significantly between NAG and GC, three that distinguished NAG from DU, and eight that differed between DU and GC. The IgG glycosylation signature may be useful as a predictive marker for gastric cancer.
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Affiliation(s)
- L Renee Ruhaak
- Department of Chemistry, University of California, Davis, CA, 95616
| | - Donald A Barkauskas
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, 90089
| | - Javier Torres
- Infectious Diseases Research Unit, Instituto Mexicano del Seguro Social, Mexico
| | - Cara L Cooke
- Departments of Medicine and Microbiology & Immunology; Center for Comparative Medicine, University of California, Davis School of Medicine, Davis, CA, 95616
| | - Lauren D Wu
- Department of Chemistry, University of California, Davis, CA, 95616
| | - Carol Stroble
- Department of Chemistry, University of California, Davis, CA, 95616
| | - Sureyya Ozcan
- Department of Chemistry, University of California, Davis, CA, 95616
| | | | | | - David M Rocke
- Department of Biomedical Engineering, University of California, Davis, CA, 95616 ; Division of Biostatistics, Department of Public Health Sciences, University of California, Davis, CA, 95616
| | - Carlito B Lebrilla
- Department of Chemistry, University of California, Davis, CA, 95616 ; Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616
| | - Jay V Solnick
- Departments of Medicine and Microbiology & Immunology; Center for Comparative Medicine, University of California, Davis School of Medicine, Davis, CA, 95616
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127
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Zhang Q, Zhang Q, Xiong Z, Wan H, Chen X, Zou H. Facile preparation of carbon-functionalized ordered magnetic mesoporous silica composites for highly selective enrichment of N-glycans. RSC Adv 2015. [DOI: 10.1039/c5ra11998g] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A novel carbon-functionalized ordered magnetic mesoporous silica composite was designed and synthesized.
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Affiliation(s)
- Quanqing Zhang
- Division of Metrology in Chemistry
- National Institute of Metrology
- Beijing 100029
- China
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
| | - Qinghe Zhang
- Division of Metrology in Chemistry
- National Institute of Metrology
- Beijing 100029
- China
| | - Zhichao Xiong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Hao Wan
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Xiaoting Chen
- Division of Metrology in Chemistry
- National Institute of Metrology
- Beijing 100029
- China
| | - Hanfa Zou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
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128
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Stavenhagen K, Kolarich D, Wuhrer M. Clinical Glycomics Employing Graphitized Carbon Liquid Chromatography-Mass Spectrometry. Chromatographia 2014; 78:307-320. [PMID: 25750456 PMCID: PMC4346670 DOI: 10.1007/s10337-014-2813-7] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/25/2014] [Accepted: 11/13/2014] [Indexed: 12/25/2022]
Abstract
Glycoconjugates and free glycan are involved in a variety of biological processes such as cell-cell interaction and cell trafficking. Alterations in the complex glycosylation machinery have been correlated with various pathological processes including cancer progression and metastasis. Mass Spectrometry (MS) has evolved as one of the most powerful tools in glycomics and glycoproteomics and in combination with porous graphitized carbon-liquid chromatography (PGC-LC) it is a versatile and sensitive technique for the analysis of glycans and to some extent also glycopeptides. PGC-LC-ESI-MS analysis is characterized by a high isomer separation power enabling a specific glycan compound analysis on the level of individual structures. This allows the investigation of the biological relevance of particular glycan structures and glycan features. Consequently, this strategy is a very powerful technique suitable for clinical research, such as cancer biomarker discovery, as well as in-depth analysis of recombinant glycoproteins. In this review, we will focus on how PGC in conjunction with MS detection can deliver specific structural information for clinical research on protein-bound N-glycans and mucin-type O-glycans. In addition, we will briefly review PGC analysis approaches for glycopeptides, glycosaminoglycans (GAGs) and human milk oligosaccharides (HMOs). The presented applications cover systems that vary vastly with regard to complexity such as purified glycoproteins, cells, tissue or body fluids revealing specific glycosylation changes associated with various biological processes including cancer and inflammation.
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Affiliation(s)
- Kathrin Stavenhagen
- Division of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Daniel Kolarich
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Wissenschaftspark Potsdam-Golm, Am Mühlenberg 1 OT Golm, 14242 Potsdam, Germany
| | - Manfred Wuhrer
- Division of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands ; Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands ; Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
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129
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Lee LY, Lin CH, Fanayan S, Packer NH, Thaysen-Andersen M. Differential site accessibility mechanistically explains subcellular-specific N-glycosylation determinants. Front Immunol 2014; 5:404. [PMID: 25202310 PMCID: PMC4142333 DOI: 10.3389/fimmu.2014.00404] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Accepted: 08/07/2014] [Indexed: 12/25/2022] Open
Abstract
Glycoproteins perform extra- and intracellular functions in innate and adaptive immunity by lectin-based interactions to exposed glyco-determinants. Herein, we document and mechanistically explain the formation of subcellular-specific N-glycosylation determinants on glycoproteins trafficking through the shared biosynthetic machinery of human cells. LC-MS/MS-based quantitative glycomics showed that the secreted glycoproteins of eight human breast epithelial cells displaying diverse geno- and phenotypes consistently displayed more processed, primarily complex type, N-glycans than the high-mannose-rich microsomal glycoproteins. Detailed subcellular glycome profiling of proteins derived from three breast cell lines (MCF7/MDA468/MCF10A) demonstrated that secreted glycoproteins displayed significantly more α-sialylation and α1,6-fucosylation, but less α-mannosylation, than both the intermediately glycan-processed cell-surface glycoproteomes and the under-processed microsomal glycoproteomes. Subcellular proteomics and gene ontology revealed substantial presence of endoplasmic reticulum resident glycoproteins in the microsomes and confirmed significant enrichment of secreted and cell-surface glycoproteins in the respective subcellular fractions. The solvent accessibility of the glycosylation sites on maturely folded proteins of the 100 most abundant putative N-glycoproteins observed uniquely in the three subcellular glycoproteomes correlated with the glycan type processing thereby mechanistically explaining the formation of subcellular-specific N-glycosylation. In conclusion, human cells have developed mechanisms to simultaneously and reproducibly generate subcellular-specific N-glycosylation using a shared biosynthetic machinery. This aspect of protein-specific glycosylation is important for structural and functional glycobiology and discussed here in the context of the spatio-temporal interaction of glyco-determinants with lectins central to infection and immunity.
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Affiliation(s)
- Ling Yen Lee
- Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Chi-Hung Lin
- Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Susan Fanayan
- Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Nicolle H. Packer
- Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, NSW, Australia
| | - Morten Thaysen-Andersen
- Department of Chemistry and Biomolecular Sciences, Biomolecular Frontiers Research Centre, Macquarie University, Sydney, NSW, Australia
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130
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Isolation and characterization of glycophorin from carp red blood cell membranes. MEMBRANES 2014; 4:491-508. [PMID: 25110961 PMCID: PMC4194046 DOI: 10.3390/membranes4030491] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Revised: 07/22/2014] [Accepted: 07/25/2014] [Indexed: 11/30/2022]
Abstract
We isolated a high-purity carp glycophorin from carp erythrocyte membranes following extraction using the lithium diiodosalicylate (LIS)-phenol method and streptomycin treatment. The main carp glycophorin was observed to locate at the position of the carp and human band-3 proteins on an SDS-polyacrylamide gel. Only the N-glycolylneuraminic acid (NeuGc) form of sialic acid was detected in the carp glycophorin. The oligosaccharide fraction was separated into two components (P-1 and P-2) using a Glyco-Pak DEAE column. We observed bacteriostatic activity against five strains of bacteria, including two known fish pathogens. Fractions from the carp erythrocyte membrane, the glycophorin oligosaccharide and the P-1 also exhibited bacteriostatic activity; whereas the glycolipid fraction and the glycophorin fraction without sialic acid did not show the activity. The carp glycophorin molecules attach to the flagellum of V. anguillarum or the cell surface of M. luteus and inhibited bacterial growth.
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131
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Bubka M, Link-Lenczowski P, Janik M, Pocheć E, Lityńska A. Overexpression of N-acetylglucosaminyltransferases III and V in human melanoma cells. Implications for MCAM N-glycosylation. Biochimie 2014; 103:37-49. [DOI: 10.1016/j.biochi.2014.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 04/01/2014] [Indexed: 01/25/2023]
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132
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Sun B, Hood L. Protein-centric N-glycoproteomics analysis of membrane and plasma membrane proteins. J Proteome Res 2014; 13:2705-14. [PMID: 24754784 PMCID: PMC4053080 DOI: 10.1021/pr500187g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
![]()
The advent of proteomics technology
has transformed our understanding
of biological membranes. The challenges for studying membrane proteins
have inspired the development of many analytical and bioanalytical
tools, and the techniques of glycoproteomics have emerged as an effective
means to enrich and characterize membrane and plasma-membrane proteomes.
This Review summarizes the development of various glycoproteomics
techniques to overcome the hurdles formed by the unique structures
and behaviors of membrane proteins with a focus on N-glycoproteomics.
Example contributions of N-glycoproteomics to the understanding of
membrane biology are provided, and the areas that require future technical
breakthroughs are discussed.
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Affiliation(s)
- Bingyun Sun
- Department of Chemistry, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A1S6, Canada
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133
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Anumula KR. Single tag for total carbohydrate analysis. Anal Biochem 2014; 457:31-7. [PMID: 24769375 DOI: 10.1016/j.ab.2014.04.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 04/14/2014] [Accepted: 04/17/2014] [Indexed: 11/18/2022]
Abstract
Anthranilic acid (2-aminobenzoic acid, 2-AA) has the remarkable property of reacting rapidly with every type of reducing carbohydrate. Reactivity of 2-AA with carbohydrates in aqueous solutions surpasses all other tags reported to date. This unique capability is attributed to the strategically located -COOH which accelerates Schiff base formation. Monosaccharides, oligosaccharides (N-, O-, and lipid linked and glycans in secretory fluids), glycosaminoglycans, and polysaccharides can be easily labeled with 2-AA. With 2-AA, labeling is simple in aqueous solutions containing proteins, peptides, buffer salts, and other ingredients (e.g., PNGase F, glycosidase, and transferase reaction mixtures). In contrast, other tags require relatively pure glycans for labeling in anhydrous dimethyl sulfoxide-acetic acid medium. Acidic conditions are known to cause desialylation, thus requiring a great deal of attention to sample preparation. Simpler labeling is achieved with 2-AA within 30-60 min in mild acetate-borate buffered solution. 2-AA provides the highest sensitivity and resolution in chromatographic methods for carbohydrate analysis in a simple manner. Additionally, 2-AA is uniquely qualified for quantitative analysis by mass spectrometry in the negative mode. Analyses of 2-AA-labeled carbohydrates by electrophoresis and other techniques have been reported. Examples cited here demonstrate that 2-AA is the universal tag for total carbohydrate analysis.
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134
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Liu J, Wang F, Zhu J, Mao J, Liu Z, Cheng K, Qin H, Zou H. Highly efficient N-glycoproteomic sample preparation by combining C18 and graphitized carbon adsorbents. Anal Bioanal Chem 2014; 406:3103-9. [DOI: 10.1007/s00216-014-7716-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/17/2014] [Accepted: 02/20/2014] [Indexed: 01/07/2023]
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135
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Chong SL, Virkki L, Maaheimo H, Juvonen M, Derba-Maceluch M, Koutaniemi S, Roach M, Sundberg B, Tuomainen P, Mellerowicz EJ, Tenkanen M. O-Acetylation of glucuronoxylan in Arabidopsis thaliana wild type and its change in xylan biosynthesis mutants. Glycobiology 2014; 24:494-506. [DOI: 10.1093/glycob/cwu017] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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136
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Sun N, Deng C, Li Y, Zhang X. Highly Selective Enrichment of N-Linked Glycan by Carbon-Functionalized Ordered Graphene/Mesoporous Silica Composites. Anal Chem 2014; 86:2246-50. [DOI: 10.1021/ac404103r] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Nianrong Sun
- Department
of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Chunhui Deng
- Department
of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Yan Li
- Pharmaceutical
Analysis Department, School of Pharmacy, Fudan University, Shanghai 201203, China
| | - Xiangmin Zhang
- Department
of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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137
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Lichti CF, Wildburger NC, Emmett MR, Mostovenko E, Shavkunov AS, Strain SK, Nilsson CL. Post-translational Modifications in the Human Proteome. TRANSLATIONAL BIOINFORMATICS 2014. [DOI: 10.1007/978-94-017-9202-8_6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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138
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Yang S, Toghi Eshghi S, Chiu H, DeVoe DL, Zhang H. Glycomic analysis by glycoprotein immobilization for glycan extraction and liquid chromatography on microfluidic chip. Anal Chem 2013; 85:10117-25. [PMID: 24111616 PMCID: PMC3867136 DOI: 10.1021/ac4013013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Glycosylation is one of the most common protein modifications and profoundly regulates many biological processes. Aberrant glycosylation is reported to associate with diseases such as cancers, human immunodeficiency virus, and immune disorders. It is considerably important to study protein glycosylation and the associated glycans for diagnostics and disease prognostics. Unlike other protein modifications, glycans attached to proteins are enormously complex. Therefore, the comprehensive analysis of glycans from biological or clinical samples is an unmet technical challenge. Development of the high-throughput method will facilitate the glycomics analysis. In this study, we developed a novel method for the high-throughput analysis of N-glycans from glycoproteins using glycoprotein immobilization for glycan extraction (GIG) coupled with liquid chromatography (LC) in an integrated microfluidic platform (chipLC). The separated glycans were then analyzed by mass spectrometry. Briefly, proteins were first immobilized on a solid support. Glycans on immobilized glycoproteins were modified on solid phase to increase the detection and structure analysis. N-Glycans were then enzymatically released and subsequentially separated by porous graphitized carbon particles packed in the same device. By applying the GIG-chipLC for glycomic analysis of human sera, we identified N-glycans with 148 distinct N-glycan masses. The platform was used to analyze N-glycans from mouse heart tissue and serum. The extracted N-glycans from tissues indicated that unique unsialylated N-glycans were detected in tissues that were missing from the proximal or distal serum, whereas common N-glycans from tissues and serum have mature and sialylated structures. The GIG-chipLC provides a simple and robust platform for glycomic analysis of complex biological and clinical samples.
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Affiliation(s)
- Shuang Yang
- Department of Pathology, Johns Hopkins University , Baltimore, Maryland 21231, United States
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139
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Manabe Y, Verhertbruggen Y, Gille S, Harholt J, Chong SL, Pawar PMA, Mellerowicz EJ, Tenkanen M, Cheng K, Pauly M, Scheller HV. Reduced Wall Acetylation proteins play vital and distinct roles in cell wall O-acetylation in Arabidopsis. PLANT PHYSIOLOGY 2013; 163:1107-17. [PMID: 24019426 PMCID: PMC3813637 DOI: 10.1104/pp.113.225193] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2013] [Accepted: 09/03/2013] [Indexed: 05/17/2023]
Abstract
The Reduced Wall Acetylation (RWA) proteins are involved in cell wall acetylation in plants. Previously, we described a single mutant, rwa2, which has about 20% lower level of O-acetylation in leaf cell walls and no obvious growth or developmental phenotype. In this study, we generated double, triple, and quadruple loss-of-function mutants of all four members of the RWA family in Arabidopsis (Arabidopsis thaliana). In contrast to rwa2, the triple and quadruple rwa mutants display severe growth phenotypes revealing the importance of wall acetylation for plant growth and development. The quadruple rwa mutant can be completely complemented with the RWA2 protein expressed under 35S promoter, indicating the functional redundancy of the RWA proteins. Nevertheless, the degree of acetylation of xylan, (gluco)mannan, and xyloglucan as well as overall cell wall acetylation is affected differently in different combinations of triple mutants, suggesting their diversity in substrate preference. The overall degree of wall acetylation in the rwa quadruple mutant was reduced by 63% compared with the wild type, and histochemical analysis of the rwa quadruple mutant stem indicates defects in cell differentiation of cell types with secondary cell walls.
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Affiliation(s)
- Yuzuki Manabe
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, California 94608 (Y.M., Y.V., H.V.S.); Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (Y.M., Y.V., H.V.S.)
- Energy Biosciences Institute, Berkeley, California 94720 (S.G., K.C., M.P.)
- Department of Plant and Environmental Sciences, University of Copenhagen, DK–1871 Frederiksberg, Denmark (J.H.)
- Department of Food and Environmental Sciences, University of Helsinki, FI–00014 Helsinki, Finland (S.-L.C., M.T.)
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden (P.M.-A.P., E.J.M); and
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.P., H.V.S.)
| | - Yves Verhertbruggen
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, California 94608 (Y.M., Y.V., H.V.S.); Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (Y.M., Y.V., H.V.S.)
- Energy Biosciences Institute, Berkeley, California 94720 (S.G., K.C., M.P.)
- Department of Plant and Environmental Sciences, University of Copenhagen, DK–1871 Frederiksberg, Denmark (J.H.)
- Department of Food and Environmental Sciences, University of Helsinki, FI–00014 Helsinki, Finland (S.-L.C., M.T.)
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden (P.M.-A.P., E.J.M); and
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.P., H.V.S.)
| | | | - Jesper Harholt
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, California 94608 (Y.M., Y.V., H.V.S.); Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (Y.M., Y.V., H.V.S.)
- Energy Biosciences Institute, Berkeley, California 94720 (S.G., K.C., M.P.)
- Department of Plant and Environmental Sciences, University of Copenhagen, DK–1871 Frederiksberg, Denmark (J.H.)
- Department of Food and Environmental Sciences, University of Helsinki, FI–00014 Helsinki, Finland (S.-L.C., M.T.)
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden (P.M.-A.P., E.J.M); and
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.P., H.V.S.)
| | - Sun-Li Chong
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, California 94608 (Y.M., Y.V., H.V.S.); Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (Y.M., Y.V., H.V.S.)
- Energy Biosciences Institute, Berkeley, California 94720 (S.G., K.C., M.P.)
- Department of Plant and Environmental Sciences, University of Copenhagen, DK–1871 Frederiksberg, Denmark (J.H.)
- Department of Food and Environmental Sciences, University of Helsinki, FI–00014 Helsinki, Finland (S.-L.C., M.T.)
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden (P.M.-A.P., E.J.M); and
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.P., H.V.S.)
| | - Prashant Mohan-Anupama Pawar
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, California 94608 (Y.M., Y.V., H.V.S.); Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (Y.M., Y.V., H.V.S.)
- Energy Biosciences Institute, Berkeley, California 94720 (S.G., K.C., M.P.)
- Department of Plant and Environmental Sciences, University of Copenhagen, DK–1871 Frederiksberg, Denmark (J.H.)
- Department of Food and Environmental Sciences, University of Helsinki, FI–00014 Helsinki, Finland (S.-L.C., M.T.)
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden (P.M.-A.P., E.J.M); and
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.P., H.V.S.)
| | - Ewa J. Mellerowicz
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, California 94608 (Y.M., Y.V., H.V.S.); Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (Y.M., Y.V., H.V.S.)
- Energy Biosciences Institute, Berkeley, California 94720 (S.G., K.C., M.P.)
- Department of Plant and Environmental Sciences, University of Copenhagen, DK–1871 Frederiksberg, Denmark (J.H.)
- Department of Food and Environmental Sciences, University of Helsinki, FI–00014 Helsinki, Finland (S.-L.C., M.T.)
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden (P.M.-A.P., E.J.M); and
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.P., H.V.S.)
| | - Maija Tenkanen
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, California 94608 (Y.M., Y.V., H.V.S.); Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (Y.M., Y.V., H.V.S.)
- Energy Biosciences Institute, Berkeley, California 94720 (S.G., K.C., M.P.)
- Department of Plant and Environmental Sciences, University of Copenhagen, DK–1871 Frederiksberg, Denmark (J.H.)
- Department of Food and Environmental Sciences, University of Helsinki, FI–00014 Helsinki, Finland (S.-L.C., M.T.)
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden (P.M.-A.P., E.J.M); and
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.P., H.V.S.)
| | - Kun Cheng
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, California 94608 (Y.M., Y.V., H.V.S.); Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (Y.M., Y.V., H.V.S.)
- Energy Biosciences Institute, Berkeley, California 94720 (S.G., K.C., M.P.)
- Department of Plant and Environmental Sciences, University of Copenhagen, DK–1871 Frederiksberg, Denmark (J.H.)
- Department of Food and Environmental Sciences, University of Helsinki, FI–00014 Helsinki, Finland (S.-L.C., M.T.)
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden (P.M.-A.P., E.J.M); and
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.P., H.V.S.)
| | - Markus Pauly
- Joint BioEnergy Institute, Feedstocks Division, Emeryville, California 94608 (Y.M., Y.V., H.V.S.); Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (Y.M., Y.V., H.V.S.)
- Energy Biosciences Institute, Berkeley, California 94720 (S.G., K.C., M.P.)
- Department of Plant and Environmental Sciences, University of Copenhagen, DK–1871 Frederiksberg, Denmark (J.H.)
- Department of Food and Environmental Sciences, University of Helsinki, FI–00014 Helsinki, Finland (S.-L.C., M.T.)
- Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 901 83 Umea, Sweden (P.M.-A.P., E.J.M); and
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720 (M.P., H.V.S.)
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140
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Anzengruber J, Pabst M, Neumann L, Sekot G, Heinl S, Grabherr R, Altmann F, Messner P, Schäffer C. Protein O-glucosylation in Lactobacillus buchneri. Glycoconj J 2013; 31:117-31. [PMID: 24162649 DOI: 10.1007/s10719-013-9505-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/04/2013] [Accepted: 10/07/2013] [Indexed: 02/02/2023]
Abstract
Based on the previous demonstration of surface (S-) layer protein glycosylation in Lactobacillus buchneri 41021/251 and because of general advantages of lactic acid bacteria for applied research, protein glycosylation in this bacterial species was investigated in detail. The cell surface of L. buchneri CD034 is completely covered with an oblique 2D crystalline array (lattice parameters, a = 5.9 nm; b = 6.2 nm; γ ~ 77°) formed by self-assembly of the S-layer protein SlpB. Biochemical and mass spectrometric analyses revealed that SlpB is the most abundant protein and that it is O-glycosylated at four serine residues within the sequence S(152)-A-S(154)-S(155)-A-S(157) with, on average, seven Glc(α1-6) residues, each. Subcellular fractionation of strain CD034 indicated a sequential order of SlpB export and glucosylation as evidenced by lack of glucosylation of cytosolic SlpB. Protein glycosylation analysis was extended to strain L. buchneri NRRL B-30929 where an analogous glucosylation scenario could be detected, with the S-layer glycoprotein SlpN containing an O-glycosylation motif identical to that of SlpB. This corroborates previous data on S-layer protein glucosylation of strain 41021/251 and let us propose a species-wide S-layer protein O-glucosylation in L. buchneri targeted at the sequence motif S-A-S-S-A-S. Search of the L. buchneri genomes for the said glucosylation motif revealed one further ORF, encoding the putative glycosyl-hydrolase LbGH25B and LbGH25N in L. buchneri CD034 and NRRL B-30929, respectively, for which we have indications of a glycosylation comparable to that of the S-layer proteins. These findings demonstrate the presence of a distinct protein O-glucosylation system in Gram-positive and beneficial microbes.
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Affiliation(s)
- Julia Anzengruber
- Department of NanoBiotechnology, NanoGlycobiology unit, Universität für Bodenkultur Wien, Muthgasse 11, 1190, Vienna, Austria,
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141
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Vuong TV, Vesterinen AH, Foumani M, Juvonen M, Seppälä J, Tenkanen M, Master ER. Xylo- and cello-oligosaccharide oxidation by gluco-oligosaccharide oxidase from Sarocladium strictum and variants with reduced substrate inhibition. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:148. [PMID: 24119501 PMCID: PMC4015748 DOI: 10.1186/1754-6834-6-148] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Accepted: 10/04/2013] [Indexed: 05/21/2023]
Abstract
BACKGROUND The oxidation of carbohydrates from lignocellulose can facilitate the synthesis of new biopolymers and biochemicals, and also reduce sugar metabolism by lignocellulolytic microorganisms, reserving aldonates for fermentation to biofuels. Although oxidoreductases that oxidize cellulosic hydrolysates have been well characterized, none have been reported to oxidize substituted or branched xylo-oligosaccharides. Moreover, this is the first report that identifies amino acid substitutions leading to GOOX variants with reduced substrate inhibition. RESULTS The recombinant wild type gluco-oligosaccharide oxidase (GOOX) from the fungus Sarocladium strictum, along with variants that were generated by site-directed mutagenesis, retained the FAD cofactor, and showed high activity on cello-oligosaccharide and xylo-oligosaccharides, including substituted and branched xylo-oligosaccharides. Mass spectrometric analyses confirmed that GOOX introduces one oxygen atom to oxidized products, and 1H NMR and tandem mass spectrometry analysis confirmed that oxidation was restricted to the anomeric carbon. The A38V mutation, which is close to a predicted divalent ion-binding site in the FAD-binding domain of GOOX but 30 Å away from the active site, significantly increased the kcat and catalytic efficiency of the enzyme on all oligosaccharides. Eight amino acid substitutions were separately introduced to the substrate-binding domain of GOOX-VN (at positions Y72, E247, W351, Q353 and Q384). In all cases, the Km of the enzyme variant was higher than that of GOOX, supporting the role of corresponding residues in substrate binding. Most notably, W351A increased Km values by up to two orders of magnitude while also increasing kcat up to 3-fold on cello- and xylo-oligosaccharides and showing no substrate inhibition. CONCLUSIONS This study provides further evidence that S. strictum GOOX has broader substrate specificity than the enzyme name implies, and that substrate inhibition can be reduced by removing aromatic side chains in the -2 binding subsite. Of the enzyme variants, W351A might be particularly advantageous when oxidizing oligosaccharides present at high substrate concentrations often experienced in industrial processes.
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Affiliation(s)
- Thu V Vuong
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Arja-Helena Vesterinen
- Department of Biotechnology and Chemical Technology, Aalto University, Kemistintie 1 D1, Espoo 02150, Finland
| | - Maryam Foumani
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
| | - Minna Juvonen
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, Helsinki 00014, Finland
| | - Jukka Seppälä
- Department of Biotechnology and Chemical Technology, Aalto University, Kemistintie 1 D1, Espoo 02150, Finland
| | - Maija Tenkanen
- Department of Food and Environmental Sciences, University of Helsinki, P.O. Box 27, Helsinki 00014, Finland
| | - Emma R Master
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, Ontario, M5S 3E5, Canada
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142
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Chevreux G, Faid V, Scohyers JM, Bihoreau N. N-/O-glycosylation analysis of human FVIIa produced in the milk of transgenic rabbits. Glycobiology 2013; 23:1531-46. [PMID: 24092837 PMCID: PMC3816631 DOI: 10.1093/glycob/cwt085] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Human coagulation factor VIIa is a glycoprotein that promotes haemostasis through activation of the coagulation cascade extrinsic pathway. Most haemophilia A/B patients with inhibitors are treated by injection of plasma-derived or recombinant FVIIa. The use of recombinant products raises questions about the ability of the host cell to produce efficiently post-translationally modified proteins. Glycosylation is especially critical considering that it can modulate protein safety and efficacy. The present paper reports the N-/O-glycosylation pattern of a new recombinant human factor VIIa expressed in the mammary glands of transgenic rabbits. Glycosylation was investigated by chromatography and advanced mass spectrometry techniques for glycan identification and quantitation. Mass spectrometry (MS)/MS analyses were performed to confirm the glycan structures as well as the position and branching of specific monosaccharides or substituents. The two N-glycosylation sites were found to be fully occupied mostly by mono- and bi-sialylated biantennary complex-type structures, the major form being A2G2S1. Some oligomannose/hybrid structures were retrieved in lower abundance, the major ones being GlcNAcα1,O-phosphorylated at the C6-position of a Man residue (Man-6-(GlcNAcα1,O-)phosphate motif) as commonly observed on lysosomal proteins. No immunogenic glycotopes such as Galili (Galα1,3Gal) and HD antigens (N-glycolylneuraminic acid (NeuGc)) were detected. Concerning O-glycosylation, the product exhibited O-fucose and O-glucose-(xylose)0, 1, 2 motifs as expected. The N-glycosylation consistency was also investigated by varying production parameters such as the period of lactation, the number of consecutive lactations and rabbit generations. Results show that the transgenesis technology is suitable for the long-term production of rhFVIIa with a reproducible glycosylation pattern.
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Affiliation(s)
- Guillaume Chevreux
- Analytical Department, LFB Biotechnologies, 3 Avenue des Tropiques, Les Ulis, 91942 Courtaboeuf, France
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143
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Structural characterization of the N-glycosylation of individual soybean β-conglycinin subunits. J Chromatogr A 2013; 1313:96-102. [DOI: 10.1016/j.chroma.2013.09.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Revised: 08/21/2013] [Accepted: 09/05/2013] [Indexed: 11/17/2022]
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144
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Pabst M, Fischl RM, Brecker L, Morelle W, Fauland A, Köfeler H, Altmann F, Léonard R. Rhamnogalacturonan II structure shows variation in the side chains monosaccharide composition and methylation status within and across different plant species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:61-72. [PMID: 23802881 DOI: 10.1111/tpj.12271] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Revised: 06/18/2013] [Accepted: 06/21/2013] [Indexed: 05/08/2023]
Abstract
A paradigm regarding rhamnogalacturonans II (RGII) is their strictly conserved structure within a given plant. We developed and employed a fast structural characterization method based on chromatography and mass spectrometry, allowing analysis of RGII side chains from microgram amounts of cell wall. We found that RGII structures are much more diverse than so far described. In chain A of wild-type plants, up to 45% of the l-fucose is substituted by l-galactose, a state that is seemingly uncorrelated with RGII dimerization capacity. This led us to completely reinvestigate RGII structures of the Arabidopsis thaliana fucose-deficient mutant mur1, which provided insights into RGII chain A biosynthesis, and suggested that chain A truncation, rather than l-fucose to l-galactose substitution, is responsible for the mur1 dwarf phenotype. Mass spectrometry data for chain A coupled with NMR analysis revealed a high degree of methyl esterification of its glucuronic acid, providing a plausible explanation for the puzzling RGII antibody recognition. The β-galacturonic acid of chain A exhibits up to two methyl etherifications in an organ-specific manner. Combined with variation in the length of side chain B, this gives rise to a family of RGII structures instead of the unique structure described up to now. These findings pave the way for studies on the physiological roles of modulation of RGII composition.
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Affiliation(s)
- Martin Pabst
- Department of Chemistry, University of Natural Resources and Life Sciences, 1190, Vienna, Austria
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145
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Ruhaak LR, Nguyen UT, Stroble C, Taylor SL, Taguchi A, Hanash SM, Lebrilla CB, Kim K, Miyamoto S. Enrichment strategies in glycomics-based lung cancer biomarker development. Proteomics Clin Appl 2013; 7:664-76. [PMID: 23640812 PMCID: PMC3884000 DOI: 10.1002/prca.201200131] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2012] [Revised: 01/11/2013] [Accepted: 02/12/2013] [Indexed: 12/25/2022]
Abstract
PURPOSE There is a need to identify better glycan biomarkers for diagnosis, early detection, and treatment monitoring in lung cancer using biofluids such as blood. Biofluids are complex mixtures of proteins dominated by a few high abundance proteins that may not have specificity for lung cancer. Therefore, two methods for protein enrichment were evaluated; affinity capturing of IgG and enrichment of medium abundance proteins, thus allowing us to determine which method yields the best candidate glycan biomarkers for lung cancer. EXPERIMENTAL DESIGN N-glycans isolated from plasma samples from 20 cases of lung adenocarcinoma and 20 matched controls were analyzed using nLC-PGC-chip-TOF-MS (where PGC is porous-graphitized carbon). N-glycan profiles were obtained for five different fractions: total plasma, isolated IgG, IgG-depleted plasma, and the bound and flow-through fractions of protein enrichment. RESULTS Four glycans differed significantly (false discovery rate, FDR < 0.05) between cases and controls in whole unfractionated plasma, while four other glycans differed significantly by cancer status in the IgG fraction. No significant glycan differences were observed in the other fractions. CONCLUSIONS AND CLINICAL RELEVANCE These results confirm that the N-glycan profile in plasma of lung cancer patients is different from healthy controls and appears to be dominated by alterations in relatively abundant proteins.
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Affiliation(s)
- L Renee Ruhaak
- Department of Chemistry, University of California Davis, Davis, CA 95616, USA.
| | - Uyen Thao Nguyen
- Division of Biostatistics, Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - Carol Stroble
- Department of Chemistry, University of California Davis, Davis, CA, USA
- Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Sandra L Taylor
- Division of Biostatistics, Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - Ayumu Taguchi
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, WA, USA
| | - Samir M Hanash
- Division of Public Health Sciences, Fred Hutchison Cancer Research Center, Seattle, WA, USA
- Department of Clinical Cancer Prevention - Research, Clinical Cancer Prevention, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | | | - Kyoungmi Kim
- Division of Biostatistics, Department of Public Health Sciences, University of California Davis, Davis, CA, USA
| | - Suzanne Miyamoto
- Division of Hematology and Oncology, University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
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146
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Type and branched pattern of N-glycans and their structural effect on the chicken egg allergen ovotransferrin: a comparison with ovomucoid. Glycoconj J 2013; 31:41-50. [DOI: 10.1007/s10719-013-9498-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2013] [Revised: 08/10/2013] [Accepted: 08/20/2013] [Indexed: 10/26/2022]
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147
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Nishikaze T, Kawabata SI, Tanaka K. Boron forms unexpected glycopeptide derivatives during MALDI-MS experiment. JOURNAL OF MASS SPECTROMETRY : JMS 2013; 48:1005-1009. [PMID: 24078240 DOI: 10.1002/jms.3246] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2013] [Revised: 06/07/2013] [Accepted: 06/17/2013] [Indexed: 06/02/2023]
Affiliation(s)
- Takashi Nishikaze
- Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto, 604-8511, Japan
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148
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Mun JY, Lee KJ, Seo H, Sung MS, Cho YS, Lee SG, Kwon O, Oh DB. Efficient Adhesion-Based Plasma Membrane Isolation for Cell Surface N-Glycan Analysis. Anal Chem 2013; 85:7462-70. [DOI: 10.1021/ac401431u] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
| | | | | | - Min-Sun Sung
- Biosystems and
Bioengineering
Program, University of Science and Technology (UST), Daejeon 305-350, South Korea
| | | | - Seung-Goo Lee
- Biosystems and
Bioengineering
Program, University of Science and Technology (UST), Daejeon 305-350, South Korea
| | - Ohsuk Kwon
- Biosystems and
Bioengineering
Program, University of Science and Technology (UST), Daejeon 305-350, South Korea
| | - Doo-Byoung Oh
- Biosystems and
Bioengineering
Program, University of Science and Technology (UST), Daejeon 305-350, South Korea
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149
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Wang C, Yuan J, Li X, Wang Z, Huang L. Sulfonyl hydrazine-functionalized polymer as a specific capturer of reducing glycans from complex samples for high-throughput analysis by electrospray ionization mass spectrometry. Analyst 2013; 138:5344-56. [PMID: 23875183 DOI: 10.1039/c3an00931a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Qualitative and quantitative studies of glycosylation patterns of various biologically important proteins represent a key field for the understanding of their complex structure-function relationships. However, the analysis of glycoprotein glycans is usually undermined by tedious sample processing steps prior to detection, including deproteination, desalting and removal of some other non-glycan impurities, which results in considerable sample loss and increased difficulty of quantitative analysis. Herein we report a facile and versatile method for the quantitative isolation of reducing glycans from complex samples using sulfonyl hydrazine-functionalized polystyrene (SHPS) beads, namely the SHPS-based glycan capturing procedure. This method allows the chemoselective and efficient condensation of the aldehyde group of reducing glycans with the active sulfonyl hydrazine group of SHPS beads under anhydrous conditions, resulting in the formation of sulfonyl hydrazone conjugates. The non-glycan components in samples, such as proteins, salts and some other impurities, can be completely removed by washing the sulfonyl hydrazone conjugates. Regeneration of the reducing glycans can be performed via mild hydrolysis of the washed sulfonyl hydrazone conjugates. This procedure is compatible with almost all the current techniques for the derivatization or detection of reducing glycans. We have obtained essential data for this method, including optimized reaction conditions, linearity and reproducibility for glycan quantitation, as well as a final glycan recovery ratio. Moreover, mass spectrometric analysis of the glycans from some complex biological samples, including milk, human blood plasma and fetal bovine serum, was achieved, demonstrating good applicability of this novel procedure.
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Affiliation(s)
- Chengjian Wang
- Educational Ministry Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Science, Northwest University, Xi'an 710069, China
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150
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Cosgrave EFJ, Struwe WB, Hayes JM, Harvey DJ, Wormald MR, Rudd PM. N-Linked Glycan Structures of the Human Fcγ Receptors Produced in NS0 Cells. J Proteome Res 2013; 12:3721-37. [DOI: 10.1021/pr400344h] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Eoin F. J. Cosgrave
- NIBRT Glycobiology Group, National Institute for Bioprocessing Research and Training, Foster’s Avenue, Mount Merrion, Blackrock, County Dublin,
Ireland
- Pharmaceutical
Life Sciences
Group, Waters Corporation, 34 Maple Street,
Milford, Massachusetts 01757, United States
| | - Weston B. Struwe
- NIBRT Glycobiology Group, National Institute for Bioprocessing Research and Training, Foster’s Avenue, Mount Merrion, Blackrock, County Dublin,
Ireland
- Chemistry Research Laboratory,
Department of Chemistry, University of Oxford, Oxford OX1 3TA, United Kingdom
| | - Jerrard M. Hayes
- NIBRT Glycobiology Group, National Institute for Bioprocessing Research and Training, Foster’s Avenue, Mount Merrion, Blackrock, County Dublin,
Ireland
| | - David J. Harvey
- Oxford Glycobiology Institute,
Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Mark R. Wormald
- Oxford Glycobiology Institute,
Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Pauline M. Rudd
- NIBRT Glycobiology Group, National Institute for Bioprocessing Research and Training, Foster’s Avenue, Mount Merrion, Blackrock, County Dublin,
Ireland
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