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Okada T, Teramoto T, Ihara H, Ikeda Y, Kakuta Y. Crystal structure of mango α1,3/α1,4-fucosyltransferase elucidates unique elements that regulate Lewis A-dominant oligosaccharide assembly. Glycobiology 2024; 34:cwae015. [PMID: 38376259 DOI: 10.1093/glycob/cwae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 01/28/2024] [Accepted: 02/14/2024] [Indexed: 02/21/2024] Open
Abstract
In various organisms, α1,3/α1,4-fucosyltransferases (CAZy GT10 family enzymes) mediate the assembly of type I (Galβ1,3GlcNAc) and/or type II (Galβ1,4GlcNAc)-based Lewis structures that are widely distributed in glycoconjugates. Unlike enzymes of other species, plant orthologues show little fucosyltransferase activity for type II-based glycans and predominantly catalyze the assembly of the Lewis A structure [Galβ1,3(Fucα1,4)GlcNAc] on the type I disaccharide unit of their substrates. However, the structural basis underlying this unique substrate selectivity remains elusive. In this study, we investigated the structure-function relationship of MiFUT13A, a mango α1,3/α1,4-fucosyltransferase. The prepared MiFUT13A displayed distinct α1,4-fucosyltransferase activity. Consistent with the enzymatic properties of this molecule, X-ray crystallography revealed that this enzyme has a typical GT-B fold-type structure containing a set of residues that are responsible for its SN2-like catalysis. Site-directed mutagenesis and molecular docking analyses proposed a rational binding mechanism for type I oligosaccharides. Within the catalytic cleft, the pocket surrounding Trp121 serves as a binding site, anchoring the non-reducing terminal β1,3-galactose that belongs to the type I disaccharide unit. Furthermore, Glu177 was postulated to function as a general base catalyst through its interaction with the 4-hydroxy group of the acceptor N-acetylglucosamine residue. Adjacent residues, specifically Thr120, Thr157 and Asp175 were speculated to assist in binding of the reducing terminal residues. Intriguingly, these structural elements were not fully conserved in mammalian orthologue which also shows predominant α1,4-fucosyltransferase activity. In conclusion, we have proposed that MiFUT13A generates the Lewis A structure on type I glycans through a distinct mechanism, divergent from that of mammalian enzymes.
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Affiliation(s)
- Takahiro Okada
- Division of Molecular Cell Biology, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501, Japan
| | - Takamasa Teramoto
- Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Hideyuki Ihara
- Division of Molecular Cell Biology, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501, Japan
| | - Yoshitaka Ikeda
- Division of Molecular Cell Biology, Department of Biomolecular Sciences, Faculty of Medicine, Saga University, 5-1-1 Nabeshima, Saga 849-8501, Japan
| | - Yoshimitsu Kakuta
- Laboratory of Biophysical Chemistry, Department of Bioscience and Biotechnology, Faculty of Agriculture, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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2
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Chen MM, Kopittke PM, Zhao FJ, Wang P. Applications and opportunities of click chemistry in plant science. TRENDS IN PLANT SCIENCE 2024; 29:167-178. [PMID: 37612212 DOI: 10.1016/j.tplants.2023.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/29/2023] [Accepted: 07/19/2023] [Indexed: 08/25/2023]
Abstract
The Nobel Prize in Chemistry for 2022 was awarded to the pioneers of Lego-like 'click chemistry': combinatorial chemistry with remarkable modularity and diversity. It has been applied to a wide variety of biological systems, from microorganisms to plants and animals, including humans. Although click chemistry is a powerful chemical biology tool, comparatively few studies have examined its potential in plant science. Here, we review click chemistry reactions and their applications in plant systems, highlighting the activity-based probes and metabolic labeling strategies combined with bioorthogonal click chemistry to visualize plant biological processes. These applications offer new opportunities to explore and understand the underlying molecular mechanisms regulating plant composition, growth, metabolism, defense, and immune responses.
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Affiliation(s)
- Ming-Ming Chen
- Centre of Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peter M Kopittke
- School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Queensland, 4072, Australia
| | - Fang-Jie Zhao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Peng Wang
- Centre of Agriculture and Health, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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3
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Hrmova M, Zimmer J, Bulone V, Fincher GB. Enzymes in 3D: Synthesis, remodelling, and hydrolysis of cell wall (1,3;1,4)-β-glucans. PLANT PHYSIOLOGY 2023; 194:33-50. [PMID: 37594400 PMCID: PMC10762513 DOI: 10.1093/plphys/kiad415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 06/09/2023] [Indexed: 08/19/2023]
Abstract
Recent breakthroughs in structural biology have provided valuable new insights into enzymes involved in plant cell wall metabolism. More specifically, the molecular mechanism of synthesis of (1,3;1,4)-β-glucans, which are widespread in cell walls of commercially important cereals and grasses, has been the topic of debate and intense research activity for decades. However, an inability to purify these integral membrane enzymes or apply transgenic approaches without interpretative problems associated with pleiotropic effects has presented barriers to attempts to define their synthetic mechanisms. Following the demonstration that some members of the CslF sub-family of GT2 family enzymes mediate (1,3;1,4)-β-glucan synthesis, the expression of the corresponding genes in a heterologous system that is free of background complications has now been achieved. Biochemical analyses of the (1,3;1,4)-β-glucan synthesized in vitro, combined with 3-dimensional (3D) cryogenic-electron microscopy and AlphaFold protein structure predictions, have demonstrated how a single CslF6 enzyme, without exogenous primers, can incorporate both (1,3)- and (1,4)-β-linkages into the nascent polysaccharide chain. Similarly, 3D structures of xyloglucan endo-transglycosylases and (1,3;1,4)-β-glucan endo- and exohydrolases have allowed the mechanisms of (1,3;1,4)-β-glucan modification and degradation to be defined. X-ray crystallography and multi-scale modeling of a broad specificity GH3 β-glucan exohydrolase recently revealed a previously unknown and remarkable molecular mechanism with reactant trajectories through which a polysaccharide exohydrolase can act with a processive action pattern. The availability of high-quality protein 3D structural predictions should prove invaluable for defining structures, dynamics, and functions of other enzymes involved in plant cell wall metabolism in the immediate future.
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Affiliation(s)
- Maria Hrmova
- School of Agriculture, Food and Wine, and the Waite Research Institute, University of Adelaide, Glen Osmond, South Australia 5064, Australia
| | - Jochen Zimmer
- Howard Hughes Medical Institute and Department of Molecular Physiology and Biological Physics, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Vincent Bulone
- College of Medicine and Public Health, Flinders University, Bedford Park, South Australia 5042, Australia
- Division of Glycoscience, Department of Chemistry, KTH Royal Institute of Technology, Alba Nova University Centre, 106 91 Stockholm, Sweden
| | - Geoffrey B Fincher
- School of Agriculture, Food and Wine, and the Waite Research Institute, University of Adelaide, Glen Osmond, South Australia 5064, Australia
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4
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Kadirvelraj R, Boruah BM, Wang S, Chapla D, Huang C, Ramiah A, Hudson KL, Prudden AR, Boons GJ, Withers SG, Wood ZA, Moremen KW. Structural basis for Lewis antigen synthesis by the α1,3-fucosyltransferase FUT9. Nat Chem Biol 2023; 19:1022-1030. [PMID: 37202521 PMCID: PMC10726971 DOI: 10.1038/s41589-023-01345-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 04/20/2023] [Indexed: 05/20/2023]
Abstract
Mammalian cell surface and secreted glycoproteins exhibit remarkable glycan structural diversity that contributes to numerous physiological and pathogenic interactions. Terminal glycan structures include Lewis antigens synthesized by a collection of α1,3/4-fucosyltransferases (CAZy GT10 family). At present, the only available crystallographic structure of a GT10 member is that of the Helicobacter pylori α1,3-fucosyltransferase, but mammalian GT10 fucosyltransferases are distinct in sequence and substrate specificity compared with the bacterial enzyme. Here, we determined crystal structures of human FUT9, an α1,3-fucosyltransferase that generates Lewisx and Lewisy antigens, in complex with GDP, acceptor glycans, and as a FUT9-donor analog-acceptor Michaelis complex. The structures reveal substrate specificity determinants and allow prediction of a catalytic model supported by kinetic analyses of numerous active site mutants. Comparisons with other GT10 fucosyltransferases and GT-B fold glycosyltransferases provide evidence for modular evolution of donor- and acceptor-binding sites and specificity for Lewis antigen synthesis among mammalian GT10 fucosyltransferases.
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Affiliation(s)
- Renuka Kadirvelraj
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
| | - Bhargavi M Boruah
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Shuo Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Chin Huang
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Annapoorani Ramiah
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Kieran L Hudson
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Department of Chemistry, University of Georgia, Athens, GA, USA
| | - Stephen G Withers
- Department of Biochemistry and Molecular Biology, Department of Chemistry, University of British Columbia, Vancouver, British Columbia, Canada
| | - Zachary A Wood
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA.
| | - Kelley W Moremen
- Department of Biochemistry & Molecular Biology, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
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5
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Yang X, Jiang Z, He J, Shen L. iTRAQ-Based Quantitative Proteomics Unveils Protein Dynamics in the Root of Solanum melongena L. under Waterlogging Stress Conditions. Life (Basel) 2023; 13:1399. [PMID: 37374181 DOI: 10.3390/life13061399] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/29/2023] Open
Abstract
Waterlogging poses significant abiotic stress that endangers the survival of plants, including crops. In response, plants dramatically change their physiology to enhance their tolerance to waterlogging, such as proteome reconfiguration. Here, we utilized isobaric tags for the relative and absolute quantitation (iTRAQ)-based protein labeling technique to examine the proteomic changes induced by waterlogging in the roots of Solanum melongena L., a solanaceous plant. The plants were subjected to 6, 12, and 24 h of waterlogging stress at the flowering stage. Of the 4074 identified proteins, compared to the control, the abundance of the proteins increased and decreased in 165 and 78 proteins, respectively, in 6 h of treatments; 219 and 89 proteins, respectively, in 12 h of treatments; and 126 and 127 proteins, respectively, in 24 h of treatments. The majority of these differentially regulated proteins participated in processes such as energy metabolism, amino acid biosynthesis, signal transduction, and nitrogen metabolism. Fructose-bisphosphate aldolase and three alcohol dehydrogenase genes, in particular, were up- or down-regulated in waterlogging-treated Solanum melongena roots, suggesting that some proteins related to anaerobic metabolism (glycolysis and fermentation) may play vital roles in protecting its roots from waterlogging stress to enable long-term survival. Overall, this research not only offers a comprehensive dataset of protein alterations in waterlogged Solanum melongena roots but also insights into the mechanisms by which solanaceous plants adapt to waterlogging stress.
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Affiliation(s)
- Xu Yang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Zheng Jiang
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Jie He
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
| | - Lei Shen
- College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou 225009, China
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6
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Li H, Chapla D, Amos RA, Ramiah A, Moremen KW, Li H. Structural basis for heparan sulfate co-polymerase action by the EXT1-2 complex. Nat Chem Biol 2023; 19:565-574. [PMID: 36593275 PMCID: PMC10160006 DOI: 10.1038/s41589-022-01220-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/31/2022] [Indexed: 01/04/2023]
Abstract
Heparan sulfate (HS) proteoglycans are extended (-GlcAβ1,4GlcNAcα1,4-)n co-polymers containing decorations of sulfation and epimerization that are linked to cell surface and extracellular matrix proteins. In mammals, HS repeat units are extended by an obligate heterocomplex of two exostosin family members, EXT1 and EXT2, where each protein monomer contains distinct GT47 (GT-B fold) and GT64 (GT-A fold) glycosyltransferase domains. In this study, we generated human EXT1-EXT2 (EXT1-2) as a functional heterocomplex and determined its structure in the presence of bound donor and acceptor substrates. Structural data and enzyme activity of catalytic site mutants demonstrate that only two of the four glycosyltransferase domains are major contributors to co-polymer syntheses: the EXT1 GT-B fold β1,4GlcA transferase domain and the EXT2 GT-A fold α1,4GlcNAc transferase domain. The two catalytic sites are over 90 Å apart, indicating that HS is synthesized by a dissociative process that involves a single catalytic site on each monomer.
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Affiliation(s)
- Hua Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Robert A Amos
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Annapoorani Ramiah
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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7
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McFarlane HE. Open questions in plant cell wall synthesis. JOURNAL OF EXPERIMENTAL BOTANY 2023:erad110. [PMID: 36961357 DOI: 10.1093/jxb/erad110] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Indexed: 06/18/2023]
Abstract
Plant cells are surrounded by strong yet flexible polysaccharide-based cell walls that support the cell while also allowing growth by cell expansion. Plant cell wall research has advanced tremendously in recent years. Sequenced genomes of many model and crop plants have facilitated cataloging and characterization of many enzymes involved in cell wall synthesis. Structural information has been generated for several important cell wall synthesizing enzymes. Important tools have been developed including antibodies raised against a variety of cell wall polysaccharides and glycoproteins, collections of enzyme clones and synthetic glycan arrays for characterizing enzymes, herbicides that specifically affect cell wall synthesis, live-cell imaging probes to track cell wall synthesis, and an inducible secondary cell wall synthesis system. Despite these advances, and often because of the new information they provide, many open questions about plant cell wall polysaccharide synthesis persist. This article highlights some of the key questions that remain open, reviews the data supporting different hypotheses that address these questions, and discusses technological developments that may answer these questions in the future.
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Affiliation(s)
- Heather E McFarlane
- Department of Cell & Systems Biology, University of Toronto, 25 Harbord St., Toronto, ON, M5S 3G5, Canada
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8
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Prabhakar PK, Pereira JH, Taujale R, Shao W, Bharadwaj VS, Chapla D, Yang JY, Bomble YJ, Moremen KW, Kannan N, Hammel M, Adams PD, Scheller HV, Urbanowicz BR. Structural and biochemical insight into a modular β-1,4-galactan synthase in plants. NATURE PLANTS 2023; 9:486-500. [PMID: 36849618 PMCID: PMC10115243 DOI: 10.1038/s41477-023-01358-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 01/25/2023] [Indexed: 05/18/2023]
Abstract
Rhamnogalacturonan I (RGI) is a structurally complex pectic polysaccharide with a backbone of alternating rhamnose and galacturonic acid residues substituted with arabinan and galactan side chains. Galactan synthase 1 (GalS1) transfers galactose and arabinose to either extend or cap the β-1,4-galactan side chains of RGI, respectively. Here we report the structure of GalS1 from Populus trichocarpa, showing a modular protein consisting of an N-terminal domain that represents the founding member of a new family of carbohydrate-binding module, CBM95, and a C-terminal glycosyltransferase family 92 (GT92) catalytic domain that adopts a GT-A fold. GalS1 exists as a dimer in vitro, with stem domains interacting across the chains in a 'handshake' orientation that is essential for maintaining stability and activity. In addition to understanding the enzymatic mechanism of GalS1, we gained insight into the donor and acceptor substrate binding sites using deep evolutionary analysis, molecular simulations and biochemical studies. Combining all the results, a mechanism for GalS1 catalysis and a new model for pectic galactan side-chain addition are proposed.
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Affiliation(s)
- Pradeep Kumar Prabhakar
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, USA
| | - Jose Henrique Pereira
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Rahil Taujale
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Wanchen Shao
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Vivek S Bharadwaj
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Digantkumar Chapla
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Yannick J Bomble
- Biosciences Center, National Renewable Energy Laboratory, Golden, CO, USA
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Michal Hammel
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Paul D Adams
- Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Bioengineering, University of California, Berkeley, CA, USA
| | - Henrik V Scheller
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Breeanna R Urbanowicz
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oakridge, TN, USA.
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9
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2017-2018. MASS SPECTROMETRY REVIEWS 2023; 42:227-431. [PMID: 34719822 DOI: 10.1002/mas.21721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 07/26/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
This review is the tenth update of the original article published in 1999 on the application of matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2018. Also included are papers that describe methods appropriate to glycan and glycoprotein analysis by MALDI, such as sample preparation techniques, even though the ionization method is not MALDI. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, new methods, matrices, derivatization, MALDI imaging, fragmentation and the use of arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Most of the applications are presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. The reported work shows increasing use of combined new techniques such as ion mobility and highlights the impact that MALDI imaging is having across a range of diciplines. MALDI is still an ideal technique for carbohydrate analysis and advancements in the technique and the range of applications continue steady progress.
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Affiliation(s)
- David J Harvey
- Nuffield Department of Medicine, Target Discovery Institute, University of Oxford, Oxford, UK
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10
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Amos RA, Atmodjo MA, Huang C, Gao Z, Venkat A, Taujale R, Kannan N, Moremen KW, Mohnen D. Polymerization of the backbone of the pectic polysaccharide rhamnogalacturonan I. NATURE PLANTS 2022; 8:1289-1303. [PMID: 36357524 PMCID: PMC10115348 DOI: 10.1038/s41477-022-01270-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 10/05/2022] [Indexed: 06/10/2023]
Abstract
Rhamnogalacturonan I (RG-I) is a major plant cell wall pectic polysaccharide defined by its repeating disaccharide backbone structure of [4)-α-D-GalA-(1,2)-α-L-Rha-(1,]. A family of RG-I:Rhamnosyltransferases (RRT) has previously been identified, but synthesis of the RG-I backbone has not been demonstrated in vitro because the identity of Rhamnogalacturonan I:Galaturonosyltransferase (RG-I:GalAT) was unknown. Here a putative glycosyltransferase, At1g28240/MUCI70, is shown to be an RG-I:GalAT. The name RGGAT1 is proposed to reflect the catalytic activity of this enzyme. When incubated together with the rhamnosyltransferase RRT4, the combined activities of RGGAT1 and RRT4 result in elongation of RG-I acceptors in vitro into a polymeric product. RGGAT1 is a member of a new GT family categorized as GT116, which does not group into existing GT-A clades and is phylogenetically distinct from the GALACTURONOSYLTRANSFERASE (GAUT) family of GalA transferases that synthesize the backbone of the pectin homogalacturonan. RGGAT1 has a predicted GT-A fold structure but employs a metal-independent catalytic mechanism that is rare among glycosyltransferases with this fold type. The identification of RGGAT1 and the 8-member Arabidopsis GT116 family provides a new avenue for studying the mechanism of RG-I synthesis and the function of RG-I in plants.
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Affiliation(s)
- Robert A Amos
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Melani A Atmodjo
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Chin Huang
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Zhongwei Gao
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Aarya Venkat
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Rahil Taujale
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Natarajan Kannan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
| | - Kelley W Moremen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Debra Mohnen
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.
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11
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Julian JD, Zabotina OA. Xyloglucan Biosynthesis: From Genes to Proteins and Their Functions. FRONTIERS IN PLANT SCIENCE 2022; 13:920494. [PMID: 35720558 PMCID: PMC9201394 DOI: 10.3389/fpls.2022.920494] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 05/13/2022] [Indexed: 05/12/2023]
Abstract
The plant's recalcitrant cell wall is composed of numerous polysaccharides, including cellulose, hemicellulose, and pectin. The most abundant hemicellulose in dicot cell walls is xyloglucan, which consists of a β-(1- > 4) glucan backbone with α-(1- > 6) xylosylation producing an XXGG or XXXG pattern. Xylose residues of xyloglucan are branched further with different patterns of arabinose, fucose, galactose, and acetylation that varies between species. Although xyloglucan research in other species lag behind Arabidopsis thaliana, significant advances have been made into the agriculturally relevant species Oryza sativa and Solanum lycopersicum, which can be considered model organisms for XXGG type xyloglucan. In this review, we will present what is currently known about xyloglucan biosynthesis in A. thaliana, O. sativa, and S. lycopersicum and discuss the recent advances in the characterization of the glycosyltransferases involved in this complex process and their organization in the Golgi.
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Affiliation(s)
- Jordan D Julian
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
| | - Olga A Zabotina
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA, United States
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12
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Wang HT, Bharadwaj VS, Yang JY, Curry TM, Moremen KW, Bomble YJ, Urbanowicz BR. Rational enzyme design for controlled functionalization of acetylated xylan for cell-free polymer biosynthesis. Carbohydr Polym 2021; 273:118564. [PMID: 34560975 DOI: 10.1016/j.carbpol.2021.118564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/02/2021] [Accepted: 08/13/2021] [Indexed: 11/18/2022]
Abstract
Xylan O-acetyltransferase 1 (XOAT1) is involved in O-acetylating the backbone of hemicellulose xylan. Recent structural analysis of XOAT1 showed two unequal lobes forming a cleft that is predicted to accommodate and position xylan acceptors into proximity with the catalytic triad. Here, we used docking and molecular dynamics simulations to investigate the optimal orientation of xylan in the binding cleft of XOAT1 and identify putative key residues (Gln445 and Arg444 on Minor lobe & Asn312, Met311 and Asp403 on Major lobe) involved in substrate interactions. Site-directed mutagenesis coupled with biochemical analyses revealed the major lobe of XOAT1 is important for xylan binding. Mutation of single key residues yielded XOAT1 variants with various enzymatic efficiencies that are applicable to one-pot synthesis of xylan polymers with different degrees of O-acetylation. Taken together, our results demonstrate the effectiveness of computational modeling in guiding enzyme engineering aimed at modulating xylan and redesigning plant cell walls.
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Affiliation(s)
- Hsin-Tzu Wang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA; Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Vivek S Bharadwaj
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, 16253 Denver West Parkway, Golden, CO 80401, USA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA; Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Thomas M Curry
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA; Department of Biochemistry and Molecular Biology, 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; Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA
| | - Yannick J Bomble
- Bioscience Center, National Renewable Energy Laboratory, 16253 Denver West Parkway, Golden, CO 80401, USA
| | - Breeanna R Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA; Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, GA 30602, USA.
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13
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Structural Insights in Mammalian Sialyltransferases and Fucosyltransferases: We Have Come a Long Way, but It Is Still a Long Way Down. Molecules 2021; 26:molecules26175203. [PMID: 34500643 PMCID: PMC8433944 DOI: 10.3390/molecules26175203] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 08/19/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022] Open
Abstract
Mammalian cell surfaces are modified with complex arrays of glycans that play major roles in health and disease. Abnormal glycosylation is a hallmark of cancer; terminal sialic acid and fucose in particular have high levels in tumor cells, with positive implications for malignancy. Increased sialylation and fucosylation are due to the upregulation of a set of sialyltransferases (STs) and fucosyltransferases (FUTs), which are potential drug targets in cancer. In the past, several advances in glycostructural biology have been made with the determination of crystal structures of several important STs and FUTs in mammals. Additionally, how the independent evolution of STs and FUTs occurred with a limited set of global folds and the diverse modular ability of catalytic domains toward substrates has been elucidated. This review highlights advances in the understanding of the structural architecture, substrate binding interactions, and catalysis of STs and FUTs in mammals. While this general understanding is emerging, use of this information to design inhibitors of STs and FUTs will be helpful in providing further insights into their role in the manifestation of cancer and developing targeted therapeutics in cancer.
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14
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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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15
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Teze D, Coines J, Fredslund F, Dubey KD, Bidart GN, Adams PD, Dueber JE, Svensson B, Rovira C, Welner DH. O-/N-/S-Specificity in Glycosyltransferase Catalysis: From Mechanistic Understanding to Engineering. ACS Catal 2021. [DOI: 10.1021/acscatal.0c04171] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- David Teze
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Joan Coines
- Departament de Química Inorgánica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - Folmer Fredslund
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Kshatresh D. Dubey
- Departament de Química Inorgánica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
| | - Gonzalo N. Bidart
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Paul D. Adams
- Department of Bioengineering, University of California, Berkeley, California 94704, United States
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - John E. Dueber
- Department of Bioengineering, University of California, Berkeley, California 94704, United States
- Biological Systems & Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Birte Svensson
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
| | - Carme Rovira
- Departament de Química Inorgánica i Orgànica and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, Barcelona 08028, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08018, Spain
| | - Ditte H. Welner
- Department of Biotechnology and Biomedicine, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
- Joint BioEnergy Institute, Emeryville, California 94608, United States
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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16
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Mendoza F, Jaña GA. The inverting mechanism of the metal ion-independent LanGT2: the first step to understand the glycosylation of natural product antibiotic precursors through QM/MM simulations. Org Biomol Chem 2021; 19:5888-5898. [PMID: 34132308 DOI: 10.1039/d1ob00544h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Glycosyltransferases (GTs) from the GT1 family are responsible for the glycosylation of various important organic structures such as terpenes, steroids and peptide antibiotics, making it one of the most intensely studied families of GTs. The target of our study, LanGT2, is a member of the GT1 family that uses an inverting mechanism for transferring olivose from TDP-olivose, the donor substrate, to the natural product tetrangulol (Tet), the precursor of the antibiotic landomycin A. X-ray crystallography in conjunction with mutagenesis experiments has revealed the catalytic significance of 3 amino acids (Ser10, Ser219 and Asp137), suggesting Asp137 as the base catalyst. In the absence of X-ray structures that include the acceptor substrate Tet, in silico experiments and MD simulations that have modeled ternary complexes propose that Asp137 could recruit a water molecule to facilitate the nucleophilic activation of Tet, since the distance between Asp137 and the nucleophile is too long to directly deprotonate the nucleophilic moiety. So far, there is no computational evidence regarding the precise mechanism by which LanGT2 catalyzes the transfer of olivose, which raises questions such as: is a water-assisted mechanism possible? and how does this metal ion-independent GT stabilize the growing negative charge of the diphosphate leaving group? In this work, the QM/MM approach was used to unravel the catalytic mechanism of LanGT2, and to identify the role of crucial catalytic amino acids at a molecular level. Our calculations show that the minimum energy path (MEP) describes an SN2-like mechanism, identifying an oxocarbenium ion-like TS in which the olivosyl moiety adopts a 4H3 conformation. Interactions established between the diphosphate group of TDP and Ser10, Ser219, Arg220 and His283 are key to stabilize the development of charge on the leaving group. Our work also suggests that a water-mediated proton transfer mechanism is feasible, in which the water molecule is key to stabilize the phenolate ion-like nucleophile in the TS. This is the first computational insight into the inverting mechanism of an antibiotic natural product GT, and its implications may serve to guide the design of new biocatalysts for natural product glycodiversification.
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Affiliation(s)
- Fernanda Mendoza
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile.
| | - Gonzalo A Jaña
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Autopista Concepción-Talcahuano 7100, Talcahuano, Chile.
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17
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Zabotina OA, Zhang N, Weerts R. Polysaccharide Biosynthesis: Glycosyltransferases and Their Complexes. FRONTIERS IN PLANT SCIENCE 2021; 12:625307. [PMID: 33679837 PMCID: PMC7933479 DOI: 10.3389/fpls.2021.625307] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/14/2021] [Indexed: 05/04/2023]
Abstract
Glycosyltransferases (GTs) are enzymes that catalyze reactions attaching an activated sugar to an acceptor substrate, which may be a polysaccharide, peptide, lipid, or small molecule. In the past decade, notable progress has been made in revealing and cloning genes encoding polysaccharide-synthesizing GTs. However, the vast majority of GTs remain structurally and functionally uncharacterized. The mechanism by which they are organized in the Golgi membrane, where they synthesize complex, highly branched polysaccharide structures with high efficiency and fidelity, is also mostly unknown. This review will focus on current knowledge about plant polysaccharide-synthesizing GTs, specifically focusing on protein-protein interactions and the formation of multiprotein complexes.
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18
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Soto MJ, Prabhakar PK, Wang HT, Backe J, Chapla D, Bartetzko M, Black IM, Azadi P, Peña MJ, Pfrengle F, Moremen KW, Urbanowicz BR, Hahn MG. AtFUT4 and AtFUT6 Are Arabinofuranose-Specific Fucosyltransferases. FRONTIERS IN PLANT SCIENCE 2021; 12:589518. [PMID: 33633757 PMCID: PMC7900004 DOI: 10.3389/fpls.2021.589518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 01/19/2021] [Indexed: 05/03/2023]
Abstract
The bulk of plant biomass is comprised of plant cell walls, which are complex polymeric networks, composed of diverse polysaccharides, proteins, polyphenolics, and hydroxyproline-rich glycoproteins (HRGPs). Glycosyltransferases (GTs) work together to synthesize the saccharide components of the plant cell wall. The Arabidopsis thaliana fucosyltransferases (FUTs), AtFUT4, and AtFUT6, are members of the plant-specific GT family 37 (GT37). AtFUT4 and AtFUT6 transfer fucose (Fuc) onto arabinose (Ara) residues of arabinogalactan (AG) proteins (AGPs) and have been postulated to be non-redundant AGP-specific FUTs. AtFUT4 and AtFUT6 were recombinantly expressed in mammalian HEK293 cells and purified for biochemical analysis. We report an updated understanding on the specificities of AtFUT4 and AtFUT6 that are involved in the synthesis of wall localized AGPs. Our findings suggest that they are selective enzymes that can utilize various arabinogalactan (AG)-like and non-AG-like oligosaccharide acceptors, and only require a free, terminal arabinofuranose. We also report with GUS promoter-reporter gene studies that AtFUT4 and AtFUT6 gene expression is sub-localized in different parts of developing A. thaliana roots.
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Affiliation(s)
- Maria J. Soto
- Lawrence Berkeley National Laboratory, DOE Joint Genome Institute, Berkeley, CA, United States
- The Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
| | - Pradeep Kumar Prabhakar
- The Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Hsin-Tzu Wang
- The Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Jason Backe
- The Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Digantkumar Chapla
- The Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Max Bartetzko
- Department of Biomolecular Systems, Max-Planck-Institute of Colloids and Interfaces, Potsdam, Germany
| | - Ian M. Black
- The Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
| | - Parastoo Azadi
- The Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Maria J. Peña
- The Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - 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, Austria
| | - Kelley W. Moremen
- The Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Breeanna R. Urbanowicz
- The Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- *Correspondence: Breeanna R. Urbanowicz,
| | - Michael G. Hahn
- The Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Department of Plant Biology, University of Georgia, Athens, GA, United States
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Michael G. Hahn,
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19
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Boruah BM, Kadirvelraj R, Liu L, Ramiah A, Li C, Zong G, Bosman GP, Yang JY, Wang LX, Boons GJ, Wood ZA, Moremen KW. Characterizing human α-1,6-fucosyltransferase (FUT8) substrate specificity and structural similarities with related fucosyltransferases. J Biol Chem 2020; 295:17027-17045. [PMID: 33004438 PMCID: PMC7863877 DOI: 10.1074/jbc.ra120.014625] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 09/28/2020] [Indexed: 12/18/2022] Open
Abstract
Mammalian Asn-linked glycans are extensively processed as they transit the secretory pathway to generate diverse glycans on cell surface and secreted glycoproteins. Additional modification of the glycan core by α-1,6-fucose addition to the innermost GlcNAc residue (core fucosylation) is catalyzed by an α-1,6-fucosyltransferase (FUT8). The importance of core fucosylation can be seen in the complex pathological phenotypes of FUT8 null mice, which display defects in cellular signaling, development, and subsequent neonatal lethality. Elevated core fucosylation has also been identified in several human cancers. However, the structural basis for FUT8 substrate specificity remains unknown.Here, using various crystal structures of FUT8 in complex with a donor substrate analog, and with four distinct glycan acceptors, we identify the molecular basis for FUT8 specificity and activity. The ordering of three active site loops corresponds to an increased occupancy for bound GDP, suggesting an induced-fit folding of the donor-binding subsite. Structures of the various acceptor complexes were compared with kinetic data on FUT8 active site mutants and with specificity data from a library of glycan acceptors to reveal how binding site complementarity and steric hindrance can tune substrate affinity. The FUT8 structure was also compared with other known fucosyltransferases to identify conserved and divergent structural features for donor and acceptor recognition and catalysis. These data provide insights into the evolution of modular templates for donor and acceptor recognition among GT-B fold glycosyltransferases in the synthesis of diverse glycan structures in biological systems.
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Affiliation(s)
- Bhargavi M Boruah
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Renuka Kadirvelraj
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA
| | - Lin Liu
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Annapoorani Ramiah
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Chao Li
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Guanghui Zong
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Gerlof P Bosman
- Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Utrecht Institute for Pharmaceutical Sciences, Utrecht, The Netherlands
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Lai-Xi Wang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland, USA
| | - Geert-Jan Boons
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA; Department of Chemical Biology and Drug Discovery, Utrecht Institute for Pharmaceutical Sciences, and Utrecht Institute for Pharmaceutical Sciences, Utrecht, The Netherlands
| | - Zachary A Wood
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA; Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia, USA.
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20
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Bharadwaj VS, Crowley MF, Peña MJ, Urbanowicz B, O'Neill M. Mechanism and Reaction Energy Landscape for Apiose Cross-Linking by Boric Acid in Rhamnogalacturonan II. J Phys Chem B 2020; 124:10117-10125. [PMID: 33112619 DOI: 10.1021/acs.jpcb.0c06920] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Rhamnogalacturonan II (RG-II)-the most complex polysaccharide known in nature-exists as a borate cross-linked dimer in the plant primary cell wall. Boric acid facilitates the formation of this cross-link on the apiosyl residues of RG-II's side chain A. Here, we detail the reaction mechanism for the cross-linking process with ab initio calculations coupled with transition state theory. We determine the formation of the first ester linkage to be the rate-limiting step of the mechanism. Our findings demonstrate that the regio- and stereospecific nature of subsequent steps in the reaction itinerary presents four distinct energetically plausible reaction pathways. This has significant implications for the overall structure of the cross-linked RG-II dimer assembly. Our transition state and reaction path analyses reveal key geometric insights that corroborate previous experimental hypotheses on borate ester formation reactions.
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Affiliation(s)
- Vivek S Bharadwaj
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Michael F Crowley
- Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Maria J Peña
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Breeanna Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States.,Department of Biochemistry and Molecular Biology, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
| | - Malcolm O'Neill
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, Georgia 30602, United States
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21
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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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22
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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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23
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Elongating maize root: zone-specific combinations of polysaccharides from type I and type II primary cell walls. Sci Rep 2020; 10:10956. [PMID: 32616810 PMCID: PMC7331734 DOI: 10.1038/s41598-020-67782-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/12/2020] [Indexed: 11/09/2022] Open
Abstract
The dynamics of cell wall polysaccharides may modulate the cell wall mechanics and thus control the expansion growth of plant cells. The unique composition of type II primary cell wall characteristic of grasses suggests that they employ specific mechanisms for cell enlargement. We characterized the transcriptomes in five zones along maize root, clustered the expression of genes for numerous glycosyltransferases and performed extensive immunohistochemical analysis to relate the changes in cell wall polysaccharides to critical stages of cell development in Poaceae. Specific patterns of cell wall formation differentiate the initiation, realization and cessation of elongation growth. Cell walls of meristem and early elongation zone represent a mixture of type I and type II specific polysaccharides. Xyloglucans and homogalacturonans are synthesized there actively together with mixed-linkage glucans and glucuronoarabinoxylans. Rhamnogalacturonans-I with the side-chains of branched 1,4-galactan and arabinan persisted in cell walls throughout the development. Thus, the machinery to generate the type I primary cell wall constituents is completely established and operates. The expression of glycosyltransferases responsible for mixed-linkage glucan and glucuronoarabinoxylan synthesis peaks at active or late elongation. These findings widen the number of jigsaw pieces which should be put together to solve the puzzle of grass cell growth.
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24
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Lunin VV, Wang HT, Bharadwaj VS, Alahuhta M, Peña MJ, Yang JY, Archer-Hartmann SA, Azadi P, Himmel ME, Moremen KW, York WS, Bomble YJ, Urbanowicz BR. Molecular Mechanism of Polysaccharide Acetylation by the Arabidopsis Xylan O-acetyltransferase XOAT1. THE PLANT CELL 2020; 32:2367-2382. [PMID: 32354790 PMCID: PMC7346548 DOI: 10.1105/tpc.20.00028] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 04/14/2020] [Accepted: 04/29/2020] [Indexed: 05/03/2023]
Abstract
Xylans are a major component of plant cell walls. O-Acetyl moieties are the dominant backbone substituents of glucuronoxylan in dicots and play a major role in the polymer-polymer interactions that are crucial for wall architecture and normal plant development. Here, we describe the biochemical, structural, and mechanistic characterization of Arabidopsis (Arabidopsis thaliana) xylan O-acetyltransferase 1 (XOAT1), a member of the plant-specific Trichome Birefringence Like (TBL) family. Detailed characterization of XOAT1-catalyzed reactions by real-time NMR confirms that it exclusively catalyzes the 2-O-acetylation of xylan, followed by nonenzymatic acetyl migration to the O-3 position, resulting in products that are monoacetylated at both O-2 and O-3 positions. In addition, we report the crystal structure of the catalytic domain of XOAT1, which adopts a unique conformation that bears some similarities to the α/β/α topology of members of the GDSL-like lipase/acylhydrolase family. Finally, we use a combination of biochemical analyses, mutagenesis, and molecular simulations to show that XOAT1 catalyzes xylan acetylation through formation of an acyl-enzyme intermediate, Ac-Ser-216, by a double displacement bi-bi mechanism involving a Ser-His-Asp catalytic triad and unconventionally uses an Arg residue in the formation of an oxyanion hole.
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Affiliation(s)
- Vladimir V Lunin
- Bioscience Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Hsin-Tzu Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Vivek S Bharadwaj
- Bioscience Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Markus Alahuhta
- Bioscience Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Maria J Peña
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | | | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Michael E Himmel
- Bioscience Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - William S York
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Yannick J Bomble
- Bioscience Center, National Renewable Energy Laboratory, Golden, Colorado 80401
| | - Breeanna R Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
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25
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Hassan MM, Yuan G, Chen JG, Tuskan GA, Yang X. Prime Editing Technology and Its Prospects for Future Applications in Plant Biology Research. BIODESIGN RESEARCH 2020; 2020:9350905. [PMID: 37849904 PMCID: PMC10530660 DOI: 10.34133/2020/9350905] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/19/2020] [Indexed: 10/19/2023] Open
Abstract
Many applications in plant biology requires editing genomes accurately including correcting point mutations, incorporation of single-nucleotide polymorphisms (SNPs), and introduction of multinucleotide insertion/deletions (indels) into a predetermined position in the genome. These types of modifications are possible using existing genome-editing technologies such as the CRISPR-Cas systems, which require induction of double-stranded breaks in the target DNA site and the supply of a donor DNA molecule that contains the desired edit sequence. However, low frequency of homologous recombination in plants and difficulty of delivering the donor DNA molecules make this process extremely inefficient. Another kind of technology known as base editing can perform precise editing; however, only certain types of modifications can be obtained, e.g., C/G-to-T/A and A/T-to-G/C. Recently, a new type of genome-editing technology, referred to as "prime editing," has been developed, which can achieve various types of editing such as any base-to-base conversion, including both transitions (C→T, G→A, A→G, and T→C) and transversion mutations (C→A, C→G, G→C, G→T, A→C, A→T, T→A, and T→G), as well as small indels without the requirement for inducing double-stranded break in the DNA. Because prime editing has wide flexibility to achieve different types of edits in the genome, it holds a great potential for developing superior crops for various purposes, such as increasing yield, providing resistance to various abiotic and biotic stresses, and improving quality of plant product. In this review, we describe the prime editing technology and discuss its limitations and potential applications in plant biology research.
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Affiliation(s)
- Md. Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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26
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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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27
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Järvå MA, Dramicanin M, Lingford JP, Mao R, John A, Jarman KE, Grinter R, Goddard-Borger ED. Structural basis of substrate recognition and catalysis by fucosyltransferase 8. J Biol Chem 2020; 295:6677-6688. [PMID: 32220931 DOI: 10.1074/jbc.ra120.013291] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/26/2020] [Indexed: 12/11/2022] Open
Abstract
Fucosylation of the innermost GlcNAc of N-glycans by fucosyltransferase 8 (FUT8) is an important step in the maturation of complex and hybrid N-glycans. This simple modification can dramatically affect the activities and half-lives of glycoproteins, effects that are relevant to understanding the invasiveness of some cancers, development of mAb therapeutics, and the etiology of a congenital glycosylation disorder. The acceptor substrate preferences of FUT8 are well-characterized and provide a framework for understanding N-glycan maturation in the Golgi; however, the structural basis of these substrate preferences and the mechanism through which catalysis is achieved remain unknown. Here we describe several structures of mouse and human FUT8 in the apo state and in complex with GDP, a mimic of the donor substrate, and with a glycopeptide acceptor substrate at 1.80-2.50 Å resolution. These structures provide insights into a unique conformational change associated with donor substrate binding, common strategies employed by fucosyltransferases to coordinate GDP, features that define acceptor substrate preferences, and a likely mechanism for enzyme catalysis. Together with molecular dynamics simulations, the structures also revealed how FUT8 dimerization plays an important role in defining the acceptor substrate-binding site. Collectively, this information significantly builds on our understanding of the core fucosylation process.
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Affiliation(s)
- Michael A Järvå
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Marija Dramicanin
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - James P Lingford
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Runyu Mao
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Alan John
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Kate E Jarman
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
| | - Ethan D Goddard-Borger
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia .,Department of Medical Biology, University of Melbourne, Parkville, Victoria 3010, Australia
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28
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Smith PJ, O'Neill MA, Backe J, York WS, Peña MJ, Urbanowicz BR. Analytical Techniques for Determining the Role of Domain of Unknown Function 579 Proteins in the Synthesis of O-Methylated Plant Polysaccharides. SLAS Technol 2020; 25:345-355. [PMID: 32204644 DOI: 10.1177/2472630320912692] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Matrix polysaccharides are a diverse group of structurally complex carbohydrates and account for a large portion of the biomass consumed as food or used to produce fuels and materials. Glucuronoxylan and arabinogalactan protein are matrix glycans that have sidechains decorated with 4-O-methyl glucuronosyl residues. Methylation is a key determinant of the physical properties of these wall glycopolymers and consequently affects both their biological function and ability to interact with other wall polymers. Indeed, there is increasing interest in determining the distribution and abundance of methyl-etherified polysaccharides in different plant species, tissues, and developmental stages. There is also a need to understand the mechanisms involved in their biosynthesis. Members of the Domain of Unknown Function (DUF) 579 family have been demonstrated to have a role in the biosynthesis of methyl-etherified glycans. Here we describe methods for the analysis of the 4-O-methyl glucuronic acid moieties that are present in sidechains of arabinogalactan proteins. These methods are then applied toward the analysis of loss-of-function mutants of two DUF579 family members that lack this modification in muro. We also present a procedure to assay DUF579 family members for enzymatic activity in vitro using acceptor oligosaccharides prepared from xylan of loss-of-function mutants. Our approach facilitates the characterization of enzymes that modify glycosyl residues during cell wall synthesis and the structures that they generate.
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Affiliation(s)
- Peter J Smith
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.,Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, OakRidge, TN, USA
| | - Malcolm A O'Neill
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - Jason Backe
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.,Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, OakRidge, TN, USA
| | - William S York
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.,Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, OakRidge, TN, USA
| | - Maria J Peña
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.,Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, OakRidge, TN, USA
| | - Breeanna R Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA.,Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, USA.,Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, OakRidge, TN, USA
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29
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McGraphery K, Schwab W. Comparative Analysis of High-Throughput Assays of Family-1 Plant Glycosyltransferases. Int J Mol Sci 2020; 21:ijms21062208. [PMID: 32210023 PMCID: PMC7139940 DOI: 10.3390/ijms21062208] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 03/20/2020] [Accepted: 03/21/2020] [Indexed: 01/16/2023] Open
Abstract
The ability of glycosyltransferases (GTs) to reduce volatility, increase solubility, and thus alter the bioavailability of small molecules through glycosylation has attracted immense attention in pharmaceutical, nutraceutical, and cosmeceutical industries. The lack of GTs known and the scarcity of high-throughput (HTP) available methods, hinders the extrapolation of further novel applications. In this study, the applicability of new GT-assays suitable for HTP screening was tested and compared with regard to harmlessness, robustness, cost-effectiveness and reproducibility. The UDP-Glo GT-assay, Phosphate GT Activity assay, pH-sensitive GT-assay, and UDP2-TR-FRET assay were applied and tailored to plant UDP GTs (UGTs). Vitis vinifera (UGT72B27) GT was subjected to glycosylation reaction with various phenolics. Substrate screening and kinetic parameters were evaluated. The pH-sensitive assay and the UDP2-TR-FRET assay were incomparable and unsuitable for HTP plant GT-1 family UGT screening. Furthermore, the UDP-Glo GT-assay and the Phosphate GT Activity assay yielded closely similar and reproducible KM, vmax, and kcat values. Therefore, with the easy experimental set-up and rapid readout, the two assays are suitable for HTP screening and quantitative kinetic analysis of plant UGTs. This research sheds light on new and emerging HTP assays, which will allow for analysis of novel family-1 plant GTs and will uncover further applications.
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Affiliation(s)
| | - Wilfried Schwab
- Correspondence: ; Tel.: +49-8161-712-912; Fax: +49-8161-712-950
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30
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Structural basis for substrate specificity and catalysis of α1,6-fucosyltransferase. Nat Commun 2020; 11:973. [PMID: 32080177 PMCID: PMC7033129 DOI: 10.1038/s41467-020-14794-z] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 01/30/2020] [Indexed: 12/22/2022] Open
Abstract
Core-fucosylation is an essential biological modification by which a fucose is transferred from GDP-β-L-fucose to the innermost N-acetylglucosamine residue of N-linked glycans. A single human enzyme α1,6-fucosyltransferase (FUT8) is the only enzyme responsible for this modification via the addition of an α-1,6-linked fucose to N-glycans. To date, the details of substrate recognition and catalysis by FUT8 remain unknown. Here, we report the crystal structure of FUT8 complexed with GDP and a biantennary complex N-glycan (G0), which provides insight into both substrate recognition and catalysis. FUT8 follows an SN2 mechanism and deploys a series of loops and an α-helix which all contribute in forming the binding site. An exosite, formed by one of these loops and an SH3 domain, is responsible for the recognition of branched sugars, making contacts specifically to the α1,3 arm GlcNAc, a feature required for catalysis. This information serves as a framework for inhibitor design, and helps to assess its potential as a therapeutic target.
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31
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Nagae M, Yamaguchi Y, Taniguchi N, Kizuka Y. 3D Structure and Function of Glycosyltransferases Involved in N-glycan Maturation. Int J Mol Sci 2020; 21:ijms21020437. [PMID: 31936666 PMCID: PMC7014118 DOI: 10.3390/ijms21020437] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 01/06/2020] [Accepted: 01/08/2020] [Indexed: 12/21/2022] Open
Abstract
Glycosylation is the most ubiquitous post-translational modification in eukaryotes. N-glycan is attached to nascent glycoproteins and is processed and matured by various glycosidases and glycosyltransferases during protein transport. Genetic and biochemical studies have demonstrated that alternations of the N-glycan structure play crucial roles in various physiological and pathological events including progression of cancer, diabetes, and Alzheimer’s disease. In particular, the formation of N-glycan branches regulates the functions of target glycoprotein, which are catalyzed by specific N-acetylglucosaminyltransferases (GnTs) such as GnT-III, GnT-IVs, GnT-V, and GnT-IX, and a fucosyltransferase, FUT8s. Although the 3D structures of all enzymes have not been solved to date, recent progress in structural analysis of these glycosyltransferases has provided insights into substrate recognition and catalytic reaction mechanisms. In this review, we discuss the biological significance and structure-function relationships of these enzymes.
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Affiliation(s)
- Masamichi Nagae
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- Correspondence: (M.N.); (Y.K.)
| | - Yoshiki Yamaguchi
- Faculty of Pharmaceutical Sciences, Tohoku Medical and Pharmaceutical University, Miyagi 981-8558, Japan;
| | - Naoyuki Taniguchi
- Department of Glyco-Oncology and Medical Biochemistry, Osaka International Cancer Institute, 3-1-69 Otemae, Chuo-ku, Osaka 541-8567, Japan;
| | - Yasuhiko Kizuka
- Center for Highly Advanced Integration of Nano and Life Sciences (G-CHAIN), Gifu University, 1-1 Yanagido, Gifu 501-1193, Japan
- Correspondence: (M.N.); (Y.K.)
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32
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Emerging structural insights into glycosyltransferase-mediated synthesis of glycans. Nat Chem Biol 2019; 15:853-864. [PMID: 31427814 DOI: 10.1038/s41589-019-0350-2] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 07/17/2019] [Indexed: 12/27/2022]
Abstract
Glycans linked to proteins and lipids play key roles in biology; thus, accurate replication of cellular glycans is crucial for maintaining function following cell division. The fact that glycans are not copied from genomic templates suggests that fidelity is provided by the catalytic templates of glycosyltransferases that accurately add sugars to specific locations on growing oligosaccharides. To form new glycosidic bonds, glycosyltransferases bind acceptor substrates and orient a specific hydroxyl group, frequently one of many, for attack of the donor sugar anomeric carbon. Several recent crystal structures of glycosyltransferases with bound acceptor substrates reveal that these enzymes have common core structures that function as scaffolds upon which variable loops are inserted to confer substrate specificity and correctly orient the nucleophilic hydroxyl group. The varied approaches for acceptor binding site assembly suggest an ongoing evolution of these loop regions provides templates for assembly of the diverse glycan structures observed in biology.
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33
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Ohashi H, Ohashi T, Misaki R, Fujiyama K. Arabidopsis thaliana α1,2-l-fucosyltransferase catalyzes the transfer of l-galactose to xyloglucan oligosaccharides. FEBS Lett 2019; 593:187-194. [PMID: 30478825 DOI: 10.1002/1873-3468.13303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 11/19/2018] [Accepted: 11/20/2018] [Indexed: 11/10/2022]
Abstract
l-Galactose (l-Gal) is one of the components of plant cell wall polysaccharides. In the GDP-l-fucose-deficient Arabidopsis thaliana mutant mur1, l-fucose (l-Fuc) residues in xyloglucan are substituted by l-Gal residues. l-Gal only differs from l-Fuc by the presence of an oxygen at C-6. Thus, we hypothesized that the A. thaliana xyloglucan α1,2-l-fucosyltransferase (AtFUT1) is also responsible for the l-galactosyl transfer to d-galactose residues in xyloglucan. In this study, we heterologously produced AtFUT1 in fission yeast and carried out an in vitro assay for the activities of AtFUT1 on GDP-l-Gal and xyloglucan oligosaccharide. We show that the recombinant AtFUT1 catalyzes l-Gal transfer to xyloglucan oligosaccharides although the initial velocity of l-Gal transfer is 3.1 times lower than that of l-Fuc transfer.
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Affiliation(s)
- Hiroyuki Ohashi
- International Center for Biotechnology, Osaka University, Suita, Japan
| | - Takao Ohashi
- International Center for Biotechnology, Osaka University, Suita, Japan
| | - Ryo Misaki
- International Center for Biotechnology, Osaka University, Suita, Japan
| | - Kazuhito Fujiyama
- International Center for Biotechnology, Osaka University, Suita, Japan
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Amos RA, Mohnen D. Critical Review of Plant Cell Wall Matrix Polysaccharide Glycosyltransferase Activities Verified by Heterologous Protein Expression. FRONTIERS IN PLANT SCIENCE 2019; 10:915. [PMID: 31379900 PMCID: PMC6646851 DOI: 10.3389/fpls.2019.00915] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 06/27/2019] [Indexed: 05/02/2023]
Abstract
The life cycle and development of plants requires the biosynthesis, deposition, and degradation of cell wall matrix polysaccharides. The structures of the diverse cell wall matrix polysaccharides influence commercially important properties of plant cells, including growth, biomass recalcitrance, organ abscission, and the shelf life of fruits. This review is a comprehensive summary of the matrix polysaccharide glycosyltransferase (GT) activities that have been verified using in vitro assays following heterologous GT protein expression. Plant cell wall (PCW) biosynthetic GTs are primarily integral transmembrane proteins localized to the endoplasmic reticulum and Golgi of the plant secretory system. The low abundance of these enzymes in plant tissues makes them particularly difficult to purify from native plant membranes in quantities sufficient for enzymatic characterization, which is essential to study the functions of the different GTs. Numerous activities in the synthesis of the major cell wall matrix glycans, including pectins, xylans, xyloglucan, mannans, mixed-linkage glucans (MLGs), and arabinogalactan components of AGP proteoglycans have been mapped to specific genes and multi-gene families. Cell wall GTs include those that synthesize the polymer backbones, those that elongate side branches with extended glycosyl chains, and those that add single monosaccharide linkages onto polysaccharide backbones and/or side branches. Three main strategies have been used to identify genes encoding GTs that synthesize cell wall linkages: analysis of membrane fractions enriched for cell wall biosynthetic activities, mutational genetics approaches investigating cell wall compositional phenotypes, and omics-directed identification of putative GTs from sequenced plant genomes. Here we compare the heterologous expression systems used to produce, purify, and study the enzyme activities of PCW GTs, with an emphasis on the eukaryotic systems Nicotiana benthamiana, Pichia pastoris, and human embryonic kidney (HEK293) cells. We discuss the enzymatic properties of GTs including kinetic rates, the chain lengths of polysaccharide products, acceptor oligosaccharide preferences, elongation mechanisms for the synthesis of long-chain polymers, and the formation of GT complexes. Future directions in the study of matrix polysaccharide biosynthesis are proposed.
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Affiliation(s)
- Robert A. Amos
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Debra Mohnen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA, United States
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- *Correspondence: Debra Mohnen
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Amos RA, Pattathil S, Yang JY, Atmodjo MA, Urbanowicz BR, Moremen KW, Mohnen D. A two-phase model for the non-processive biosynthesis of homogalacturonan polysaccharides by the GAUT1:GAUT7 complex. J Biol Chem 2018; 293:19047-19063. [PMID: 30327429 DOI: 10.1074/jbc.ra118.004463] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Revised: 10/08/2018] [Indexed: 11/06/2022] Open
Abstract
Homogalacturonan (HG) is a pectic glycan in the plant cell wall that contributes to plant growth and development and cell wall structure and function, and interacts with other glycans and proteoglycans in the wall. HG is synthesized by the galacturonosyltransferase (GAUT) gene family. Two members of this family, GAUT1 and GAUT7, form a heteromeric enzyme complex in Arabidopsis thaliana Here, we established a heterologous GAUT expression system in HEK293 cells and show that co-expression of recombinant GAUT1 with GAUT7 results in the production of a soluble GAUT1:GAUT7 complex that catalyzes elongation of HG products in vitro The reaction rates, progress curves, and product distributions exhibited major differences dependent upon small changes in the degree of polymerization (DP) of the oligosaccharide acceptor. GAUT1:GAUT7 displayed >45-fold increased catalytic efficiency with DP11 acceptors relative to DP7 acceptors. Although GAUT1:GAUT7 synthesized high-molecular-weight polymeric HG (>100 kDa) in a substrate concentration-dependent manner typical of distributive (nonprocessive) glycosyltransferases with DP11 acceptors, reactions primed with short-chain acceptors resulted in a bimodal product distribution of glycan products that has previously been reported as evidence for a processive model of GT elongation. As an alternative to the processive glycosyltransfer model, a two-phase distributive elongation model is proposed in which a slow phase, which includes the de novo initiation of HG and elongation of short-chain acceptors, is distinguished from a phase of rapid elongation of intermediate- and long-chain acceptors. Upon reaching a critical chain length of DP11, GAUT1:GAUT7 elongates HG to high-molecular-weight products.
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Affiliation(s)
- Robert A Amos
- From the Complex Carbohydrate Research Center and.,the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | | | | | - Melani A Atmodjo
- From the Complex Carbohydrate Research Center and.,the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | | | - Kelley W Moremen
- From the Complex Carbohydrate Research Center and.,the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
| | - Debra Mohnen
- From the Complex Carbohydrate Research Center and .,the Department of Biochemistry and Molecular Biology, University of Georgia, Athens, Georgia 30602
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Culbertson AT, Ehrlich JJ, Choe JY, Honzatko RB, Zabotina OA. Structure of xyloglucan xylosyltransferase 1 reveals simple steric rules that define biological patterns of xyloglucan polymers. Proc Natl Acad Sci U S A 2018; 115:6064-6069. [PMID: 29784804 PMCID: PMC6003343 DOI: 10.1073/pnas.1801105115] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The plant cell wall is primarily a polysaccharide mesh of the most abundant biopolymers on earth. Although one of the richest sources of biorenewable materials, the biosynthesis of the plant polysaccharides is poorly understood. Structures of many essential plant glycosyltransferases are unknown and suitable substrates are often unavailable for in vitro analysis. The dearth of such information impedes the development of plants better suited for industrial applications. Presented here are structures of Arabidopsis xyloglucan xylosyltransferase 1 (XXT1) without ligands and in complexes with UDP and cellohexaose. XXT1 initiates side-chain extensions from a linear glucan polymer by transferring the xylosyl group from UDP-xylose during xyloglucan biosynthesis. XXT1, a homodimer and member of the GT-A fold family of glycosyltransferases, binds UDP analogously to other GT-A fold enzymes. Structures here and the properties of mutant XXT1s are consistent with a SNi-like catalytic mechanism. Distinct from other systems is the recognition of cellohexaose by way of an extended cleft. The XXT1 dimer alone cannot produce xylosylation patterns observed for native xyloglucans because of steric constraints imposed by the acceptor binding cleft. Homology modeling of XXT2 and XXT5, the other two xylosyltransferases involved in xyloglucan biosynthesis, reveals a structurally altered cleft in XXT5 that could accommodate a partially xylosylated glucan chain produced by XXT1 and/or XXT2. An assembly of the three XXTs can produce the xylosylation patterns of native xyloglucans, suggesting the involvement of an organized multienzyme complex in the xyloglucan biosynthesis.
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Affiliation(s)
- Alan T Culbertson
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Jacqueline J Ehrlich
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Jun-Yong Choe
- Department of Biochemistry and Molecular Biology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064
| | - Richard B Honzatko
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011
| | - Olga A Zabotina
- Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames, IA 50011;
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Jensen JK, Busse‐Wicher M, Poulsen CP, Fangel JU, Smith PJ, Yang J, Peña M, Dinesen MH, Martens HJ, Melkonian M, Wong GK, Moremen KW, Wilkerson CG, Scheller HV, Dupree P, Ulvskov P, Urbanowicz BR, Harholt J. Identification of an algal xylan synthase indicates that there is functional orthology between algal and plant cell wall biosynthesis. THE NEW PHYTOLOGIST 2018; 218:1049-1060. [PMID: 29460505 PMCID: PMC5902652 DOI: 10.1111/nph.15050] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 01/14/2018] [Indexed: 05/18/2023]
Abstract
Insights into the evolution of plant cell walls have important implications for comprehending these diverse and abundant biological structures. In order to understand the evolving structure-function relationships of the plant cell wall, it is imperative to trace the origin of its different components. The present study is focused on plant 1,4-β-xylan, tracing its evolutionary origin by genome and transcriptome mining followed by phylogenetic analysis, utilizing a large selection of plants and algae. It substantiates the findings by heterologous expression and biochemical characterization of a charophyte alga xylan synthase. Of the 12 known gene classes involved in 1,4-β-xylan formation, XYS1/IRX10 in plants, IRX7, IRX8, IRX9, IRX14 and GUX occurred for the first time in charophyte algae. An XYS1/IRX10 ortholog from Klebsormidium flaccidum, designated K. flaccidumXYLAN SYNTHASE-1 (KfXYS1), possesses 1,4-β-xylan synthase activity, and 1,4-β-xylan occurs in the K. flaccidum cell wall. These data suggest that plant 1,4-β-xylan originated in charophytes and shed light on the origin of one of the key cell wall innovations to occur in charophyte algae, facilitating terrestrialization and emergence of polysaccharide-based plant cell walls.
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Affiliation(s)
- Jacob Krüger Jensen
- Department of Plant BiologyMichigan State UniversityEast LansingMI48823USA
- DOE Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48823USA
| | | | | | | | - Peter James Smith
- Complex Carbohydrate Research CenterUniversity of Georgia315 Riverbend RoadAthensGA30602USA
- BioEnergy Science CenterOak Ridge National Lab LaboratoryOak RidgeTN37831USA
| | - Jeong‐Yeh Yang
- Complex Carbohydrate Research CenterUniversity of Georgia315 Riverbend RoadAthensGA30602USA
| | - Maria‐Jesus Peña
- Complex Carbohydrate Research CenterUniversity of Georgia315 Riverbend RoadAthensGA30602USA
- BioEnergy Science CenterOak Ridge National Lab LaboratoryOak RidgeTN37831USA
| | | | - Helle Juel Martens
- Department of Plant and Environmental SciencesUniversity of Copenhagen1971Frederiksberg CDenmark
| | - Michael Melkonian
- Botanical InstituteDepartment of Biological SciencesUniversität zu KölnKölnD‐50674Germany
| | - Gane Ka‐Shu Wong
- BGI‐ShenzhenBeishan Industrial ZoneYantian DistrictShenzhen518083China
| | - Kelley W. Moremen
- Complex Carbohydrate Research CenterUniversity of Georgia315 Riverbend RoadAthensGA30602USA
| | - Curtis Gene Wilkerson
- Department of Plant BiologyMichigan State UniversityEast LansingMI48823USA
- DOE Great Lakes Bioenergy Research CenterMichigan State UniversityEast LansingMI48823USA
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMI48824USA
| | - Henrik Vibe Scheller
- Joint BioEnergy InstituteEmeryvilleCA94608USA
- Environmental Genomics and Systems Biology DivisionLawrence Berkeley National LaboratoryBerkeleyCA94720USA
| | - Paul Dupree
- Department of BiochemistryUniversity of CambridgeCambridgeCB2 1QWUK
| | - Peter Ulvskov
- Complex Carbohydrate Research CenterUniversity of Georgia315 Riverbend RoadAthensGA30602USA
| | - Breeanna Rae Urbanowicz
- Complex Carbohydrate Research CenterUniversity of Georgia315 Riverbend RoadAthensGA30602USA
- BioEnergy Science CenterOak Ridge National Lab LaboratoryOak RidgeTN37831USA
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Dallabernardina P, Ruprecht C, Smith PJ, Hahn MG, Urbanowicz BR, Pfrengle F. Automated glycan assembly of galactosylated xyloglucan oligosaccharides and their recognition by plant cell wall glycan-directed antibodies. Org Biomol Chem 2018; 15:9996-10000. [PMID: 29177276 DOI: 10.1039/c7ob02605f] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
We report the automated glycan assembly of oligosaccharides related to the plant cell wall hemicellulosic polysaccharide xyloglucan. The synthesis of galactosylated xyloglucan oligosaccharides was enabled by introducing p-methoxybenzyl (PMB) as a temporary protecting group for automated glycan assembly. The generated oligosaccharides were printed as microarrays, and the binding of a collection of xyloglucan-directed monoclonal antibodies (mAbs) to the oligosaccharides was assessed. We also demonstrated that the printed glycans can be further enzymatically modified while appended to the microarray surface by Arabidopsis thaliana xyloglucan xylosyltransferase 2 (AtXXT2).
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Affiliation(s)
- Pietro Dallabernardina
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, Am Mühlenberg 1, 14476 Potsdam, Germany.
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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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40
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Moremen KW, Ramiah A, Stuart M, Steel J, Meng L, Forouhar F, Moniz HA, Gahlay G, Gao Z, Chapla D, Wang S, Yang JY, Prabahkar PK, Johnson R, dela Rosa M, Geisler C, Nairn AV, Wu SC, Tong L, Gilbert HJ, LaBaer J, Jarvis DL. Expression system for structural and functional studies of human glycosylation enzymes. Nat Chem Biol 2018; 14:156-162. [PMID: 29251719 PMCID: PMC5774587 DOI: 10.1038/nchembio.2539] [Citation(s) in RCA: 157] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Accepted: 11/08/2017] [Indexed: 12/14/2022]
Abstract
Vertebrate glycoproteins and glycolipids are synthesized in complex biosynthetic pathways localized predominantly within membrane compartments of the secretory pathway. The enzymes that catalyze these reactions are exquisitely specific, yet few have been extensively characterized because of challenges associated with their recombinant expression as functional products. We used a modular approach to create an expression vector library encoding all known human glycosyltransferases, glycoside hydrolases, and sulfotransferases, as well as other glycan-modifying enzymes. We then expressed the enzymes as secreted catalytic domain fusion proteins in mammalian and insect cell hosts, purified and characterized a subset of the enzymes, and determined the structure of one enzyme, the sialyltransferase ST6GalNAcII. Many enzymes were produced at high yields and at similar levels in both hosts, but individual protein expression levels varied widely. This expression vector library will be a transformative resource for recombinant enzyme production, broadly enabling structure-function studies and expanding applications of these enzymes in glycochemistry and glycobiology.
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Affiliation(s)
- Kelley W. Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA
| | | | - Melissa Stuart
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
| | - Jason Steel
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Lu Meng
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA
| | - Farhad Forouhar
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027
| | - Heather A. Moniz
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA
| | - Gagandeep Gahlay
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
| | - Zhongwei Gao
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA
| | | | - Shuo Wang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA
| | - Jeong-Yeh Yang
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA
| | | | - Roy Johnson
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA
| | - Mitche dela Rosa
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA
| | - Christoph Geisler
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
| | - Alison V. Nairn
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA
| | - Sheng-Cheng Wu
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA
| | - Liang Tong
- Department of Biological Sciences, Northeast Structural Genomics Consortium, Columbia University, New York, New York 10027
| | - Harry J. Gilbert
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA
| | - Joshua LaBaer
- Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Donald L. Jarvis
- Department of Molecular Biology, University of Wyoming, Laramie, WY 82071
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Smith PJ, Wang HT, York WS, Peña MJ, Urbanowicz BR. Designer biomass for next-generation biorefineries: leveraging recent insights into xylan structure and biosynthesis. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:286. [PMID: 29213325 PMCID: PMC5708106 DOI: 10.1186/s13068-017-0973-z] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 11/20/2017] [Indexed: 05/02/2023]
Abstract
Xylans are the most abundant noncellulosic polysaccharides in lignified secondary cell walls of woody dicots and in both primary and secondary cell walls of grasses. These polysaccharides, which comprise 20-35% of terrestrial biomass, present major challenges for the efficient microbial bioconversion of lignocellulosic feedstocks to fuels and other value-added products. Xylans play a significant role in the recalcitrance of biomass to degradation, and their bioconversion requires metabolic pathways that are distinct from those used to metabolize cellulose. In this review, we discuss the key differences in the structural features of xylans across diverse plant species, how these features affect their interactions with cellulose and lignin, and recent developments in understanding their biosynthesis. In particular, we focus on how the combined structural and biosynthetic knowledge can be used as a basis for biomass engineering aimed at developing crops that are better suited as feedstocks for the bioconversion industry.
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Affiliation(s)
- Peter J. Smith
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
| | - Hsin-Tzu Wang
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
| | - William S. York
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
| | - Maria J. Peña
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
| | - Breeanna R. Urbanowicz
- Complex Carbohydrate Research Center, University of Georgia, 315 Riverbend Road, Athens, GA USA
- BioEnergy Science Center, Oak Ridge National Lab Laboratory, Oak Ridge, TN USA
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