1
|
Yun J, Jo JY, Tuomivaara ST, Lim JM. Isotope labeling strategies of glycans for mass spectrometry-based quantitative glycomics. Microchem J 2021. [DOI: 10.1016/j.microc.2021.106655] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
2
|
Kadowaki MAS, Briganti L, Evangelista DE, Echevarría-Poza A, Tryfona T, Pellegrini VOA, Nakayama DG, Dupree P, Polikarpov I. Unlocking the structural features for the xylobiohydrolase activity of an unusual GH11 member identified in a compost-derived consortium. Biotechnol Bioeng 2021; 118:4052-4064. [PMID: 34232504 DOI: 10.1002/bit.27880] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 06/28/2021] [Accepted: 07/04/2021] [Indexed: 11/08/2022]
Abstract
The heteropolysaccharide xylan is a valuable source of sustainable chemicals and materials from renewable biomass sources. A complete hydrolysis of this major hemicellulose component requires a diverse set of enzymes including endo-β-1,4-xylanases, β-xylosidases, acetylxylan esterases, α-l-arabinofuranosidases, and α-glucuronidases. Notably, the most studied xylanases from glycoside hydrolase family 11 (GH11) have exclusively been endo-β-1,4- and β-1,3-xylanases. However, a recent analysis of a metatranscriptome library from a microbial lignocellulose community revealed GH11 enzymes capable of releasing solely xylobiose from xylan. Although initial biochemical studies clearly indicated their xylobiohydrolase mode of action, the structural features that drive this new activity still remained unclear. It was also not clear whether the enzymes acted on the reducing or nonreducing end of the substrate. Here, we solved the crystal structure of MetXyn11 in the apo and xylobiose-bound forms. The structure of MetXyn11 revealed the molecular features that explain the observed pattern on xylooligosaccharides released by this nonreducing end xylobiohydrolase.
Collapse
Affiliation(s)
- Marco A S Kadowaki
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil.,PhotoBioCatalysis-Biomass transformation Lab (BTL), École Interfacultaire de Bioingénieurs (EIB), Université Libre de Bruxelles, Brussels, Belgium
| | - Lorenzo Briganti
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Danilo E Evangelista
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil.,Instituto de Criminalística de Andradina, Superintendência da Polícia Técnico Científica de São Paulo, Andradina, São Paulo, Brazil
| | | | - Theodora Tryfona
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Vanessa O A Pellegrini
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Darlan G Nakayama
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Igor Polikarpov
- Grupo de Biotecnologia Molecular, Instituto de Física de São Carlos, Universidade de São Paulo, São Carlos, São Paulo, Brazil
| |
Collapse
|
3
|
Carneiro LA, Yu L, Dupree P, Ward RJ. Characterization of a β-galactosidase from Bacillus subtilis with transgalactosylation activity. Int J Biol Macromol 2018; 120:279-287. [DOI: 10.1016/j.ijbiomac.2018.07.116] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/14/2018] [Accepted: 07/16/2018] [Indexed: 01/09/2023]
|
4
|
Smith J, Mittermayr S, Váradi C, Bones J. Quantitative glycomics using liquid phase separations coupled to mass spectrometry. Analyst 2018; 142:700-720. [PMID: 28170017 DOI: 10.1039/c6an02715f] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Post-translational modification of proteins by the attachment of glycans is governed by a variety of highly specific enzymes and is associated with fundamental impacts on the parent protein's physical, chemical and biological properties. The inherent connection between cellular physiology and specific glycosylation patterns has been shown to offer potential for diagnostic and prognostic monitoring of altered glycosylation in the disease state. Conversely, glycoprotein based biopharmaceuticals have emerged as dominant therapeutic strategies in the treatment of intricate diseases. Glycosylation present on these biopharmaceuticals represents a major critical quality attribute with impacts on both pharmacokinetics and pharmacodynamics. The structural variety of glycans, based upon their non-template driven assembly, poses a significant analytical challenge for both qualitative and quantitative analysis. Labile monosaccharide constituents, isomeric species and often low sample availability from biological sources necessitates meticulous sample handling, ultra-high-resolution analytical separation and sensitive detection techniques, respectively. In this article a critical review of analytical quantitation approaches using liquid phase separations coupled to mass spectrometry for released glycans of biopharmaceutical and biomedical significance is presented. Considerations associated with sample derivatisation strategies, ionisation, relative quantitation through isotopic as well as isobaric labelling, metabolic/enzymatic incorporation and targeted analysis are all thoroughly discussed.
Collapse
Affiliation(s)
- Josh Smith
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland. and School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, 152-160 Pearse Street, Dublin 2, D02 R590, Ireland
| | - Stefan Mittermayr
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland.
| | - Csaba Váradi
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland.
| | - Jonathan Bones
- National Institute for Bioprocessing Research and Training, Fosters Avenue, Mount Merrion, Blackrock, Dublin, A94 X099, Ireland. and School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4, D04 V1 W8, Ireland
| |
Collapse
|
5
|
Pidatala VR, Mahboubi A, Mortimer JC. Structural Characterization of Mannan Cell Wall Polysaccharides in Plants Using PACE. J Vis Exp 2017. [PMID: 29155734 PMCID: PMC5752419 DOI: 10.3791/56424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Plant cell wall polysaccharides are notoriously difficult to analyze, and most methods require expensive equipment, skilled operators, and large amounts of purified material. Here, we describe a simple method for gaining detailed polysaccharide structural information, including resolution of structural isomers. For polysaccharide analysis by gel electrophoresis (PACE), plant cell wall material is hydrolyzed with glycosyl hydrolases specific to the polysaccharide of interest (e.g., mannanases for mannan). Large format polyacrylamide gels are then used to separate the released oligosaccharides, which have been fluorescently labeled. Gels can be visualized with a modified gel imaging system (see Table of Materials). The resulting oligosaccharide fingerprint can either be compared qualitatively or, with replication, quantitatively. Linkage and branching information can be established using additional glycosyl hydrolases (e.g., mannosidases and galactosidases). Whilst this protocol describes a method for analyzing glucomannan structure, it can be applied to any polysaccharide for which characterized glycosyl hydrolases exist. Alternatively, it can be used to characterize novel glycosyl hydrolases using defined polysaccharide substrates.
Collapse
Affiliation(s)
- Venkataramana R Pidatala
- Joint BioEnergy Institute; Environmental and Systems Biology, BioSciences Division, Lawrence Berkeley National Laboratory
| | - Amir Mahboubi
- Joint BioEnergy Institute; Environmental and Systems Biology, BioSciences Division, Lawrence Berkeley National Laboratory
| | - Jenny C Mortimer
- Joint BioEnergy Institute; Environmental and Systems Biology, BioSciences Division, Lawrence Berkeley National Laboratory;
| |
Collapse
|
6
|
Albrecht S, Mittermayr S, Smith J, Martín SM, Doherty M, Bones J. Twoplex 12/13 C 6 aniline stable isotope and linkage-specific sialic acid labeling 2D-LC-MS workflow for quantitative N-glycomics. Proteomics 2017; 17. [PMID: 27891772 DOI: 10.1002/pmic.201600304] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 11/10/2016] [Accepted: 11/25/2016] [Indexed: 11/06/2022]
Abstract
Quantitative glycomics represents an actively expanding research field ranging from the discovery of disease-associated glycan alterations to the quantitative characterization of N-glycans on therapeutic proteins. Commonly used analytical platforms for comparative relative quantitation of complex glycan samples include MALDI-TOF-MS or chromatographic glycan profiling with subsequent data alignment and statistical evaluation. Limitations of such approaches include run-to-run technical variation and the potential introduction of subjectivity during data processing. Here, we introduce an offline 2D LC-MSE workflow for the fractionation and relative quantitation of twoplex isotopically labeled N-linked oligosaccharides using neutral 12 C6 and 13 C6 aniline (Δmass = 6 Da). Additional linkage-specific derivatization of sialic acids using 4-(4,6-dimethoxy-1,3,5-trizain-2-yl)-4-methylmorpholinium chloride offered simultaneous and advanced in-depth structural characterization. The potential of the method was demonstrated for the differential analysis of structurally defined N-glycans released from serum proteins of patients diagnosed with various stages of colorectal cancer. The described twoplex 12 C6 /13 C6 aniline 2D LC-MS platform is ideally suited for differential glycomic analysis of structurally complex N-glycan pools due to combination and analysis of samples in a single LC-MS injection and the associated minimization in technical variation.
Collapse
Affiliation(s)
- Simone Albrecht
- Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Stefan Mittermayr
- Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Josh Smith
- Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Silvia Millán Martín
- Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Dublin, Ireland
| | - Margaret Doherty
- Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Dublin, Ireland.,Department of Life Sciences, School of Science, Institute of Technology Sligo, Sligo, Ireland
| | - Jonathan Bones
- Characterisation and Comparability Laboratory, NIBRT - The National Institute for Bioprocessing Research and Training, Dublin, Ireland
| |
Collapse
|
7
|
Grünwald-Gruber C, Thader A, Maresch D, Dalik T, Altmann F. Determination of true ratios of different N-glycan structures in electrospray ionization mass spectrometry. Anal Bioanal Chem 2017; 409:2519-2530. [PMID: 28271226 PMCID: PMC5359385 DOI: 10.1007/s00216-017-0235-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 01/27/2017] [Indexed: 12/25/2022]
Abstract
An ideal method for the analysis of N-glycans would both identify the isomeric structure and deliver a true picture of the relative, if not absolute, amounts of the various structures in one sample. Porous graphitic carbon chromatography coupled with electrospray ionization mass spectrometry (ESI-MS) detection has emerged as a method with a particularly high potential of resolving isomeric oligosaccharides, but little attention has so far been paid to quantitation of the results obtained. In this work, we isolated a range of structures from Man5 to complex type N-glycans with zero to four sialic acids and blended them into an equimolar "glyco tune mix". When subjected to liquid chromatography-ESI-MS in positive and negative modes, the glyco tune mix clearly demonstrated the futility of quantitation of N-glycans of different overall composition, different number of sialic acids, and strongly differing size without compensation for their very different molar responses. Relative quantitation of human plasma N-glycans was performed with correction factors deduced from this external glyco tune mix. Addition of just one isotope-coded internal standard with enzymatically added 13C-galactose led to absolute quantification in the same experiment. Graphical Abstract Discrepancy between desirable (grey bars) and real (green bars) relative ion abundance of equimolar amounts of glycans in positive mode ESI-MS.
Collapse
Affiliation(s)
- Clemens Grünwald-Gruber
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Andreas Thader
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Daniel Maresch
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Thomas Dalik
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria
| | - Friedrich Altmann
- Department of Chemistry, University of Natural Resources and Life Sciences, Vienna, Muthgasse 18, 1190, Vienna, Austria.
| |
Collapse
|
8
|
Mancera-Arteu M, Giménez E, Barbosa J, Sanz-Nebot V. Identification and characterization of isomeric N-glycans of human alfa-acid-glycoprotein by stable isotope labelling and ZIC-HILIC-MS in combination with exoglycosidase digestion. Anal Chim Acta 2016; 940:92-103. [DOI: 10.1016/j.aca.2016.07.043] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 07/27/2016] [Accepted: 07/29/2016] [Indexed: 12/25/2022]
|
9
|
Cao W, Zhang W, Huang J, Jiang B, Zhang L, Yang P. Glycan reducing end dual isotopic labeling (GREDIL) for mass spectrometry-based quantitative N-glycomics. Chem Commun (Camb) 2016; 51:13603-6. [PMID: 26240031 DOI: 10.1039/c5cc05365j] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A general and effective enzymatic labeling method, termed glycan reducing end dual isotopic labeling (GREDIL), was developed for mass spectrometry-based quantitative N-glycomics.
Collapse
Affiliation(s)
- Weiqian Cao
- Institutes of Biomedical Sciences, Fudan University, Shanghai 200032, P. R. China.
| | | | | | | | | | | |
Collapse
|
10
|
Cai Y, Jiao J, Bin Z, Zhang Y, Yang P, Lu H. Glycan reductive isotope-coded amino acid labeling (GRIAL) for mass spectrometry-based quantitative N-glycomics. Chem Commun (Camb) 2015; 51:772-5. [PMID: 25421075 DOI: 10.1039/c4cc08086f] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
A general and simple labeling method, termed glycan reductive isotope-coded amino acid labeling (GRIAL), was developed for mass spectrometry-based quantitative N-glycomics.
Collapse
Affiliation(s)
- Yan Cai
- Shanghai Cancer Center and Key Laboratory of Glycoconjugates Research Ministry of Public Health, Fudan University, Shanghai 200032, P. R. China.
| | | | | | | | | | | |
Collapse
|
11
|
Mortimer JC, Faria-Blanc N, Yu X, Tryfona T, Sorieul M, Ng YZ, Zhang Z, Stott K, Anders N, Dupree P. An unusual xylan in Arabidopsis primary cell walls is synthesised by GUX3, IRX9L, IRX10L and IRX14. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:413-26. [PMID: 26043357 PMCID: PMC4528235 DOI: 10.1111/tpj.12898] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 05/22/2015] [Accepted: 05/26/2015] [Indexed: 05/04/2023]
Abstract
Xylan is a crucial component of many plant primary and secondary cell walls. However, the structure and function of xylan in the dicotyledon primary cell wall is not well understood. Here, we characterized a xylan that is specific to tissues enriched in Arabidopsis primary cell walls. Unlike previously described xylans, this xylan carries a pentose linked 1-2 to the α-1,2-d-glucuronic acid (GlcA) side chains on the β-1,4-Xyl backbone. The frequent and precisely regular spacing of GlcA substitutions every six xylosyl residues along the backbone is also unlike that previously observed in secondary cell wall xylan. Molecular genetics, in vitro assays, and expression data suggest that IRX9L, IRX10L and IRX14 are required for xylan backbone synthesis in primary cell wall synthesising tissues. IRX9 and IRX10 are not involved in the primary cell wall xylan synthesis but are functionally exchangeable with IRX9L and IRX10L. GUX3 is the only glucuronyltransferase required for the addition of the GlcA decorations on the xylan. The differences in xylan structure in primary versus secondary cell walls might reflect the different roles in cross-linking and interaction with other cell wall components.
Collapse
Affiliation(s)
- Jenny C Mortimer
- Department of Biochemistry, University of CambridgeCambridge, CB2 1QW, UK
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Joint BioEnergy InstituteBerkeley, CA, 94720, USA
| | - Nuno Faria-Blanc
- Department of Biochemistry, University of CambridgeCambridge, CB2 1QW, UK
| | - Xiaolan Yu
- Department of Biochemistry, University of CambridgeCambridge, CB2 1QW, UK
| | - Theodora Tryfona
- Department of Biochemistry, University of CambridgeCambridge, CB2 1QW, UK
| | - Mathias Sorieul
- Department of Biochemistry, University of CambridgeCambridge, CB2 1QW, UK
| | - Yao Z Ng
- Department of Biochemistry, University of CambridgeCambridge, CB2 1QW, UK
| | - Zhinong Zhang
- Department of Biochemistry, University of CambridgeCambridge, CB2 1QW, UK
| | - Katherine Stott
- Department of Biochemistry, University of CambridgeCambridge, CB2 1QW, UK
| | - Nadine Anders
- Department of Biochemistry, University of CambridgeCambridge, CB2 1QW, UK
| | - Paul Dupree
- Department of Biochemistry, University of CambridgeCambridge, CB2 1QW, UK
- *For Correspondence (e-mail )
| |
Collapse
|
12
|
Li H, Bendiak B, Siems WF, Gang DR, Hill HH. Determining the Isomeric Heterogeneity of Neutral Oligosaccharide-Alditols of Bovine Submaxillary Mucin Using Negative Ion Traveling Wave Ion Mobility Mass Spectrometry. Anal Chem 2015; 87:2228-35. [DOI: 10.1021/ac503754k] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Hongli Li
- Department
of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Brad Bendiak
- Department
of Cell and Developmental Biology, Program in Structural
Biology and Biophysics, University of Colorado, Health Sciences Center, Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - William F. Siems
- Department
of Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - David R. Gang
- Institute of Biological
Chemistry, Washington State University, Pullman, Washington 99164, United States
| | - Herbert H. Hill
- Department
of Chemistry, Washington State University, Pullman, Washington 99164, United States
| |
Collapse
|
13
|
Witt L, Pirkl A, Draude F, Peter-Katalinić J, Dreisewerd K, Mormann M. Water ice is a soft matrix for the structural characterization of glycosaminoglycans by infrared matrix-assisted laser desorption/ionization. Anal Chem 2014; 86:6439-46. [PMID: 24862464 DOI: 10.1021/ac5008706] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Glycosaminoglycans (GAGs) are a class of heterogeneous, often highly sulfated glycans that form linear chains consisting of up to 100 monosaccharide building blocks and more. GAGs are ubiquitous constituents of connective tissue, cartilage, and the extracellular matrix, where they have key functions in many important biological processes. For their characterization by mass spectrometry (MS) and tandem MS, the high molecular weight polymers are usually enzymatically digested to oligomers with a low degree of polymerization (dp), typically disaccharides. However, owing to their lability elimination of sulfate groups upon desorption/ionization is often encountered leading to a loss of information on the analyte. Here, we demonstrate that, in particular, water ice constitutes an extremely mild matrix for the analysis of highly sulfated GAG disaccharides by infrared matrix-assisted laser desorption/ionization (IR-MALDI) mass spectrometry. Depending on the degree of sulfation, next to the singly charged ionic species doubly- and even triply charged ions are formed. An unambiguous assignment of the sulfation sites becomes possible by subjecting sodium adducts of the GAGs to low-energy collision-induced dissociation tandem MS. These ionic species exhibit a remarkable stability of the sulfate substituents, allowing the formation of fragment ions retaining their sulfation that arise from either cross-ring cleavages or rupture of the glycosidic bonds, thereby allowing an unambiguous assignment of the sulfation sites.
Collapse
Affiliation(s)
- Lukas Witt
- Institute for Hygiene, University of Münster , 48149 Münster, Germany
| | | | | | | | | | | |
Collapse
|
14
|
Tryfona T, Theys TE, Wagner T, Stott K, Keegstra K, Dupree P. Characterisation of FUT4 and FUT6 α-(1 → 2)-fucosyltransferases reveals that absence of root arabinogalactan fucosylation increases Arabidopsis root growth salt sensitivity. PLoS One 2014; 9:e93291. [PMID: 24667545 PMCID: PMC3965541 DOI: 10.1371/journal.pone.0093291] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Accepted: 03/04/2014] [Indexed: 11/22/2022] Open
Abstract
Plant type II arabinogalactan (AG) polysaccharides are attached to arabinogalactan proteins (AGPs) at hydroxyproline residues, and they are very diverse and heterogeneous structures. The AG consists of a β-(1→3)-linked galactan backbone with β-(1→6)-galactan side chains that are modified mainly with arabinose, but they may also contain glucuronic acid, rhamnose or other sugars. Here, we studied the positions of fucose substitutions in AGPs, and we investigated the functions of this fucosylation. Monosaccharide analysis of Arabidopsis leaf AGP extracts revealed a significant reduction in L-Fucose content in the fut4 mutant, but not in the fut6 mutant. In addition, Fucose was reduced in the fut4 mutant in root AGP extracts and was absent in the fut4/fut6 mutant. Curiously, in all cases reduction of fucose was accompanied with a reduction in xylose levels. The fucosylated AGP structures in leaves and roots in wild type and fut mutant plants were characterised by sequential digestion with AG specific enzymes, analysis by Polysaccharide Analysis using Carbohydrate gel Electrophoresis, and Matrix Assisted Laser Desorption/Ionisation (MALDI)-Time of Flight Mass spectrometry (MS). We found that FUT4 is solely responsible for the fucosylation of AGPs in leaves. The Arabidopsis thaliana FUT4 and FUT6 genes have been previously proposed to be non-redundant AG-specific fucosyltransferases. Unexpectedly, FUT4 and FUT6 enzymes both fucosylate the same AGP structures in roots, suggesting partial redundancy to each other. Detailed structural characterisation of root AGPs with high energy MALDI-Collision Induced Dissociation MS and NMR revealed an abundant unique AG oligosaccharide structure consisting of terminal xylose attached to fucose. The loss of this structure in fut4/fut6 mutants explains the reduction of both fucose and xylose in AGP extracts. Under salt-stress growth conditions the fut4/fut6 mutant lacking AGP fucosylation exhibited a shorter root phenotype than wild type plants, implicating fucosylation of AGPs in maintaining proper cell expansion under these conditions.
Collapse
Affiliation(s)
- Theodora Tryfona
- School of Biological Sciences, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tina E. Theys
- School of Biological Sciences, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Tanya Wagner
- DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
| | - Katherine Stott
- School of Biological Sciences, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Kenneth Keegstra
- DOE Plant Research Laboratory, Michigan State University, East Lansing, Michigan, United States of America
| | - Paul Dupree
- School of Biological Sciences, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
- * E-mail:
| |
Collapse
|
15
|
Giménez E, Sanz-Nebot V, Rizzi A. Relative quantitation of glycosylation variants by stable isotope labeling of enzymatically released N-glycans using [12C]/[13C] aniline and ZIC-HILIC-ESI-TOF-MS. Anal Bioanal Chem 2013; 405:7307-19. [DOI: 10.1007/s00216-013-7178-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Revised: 06/20/2013] [Accepted: 06/25/2013] [Indexed: 10/26/2022]
|
16
|
Li X, Jackson P, Rubtsov DV, Faria-Blanc N, Mortimer JC, Turner SR, Krogh KB, Johansen KS, Dupree P. Development and application of a high throughput carbohydrate profiling technique for analyzing plant cell wall polysaccharides and carbohydrate active enzymes. BIOTECHNOLOGY FOR BIOFUELS 2013; 6:94. [PMID: 23819705 PMCID: PMC3717103 DOI: 10.1186/1754-6834-6-94] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 06/28/2013] [Indexed: 05/17/2023]
Abstract
BACKGROUND Plant cell wall polysaccharide composition varies substantially between species, organs and genotypes. Knowledge of the structure and composition of these polysaccharides, accompanied by a suite of well characterised glycosyl hydrolases will be important for the success of lignocellulosic biofuels. Current methods used to characterise enzymatically released plant oligosaccharides are relatively slow. RESULTS A method and software was developed allowing the use of a DNA sequencer to profile oligosaccharides derived from plant cell wall polysaccharides (DNA sequencer-Assisted Saccharide analysis in High throughput, DASH). An ABI 3730xl, which can analyse 96 samples simultaneously by capillary electrophoresis, was used to separate fluorophore derivatised reducing mono- and oligo-saccharides from plant cell walls. Using electrophoresis mobility markers, oligosaccharide mobilities were standardised between experiments to enable reproducible oligosaccharide identification. These mobility markers can be flexibly designed to span the mobilities of oligosaccharides under investigation, and they have a fluorescence emission that is distinct from that of the saccharide labelling. Methods for relative and absolute quantitation of oligosaccharides are described. Analysis of a large number of samples is facilitated by the DASHboard software which was developed in parallel. Use of this method was exemplified by comparing xylan structure and content in Arabidopsis thaliana mutants affected in xylan synthesis. The product profiles of specific xylanases were also compared in order to identify enzymes with unusual oligosaccharide products. CONCLUSIONS The DASH method and DASHboard software can be used to carry out large-scale analyses of the compositional variation of plant cell walls and biomass, to compare plants with mutations in plant cell wall synthesis pathways, and to characterise novel carbohydrate active enzymes.
Collapse
Affiliation(s)
- Xiaofei Li
- Department of Biochemistry, Building O, Downing Site, University of Cambridge, Cambridge CB2 1QW, UK
| | - Peter Jackson
- Department of Biochemistry, Building O, Downing Site, University of Cambridge, Cambridge CB2 1QW, UK
| | - Denis V Rubtsov
- Department of Biochemistry, Building O, Downing Site, University of Cambridge, Cambridge CB2 1QW, UK
| | - Nuno Faria-Blanc
- Department of Biochemistry, Building O, Downing Site, University of Cambridge, Cambridge CB2 1QW, UK
| | - Jenny C Mortimer
- Department of Biochemistry, Building O, Downing Site, University of Cambridge, Cambridge CB2 1QW, UK
| | - Simon R Turner
- Faculty of Life Sciences, Michael Smith Building, Oxford Road, Manchester M13 9PT, UK
| | | | | | - Paul Dupree
- Department of Biochemistry, Building O, Downing Site, University of Cambridge, Cambridge CB2 1QW, UK
| |
Collapse
|
17
|
Alley WR, Mann BF, Novotny MV. High-sensitivity analytical approaches for the structural characterization of glycoproteins. Chem Rev 2013; 113:2668-732. [PMID: 23531120 PMCID: PMC3992972 DOI: 10.1021/cr3003714] [Citation(s) in RCA: 239] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- William R. Alley
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
| | - Benjamin F. Mann
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana, United States
- National Center for Glycomics and Glycoproteomics, Indiana University, Bloomington, Indiana, United States
- Indiana University School of Medicine, Indiana University, Indianapolis, Indiana, United States
| |
Collapse
|
18
|
Novotny MV, Alley WR, Mann BF. Analytical glycobiology at high sensitivity: current approaches and directions. Glycoconj J 2013; 30:89-117. [PMID: 22945852 PMCID: PMC3586546 DOI: 10.1007/s10719-012-9444-8] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 06/29/2012] [Accepted: 08/14/2012] [Indexed: 12/30/2022]
Abstract
This review summarizes the analytical advances made during the last several years in the structural and quantitative determinations of glycoproteins in complex biological mixtures. The main analytical techniques used in the fields of glycomics and glycoproteomics involve different modes of mass spectrometry and their combinations with capillary separation methods such as microcolumn liquid chromatography and capillary electrophoresis. The need for high-sensitivity measurements have been emphasized in the oligosaccharide profiling used in the field of biomarker discovery through MALDI mass spectrometry. High-sensitivity profiling of both glycans and glycopeptides from biological fluids and tissue extracts has been aided significantly through lectin preconcentration and the uses of affinity chromatography.
Collapse
Affiliation(s)
- Milos V Novotny
- Department of Chemistry, Indiana University, Bloomington, IN, USA.
| | | | | |
Collapse
|
19
|
Alley WR, Novotny MV. Structural glycomic analyses at high sensitivity: a decade of progress. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2013; 6:237-65. [PMID: 23560930 PMCID: PMC3992932 DOI: 10.1146/annurev-anchem-062012-092609] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
The field of glycomics has recently advanced in response to the urgent need for structural characterization and quantification of complex carbohydrates in biologically and medically important applications. The recent success of analytical glycobiology at high sensitivity reflects numerous advances in biomolecular mass spectrometry and its instrumentation, capillary and microchip separation techniques, and microchemical manipulations of carbohydrate reactivity. The multimethodological approach appears to be necessary to gain an in-depth understanding of very complex glycomes in different biological systems.
Collapse
Affiliation(s)
- William R. Alley
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
| | - Milos V. Novotny
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405
- Department of Medicine, Indiana University, Indianapolis, Indiana 46202
| |
Collapse
|
20
|
Bowman MJ, Dien BS, O'Bryan PJ, Sarath G, Cotta MA. Comparative Analysis of End Point Enzymatic Digests of Arabino-Xylan Isolated from Switchgrass (Panicum virgatum L) of Varying Maturities using LC-MSn. Metabolites 2012; 2:959-82. [PMID: 24957770 PMCID: PMC3901237 DOI: 10.3390/metabo2040959] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2012] [Revised: 10/30/2012] [Accepted: 11/09/2012] [Indexed: 11/16/2022] Open
Abstract
Switchgrass (Panicum virgatum L., SG) is a perennial grass presently used for forage and being developed as a bioenergy crop for conversion of cell wall carbohydrates to biofuels. Up to 50% of the cell wall associated carbohydrates are xylan. SG was analyzed for xylan structural features at variable harvest maturities. Xylan from each of three maturities was isolated using classical alkaline extraction to yield fractions (Xyl A and B) with varying compositional ratios. The Xyl B fraction was observed to decrease with plant age. Xylan samples were subsequently prepared for structure analysis by digesting with pure endo-xylanase, which preserved side-groups, or a commercial carbohydrase preparation favored for biomass conversion work. Enzymatic digestion products were successfully permethylated and analyzed by reverse-phase liquid chromatography with mass spectrometric detection (RP-HPLC-MSn). This method is advantageous compared to prior work on plant biomass because it avoids isolation of individual arabinoxylan oligomers. The use of RP-HPLC- MSn differentiated 14 structural oligosaccharides (d.p. 3-9) from the monocomponent enzyme digestion and nine oligosaccharide structures (d.p. 3-9) from hydrolysis with a cellulase enzyme cocktail. The distribution of arabinoxylan oligomers varied depending upon the enzyme(s) applied but did not vary with harvest maturity.
Collapse
Affiliation(s)
- Michael J Bowman
- Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, 1815 N. University Street, Peoria, IL 61604, USA.
| | - Bruce S Dien
- Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, 1815 N. University Street, Peoria, IL 61604, USA.
| | - Patricia J O'Bryan
- Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, 1815 N. University Street, Peoria, IL 61604, USA.
| | - Gautam Sarath
- Department of Agriculture, Agricultural Research Service, Central-East Regional Biomass Center, 137 Keim Hall, East Campus, UNL, Lincoln, NE 68583, USA.
| | - Michael A Cotta
- Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, 1815 N. University Street, Peoria, IL 61604, USA.
| |
Collapse
|
21
|
Tryfona T, Liang HC, Kotake T, Tsumuraya Y, Stephens E, Dupree P. Structural characterization of Arabidopsis leaf arabinogalactan polysaccharides. PLANT PHYSIOLOGY 2012; 160:653-66. [PMID: 22891237 PMCID: PMC3461546 DOI: 10.1104/pp.112.202309] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Accepted: 08/06/2012] [Indexed: 05/18/2023]
Abstract
Proteins decorated with arabinogalactan (AG) have important roles in cell wall structure and plant development, yet the structure and biosynthesis of this polysaccharide are poorly understood. To facilitate the analysis of biosynthetic mutants, water-extractable arabinogalactan proteins (AGPs) were isolated from the leaves of Arabidopsis (Arabidopsis thaliana) plants and the structure of the AG carbohydrate component was studied. Enzymes able to hydrolyze specifically AG were utilized to release AG oligosaccharides. The released oligosaccharides were characterized by high-energy matrix-assisted laser desorption ionization-collision-induced dissociation mass spectrometry and polysaccharide analysis by carbohydrate gel electrophoresis. The Arabidopsis AG is composed of a β-(1→3)-galactan backbone with β-(1→6)-d-galactan side chains. The β-(1→6)-galactan side chains vary in length from one to over 20 galactosyl residues, and they are partly substituted with single α-(1→3)-l-arabinofuranosyl residues. Additionally, a substantial proportion of the β-(1→6)-galactan side chain oligosaccharides are substituted at the nonreducing termini with single 4-O-methyl-glucuronosyl residues via β-(1→6)-linkages. The β-(1→6)-galactan side chains are occasionally substituted with α-l-fucosyl. In the fucose-deficient murus1 mutant, AGPs lack these fucose modifications. This work demonstrates that Arabidopsis mutants in AGP structure can be identified and characterized. The detailed structural elucidation of the AG polysaccharides from the leaves of Arabidopsis is essential for insights into the structure-function relationships of these molecules and will assist studies on their biosynthesis.
Collapse
|
22
|
Strum JS, Kim J, Wu S, De Leoz MLA, Peacock K, Grimm R, German JB, Mills DA, Lebrilla CB. Identification and accurate quantitation of biological oligosaccharide mixtures. Anal Chem 2012; 84:7793-801. [PMID: 22897719 DOI: 10.1021/ac301128s] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Structure-specific characterization and quantitation is often required for effective functional studies of oligosaccharides. Inside the gut, HMOs are preferentially bound and catabolized by the beneficial bacteria. HMO utility by these bacteria employs structure-specific catabolism based on a number of glycosidases. Determining the activity of these enzymes requires accurate quantitation of a large number of structures. In this study, we describe a method for the quantitation of human milk oligosaccharide (HMO) structures employing LC/MS and isotopically labeled internal standards. Data analysis was accomplished with a newly developed software tool, LC/MS Searcher, that employs a reference structure library to process LC/MS data yielding structural identification with accurate quantitation. The method was used to obtain a meta-enzyme analysis of bacteria, the simultaneous characterization of all glycosidases employed by bacteria for the catabolism of milk oligosaccharides. Analysis of consumed HMO structures confirmed the utility of a β-1,3-galactosidase in Bifidobacterium longum subsp. infantis ATCC 15697 (B. infantis). In comparison, Bifidobacterium breve ATCC 15700 showed significantly less HMO catabolic activity compared to B. infantis.
Collapse
Affiliation(s)
- John S Strum
- Department of Chemistry, University of California, Davis, 95616, United States
| | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Tep S, Hincapie M, Hancock WS. The characterization and quantitation of glycomic changes in CHO cells during a bioreactor campaign. Biotechnol Bioeng 2012; 109:3007-17. [DOI: 10.1002/bit.24590] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 06/05/2012] [Accepted: 06/20/2012] [Indexed: 12/13/2022]
|
24
|
Recent developments in the detailed characterization of polymers by multidimensional chromatography. J Chromatogr A 2012; 1240:1-20. [DOI: 10.1016/j.chroma.2012.03.038] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Revised: 03/06/2012] [Accepted: 03/10/2012] [Indexed: 02/03/2023]
|
25
|
Bowman MJ, Dien BS, Hector RE, Sarath G, Cotta MA. Liquid chromatography-mass spectrometry investigation of enzyme-resistant xylooligosaccharide structures of switchgrass associated with ammonia pretreatment, enzymatic saccharification, and fermentation. BIORESOURCE TECHNOLOGY 2012; 110:437-47. [PMID: 22330596 DOI: 10.1016/j.biortech.2012.01.062] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Revised: 01/03/2012] [Accepted: 01/13/2012] [Indexed: 05/11/2023]
Abstract
Switchgrass is a potential source of renewable biomass for conversion to liquid biofuels. Efficient conversion requires effective strategies for pretreatment and enzymatic saccharification to produce fermentable sugars. Standard analysis of fermentation liquids includes detection of monosaccharides and ethanol to determine efficiency of conversion. Larger components, specifically oligosaccharides, are typically not measured due to the structural complexity of the products; however, as oligosaccharides they represent carbon available in biomass that is not converted to liquid fuels. In this study, ammonia-pretreated switchgrass was enzymatically depolymerized either independently or under simultaneous saccharification and fermentation conditions. Residual oligosaccharides were reducing end-labeled followed by hydrophilic interaction liquid chromatography mass spectrometry/mass spectrometry analysis. These data reveal 20 oligosaccharide peaks with distinct retention times and tandem mass spectrometry fragmentation patterns representing 13 different oligosaccharide compositions. All measured compositions were smaller than a chain length of six and were neither linear xylooligosaccharides nor modified with phenolic esters. This work represents a robust method to monitor and identify unhydrolyzed oligosaccharides from fermentations, thereby permitting the screening of targeted enzymatic activities to promote the complete hydrolysis of xylan.
Collapse
Affiliation(s)
- Michael J Bowman
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, 1815 N. University Street, Peoria, IL 61604, USA.
| | | | | | | | | |
Collapse
|
26
|
Bauer S. Mass spectrometry for characterizing plant cell wall polysaccharides. FRONTIERS IN PLANT SCIENCE 2012; 3:45. [PMID: 22645587 PMCID: PMC3355817 DOI: 10.3389/fpls.2012.00045] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 02/23/2012] [Indexed: 05/23/2023]
Abstract
Mass spectrometry is a selective and powerful technique to obtain identification and structural information on compounds present in complex mixtures. Since it requires only small sample amount it is an excellent tool for researchers interested in detecting changes in composition of complex carbohydrates of plants. This mini-review gives an overview of common mass spectrometry techniques applied to the analysis of plant cell wall carbohydrates. It presents examples in which mass spectrometry has been used to elucidate the structure of oligosaccharides derived from hemicelluloses and pectins and illustrates how information on sequence, linkages, branching, and modifications are obtained from characteristic fragmentation patterns.
Collapse
Affiliation(s)
- Stefan Bauer
- Energy Biosciences Institute, University of CaliforniaBerkeley, CA, USA
| |
Collapse
|
27
|
Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2007-2008. MASS SPECTROMETRY REVIEWS 2012; 31:183-311. [PMID: 21850673 DOI: 10.1002/mas.20333] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2010] [Revised: 01/04/2011] [Accepted: 01/04/2011] [Indexed: 05/31/2023]
Abstract
This review is the fifth update of the original review, published in 1999, on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2008. The first section of the review covers fundamental studies, fragmentation of carbohydrate ions, use of derivatives and new software developments for analysis of carbohydrate spectra. Among newer areas of method development are glycan arrays, MALDI imaging and the use of ion mobility spectrometry. The second section of the review discusses applications of MALDI MS to the analysis of different types of carbohydrate. Specific compound classes that are covered include carbohydrate polymers from plants, N- and O-linked glycans from glycoproteins, biopharmaceuticals, glycated proteins, glycolipids, glycosides and various other natural products. There is a short section on the use of MALDI mass spectrometry for the study of enzymes involved in glycan processing and a section on the use of MALDI MS to monitor products of the chemical synthesis of carbohydrates with emphasis on carbohydrate-protein complexes and glycodendrimers. Corresponding analyses by electrospray ionization now appear to outnumber those performed by MALDI and the amount of literature makes a comprehensive review on this technique impractical. However, most of the work relating to sample preparation and glycan synthesis is equally relevant to electrospray and, consequently, those proposing analyses by electrospray should also find material in this review of interest.
Collapse
Affiliation(s)
- David J Harvey
- Oxford Glycobiology Institute, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
| |
Collapse
|
28
|
A general approach for the purification and quantitative glycomic analysis of human plasma. Anal Bioanal Chem 2012; 402:2687-700. [DOI: 10.1007/s00216-012-5712-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 12/28/2011] [Accepted: 01/04/2012] [Indexed: 11/26/2022]
|
29
|
Glycosyl transferases in family 61 mediate arabinofuranosyl transfer onto xylan in grasses. Proc Natl Acad Sci U S A 2012; 109:989-93. [PMID: 22215597 DOI: 10.1073/pnas.1115858109] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Xylan, a hemicellulosic component of the plant cell wall, is one of the most abundant polysaccharides in nature. In contrast to dicots, xylan in grasses is extensively modified by α-(1,2)- and α-(1,3)-linked arabinofuranose. Despite the importance of grass arabinoxylan in human and animal nutrition and for bioenergy, the enzymes adding the arabinosyl substitutions are unknown. Here we demonstrate that knocking-down glycosyltransferase (GT) 61 expression in wheat endosperm strongly decreases α-(1,3)-linked arabinosyl substitution of xylan. Moreover, heterologous expression of wheat and rice GT61s in Arabidopsis leads to arabinosylation of the xylan, and therefore provides gain-of-function evidence for α-(1,3)-arabinosyltransferase activity. Thus, GT61 proteins play a key role in arabinoxylan biosynthesis and therefore in the evolutionary divergence of grass cell walls.
Collapse
|
30
|
Tep S, Hincapie M, Hancock WS. A MALDI-TOF MS method for the simultaneous and quantitative analysis of neutral and sialylated glycans of CHO-expressed glycoproteins. Carbohydr Res 2012; 347:121-9. [DOI: 10.1016/j.carres.2011.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/04/2011] [Accepted: 10/06/2011] [Indexed: 01/05/2023]
|
31
|
Leijdekkers A, Sanders M, Schols H, Gruppen H. Characterizing plant cell wall derived oligosaccharides using hydrophilic interaction chromatography with mass spectrometry detection. J Chromatogr A 2011; 1218:9227-35. [DOI: 10.1016/j.chroma.2011.10.068] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2011] [Revised: 10/19/2011] [Accepted: 10/24/2011] [Indexed: 10/15/2022]
|
32
|
Ropartz D, Bodet PE, Przybylski C, Gonnet F, Daniel R, Fer M, Helbert W, Bertrand D, Rogniaux H. Performance evaluation on a wide set of matrix-assisted laser desorption ionization matrices for the detection of oligosaccharides in a high-throughput mass spectrometric screening of carbohydrate depolymerizing enzymes. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:2059-70. [PMID: 21698689 DOI: 10.1002/rcm.5060] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Compared to other analytical methods, matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) presents several unique advantages for the structural characterization of degradation products of carbohydrates. Our final goal is to implement this technique as a high-throughput platform, with the aim of exploring natural bio-diversity to discover new carbohydrate depolymerizing enzymes. In this approach, a variety of carbohydrates will be used as enzymes substrates and MALDI-MS will be employed to monitor the oligosaccharides produced. One drawback of MALDI, however, is that the choice of the matrix is largely dependent on the chemical properties of the analyte. In this context, our objective in the present work was to find the smallest set of MALDI matrices able to detect chemically heterogeneous oligosaccharides. This was done through the performance evaluation of more than 40 MALDI matrices preparations. Homogeneity of analyte-matrix deposits was considered as a critical feature, especially since the final objective is to fully automate the analyses. Evaluation of the matrices was done by means of a rigorous statistical approach. Amongst all tested compounds, our work proposes the use of the DHB/DMA ionic matrix as the most generic matrix, for rapid detection of a variety of polysaccharides including neutral, anionic, methylated, sulfated, and acetylated compounds. The selected matrices were then used to screen crude bacterial incubation media for the detection of enzymatic degradation products.
Collapse
Affiliation(s)
- David Ropartz
- INRA UR1268 Biopolymères Interactions Assemblages, Plate-Forme BIBS, F-44316 Nantes, France.
| | | | | | | | | | | | | | | | | |
Collapse
|
33
|
Bowman MJ, Dien BS, O'Bryan PJ, Sarath G, Cotta MA. Selective chemical oxidation and depolymerization of switchgrass [corrected] (Panicum virgatum L.) xylan with [corrected] oligosaccharide product analysis by mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2011; 25:941-950. [PMID: 21416531 DOI: 10.1002/rcm.4949] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 01/20/2011] [Accepted: 01/20/2011] [Indexed: 05/30/2023]
Abstract
Xylan is a barrier to enzymatic hydrolysis of plant cell walls. It is well accepted that the xylan layer needs to be removed to efficiently hydrolyze cellulose; consequently, pretreatment conditions are (in part) optimized for maximal xylan depolymerization or displacement. Xylan consists of a long chain of β-1,4-linked xylose units substituted with arabinose (typically α-1,3-linked in grasses) and glucuronic acid (α-1,2-linked). Xylan has been proposed to have a structural function in plants and therefore may play a role in determining biomass reactivity to pretreatment. It has been proposed that substitutions along xylan chains are not random and, based upon studies of pericarp xylan, are organized in domains that have specific structural functions. Analysis of intact xylan is problematic because of its chain length (> degree of polymerization (d.p.) 100) and heterogeneous side groups. Traditionally, enzymatic end-point products have been characterized due to the limited products generated. Analysis of resultant arabino-xylo-oligosaccharides by mass spectrometry is complicated by the isobaric pentose sugars that primarily compose xylan. In this report, the variation in pentose ring structures was exploited for selective oxidation of the arabinofuranose primary alcohols followed by acid depolymerization to provide oligosaccharides with modified arabinose branches intact. Switchgrass samples were analyzed by hydrophilic interaction chromatography (HILIC)-liquid chromatography (LC)-mass spectrometry/mass spectrometry (MSMS) and off-line nanospray MS to demonstrate the utility of this chemistry for determination of primary hydroxyl groups on oligosaccharide structures, with potential applications for determining the sequence of arabino-xylo-oligosaccharides present in plant cell wall material.
Collapse
Affiliation(s)
- Michael J Bowman
- USDA, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, 1815 North University Street, Peoria, IL 61604, USA.
| | | | | | | | | |
Collapse
|
34
|
Ruhaak LR, Zauner G, Huhn C, Bruggink C, Deelder AM, Wuhrer M. Glycan labeling strategies and their use in identification and quantification. Anal Bioanal Chem 2010; 397:3457-81. [PMID: 20225063 PMCID: PMC2911528 DOI: 10.1007/s00216-010-3532-z] [Citation(s) in RCA: 366] [Impact Index Per Article: 26.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Revised: 01/22/2010] [Accepted: 01/22/2010] [Indexed: 12/28/2022]
Abstract
Most methods for the analysis of oligosaccharides from biological sources require a glycan derivatization step: glycans may be derivatized to introduce a chromophore or fluorophore, facilitating detection after chromatographic or electrophoretic separation. Derivatization can also be applied to link charged or hydrophobic groups at the reducing end to enhance glycan separation and mass-spectrometric detection. Moreover, derivatization steps such as permethylation aim at stabilizing sialic acid residues, enhancing mass-spectrometric sensitivity, and supporting detailed structural characterization by (tandem) mass spectrometry. Finally, many glycan labels serve as a linker for oligosaccharide attachment to surfaces or carrier proteins, thereby allowing interaction studies with carbohydrate-binding proteins. In this review, various aspects of glycan labeling, separation, and detection strategies are discussed.
Collapse
Affiliation(s)
- L. R. Ruhaak
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300RC Leiden, The Netherlands
| | - G. Zauner
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300RC Leiden, The Netherlands
| | - C. Huhn
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300RC Leiden, The Netherlands
| | - C. Bruggink
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300RC Leiden, The Netherlands
| | - A. M. Deelder
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300RC Leiden, The Netherlands
| | - M. Wuhrer
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300RC Leiden, The Netherlands
| |
Collapse
|
35
|
Bowman MJ, Zaia J. Comparative glycomics using a tetraplex stable-isotope coded tag. Anal Chem 2010; 82:3023-31. [PMID: 20230064 DOI: 10.1021/ac100108w] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This study illustrates the utility of tetraplex stable isotope coded tags in mass spectrometric glycomics using three carbohydrate classes. The teteraplex tags allow for the direct comparison of glycan compositions within four samples using capillary scale hydrophilic interaction chromatography with online mass spectrometry. In addition, the ability to discern glycan structural isomers is shown based on the tandem mass spectra of each composition using nanospray ionization. Results are shown for chondroitin sulfate proteoglycans, low molecular weight heparins, full length heparins, and N-glycans from alpha-1-acid glycoproteins from four mammalian species. The data demonstrate the value of the tetraplex stable isotope tagging approach for producing high-quality glycomics compositional profiling and fine structural analysis.
Collapse
Affiliation(s)
- Michael J Bowman
- Boston University School of Medicine, Department of Biochemistry, Center for Biomedical Mass Spectrometry, Boston, Massachusetts 02118, USA
| | | |
Collapse
|
36
|
Prien JM, Prater BD, Qin Q, Cockrill SL. Mass spectrometric-based stable isotopic 2-aminobenzoic acid glycan mapping for rapid glycan screening of biotherapeutics. Anal Chem 2010; 82:1498-508. [PMID: 20108906 DOI: 10.1021/ac902617t] [Citation(s) in RCA: 78] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fast, sensitive, robust methods for "high-level" glycan screening are necessary during various stages of a biotherapeutic product's lifecycle, including clone selection, process changes, and quality control for lot release testing. Traditional glycan screening involves chromatographic or electrophoretic separation-based methods, and, although reproducible, these methods can be time-consuming. Even ultrahigh-performance chromatographic and microfluidic integrated LC/MS systems, which work on the tens of minute time scale, become lengthy when hundreds of samples are to be analyzed. Comparatively, a direct infusion mass spectrometry (MS)-based glycan screening method acquires data on a millisecond time scale, exhibits exquisite sensitivity and reproducibility, and is amenable to automated peak annotation. In addition, characterization of glycan species via sequential mass spectrometry can be performed simultaneously. Here, we demonstrate a quantitative high-throughput MS-based mapping approach using stable isotope 2-aminobenzoic acid (2-AA) for rapid "high-level" glycan screening.
Collapse
Affiliation(s)
- Justin M Prien
- Analytical Sciences, Amgen, Inc., 4000 Nelson Rd., Longmont, Colorado 80503, USA.
| | | | | | | |
Collapse
|
37
|
Alley WR, Madera M, Mechref Y, Novotny MV. Chip-based reversed-phase liquid chromatography-mass spectrometry of permethylated N-linked glycans: a potential methodology for cancer-biomarker discovery. Anal Chem 2010; 82:5095-106. [PMID: 20491449 PMCID: PMC2910595 DOI: 10.1021/ac100131e] [Citation(s) in RCA: 129] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The study of protein glycosylation in biological fluids and tissues has substantial medical importance, as changes in glycan structures have now been associated with a number of diseases. Quantification of glycomic-profile changes is becoming increasingly important in the search for disease biomarkers. Here, we report a highly reproducible combination of a glycomic sample preparation/solid-phase derivatization of glycoprotein-derived N-linked glycans with their subsequent microchip-based separation and mass-spectrometric (MS) measurements. Following our previously described reductive beta-elimination for O-linked glycans with ammonia-borane complex to reduce N-linked structures, the N-linked alditol structures are effectively methylated in dimethylformamide medium to avoid artefacts in MS measurements. Reversed-phase microfluidic liquid chromatography (LC) of methylated N-linked oligosaccharide alditols resolved some closely related structures into regular retention increments, aiding in their structural assignments. Optimized LC gradients, together with nanospray MS, have been applied here in the quantitative measurements of N-linked glycans in blood serum, distinguishing breast cancer patients from control individuals.
Collapse
Affiliation(s)
- William R. Alley
- National Center for Glycomics and Glycoproteomics, Department of Chemistry, Indiana University, Bloomington, IN, USA 47405
| | - Milan Madera
- National Center for Glycomics and Glycoproteomics, Department of Chemistry, Indiana University, Bloomington, IN, USA 47405
| | - Yehia Mechref
- National Center for Glycomics and Glycoproteomics, Department of Chemistry, Indiana University, Bloomington, IN, USA 47405
- MetaCyt Biochemical Analysis Center, Department of Chemistry, Indiana University, Bloomington, IN, USA 47405
| | - Milos V. Novotny
- National Center for Glycomics and Glycoproteomics, Department of Chemistry, Indiana University, Bloomington, IN, USA 47405
| |
Collapse
|
38
|
Peš O, Preisler J. Off-line coupling of microcolumn separations to desorption mass spectrometry. J Chromatogr A 2010; 1217:3966-77. [DOI: 10.1016/j.chroma.2010.02.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 02/22/2010] [Accepted: 02/24/2010] [Indexed: 01/13/2023]
|
39
|
Hashii N, Kawasaki N, Itoh S, Nakajima Y, Harazono A, Kawanishi T, Yamaguchi T. Identification of glycoproteins carrying a target glycan-motif by liquid chromatography/multiple-stage mass spectrometry: identification of Lewis x-conjugated glycoproteins in mouse kidney. J Proteome Res 2009; 8:3415-29. [PMID: 19453144 DOI: 10.1021/pr9000527] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Certain glycan motifs in glycoproteins are involved in several biological events and diseases. To understand the roles of these motifs, a method is needed to identify the glycoproteins that carry them. We previously demonstrated that liquid chromatography-multiple-stage mass spectrometry (LC-MSn) allowed for differentiation of oligosaccharides attached to Lewis-motifs, such as Lewisx(Lex, Galbeta1-4(Fucalpha1-3)GlcNAc) from other glycans. We successfully discriminated Lex-conjugated oligosaccharides from other N-linked oligosaccharides derived from mouse kidney proteins by using Lewis-motif-distinctive ions, a deoxyhexose (dHex)+hexose (Hex)+N-acetylhexsosamine (HexNAc) fragment (m/z 512), and a Hex+HexNAc fragment (m/z 366). In the present study, we demonstrated that this method could be used to identify the Lex-conjugated glycoproteins. All proteins in the mouse kidney were digested into peptides, and the fucosylated glycopeptides were enriched by lectin-affinity chromatography. The resulting fucosylated glycopeptides were subjected to two different runs of LC-MSn using a Fourier- transform ion cyclotron resonance mass spectrometer (FTICR-MS) and an ion trap-type mass spectrometer. After the first run, we picked out product ion spectra of the expected Lex-conjugated glycopeptides based on the presence of Lewis-motif-distinctive ions and assigned a peptide+HexNAc or peptide+(dHex)HexNAc fragment in each spectrum. Then the fucosylated glycopeptides were subjected to a second run in which the peptide-related fragments were set as precursor ions. We successfully identified gamma-glutamyl transpeptidase 1 (gamma-GTP1), low-density lipoprotein receptor-related protein 2 (LRP2), and a cubilin precursor as Lex-conjugated glycoproteins by sequencing of 2-5 glycopeptides. In addition, it was deduced that cadherin 16, dipeptidase I, H-2 class I histocompatibility antigen, K-K alpha precursor (H2-Kk), and alanyl (membrane) aminopeptidase could be Lex-conjugated glycoproteins from the good agreement between the experimental and theoretical masses and fragment patterns. The results indicated that our method could be applicable for the identification and screening of glycoproteins carrying target glycan-motifs, such as Lewis epitopes.
Collapse
Affiliation(s)
- Noritaka Hashii
- Division of Biological Chemistry and Biologicals, National Institute of Health Sciences, 1-18-1 Kamiyouga, Setagaya-ku, Tokyo 158-8501, Japan
| | | | | | | | | | | | | |
Collapse
|
40
|
Xia B, Feasley CL, Sachdev GP, Smith DF, Cummings RD. Glycan reductive isotope labeling for quantitative glycomics. Anal Biochem 2009; 387:162-70. [PMID: 19454239 DOI: 10.1016/j.ab.2009.01.028] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2008] [Revised: 01/16/2009] [Accepted: 01/19/2009] [Indexed: 12/12/2022]
Abstract
Many diseases and disorders are characterized by quantitative and/or qualitative changes in complex carbohydrates. Mass spectrometry methods show promise in monitoring and detecting these important biological changes. Here we report a new glycomics method, termed glycan reductive isotope labeling (GRIL), where free glycans are derivatized by reductive amination with the differentially coded stable isotope tags [(12)C(6)]aniline and [(13)C(6)]aniline. These dual-labeled aniline-tagged glycans can be recovered by reverse-phase chromatography and can be quantified based on ultraviolet (UV) absorbance and relative ion abundances. Unlike previously reported isotopically coded reagents for glycans, GRIL does not contain deuterium, which can be chromatographically resolved. Our method shows no chromatographic resolution of differentially labeled glycans. Mixtures of differentially tagged glycans can be directly compared and quantified using mass spectrometric techniques. We demonstrate the use of GRIL to determine relative differences in glycan amount and composition. We analyze free glycans and glycans enzymatically or chemically released from a variety of standard glycoproteins, as well as human and mouse serum glycoproteins, using this method. This technique allows linear relative quantitation of glycans over a 10-fold concentration range and can accurately quantify sub-picomole levels of released glycans, providing a needed advancement in the field of glycomics.
Collapse
Affiliation(s)
- Baoyun Xia
- Department of Biochemistry and Glycomics Center at Emory University, Emory University School of Medicine, Atlanta, GA 30322, USA
| | | | | | | | | |
Collapse
|