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Kundalia PH, Pažitná L, Kianičková K, Jáné E, Lorencová L, Katrlík J. A Holistic 4D Approach to Optimize Intrinsic and Extrinsic Factors Contributing to Variability in Microarray Biosensing in Glycomics. SENSORS (BASEL, SWITZERLAND) 2023; 23:5362. [PMID: 37420529 DOI: 10.3390/s23125362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/27/2023] [Accepted: 06/04/2023] [Indexed: 07/09/2023]
Abstract
Protein-carbohydrate interactions happen to be a crucial facet of biology, discharging a myriad of functions. Microarrays have become a premier choice to discern the selectivity, sensitivity and breadth of these interactions in a high-throughput manner. The precise recognition of target glycan ligands among the plethora of others is central for any glycan-targeting probe being tested by microarray analyses. Ever since the introduction of the microarray as an elemental tool for high-throughput glycoprofiling, numerous distinct array platforms possessing different customizations and assemblies have been developed. Accompanying these customizations are various factors ushering variances across array platforms. In this primer, we investigate the influence of various extrinsic factors, namely printing parameters, incubation procedures, analyses and array storage conditions on the protein-carbohydrate interactions and evaluate these factors for the optimal performance of microarray glycomics analysis. We hereby propose a 4D approach (Design-Dispense-Detect-Deduce) to minimize the effect of these extrinsic factors on glycomics microarray analyses and thereby streamline cross-platform analyses and comparisons. This work will aid in optimizing microarray analyses for glycomics, minimize cross-platform disparities and bolster the further development of this technology.
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Affiliation(s)
- Paras H Kundalia
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, SK-84538 Bratislava, Slovakia
| | - Lucia Pažitná
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, SK-84538 Bratislava, Slovakia
| | - Kristína Kianičková
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, SK-84538 Bratislava, Slovakia
| | - Eduard Jáné
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, SK-84538 Bratislava, Slovakia
| | - Lenka Lorencová
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, SK-84538 Bratislava, Slovakia
| | - Jaroslav Katrlík
- Department of Glycobiotechnology, Institute of Chemistry, Slovak Academy of Sciences, SK-84538 Bratislava, Slovakia
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2
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Ang ME, Cowley JM, Yap K, Hahn MG, Mikkelsen D, Tucker MR, Williams BA, Burton RA. Novel constituents of Salvia hispanica L. (chia) nutlet mucilage and the improved in vitro fermentation of nutlets when ground. Food Funct 2023; 14:1401-1414. [PMID: 36637177 DOI: 10.1039/d2fo03002k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Upon wetting, chia (Salvia hispanica L.) nutlets produce a gel-like capsule of polysaccharides called mucilage that comprises a significant part of their dietary fibre content. Seed/nutlet mucilage is often used as a texture modifying hydrocolloid and bulking dietary fibre due to its water-binding ability, though the utility of mucilage from different sources is highly structure-function dependent. The composition and structure of chia nutlet mucilage is poorly defined, and a better understanding will aid in exploiting its dietary fibre functionality, particularly if, and how, it is utilised by gut microbiota. In this study, microscopy, chromatography, mass spectrometry and glycome profiling techniques showed that chia nutlet mucilage is highly complex, layered, and contains several polymer types. The mucilage comprises a novel xyloamylose containing both β-linked-xylose and α-linked-glucose, a near-linear xylan that may be sparsely substituted, a modified cellulose domain, and abundant alcohol-soluble oligosaccharides. To assess the dietary fibre functionality of chia nutlet mucilage, an in vitro cumulative gas production technique was used to determine the fermentability of different chia nutlet preparations. The complex nature of chia nutlet mucilage led to poor fermentation where the oligosaccharides appeared to be the only fermentable substrate present in the mucilage. Of note, ground chia nutlets were better fermented than intact whole nutlets, as judged by short chain fatty acid production. Therefore, it is suggested that the benefits of eating chia as a "superfood", could be notably enhanced if the nutlets are ground rather than being consumed whole, improving the bioaccessibility of key nutrients including dietary fibre.
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Affiliation(s)
- Main Ern Ang
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA 5064, Australia.
| | - James M Cowley
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA 5064, Australia.
| | - Kuok Yap
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA 5064, Australia.
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd, Athens, GA 30602, USA
| | - Deirdre Mikkelsen
- The University of Queensland, Australian Research Council Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, St Lucia, QLD 4072, Australia.,School of Agriculture and Food Sciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Matthew R Tucker
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA 5064, Australia.
| | - Barbara A Williams
- The University of Queensland, Australian Research Council Centre of Excellence in Plant Cell Walls, Centre for Nutrition and Food Sciences, Queensland Alliance for Agriculture and Food Innovation, St Lucia, QLD 4072, Australia
| | - Rachel A Burton
- School of Agriculture, Food and Wine, University of Adelaide, Glen Osmond, SA 5064, Australia.
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3
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Silva CJ, Adaskaveg JA, Mesquida-Pesci SD, Ortega-Salazar IB, Pattathil S, Zhang L, Hahn MG, van Kan JAL, Cantu D, Powell ALT, Blanco-Ulate B. Botrytis cinerea infection accelerates ripening and cell wall disassembly to promote disease in tomato fruit. PLANT PHYSIOLOGY 2023; 191:575-590. [PMID: 36053186 PMCID: PMC9806607 DOI: 10.1093/plphys/kiac408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 08/09/2022] [Indexed: 06/15/2023]
Abstract
Postharvest fungal pathogens benefit from the increased host susceptibility that occurs during fruit ripening. In unripe fruit, pathogens often remain quiescent and unable to cause disease until ripening begins, emerging at this point into destructive necrotrophic lifestyles that quickly result in fruit decay. Here, we demonstrate that one such pathogen, Botrytis cinerea, actively induces ripening processes to facilitate infections and promote disease in tomato (Solanum lycopersicum). Assessments of ripening progression revealed that B. cinerea accelerated external coloration, ethylene production, and softening in unripe fruit, while mRNA sequencing of inoculated unripe fruit confirmed the corresponding upregulation of host genes involved in ripening processes, such as ethylene biosynthesis and cell wall degradation. Furthermore, an enzyme-linked immunosorbent assay (ELISA)-based glycomics technique used to assess fruit cell wall polysaccharides revealed remarkable similarities in the cell wall polysaccharide changes caused by both infections of unripe fruit and ripening of healthy fruit, particularly in the increased accessibility of pectic polysaccharides. Virulence and additional ripening assessment experiments with B. cinerea knockout mutants showed that induction of ripening depends on the ability to infect the host and break down pectin. The B. cinerea double knockout Δbc polygalacturonase1 Δbc polygalacturonase2 lacking two critical pectin degrading enzymes was incapable of emerging from quiescence even long after the fruit had ripened at its own pace, suggesting that the failure to accelerate ripening severely inhibits fungal survival on unripe fruit. These findings demonstrate that active induction of ripening in unripe tomato fruit is an important infection strategy for B. cinerea.
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Affiliation(s)
- Christian J Silva
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Jaclyn A Adaskaveg
- Department of Plant Sciences, University of California, Davis, California, USA
| | | | | | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
- Mascoma LLC (Lallemand, Inc.), Lebanon, New Hampshire 03766, USA
| | - Lisha Zhang
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
- Center of Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Jan A L van Kan
- Laboratory of Phytopathology, Wageningen University, Wageningen, The Netherlands
| | - Dario Cantu
- Department of Viticulture and Enology, University of California, Davis, California, USA
| | - Ann L T Powell
- Department of Plant Sciences, University of California, Davis, California, USA
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4
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Ruprecht C, Blaukopf M, Pfrengle F. Synthetic fragments of plant polysaccharides as tools for cell wall biology. Curr Opin Chem Biol 2022; 71:102208. [PMID: 36108403 DOI: 10.1016/j.cbpa.2022.102208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 08/08/2022] [Accepted: 08/09/2022] [Indexed: 01/27/2023]
Abstract
A sustainable bioeconomy that includes increased agricultural productivity and new technologies to convert renewable biomass to value-added products may help meet the demands of a growing world population for food, energy and materials. The potential use of plant biomass is determined by the properties of the cell walls, consisting of polysaccharides, proteins, and the polyphenolic polymer lignin. Comprehensive knowledge of cell wall glycan structure and biosynthesis is therefore essential for optimal utilization. However, several areas of plant cell wall research are hampered by a lack of available pure oligosaccharide samples that represent structural features of cell wall glycans. Here, we provide an update on recent chemical syntheses of plant cell wall oligosaccharides and their application in characterizing plant cell wall-directed antibodies and carbohydrate-active enzymes including glycosyltransferases and glycosyl hydrolases, with a particular focus on glycan array technology.
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Affiliation(s)
- Colin Ruprecht
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Markus Blaukopf
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria
| | - Fabian Pfrengle
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Muthgasse 18, 1190 Vienna, Austria.
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5
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Affiliation(s)
- Xiaona Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
| | - You Yang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, Engineering Research Center of Pharmaceutical Process Chemistry, Ministry of Education School of Pharmacy, East China University of Science and Technology 130 Meilong Road Shanghai 200237 China
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6
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Understanding the structure and composition of recalcitrant oligosaccharides in hydrolysate using high-throughput biotin-based glycome profiling and mass spectrometry. Sci Rep 2022; 12:2521. [PMID: 35169269 PMCID: PMC8847591 DOI: 10.1038/s41598-022-06530-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 01/24/2022] [Indexed: 11/18/2022] Open
Abstract
Novel Immunological and Mass Spectrometry Methods for Comprehensive Analysis of Recalcitrant Oligosaccharides in AFEX Pretreated Corn Stover. Lignocellulosic biomass is a sustainable alternative to fossil fuel and is extensively used for developing bio-based technologies to produce products such as food, feed, fuel, and chemicals. The key to these technologies is to develop cost competitive processes to convert complex carbohydrates present in plant cell wall to simple sugars such as glucose, xylose, and arabinose. Since lignocellulosic biomass is highly recalcitrant, it must undergo a combination of thermochemical treatment such as Ammonia Fiber Expansion (AFEX), dilute acid (DA), Ionic Liquid (IL) and biological treatment such as enzyme hydrolysis and microbial fermentation to produce desired products. However, when using commercial fungal enzymes during hydrolysis, only 75–85% of the soluble sugars generated are monomeric sugars, while the remaining 15–25% are soluble recalcitrant oligosaccharides that cannot be easily utilized by microorganisms. Previously, we successfully separated and purified the soluble recalcitrant oligosaccharides using a combination of charcoal and celite-based separation followed by size exclusion chromatography and studies their inhibitory properties on enzymes. We discovered that the oligosaccharides with higher degree of polymerization (DP) containing methylated uronic acid substitutions were more recalcitrant towards commercial enzyme mixtures than lower DP and neutral oligosaccharides. Here, we report the use of several complementary techniques that include glycome profiling using plant biomass glycan specific monoclonal antibodies (mAbs) to characterize sugar linkages in plant cell walls and enzymatic hydrolysate, matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) using structurally-informative diagnostic peaks offered by negative ion post-secondary decay spectra, gas chromatography followed by mass spectrometry (GC–MS) to characterize oligosaccharide sugar linkages with and without derivatization. Since oligosaccharides (DP 4–20) are small, it is challenging to mobilize these molecules for mAbs binding and characterization. To overcome this problem, we have applied a new biotin-coupling based oligosaccharide immobilization method that successfully tagged most of the low DP soluble oligosaccharides on to a micro-plate surface followed by specific linkage analysis using mAbs in a high-throughput system. This new approach will help develop more advanced versions of future high throughput glycome profiling methods that can be used to separate and characterize oligosaccharides present in biomarkers for diagnostic applications.
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7
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Ruprecht C, Pfrengle F. Synthetic Plant Glycan Microarrays as Tools for Plant Biology. Methods Mol Biol 2022; 2460:115-125. [PMID: 34972933 DOI: 10.1007/978-1-0716-2148-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Chemically synthesized plant oligosaccharides have recently evolved as powerful molecular tools for plant cell wall biology. Synthetic plant glycan microarrays equipped with these oligosaccharides enable high-throughput analyses of glycan-binding proteins and carbohydrate-active enzymes. To produce these glycan microarrays, small amounts of glycan solution are printed on suitable surfaces for covalent or non-covalent immobilization. Synthetic plant glycan microarrays have been used for example to map the epitopes of plant cell wall-directed antibodies, to characterize glycosyl hydrolases and glycosyl transferases, and to analyze lectin binding. In this chapter, detailed experimental procedures for the production of synthetic glycan microarrays and their use for the characterization of cell wall glycan-directed antibodies are described.
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Affiliation(s)
- Colin Ruprecht
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Fabian Pfrengle
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.
- Department of Chemistry, University of Natural Resources and Life Sciences Vienna, Vienna, Austria.
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8
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Fittolani G, Tyrikos-Ergas T, Vargová D, Chaube MA, Delbianco M. Progress and challenges in the synthesis of sequence controlled polysaccharides. Beilstein J Org Chem 2021; 17:1981-2025. [PMID: 34386106 PMCID: PMC8353590 DOI: 10.3762/bjoc.17.129] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/22/2021] [Indexed: 01/15/2023] Open
Abstract
The sequence, length and substitution of a polysaccharide influence its physical and biological properties. Thus, sequence controlled polysaccharides are important targets to establish structure-properties correlations. Polymerization techniques and enzymatic methods have been optimized to obtain samples with well-defined substitution patterns and narrow molecular weight distribution. Chemical synthesis has granted access to polysaccharides with full control over the length. Here, we review the progress towards the synthesis of well-defined polysaccharides. For each class of polysaccharides, we discuss the available synthetic approaches and their current limitations.
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Affiliation(s)
- Giulio Fittolani
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Theodore Tyrikos-Ergas
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195 Berlin, Germany
| | - Denisa Vargová
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Manishkumar A Chaube
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
| | - Martina Delbianco
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany
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9
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Low KE, Xing X, Moote PE, Inglis GD, Venketachalam S, Hahn MG, King ML, Tétard-Jones CY, Jones DR, Willats WGT, Slominski BA, Abbott DW. Combinatorial Glycomic Analyses to Direct CAZyme Discovery for the Tailored Degradation of Canola Meal Non-Starch Dietary Polysaccharides. Microorganisms 2020; 8:microorganisms8121888. [PMID: 33260318 PMCID: PMC7761036 DOI: 10.3390/microorganisms8121888] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/17/2020] [Accepted: 11/20/2020] [Indexed: 12/12/2022] Open
Abstract
Canola meal (CM), the protein-rich by-product of canola oil extraction, has shown promise as an alternative feedstuff and protein supplement in poultry diets, yet its use has been limited due to the abundance of plant cell wall fibre, specifically non-starch polysaccharides (NSP) and lignin. The addition of exogenous enzymes to promote the digestion of CM NSP in chickens has potential to increase the metabolizable energy of CM. We isolated chicken cecal bacteria from a continuous-flow mini-bioreactor system and selected for those with the ability to metabolize CM NSP. Of 100 isolates identified, Bacteroides spp. and Enterococcus spp. were the most common species with these capabilities. To identify enzymes specifically for the digestion of CM NSP, we used a combination of glycomics techniques, including enzyme-linked immunosorbent assay characterization of the plant cell wall fractions, glycosidic linkage analysis (methylation-GC-MS analysis) of CM NSP and their fractions, bacterial growth profiles using minimal media supplemented with CM NSP, and the sequencing and de novo annotation of bacterial genomes of high-efficiency CM NSP utilizing bacteria. The SACCHARIS pipeline was used to select plant cell wall active enzymes for recombinant production and characterization. This approach represents a multidisciplinary innovation platform to bioprospect endogenous CAZymes from the intestinal microbiota of herbivorous and omnivorous animals which is adaptable to a variety of applications and dietary polysaccharides.
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Affiliation(s)
- Kristin E. Low
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (K.E.L.); (X.X.); (P.E.M.); (G.D.I.); (M.L.K.); (D.R.J.)
| | - Xiaohui Xing
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (K.E.L.); (X.X.); (P.E.M.); (G.D.I.); (M.L.K.); (D.R.J.)
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Paul E. Moote
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (K.E.L.); (X.X.); (P.E.M.); (G.D.I.); (M.L.K.); (D.R.J.)
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - G. Douglas Inglis
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (K.E.L.); (X.X.); (P.E.M.); (G.D.I.); (M.L.K.); (D.R.J.)
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Sivasankari Venketachalam
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (S.V.); (M.G.H.)
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Michael G. Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA; (S.V.); (M.G.H.)
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
| | - Marissa L. King
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (K.E.L.); (X.X.); (P.E.M.); (G.D.I.); (M.L.K.); (D.R.J.)
| | - Catherine Y. Tétard-Jones
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK; (C.Y.T.-J.); (W.G.T.W.)
| | - Darryl R. Jones
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (K.E.L.); (X.X.); (P.E.M.); (G.D.I.); (M.L.K.); (D.R.J.)
| | - William G. T. Willats
- School of Natural and Environmental Sciences, Newcastle University, Newcastle Upon Tyne NE1 7RU, UK; (C.Y.T.-J.); (W.G.T.W.)
| | - Bogdan A. Slominski
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada;
| | - D. Wade Abbott
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB T1J 4B1, Canada; (K.E.L.); (X.X.); (P.E.M.); (G.D.I.); (M.L.K.); (D.R.J.)
- Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Correspondence:
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10
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Ruprecht C, Bartetzko MP, Senf D, Lakhina A, Smith PJ, Soto MJ, Oh H, Yang J, Chapla D, Varon Silva D, Clausen MH, Hahn MG, Moremen KW, Urbanowicz BR, Pfrengle F. A Glycan Array‐Based Assay for the Identification and Characterization of Plant Glycosyltransferases. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202003105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Colin Ruprecht
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
- Present address: Department of Chemistry University of Natural Resources and Life Sciences Vienna Muthgasse 18 1190 Vienna Austria
| | - Max P. Bartetzko
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
- Institute of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Deborah Senf
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
- Institute of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Anna Lakhina
- Complex Carbohydrate Research Center University of Georgia 315 Riverbend Road Athens GA 30602 USA
| | - Peter J. Smith
- Complex Carbohydrate Research Center University of Georgia 315 Riverbend Road Athens GA 30602 USA
| | - Maria J. Soto
- Complex Carbohydrate Research Center University of Georgia 315 Riverbend Road Athens GA 30602 USA
- Present address: US Department of Energy Joint Genome Institute (JGI) Berkeley CA 94702 USA
| | - Hyunil Oh
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
- Institute of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
| | - Jeong‐Yeh Yang
- Complex Carbohydrate Research Center University of Georgia 315 Riverbend Road Athens GA 30602 USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center University of Georgia 315 Riverbend Road Athens GA 30602 USA
| | - Daniel Varon Silva
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
| | - Mads H. Clausen
- Center for Nanomedicine and Theranostics Department of Chemistry Technical University of Denmark Kemitorvet 207 2800 Kgs. Lyngby Denmark
| | - Michael G. Hahn
- Complex Carbohydrate Research Center University of Georgia 315 Riverbend Road Athens GA 30602 USA
| | - Kelley W. Moremen
- Complex Carbohydrate Research Center University of Georgia 315 Riverbend Road Athens GA 30602 USA
| | - Breeanna R. Urbanowicz
- Complex Carbohydrate Research Center University of Georgia 315 Riverbend Road Athens GA 30602 USA
| | - Fabian Pfrengle
- Department of Biomolecular Systems Max Planck Institute of Colloids and Interfaces Am Mühlenberg 1 14476 Potsdam Germany
- Institute of Chemistry and Biochemistry Freie Universität Berlin Arnimallee 22 14195 Berlin Germany
- Present address: Department of Chemistry University of Natural Resources and Life Sciences Vienna Muthgasse 18 1190 Vienna Austria
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11
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Ruprecht C, Bartetzko MP, Senf D, Lakhina A, Smith PJ, Soto MJ, Oh H, Yang J, Chapla D, Varon Silva D, Clausen MH, Hahn MG, Moremen KW, Urbanowicz BR, Pfrengle F. A Glycan Array-Based Assay for the Identification and Characterization of Plant Glycosyltransferases. Angew Chem Int Ed Engl 2020; 59:12493-12498. [PMID: 32396713 PMCID: PMC7383710 DOI: 10.1002/anie.202003105] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 04/22/2020] [Indexed: 12/19/2022]
Abstract
Growing plants with modified cell wall compositions is a promising strategy to improve resistance to pathogens, increase biomass digestibility, and tune other important properties. In order to alter biomass architecture, a detailed knowledge of cell wall structure and biosynthesis is a prerequisite. We report here a glycan array-based assay for the high-throughput identification and characterization of plant cell wall biosynthetic glycosyltransferases (GTs). We demonstrate that different heterologously expressed galactosyl-, fucosyl-, and xylosyltransferases can transfer azido-functionalized sugar nucleotide donors to selected synthetic plant cell wall oligosaccharides on the array and that the transferred monosaccharides can be visualized "on chip" by a 1,3-dipolar cycloaddition reaction with an alkynyl-modified dye. The opportunity to simultaneously screen thousands of combinations of putative GTs, nucleotide sugar donors, and oligosaccharide acceptors will dramatically accelerate plant cell wall biosynthesis research.
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Affiliation(s)
- Colin Ruprecht
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Present address: Department of ChemistryUniversity of Natural Resources and Life Sciences ViennaMuthgasse 181190ViennaAustria
| | - Max P. Bartetzko
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Deborah Senf
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Anna Lakhina
- Complex Carbohydrate Research CenterUniversity of Georgia315 Riverbend RoadAthensGA30602USA
| | - Peter J. Smith
- Complex Carbohydrate Research CenterUniversity of Georgia315 Riverbend RoadAthensGA30602USA
| | - Maria J. Soto
- Complex Carbohydrate Research CenterUniversity of Georgia315 Riverbend RoadAthensGA30602USA
- Present address: US Department of Energy Joint Genome Institute (JGI)BerkeleyCA94702USA
| | - Hyunil Oh
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
| | - Jeong‐Yeh Yang
- Complex Carbohydrate Research CenterUniversity of Georgia315 Riverbend RoadAthensGA30602USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research CenterUniversity of Georgia315 Riverbend RoadAthensGA30602USA
| | - Daniel Varon Silva
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
| | - Mads H. Clausen
- Center for Nanomedicine and TheranosticsDepartment of ChemistryTechnical University of DenmarkKemitorvet 2072800 Kgs.LyngbyDenmark
| | - Michael G. Hahn
- Complex Carbohydrate Research CenterUniversity of Georgia315 Riverbend RoadAthensGA30602USA
| | - Kelley W. Moremen
- Complex Carbohydrate Research CenterUniversity of Georgia315 Riverbend RoadAthensGA30602USA
| | - Breeanna R. Urbanowicz
- Complex Carbohydrate Research CenterUniversity of Georgia315 Riverbend RoadAthensGA30602USA
| | - Fabian Pfrengle
- Department of Biomolecular SystemsMax Planck Institute of Colloids and InterfacesAm Mühlenberg 114476PotsdamGermany
- Institute of Chemistry and BiochemistryFreie Universität BerlinArnimallee 2214195BerlinGermany
- Present address: Department of ChemistryUniversity of Natural Resources and Life Sciences ViennaMuthgasse 181190ViennaAustria
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12
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Pfrengle F. Automated Glycan Assembly of Plant Cell Wall Oligosaccharides. Methods Mol Biol 2020; 2149:503-512. [PMID: 32617953 DOI: 10.1007/978-1-0716-0621-6_28] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Synthetic cell wall oligosaccharides are promising molecular tools for investigating the structure and function of plant cell walls. Their well-defined structure and high purity prevents misinterpretations of experimental data, and the possibility to introduce chemical handles provides means for easier localization and detection. Automated glycan assembly as emerged has a powerful new method for the efficient preparation of oligosaccharide libraries. We recently made use of this technology to prepare a collection of plant cell wall glycans for cell wall research. In this chapter, detailed experimental procedures for the automated synthesis of oligosaccharides that are ready for use in biological assays are described.
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Affiliation(s)
- Fabian Pfrengle
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.
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13
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Prabhakar PK, Wang HT, Smith PJ, Yang JY, Barnes WJ, Peña MJ, Moremen KW, Urbanowicz BR. Heterologous expression of plant glycosyltransferases for biochemistry and structural biology. Methods Cell Biol 2020; 160:145-165. [PMID: 32896313 PMCID: PMC7593805 DOI: 10.1016/bs.mcb.2020.05.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
Much of the carbon captured by photosynthesis is converted into the polysaccharides that constitute plant cell walls. These complex macrostructures are composed of cellulose, hemicellulose, and pectins, together with small amounts of structural proteins, minerals, and in many cases lignin. Wall components assemble and interact with one another to produce dynamic structures with many capabilities, including providing mechanical support to plant structures and determining plant cell shape and size. Despite their abundance, major gaps in our knowledge of the synthesis of the building blocks of these polymers remain, largely due to ineffective methods for expression and purification of active synthetic enzymes for in vitro biochemical analyses. The hemicellulosic polysaccharide, xyloglucan, comprises up to 25% of the dry weight of primary cell walls in plants. Most of the knowledge about the glycosyltransferases (GTs) involved in the xyloglucan biosynthetic pathway has been derived from the identification and carbohydrate analysis of knockout mutants, lending little information on how the catalytic biosynthesis of xyloglucan occurs in planta. In this chapter we describe methods for the heterologous expression of plant GTs using the HEK293 expression platform. As a demonstration of the utility of this platform, nine xyloglucan-relevant GTs from three different CAZy families were evaluated, and methods for expression, purification, and construct optimization are described for biochemical and structural characterization.
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Affiliation(s)
- Pradeep K Prabhakar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, United States
| | - Hsin-Tzu Wang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, United States
| | - Peter J Smith
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, United States
| | - Jeong-Yeh Yang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - William J Barnes
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Maria J Peña
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, United States
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Breeanna R Urbanowicz
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States; Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States; Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, United States.
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14
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Ruprecht C, Geissner A, Seeberger PH, Pfrengle F. Practical considerations for printing high-density glycan microarrays to study weak carbohydrate-protein interactions. Carbohydr Res 2019; 481:31-35. [PMID: 31228654 DOI: 10.1016/j.carres.2019.06.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/03/2019] [Accepted: 06/12/2019] [Indexed: 12/22/2022]
Abstract
Interactions of carbohydrates and proteins are essential for many biological processes and glycan microarrays have emerged as powerful tools to rapidly assess these carbohydrate-protein interactions. Diverse platforms to immobilize glycans on glass slides for subsequent probing of the specificities of glycan-binding proteins (GBPs) have evolved. It has been suggested that high local glycan density on microarrays is crucial for detecting low-affinity interactions. To determine the influence of printing efficacy on GBP binding, we compared N-hydroxyl succinimide (NHS)-ester activated glass slides from three different manufacturers and evaluated two different printing buffers. Large differences in binding efficacies of Concanavalin A, peanut agglutinin, and Ricinus communis agglutinin 120 were observed. On some slides, low affinity interactions were missed altogether. Addition of polyethylenglycol (PEG) 400 to the printing buffer significantly enhanced the sensitivity of the binding assays. After monitoring printing efficacy over prolonged printing times, substantial effects resulting from progressing hydrolysis of the NHS-esters during the printing run on one type of slides were found. Printing efficiency of glycans strongly depends on the type of NHS-ester activated slides, the printing buffer, and the printing time. We provide practical advice for selecting the right printing conditions for particular applications.
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Affiliation(s)
- Colin Ruprecht
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Andreas Geissner
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Fabian Pfrengle
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany; Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany.
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15
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Le Mai Hoang K, Pardo-Vargas A, Zhu Y, Yu Y, Loria M, Delbianco M, Seeberger PH. Traceless Photolabile Linker Expedites the Chemical Synthesis of Complex Oligosaccharides by Automated Glycan Assembly. J Am Chem Soc 2019; 141:9079-9086. [PMID: 31091089 PMCID: PMC6750752 DOI: 10.1021/jacs.9b03769] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Automated glycan
assembly (AGA) aims at accelerating access to
synthetic oligosaccharides to meet the demand for defined glycans
as tools for molecular glycobiology. The linkers used to connect the
growing glycan chain to the solid support play a pivotal role in the
synthesis strategy as they determine all chemical conditions used
during the synthesis and the form of the glycan obtained at the end
of it. Here, we describe a traceless photolabile linker used to prepare
carbohydrates with a free reducing end. Modification of the o-nitrobenzyl scaffold of the linker is key to high yields
and compatibility with the AGA workflow. The assembly of an asymmetrical
biantennary N-glycan from oligosaccharide fragments
prepared by AGA and linear as well as branched β-oligoglucans
is described to illustrate the power of the method. These substrates
will serve as standards and biomarkers to examine the unique specificity
of glycosyl hydrolases.
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Affiliation(s)
- Kim Le Mai Hoang
- Department of Biomolecular Systems , Max-Planck-Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany
| | - Alonso Pardo-Vargas
- Department of Biomolecular Systems , Max-Planck-Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany.,Institute of Chemistry and Biochemistry , Freie Universität Berlin , Arnimallee 22 , 14195 Berlin , Germany
| | - Yuntao Zhu
- Department of Biomolecular Systems , Max-Planck-Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany
| | - Yang Yu
- Department of Biomolecular Systems , Max-Planck-Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany.,Institute of Chemistry and Biochemistry , Freie Universität Berlin , Arnimallee 22 , 14195 Berlin , Germany
| | - Mirco Loria
- Institute of Chemistry and Biochemistry , Freie Universität Berlin , Arnimallee 22 , 14195 Berlin , Germany
| | - Martina Delbianco
- Department of Biomolecular Systems , Max-Planck-Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems , Max-Planck-Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany.,Institute of Chemistry and Biochemistry , Freie Universität Berlin , Arnimallee 22 , 14195 Berlin , Germany
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16
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Okekeogbu IO, Pattathil S, González Fernández-Niño SM, Aryal UK, Penning BW, Lao J, Heazlewood JL, Hahn MG, McCann MC, Carpita NC. Glycome and Proteome Components of Golgi Membranes Are Common between Two Angiosperms with Distinct Cell-Wall Structures. THE PLANT CELL 2019; 31:1094-1112. [PMID: 30914498 PMCID: PMC6533026 DOI: 10.1105/tpc.18.00755] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 02/28/2019] [Accepted: 03/24/2019] [Indexed: 05/20/2023]
Abstract
The plant endoplasmic reticulum-Golgi apparatus is the site of synthesis, assembly, and trafficking of all noncellulosic polysaccharides, proteoglycans, and proteins destined for the cell wall. As grass species make cell walls distinct from those of dicots and noncommelinid monocots, it has been assumed that the differences in cell-wall composition stem from differences in biosynthetic capacities of their respective Golgi. However, immunosorbence-based screens and carbohydrate linkage analysis of polysaccharides in Golgi membranes, enriched by flotation centrifugation from etiolated coleoptiles of maize (Zea mays) and leaves of Arabidopsis (Arabidopsis thaliana), showed that arabinogalactan-proteins and arabinans represent substantial portions of the Golgi-resident polysaccharides not typically found in high abundance in cell walls of either species. Further, hemicelluloses accumulated in Golgi at levels that contrasted with those found in their respective cell walls, with xyloglucans enriched in maize Golgi, and xylans enriched in Arabidopsis. Consistent with this finding, maize Golgi membranes isolated by flotation centrifugation and enriched further by free-flow electrophoresis, yielded >200 proteins known to function in the biosynthesis and metabolism of cell-wall polysaccharides common to all angiosperms, and not just those specific to cell-wall type. We propose that the distinctive compositions of grass primary cell walls compared with other angiosperms result from differential gating or metabolism of secreted polysaccharides post-Golgi by an as-yet unknown mechanism, and not necessarily by differential expression of genes encoding specific synthase complexes.
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Affiliation(s)
- Ikenna O Okekeogbu
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | | | | | - Bryan W Penning
- U.S. Department of Agriculture, Agricultural Research Service, Corn, Soybean and Wheat Quality Research, Wooster, Ohio 44691
| | - Jeemeng Lao
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Joshua L Heazlewood
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
| | - Maureen C McCann
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
| | - Nicholas C Carpita
- Department of Botany & Plant Pathology, Purdue University, West Lafayette, Indiana 47907
- Department of Biological Sciences, Purdue University, West Lafayette, Indiana 47907
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907
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17
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Abstract
The intrinsic complexity of carbohydrate structures has hampered access to pure glycans and hence impeded progress in the glycosciences. Automated Glycan Assembly (AGA) has facilitated the procurement of synthetic glycans, to be used in diagnostics, vaccine development, enzyme characterization and structure-function relationship studies. A general approach for obtaining complex glycans from mammalian, bacterial, fungal and plant classes provides molecular tools for glycobiology research. Recent advances in AGA technology pave the way for the production of novel carbohydrate materials. This perspective describes the state-of-the art of AGA and aspects of the technology where additional improvements are needed.
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Affiliation(s)
- Mónica Guberman
- Department of Biomolecular Systems , Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany.,Department of Chemistry and Biochemistry , Freie Universität Berlin , Arnimalle 22 , 14195 Berlin , Germany
| | - Peter H Seeberger
- Department of Biomolecular Systems , Max Planck Institute of Colloids and Interfaces , Am Mühlenberg 1 , 14476 Potsdam , Germany
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18
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Wilkop T, Pattathil S, Ren G, Davis DJ, Bao W, Duan D, Peralta AG, Domozych DS, Hahn MG, Drakakaki G. A Hybrid Approach Enabling Large-Scale Glycomic Analysis of Post-Golgi Vesicles Reveals a Transport Route for Polysaccharides. THE PLANT CELL 2019; 31:627-644. [PMID: 30760563 PMCID: PMC6482635 DOI: 10.1105/tpc.18.00854] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Revised: 01/22/2019] [Accepted: 02/12/2019] [Indexed: 05/10/2023]
Abstract
The plant endomembrane system facilitates the transport of polysaccharides, associated enzymes, and glycoproteins through its dynamic pathways. Although enzymes involved in cell wall biosynthesis have been identified, little is known about the endomembrane-based transport of glycan components. This is partially attributed to technical challenges in biochemically determining polysaccharide cargo in specific vesicles. Here, we introduce a hybrid approach addressing this limitation. By combining vesicle isolation with a large-scale carbohydrate antibody arraying technique, we charted an initial large-scale map describing the glycome profile of the SYNTAXIN OF PLANTS61 (SYP61) trans-Golgi network compartment in Arabidopsis (Arabidopsis thaliana). A library of antibodies recognizing specific noncellulosic carbohydrate epitopes allowed us to identify a range of diverse glycans, including pectins, xyloglucans (XyGs), and arabinogalactan proteins in isolated vesicles. Changes in XyG- and pectin-specific epitopes in the cell wall of an Arabidopsis SYP61 mutant corroborate our findings. Our data provide evidence that SYP61 vesicles are involved in the transport and deposition of structural polysaccharides and glycoproteins. Adaptation of our methodology can enable studies characterizing the glycome profiles of various vesicle populations in plant and animal systems and their respective roles in glycan transport defined by subcellular markers, developmental stages, or environmental stimuli.
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Affiliation(s)
- Thomas Wilkop
- Department of Plant Sciences, University of California, Davis, California 95616
- Light Microscopy Core, University of Kentucky, Lexington, Kentucky 40536
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712
| | - Guangxi Ren
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Destiny J Davis
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Wenlong Bao
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Dechao Duan
- Department of Plant Sciences, University of California, Davis, California 95616
| | - Angelo G Peralta
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712
| | - David S Domozych
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York 12866
| | - Michael G Hahn
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602-4712
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602-7271
| | - Georgia Drakakaki
- Department of Plant Sciences, University of California, Davis, California 95616
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19
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Bartetzko MP, Pfrengle F. Automated Glycan Assembly of Plant Oligosaccharides and Their Application in Cell-Wall Biology. Chembiochem 2019; 20:877-885. [PMID: 30427113 DOI: 10.1002/cbic.201800641] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Indexed: 12/12/2022]
Abstract
The plant cell wall provides the richest available resource of fermentable carbohydrates and biobased materials. The main component of plant cell walls is cellulose, which is the most abundant biomolecule on earth. Apart from cellulose, which is constructed from relatively simple β-1,4-glucan chains, plant cell walls also contain structurally more complex heteropolysaccharides (hemicellulose and pectin), as well as lignin and cell-wall proteins. A detailed understanding of the molecular structures, functions, and biosyntheses of cell-wall components is required to further promote their industrial use. Plant cell-wall research is, to a large degree, hampered by a lsack of available well-defined oligosaccharide samples that represent the structural features of cell-wall glycans. One technique to access these oligosaccharides is automated glycan assembly; a technique in which monosaccharide building blocks are, similarly to automated peptide and oligonucleotide chemistry, successively added to a linker-functionalized resin in a fully automated manner. Herein, recent research into the automated glycan assembly of different classes of cell-wall glycans used as molecular tools for cell-wall biology is discussed. More than 60 synthetic oligosaccharides were prepared and printed as microarrays for screening monoclonal antibodies that recognize plant cell-wall polysaccharides. The synthesized oligosaccharides have also been used to investigate glycosyltransferases and glycoside hydrolases, which are involved in synthesis and degradation of plant cell walls, as well as for the analysis of cell-wall-remodeling enzymes.
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Affiliation(s)
- Max P Bartetzko
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Fabian Pfrengle
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
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20
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da Costa RMF, Pattathil S, Avci U, Winters A, Hahn MG, Bosch M. Desirable plant cell wall traits for higher-quality miscanthus lignocellulosic biomass. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:85. [PMID: 31011368 PMCID: PMC6463665 DOI: 10.1186/s13068-019-1426-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 04/05/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Lignocellulosic biomass from dedicated energy crops such as Miscanthus spp. is an important tool to combat anthropogenic climate change. However, we still do not exactly understand the sources of cell wall recalcitrance to deconstruction, which hinders the efficient biorefining of plant biomass into biofuels and bioproducts. RESULTS We combined detailed phenotyping, correlation studies and discriminant analyses, to identify key significantly distinct variables between miscanthus organs, genotypes and most importantly, between saccharification performances. Furthermore, for the first time in an energy crop, normalised total quantification of specific cell wall glycan epitopes is reported and correlated with saccharification. CONCLUSIONS In stems, lignin has the greatest impact on recalcitrance. However, in leaves, matrix glycans and their decorations have determinant effects, highlighting the importance of biomass fine structures, in addition to more commonly described cell wall compositional features. The results of our interrogation of the miscanthus cell wall promote the concept that desirable cell wall traits for increased biomass quality are highly dependent on the target biorefining products. Thus, for the development of biorefining ideotypes, instead of a generalist miscanthus variety, more realistic and valuable approaches may come from defining a collection of specialised cultivars, adapted to specific conditions and purposes.
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Affiliation(s)
- Ricardo M. F. da Costa
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EE UK
- Present Address: Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Sivakumar Pattathil
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602-4712 USA
- Present Address: Mascoma LLC (Lallemand, Inc.), 67 Etna Road, Lebanon, NH 03766 USA
| | - Utku Avci
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602-4712 USA
- Present Address: Faculty of Engineering, Bioengineering Department, Recep Tayyip Erdogan University, 53100 Rize, Turkey
| | - Ana Winters
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EE UK
| | - Michael G. Hahn
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Rd., Athens, GA 30602-4712 USA
- DOE-BioEnergy Science Center (BESC), Oak Ridge National Laboratory, Oak Ridge, TN 37831 USA
| | - Maurice Bosch
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Plas Gogerddan, Aberystwyth, Ceredigion, SY23 3EE UK
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21
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Pardo-Vargas A, Delbianco M, Seeberger PH. Automated glycan assembly as an enabling technology. Curr Opin Chem Biol 2018; 46:48-55. [DOI: 10.1016/j.cbpa.2018.04.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Revised: 04/09/2018] [Accepted: 04/16/2018] [Indexed: 12/16/2022]
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22
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Panza M, Pistorio SG, Stine KJ, Demchenko AV. Automated Chemical Oligosaccharide Synthesis: Novel Approach to Traditional Challenges. Chem Rev 2018; 118:8105-8150. [PMID: 29953217 PMCID: PMC6522228 DOI: 10.1021/acs.chemrev.8b00051] [Citation(s) in RCA: 194] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Advances in carbohydrate chemistry have certainly made common oligosaccharides much more accessible. However, many current methods still rely heavily upon specialized knowledge of carbohydrate chemistry. The application of automated technologies to chemical and life science applications such as genomics and proteomics represents a vibrant field. These automated technologies also present opportunities for their application to organic synthesis, including that of the synthesis of oligosaccharides. However, application of automated methods to the synthesis of carbohydrates is an underdeveloped area as compared to other classes of biomolecules. The overarching goal of this review article is to present the advances that have been made at the interface of carbohydrate chemistry and automated technology.
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Affiliation(s)
- Matteo Panza
- Department of Chemistry and Biochemistry, University of Missouri–St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Salvatore G. Pistorio
- Department of Chemistry and Biochemistry, University of Missouri–St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Keith J. Stine
- Department of Chemistry and Biochemistry, University of Missouri–St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
| | - Alexei V. Demchenko
- Department of Chemistry and Biochemistry, University of Missouri–St. Louis, One University Boulevard, St. Louis, Missouri 63121, United States
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23
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Ruprecht C, Dallabernardina P, Smith PJ, Urbanowicz BR, Pfrengle F. Analyzing Xyloglucan Endotransglycosylases by Incorporating Synthetic Oligosaccharides into Plant Cell Walls. Chembiochem 2018; 19:793-798. [PMID: 29384258 DOI: 10.1002/cbic.201700638] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Indexed: 12/29/2022]
Abstract
The plant cell wall is a cellular exoskeleton consisting predominantly of a complex polysaccharide network that defines the shape of cells. During growth, this network can be loosened through the action of xyloglucan endotransglycosylases (XETs), glycoside hydrolases that "cut and paste" xyloglucan polysaccharides through a transglycosylation process. We have analyzed cohorts of XETs in different plant species to evaluate the substrate specificities of xyloglucan acceptors by using a set of synthetic oligosaccharides obtained by automated glycan assembly. The ability of XETs to incorporate the oligosaccharides into polysaccharides printed as microarrays and into stem sections of Arabidopsis thaliana, beans, and peas was assessed. We found that single xylose substitutions are sufficient for transfer, and xylosylation of the terminal glucose residue is not required by XETs, independent of plant species. To obtain information on the potential xylosylation pattern of the natural acceptor of XETs, that is, the nonreducing end of xyloglucan, we further tested the activity of xyloglucan xylosyl transferase (XXT) 2 on the synthetic xyloglucan oligosaccharides. These data shed light on inconsistencies between previous studies towards determining the acceptor substrate specificities of XETs and have important implications for further understanding plant cell wall polysaccharide synthesis and remodeling.
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Affiliation(s)
- Colin Ruprecht
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, 14195, Berlin, Germany
| | - Pietro Dallabernardina
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, 14195, Berlin, Germany
| | - Peter J Smith
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Breeanna R Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA, 30602, USA
| | - Fabian Pfrengle
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476, Potsdam, Germany.,Freie Universität Berlin, Institute of Chemistry and Biochemistry, Arnimallee 22, 14195, Berlin, Germany
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Rydahl MG, Hansen AR, Kračun SK, Mravec J. Report on the Current Inventory of the Toolbox for Plant Cell Wall Analysis: Proteinaceous and Small Molecular Probes. FRONTIERS IN PLANT SCIENCE 2018; 9:581. [PMID: 29774041 PMCID: PMC5943554 DOI: 10.3389/fpls.2018.00581] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/13/2018] [Indexed: 05/18/2023]
Abstract
Plant cell walls are highly complex structures composed of diverse classes of polysaccharides, proteoglycans, and polyphenolics, which have numerous roles throughout the life of a plant. Significant research efforts aim to understand the biology of this cellular organelle and to facilitate cell-wall-based industrial applications. To accomplish this, researchers need to be provided with a variety of sensitive and specific detection methods for separate cell wall components, and their various molecular characteristics in vitro as well as in situ. Cell wall component-directed molecular detection probes (in short: cell wall probes, CWPs) are an essential asset to the plant glycobiology toolbox. To date, a relatively large set of CWPs has been produced-mainly consisting of monoclonal antibodies, carbohydrate-binding modules, synthetic antibodies produced by phage display, and small molecular probes. In this review, we summarize the state-of-the-art knowledge about these CWPs; their classification and their advantages and disadvantages in different applications. In particular, we elaborate on the recent advances in non-conventional approaches to the generation of novel CWPs, and identify the remaining gaps in terms of target recognition. This report also highlights the addition of new "compartments" to the probing toolbox, which is filled with novel chemical biology tools, such as metabolic labeling reagents and oligosaccharide conjugates. In the end, we also forecast future developments in this dynamic field.
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Affiliation(s)
- Maja G. Rydahl
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Aleksander R. Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Stjepan K. Kračun
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- GlycoSpot IVS, Frederiksberg, Denmark
| | - Jozef Mravec
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
- *Correspondence: Jozef Mravec
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