1
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Thuy NT, Kim H, Hong S. Antagonistic functions of CTL1 and SUH1 mediate cell wall assembly in Arabidopsis. PLANT DIRECT 2024; 8:e580. [PMID: 38525472 PMCID: PMC10960159 DOI: 10.1002/pld3.580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2023] [Revised: 02/06/2024] [Accepted: 02/29/2024] [Indexed: 03/26/2024]
Abstract
Plant genomes contain numerous genes encoding chitinase-like (CTL) proteins, which have a similar protein structure to chitinase belonging to the glycoside hydrolase (GH) family but lack the chitinolytic activity to cleave the β-1,4-glycosidic bond in chitins, polymers of N-acetylglucosamine. CTL1 mutations found in rice and Arabidopsis have caused pleiotropic developmental defects, including altered cell wall composition and decreased abiotic stress tolerance, likely due to reduced cellulose content. In this study, we identified suppressor of hot2 1 (suh1) as a genetic suppressor of the ctl1 hot2-1 mutation in Arabidopsis. The mutation in SUH1 restored almost all examined ctl1 hot2-1 defects to nearly wild-type levels or at least partially. SUH1 encodes a Golgi-located type II membrane protein with glycosyltransferase (GT) activity, and its mutations lead to a reduction in cellulose content and hypersensitivity to cellulose biosynthesis inhibitors, although to a lesser extent than ctl1 hot2-1 mutation. The SUH1 promoter fused with the GUS reporter gene exhibited GUS activity in interfascicular fibers and xylem in stems; meanwhile, the ctl1 hot2-1 mutation significantly increased this activity. Our findings provide genetic and molecular evidence that the antagonistic activities of CTL1 and SUH1 play an essential role in assembling the cell wall in Arabidopsis.
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Affiliation(s)
- Nguyen Thi Thuy
- Department of the Integrative Food, Bioscience, and Biotechnology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
| | - Hyun‐Jung Kim
- Department of the Integrative Food, Bioscience, and Biotechnology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
| | - Suk‐Whan Hong
- Department of the Integrative Food, Bioscience, and Biotechnology, College of Agriculture and Life SciencesChonnam National UniversityGwangjuKorea
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2
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Wannitikul P, Wattana-Amorn P, Sathitnaitham S, Sakulkoo J, Suttangkakul A, Wonnapinij P, Bassel GW, Simister R, Gomez LD, Vuttipongchaikij S. Disruption of a DUF247 Containing Protein Alters Cell Wall Polysaccharides and Reduces Growth in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2023; 12:1977. [PMID: 37653894 PMCID: PMC10221614 DOI: 10.3390/plants12101977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 09/02/2023]
Abstract
Plant cell wall biosynthesis is a complex process that requires proteins and enzymes from glycan synthesis to wall assembly. We show that disruption of At3g50120 (DUF247-1), a member of the DUF247 multigene family containing 28 genes in Arabidopsis, results in alterations to the structure and composition of cell wall polysaccharides and reduced growth and plant size. An ELISA using cell wall antibodies shows that the mutants also exhibit ~50% reductions in xyloglucan (XyG), glucuronoxylan (GX) and heteromannan (HM) epitopes in the NaOH fraction and ~50% increases in homogalacturonan (HG) epitopes in the CDTA fraction. Furthermore, the polymer sizes of XyGs and GXs are reduced with concomitant increases in short-chain polymers, while those of HGs and mHGs are slightly increased. Complementation using 35S:DUF247-1 partially recovers the XyG and HG content, but not those of GX and HM, suggesting that DUF247-1 is more closely associated with XyGs and HGs. DUF247-1 is expressed throughout Arabidopsis, particularly in vascular and developing tissues, and its disruption affects the expression of other gene members, indicating a regulatory control role within the gene family. Our results demonstrate that DUF247-1 is required for normal cell wall composition and structure and Arabidopsis growth.
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Affiliation(s)
- Pitchaporn Wannitikul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Pakorn Wattana-Amorn
- Special Research Unit for Advanced Magnetic Resonance and Center of Excellence for Innovation in Chemistry, Department of Chemistry, Faculty of Science, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand;
| | - Sukhita Sathitnaitham
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Jenjira Sakulkoo
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
| | - Anongpat Suttangkakul
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
| | - Passorn Wonnapinij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - George W. Bassel
- School of Life Sciences, The University of Warwick, Coventry CV4 7AL, UK;
| | - Rachael Simister
- CNAP, Department of Biology, University of York, Heslington, York YO10 5DD, UK; (R.S.); (L.D.G.)
| | - Leonardo D. Gomez
- CNAP, Department of Biology, University of York, Heslington, York YO10 5DD, UK; (R.S.); (L.D.G.)
| | - Supachai Vuttipongchaikij
- Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand; (P.W.); (S.S.); (J.S.); (A.S.); (P.W.)
- Center of Advanced studies for Tropical Natural Resources, Kasetsart University, Ngam Wong Wan Road, Chattuchak, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
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3
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Leszczuk A, Kalaitzis P, Kulik J, Zdunek A. Review: structure and modifications of arabinogalactan proteins (AGPs). BMC PLANT BIOLOGY 2023; 23:45. [PMID: 36670377 PMCID: PMC9854139 DOI: 10.1186/s12870-023-04066-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 01/13/2023] [Indexed: 06/17/2023]
Abstract
The aim of this report is to provide general information on the molecular structure and synthesis of arabinogalactan proteins (AGPs) in association to their physiological significance. Assessment of genetic modifications of the activity of enzymes involved in the AGP biosynthesis is an efficient tool to study AGP functions. Thus, P4H (prolyl 4 hydroxylase) mutants, GLCAT (β-glucuronosyltransferase) mutants, and GH43 (glycoside hydrolase family 43) mutants have been described. We focused on the overview of AGPs modifications observed at the molecular, cellular, and organ levels. Inhibition of the hydroxylation process results in an increase in the intensity of cell divisions and thus, has an impact on root system length and leaf area. In turn, overexpression of P4H genes stimulates the density of root hairs. A mutation in GLCAT genes responsible for the transfer of glucuronic acid to the AGP molecule revealed that the reduction of GlcA in AGP disrupts the substantial assembly of the primary cell wall. Furthermore, silencing of genes encoding GH43, which has the ability to hydrolyze the AGP glycan by removing incorrectly synthesized β-1,3-galactans, induces changes in the abundance of other cell wall constituents, which finally leads to root growth defects. This information provides insight into AGPs as a crucial players in the structural interactions present in the plant extracellular matrix.
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Affiliation(s)
- Agata Leszczuk
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland
| | - Panagiotis Kalaitzis
- Department of Horticultural Genetics and Biotechnology, Mediterranean Agronomic Institute of Chania, Chania, P.O. Box 85, 73100 Chania, Greece
| | - Joanna Kulik
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland
| | - Artur Zdunek
- Institute of Agrophysics, Polish Academy of Sciences, Doświadczalna 4, 20-290 Lublin, Poland
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4
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Kurze E, Wüst M, Liao J, McGraphery K, Hoffmann T, Song C, Schwab W. Structure-function relationship of terpenoid glycosyltransferases from plants. Nat Prod Rep 2021; 39:389-409. [PMID: 34486004 DOI: 10.1039/d1np00038a] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Covering: up to 2021Terpenoids are physiologically active substances that are of great importance to humans. Their physicochemical properties are modified by glycosylation, in terms of polarity, volatility, solubility and reactivity, and their bioactivities are altered accordingly. Significant scientific progress has been made in the functional study of glycosylated terpenes and numerous plant enzymes involved in regio- and enantioselective glycosylation have been characterized, a reaction that remains chemically challenging. Crucial clues to the mechanism of terpenoid glycosylation were recently provided by the first crystal structures of a diterpene glycosyltransferase UGT76G1. Here, we review biochemically characterized terpenoid glycosyltransferases, compare their functions and primary structures, discuss their acceptor and donor substrate tolerance and product specificity, and elaborate features of the 3D structures of the first terpenoid glycosyltransferases from plants.
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Affiliation(s)
- Elisabeth Kurze
- Biotechnology of Natural Products, TUM School of Life Sciences, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany.
| | - Matthias Wüst
- Chair of Food Chemistry, Institute of Nutritional and Food Sciences, University of Bonn, Endenicher Allee 19C, 53115 Bonn, Germany.
| | - Jieren Liao
- Biotechnology of Natural Products, TUM School of Life Sciences, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany.
| | - Kate McGraphery
- Biotechnology of Natural Products, TUM School of Life Sciences, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany.
| | - Thomas Hoffmann
- Biotechnology of Natural Products, TUM School of Life Sciences, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany.
| | - Chuankui Song
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University Hefei, Anhui 230036, People's Republic of China.
| | - Wilfried Schwab
- Biotechnology of Natural Products, TUM School of Life Sciences, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany. .,State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University Hefei, Anhui 230036, People's Republic of China.
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5
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Silva J, Ferraz R, Dupree P, Showalter AM, Coimbra S. Three Decades of Advances in Arabinogalactan-Protein Biosynthesis. FRONTIERS IN PLANT SCIENCE 2020; 11:610377. [PMID: 33384708 PMCID: PMC7769824 DOI: 10.3389/fpls.2020.610377] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 11/23/2020] [Indexed: 05/18/2023]
Abstract
Arabinogalactan-proteins (AGPs) are a large, complex, and highly diverse class of heavily glycosylated proteins that belong to the family of cell wall hydroxyproline-rich glycoproteins. Approximately 90% of the molecules consist of arabinogalactan polysaccharides, which are composed of arabinose and galactose as major sugars and minor sugars such as glucuronic acid, fucose, and rhamnose. About half of the AGP family members contain a glycosylphosphatidylinositol (GPI) lipid anchor, which allows for an association with the outer leaflet of the plasma membrane. The mysterious AGP family has captivated the attention of plant biologists for several decades. This diverse family of glycoproteins is widely distributed in the plant kingdom, including many algae, where they play fundamental roles in growth and development processes. The journey of AGP biosynthesis begins with the assembly of amino acids into peptide chains of proteins. An N-terminal signal peptide directs AGPs toward the endoplasmic reticulum, where proline hydroxylation occurs and a GPI anchor may be added. GPI-anchored AGPs, as well as unanchored AGPs, are then transferred to the Golgi apparatus, where extensive glycosylation occurs by the action of a variety glycosyltransferase enzymes. Following glycosylation, AGPs are transported by secretory vesicles to the cell wall or to the extracellular face of the plasma membrane (in the case of GPI-anchored AGPs). GPI-anchored proteins can be released from the plasma membrane into the cell wall by phospholipases. In this review, we present an overview of the accumulated knowledge on AGP biosynthesis over the past three decades. Particular emphasis is placed on the glycosylation of AGPs as the sugar moiety is essential to their function. Recent genetics and genomics approaches have significantly contributed to a broader knowledge of AGP biosynthesis. However, many questions remain to be elucidated in the decades ahead.
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Affiliation(s)
- Jessy Silva
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Ricardo Ferraz
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Allan M. Showalter
- Department of Environmental and Plant Biology, Molecular and Cellular Biology Program, Ohio University, Athens, OH, United States
| | - Sílvia Coimbra
- Departamento de Biologia, Faculdade de Ciências da Universidade do Porto, Porto, Portugal
- LAQV Requimte, Sustainable Chemistry, Universidade do Porto, Porto, Portugal
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6
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Li K, Chen Y, Luo Y, Huang F, Zhao C, Cheng F, Xiang X, Pan G. A 22-bp deletion in OsPLS3 gene encoding a DUF266-containing protein is implicated in rice leaf senescence. PLANT MOLECULAR BIOLOGY 2018; 98:19-32. [PMID: 30117035 DOI: 10.1007/s11103-018-0758-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2018] [Accepted: 07/18/2018] [Indexed: 05/04/2023]
Abstract
Key message The OsPLS3 locus was isolated by map-based cloning that encodes a DUF266-containing protein. OsPLS3 regulates the onset of leaf senescence in rice. Glycosyltransferases (GTs) are one of the most important enzyme groups required for the modification of plant secondary metabolites and play a crucial role in plant growth and development, however the biological functions of most GTs remain elusive. We reported here the identification and characterization of a novel Oryza sativa premature leaf senescence mutant (ospls3). Through map-based cloning strategy, we determined that 22-bp deletion in the OsPLS3 gene encoding a domain of unknown function 266 (DUF266)-containing protein, a member of GT14-like, underlies the premature leaf senescence phenotype in the ospls3 mutant. The OsPLS3 mRNA levels progressively declined with the age-dependent leaf senescence in wild-type rice, implying a negative role of OsPLS3 in regulating leaf senescence. Physiological analysis, and histochemical staining and transmission electron microscopy assays indicated that the ospls3 mutant accumulated higher levels of ethylene and reactive oxygen species than its wild type. Furthermore, the ospls3 mutant showed hypersensitivity to exogenous 1-aminocyclopropane-1-carboxylic acid, H2O2 and high level of cytokinins. Our results indicated that the DUF266-containing gene OsPLS3 plays an important role in the onset of leaf senescence, in part through cytokinin and ethylene signaling in rice.
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Affiliation(s)
- Kunyu Li
- Department of Agronomy, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yaodong Chen
- Department of Agronomy, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Yanmin Luo
- Department of Agronomy, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Fudeng Huang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, People's Republic of China
| | - Chaoyue Zhao
- Department of Agronomy, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Fangmin Cheng
- Department of Agronomy, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Xun Xiang
- Experimental Teaching Center, College of Agriculture and Biotechnology, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China
| | - Gang Pan
- Department of Agronomy, Zijingang Campus, Zhejiang University, Hangzhou, 310058, People's Republic of China.
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7
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Smith DK, Harper JF, Wallace IS. A potential role for protein O-fucosylation during pollen-pistil interactions. PLANT SIGNALING & BEHAVIOR 2018; 13:e1467687. [PMID: 29939807 PMCID: PMC6103288 DOI: 10.1080/15592324.2018.1467687] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 04/12/2018] [Indexed: 05/28/2023]
Abstract
Putative protein O-fucosyltransferases (POFTs) represent a large family of Glycosyl Transferase family 65 domain-containing proteins in land plants, with at least 39 proposed members in the Arabidopsis thaliana genome alone. We recently identified a member of this family, AtOFT1 (At3g05320), in which loss-of-function mutants display impaired sexual reproduction that was linked to a defective male gamete. Specifically, oft1 mutant pollen tubes are ineffective at penetrating the stigma-style interface leading to a drastic reduction in seed set and a nearly 2000-fold reduction in pollen transmission. Our findings establish that AtOFT1 plays a critical role in pollen tube penetration through the stigma/style in Arabidopsis and further suggest an important role for protein O-glycosylation events that potentially influence pollen tube mechanical strength or the ability to respond to positional guidance cues during the process of tube growth and fertilization.
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Affiliation(s)
- D. K. Smith
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, USA
| | - J. F. Harper
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, USA
| | - I. S. Wallace
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, Reno, NV, USA
- Department of Chemistry, University of Nevada, Reno, Reno, NV, USA
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8
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Verger S, Chabout S, Gineau E, Mouille G. Cell adhesion in plants is under the control of putative O-fucosyltransferases. Development 2016; 143:2536-40. [PMID: 27317803 PMCID: PMC4958334 DOI: 10.1242/dev.132308] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2015] [Accepted: 06/02/2016] [Indexed: 12/12/2022]
Abstract
Cell-to-cell adhesion in plants is mediated by the cell wall and the presence of a pectin-rich middle lamella. However, we know very little about how the plant actually controls and maintains cell adhesion during growth and development and how it deals with the dynamic cell wall remodeling that takes place. Here we investigate the molecular mechanisms that control cell adhesion in plants. We carried out a genetic suppressor screen and a genetic analysis of cell adhesion-defective Arabidopsis thaliana mutants. We identified a genetic suppressor of a cell adhesion defect affecting a putative O-fucosyltransferase. Furthermore, we show that the state of cell adhesion is not directly linked with pectin content in the cell wall but instead is associated with altered pectin-related signaling. Our results suggest that cell adhesion is under the control of a feedback signal from the state of the pectin in the cell wall. Such a mechanism could be necessary for the control and maintenance of cell adhesion during growth and development. Highlighted article: Pectin-related signaling, rather than absolute pectin levels, are proposed to contribute to cell adhesion during growth and development in Arabidopsis thaliana.
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Affiliation(s)
- Stéphane Verger
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France Université Paris-Sud, Université Paris-Saclay, 91405 Orsay Cedex, France
| | - Salem Chabout
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
| | - Emilie Gineau
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
| | - Grégory Mouille
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026 Versailles Cedex, France
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9
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Tiwari P, Sangwan RS, Sangwan NS. Plant secondary metabolism linked glycosyltransferases: An update on expanding knowledge and scopes. Biotechnol Adv 2016; 34:714-739. [PMID: 27131396 DOI: 10.1016/j.biotechadv.2016.03.006] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 02/06/2016] [Accepted: 03/19/2016] [Indexed: 02/04/2023]
Abstract
The multigene family of enzymes known as glycosyltransferases or popularly known as GTs catalyze the addition of carbohydrate moiety to a variety of synthetic as well as natural compounds. Glycosylation of plant secondary metabolites is an emerging area of research in drug designing and development. The unsurpassing complexity and diversity among natural products arising due to glycosylation type of alterations including glycodiversification and glycorandomization are emerging as the promising approaches in pharmacological studies. While, some GTs with broad spectrum of substrate specificity are promising candidates for glycoengineering while others with stringent specificity pose limitations in accepting molecules and performing catalysis. With the rising trends in diseases and the efficacy/potential of natural products in their treatment, glycosylation of plant secondary metabolites constitutes a key mechanism in biogeneration of their glycoconjugates possessing medicinal properties. The present review highlights the role of glycosyltransferases in plant secondary metabolism with an overview of their identification strategies, catalytic mechanism and structural studies on plant GTs. Furthermore, the article discusses the biotechnological and biomedical application of GTs ranging from detoxification of xenobiotics and hormone homeostasis to the synthesis of glycoconjugates and crop engineering. The future directions in glycosyltransferase research should focus on the synthesis of bioactive glycoconjugates via metabolic engineering and manipulation of enzyme's active site leading to improved/desirable catalytic properties. The multiple advantages of glycosylation in plant secondary metabolomics highlight the increasing significance of the GTs, and in near future, the enzyme superfamily may serve as promising path for progress in expanding drug targets for pharmacophore discovery and development.
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Affiliation(s)
- Pragya Tiwari
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Lucknow 226015, India
| | - Rajender Singh Sangwan
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Lucknow 226015, India; Center of Innovative and Applied Bioprocessing (CIAB), A National Institute under Department of Biotechnology, Government of India, C-127, Phase-8, Industrial Area, S.A.S. Nagar, Mohali 160071, Punjab, India
| | - Neelam S Sangwan
- Department of Metabolic and Structural Biology, CSIR-Central Institute of Medicinal and Aromatic Plants (CSIR-CIMAP), P.O. CIMAP, Lucknow 226015, India.
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10
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Khor BY, Tye GJ, Lim TS, Choong YS. General overview on structure prediction of twilight-zone proteins. Theor Biol Med Model 2015; 12:15. [PMID: 26338054 PMCID: PMC4559291 DOI: 10.1186/s12976-015-0014-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 08/27/2015] [Indexed: 01/02/2023] Open
Abstract
Protein structure prediction from amino acid sequence has been one of the most challenging aspects in computational structural biology despite significant progress in recent years showed by critical assessment of protein structure prediction (CASP) experiments. When experimentally determined structures are unavailable, the predictive structures may serve as starting points to study a protein. If the target protein consists of homologous region, high-resolution (typically <1.5 Å) model can be built via comparative modelling. However, when confronted with low sequence similarity of the target protein (also known as twilight-zone protein, sequence identity with available templates is less than 30%), the protein structure prediction has to be initiated from scratch. Traditionally, twilight-zone proteins can be predicted via threading or ab initio method. Based on the current trend, combination of different methods brings an improved success in the prediction of twilight-zone proteins. In this mini review, the methods, progresses and challenges for the prediction of twilight-zone proteins were discussed.
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Affiliation(s)
- Bee Yin Khor
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia.
| | - Gee Jun Tye
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 11800, Minden, Penang, Malaysia.
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11
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Khor BY, Tye GJ, Lim TS, Noordin R, Choong YS. The structure and dynamics of BmR1 protein from Brugia malayi: in silico approaches. Int J Mol Sci 2014; 15:11082-99. [PMID: 24950179 PMCID: PMC4100200 DOI: 10.3390/ijms150611082] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2014] [Revised: 03/25/2014] [Accepted: 06/04/2014] [Indexed: 12/27/2022] Open
Abstract
Brugia malayi is a filarial nematode, which causes lymphatic filariasis in humans. In 1995, the disease has been identified by the World Health Organization (WHO) as one of the second leading causes of permanent and long-term disability and thus it is targeted for elimination by year 2020. Therefore, accurate filariasis diagnosis is important for management and elimination programs. A recombinant antigen (BmR1) from the Bm17DIII gene product was used for antibody-based filariasis diagnosis in "Brugia Rapid". However, the structure and dynamics of BmR1 protein is yet to be elucidated. Here we study the three dimensional structure and dynamics of BmR1 protein using comparative modeling, threading and ab initio protein structure prediction. The best predicted structure obtained via an ab initio method (Rosetta) was further refined and minimized. A total of 5 ns molecular dynamics simulation were performed to investigate the packing of the protein. Here we also identified three epitopes as potential antibody binding sites from the molecular dynamics average structure. The structure and epitopes obtained from this study can be used to design a binder specific against BmR1, thus aiding future development of antigen-based filariasis diagnostics to complement the current diagnostics.
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Affiliation(s)
- Bee Yin Khor
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang 11800, Malaysia.
| | - Gee Jun Tye
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang 11800, Malaysia.
| | - Theam Soon Lim
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang 11800, Malaysia.
| | - Rahmah Noordin
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang 11800, Malaysia.
| | - Yee Siew Choong
- Institute for Research in Molecular Medicine, Universiti Sains Malaysia, Minden, Penang 11800, Malaysia.
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12
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Mewalal R, Mizrachi E, Mansfield SD, Myburg AA. Cell wall-related proteins of unknown function: missing links in plant cell wall development. PLANT & CELL PHYSIOLOGY 2014; 55:1031-43. [PMID: 24683037 DOI: 10.1093/pcp/pcu050] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Lignocellulosic biomass is an important feedstock for the pulp and paper industry as well as emerging biofuel and biomaterial industries. However, the recalcitrance of the secondary cell wall to chemical or enzymatic degradation remains a major hurdle for efficient extraction of economically important biopolymers such as cellulose. It has been estimated that approximately 10-15% of about 27,000 protein-coding genes in the Arabidopsis genome are dedicated to cell wall development; however, only about 130 Arabidopsis genes thus far have experimental evidence validating cell wall function. While many genes have been implicated through co-expression analysis with known genes, a large number are broadly classified as proteins of unknown function (PUFs). Recently the functionality of some of these unknown proteins in cell wall development has been revealed using reverse genetic approaches. Given the large number of cell wall-related PUFs, how do we approach and subsequently prioritize the investigation of such unknown genes that may be essential to or influence plant cell wall development and structure? Here, we address the aforementioned question in two parts; we first identify the different kinds of PUFs based on known and predicted features such as protein domains. Knowledge of inherent features of PUFs may allow for functional inference and a concomitant link to biological context. Secondly, we discuss omics-based technologies and approaches that are helping identify and prioritize cell wall-related PUFs by functional association. In this way, hypothesis-driven experiments can be designed for functional elucidation of many proteins that remain missing links in our understanding of plant cell wall biosynthesis.
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Affiliation(s)
- Ritesh Mewalal
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Eshchar Mizrachi
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Hatfield, Pretoria, 0028, South Africa
| | - Shawn D Mansfield
- Department of Wood Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Private bag X20, Hatfield, Pretoria, 0028, South Africa
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13
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Sánchez-Rodríguez A, Tytgat HLP, Winderickx J, Vanderleyden J, Lebeer S, Marchal K. A network-based approach to identify substrate classes of bacterial glycosyltransferases. BMC Genomics 2014; 15:349. [PMID: 24885406 PMCID: PMC4039749 DOI: 10.1186/1471-2164-15-349] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2013] [Accepted: 04/16/2014] [Indexed: 01/03/2023] Open
Abstract
Background Bacterial interactions with the environment- and/or host largely depend on the bacterial glycome. The specificities of a bacterial glycome are largely determined by glycosyltransferases (GTs), the enzymes involved in transferring sugar moieties from an activated donor to a specific substrate. Of these GTs their coding regions, but mainly also their substrate specificity are still largely unannotated as most sequence-based annotation flows suffer from the lack of characterized sequence motifs that can aid in the prediction of the substrate specificity. Results In this work, we developed an analysis flow that uses sequence-based strategies to predict novel GTs, but also exploits a network-based approach to infer the putative substrate classes of these predicted GTs. Our analysis flow was benchmarked with the well-documented GT-repertoire of Campylobacter jejuni NCTC 11168 and applied to the probiotic model Lactobacillus rhamnosus GG to expand our insights in the glycosylation potential of this bacterium. In L. rhamnosus GG we could predict 48 GTs of which eight were not previously reported. For at least 20 of these GTs a substrate relation was inferred. Conclusions We confirmed through experimental validation our prediction of WelI acting upstream of WelE in the biosynthesis of exopolysaccharides. We further hypothesize to have identified in L. rhamnosus GG the yet undiscovered genes involved in the biosynthesis of glucose-rich glycans and novel GTs involved in the glycosylation of proteins. Interestingly, we also predict GTs with well-known functions in peptidoglycan synthesis to also play a role in protein glycosylation. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-349) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Sarah Lebeer
- Department of Microbial and Molecular Systems, KU Leuven, Centre of Microbial and Plant Genetics, Kasteelpark Arenberg 20, box 2460, Leuven B-3001, Belgium.
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14
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Ulvskov P, Paiva DS, Domozych D, Harholt J. Classification, naming and evolutionary history of glycosyltransferases from sequenced green and red algal genomes. PLoS One 2013; 8:e76511. [PMID: 24146880 PMCID: PMC3797821 DOI: 10.1371/journal.pone.0076511] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2013] [Accepted: 08/28/2013] [Indexed: 02/06/2023] Open
Abstract
The Archaeplastida consists of three lineages, Rhodophyta, Virideplantae and Glaucophyta. The extracellular matrix of most members of the Rhodophyta and Viridiplantae consists of carbohydrate-based or a highly glycosylated protein-based cell wall while the Glaucophyte covering is poorly resolved. In order to elucidate possible evolutionary links between the three advanced lineages in Archaeplastida, a genomic analysis was initiated. Fully sequenced genomes from the Rhodophyta and Virideplantae and the well-defined CAZy database on glycosyltransferases were included in the analysis. The number of glycosyltransferases found in the Rhodophyta and Chlorophyta are generally much lower then in land plants (Embryophyta). Three specific features exhibited by land plants increase the number of glycosyltransferases in their genomes: (1) cell wall biosynthesis, the more complex land plant cell walls require a larger number of glycosyltransferases for biosynthesis, (2) a richer set of protein glycosylation, and (3) glycosylation of secondary metabolites, demonstrated by a large proportion of family GT1 being involved in secondary metabolite biosynthesis. In a comparative analysis of polysaccharide biosynthesis amongst the taxa of this study, clear distinctions or similarities were observed in (1) N-linked protein glycosylation, i.e., Chlorophyta has different mannosylation and glucosylation patterns, (2) GPI anchor biosynthesis, which is apparently missing in the Rhodophyta and truncated in the Chlorophyta, (3) cell wall biosynthesis, where the land plants have unique cell wall related polymers not found in green and red algae, and (4) O-linked glycosylation where comprehensive orthology was observed in glycosylation between the Chlorophyta and land plants but not between the target proteins.
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Affiliation(s)
- Peter Ulvskov
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Dionisio Soares Paiva
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - David Domozych
- Department of Biology and Skidmore Microscopy Imaging Center, Skidmore College, Saratoga Springs, New York, United States of America
| | - Jesper Harholt
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
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15
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Wang Y, Mortimer JC, Davis J, Dupree P, Keegstra K. Identification of an additional protein involved in mannan biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 73:105-17. [PMID: 22966747 PMCID: PMC3558879 DOI: 10.1111/tpj.12019] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/24/2012] [Accepted: 09/07/2012] [Indexed: 05/18/2023]
Abstract
Galactomannans comprise a β-1,4-mannan backbone substituted with α-1,6-galactosyl residues. Genes encoding the enzymes that are primarily responsible for backbone synthesis and side-chain addition of galactomannans were previously identified and characterized. To identify additional genes involved in galactomannan biosynthesis, we previously performed deep EST profiling of fenugreek (Trigonella foenum-graecum L.) seed endosperm, which accumulates large quantities of galactomannans as a reserve carbohydrate during seed development. One of the candidate genes encodes a protein that is likely to be a glycosyltransferase. Because this protein is involved in mannan biosynthesis, we named it 'mannan synthesis-related' (MSR). Here, we report the characterization of a fenugreek MSR gene (TfMSR) and its two Arabidopsis homologs, AtMSR1 and AtMSR2. TfMSR was highly and specifically expressed in the endosperm. TfMSR, AtMSR1 and AtMSR2 proteins were all determined to be localized to the Golgi by fluorescence confocal microscopy. The level of mannosyl residues in stem glucomannans decreased by approximately 40% for Arabidopsis msr1 single T-DNA insertion mutants and by more than 50% for msr1 msr2 double mutants, but remained unchanged for msr2 single mutants. In addition, in vitro mannan synthase activity from the stems of msr1 single and msr1 msr2 double mutants also decreased. Expression of AtMSR1 or AtMSR2 in the msr1 msr2 double mutant completely or partially restored mannosyl levels. From these results, we conclude that the MSR protein is important for mannan biosynthesis, and offer some ideas about its role.
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Affiliation(s)
- Yan Wang
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Energy Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, 48824, USA
| | | | - Jonathan Davis
- Department of Energy Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
| | - Paul Dupree
- Department of Biochemistry, University of CambridgeCambridge, CB2 1QW, UK
| | - Kenneth Keegstra
- Great Lakes Bioenergy Research Center, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Energy Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Plant Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, 48824, USA
- *For correspondence (e-mail )
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16
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Voxeur A, André A, Breton C, Lerouge P. Identification of putative rhamnogalacturonan-II specific glycosyltransferases in Arabidopsis using a combination of bioinformatics approaches. PLoS One 2012; 7:e51129. [PMID: 23272088 PMCID: PMC3522684 DOI: 10.1371/journal.pone.0051129] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 10/31/2012] [Indexed: 01/24/2023] Open
Abstract
Rhamnogalacturonan-II (RG-II) is a complex plant cell wall polysaccharide that is composed of an α(1,4)-linked homogalacturonan backbone substituted with four side chains. It exists in the cell wall in the form of a dimer that is cross-linked by a borate di-ester. Despite its highly complex structure, RG-II is evolutionarily conserved in the plant kingdom suggesting that this polymer has fundamental functions in the primary wall organisation. In this study, we have set up a bioinformatics strategy aimed at identifying putative glycosyltransferases (GTs) involved in RG-II biosynthesis. This strategy is based on the selection of candidate genes encoding type II membrane proteins that are tightly coexpressed in both rice and Arabidopsis with previously characterised genes encoding enzymes involved in the synthesis of RG-II and exhibiting an up-regulation upon isoxaben treatment. This study results in the final selection of 26 putative Arabidopsis GTs, including 10 sequences already classified in the CAZy database. Among these CAZy sequences, the screening protocol allowed the selection of α-galacturonosyltransferases involved in the synthesis of α4-GalA oligogalacturonides present in both homogalacturonans and RG-II, and two sialyltransferase-like sequences previously proposed to be involved in the transfer of Kdo and/or Dha on the pectic backbone of RG-II. In addition, 16 non-CAZy GT sequences were retrieved in the present study. Four of them exhibited a GT-A fold. The remaining sequences harbored a GT-B like fold and a fucosyltransferase signature. Based on homologies with glycosyltransferases of known functions, putative roles in the RG-II biosynthesis are proposed for some GT candidates.
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Affiliation(s)
- Aline Voxeur
- Laboratoire Glyco-MEV, EA 4358, Institut de Recherche et d'Innovation Biotechnologique, University of Rouen, Mont-Saint-Aignan, France
| | - Aurélie André
- Laboratoire Glyco-MEV, EA 4358, Institut de Recherche et d'Innovation Biotechnologique, University of Rouen, Mont-Saint-Aignan, France
| | | | - Patrice Lerouge
- Laboratoire Glyco-MEV, EA 4358, Institut de Recherche et d'Innovation Biotechnologique, University of Rouen, Mont-Saint-Aignan, France
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17
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Nikolovski N, Rubtsov D, Segura MP, Miles GP, Stevens TJ, Dunkley TP, Munro S, Lilley KS, Dupree P. Putative glycosyltransferases and other plant Golgi apparatus proteins are revealed by LOPIT proteomics. PLANT PHYSIOLOGY 2012; 160:1037-51. [PMID: 22923678 PMCID: PMC3461528 DOI: 10.1104/pp.112.204263] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2012] [Accepted: 08/22/2012] [Indexed: 05/18/2023]
Abstract
The Golgi apparatus is the central organelle in the secretory pathway and plays key roles in glycosylation, protein sorting, and secretion in plants. Enzymes involved in the biosynthesis of complex polysaccharides, glycoproteins, and glycolipids are located in this organelle, but the majority of them remain uncharacterized. Here, we studied the Arabidopsis (Arabidopsis thaliana) membrane proteome with a focus on the Golgi apparatus using localization of organelle proteins by isotope tagging. By applying multivariate data analysis to a combined data set of two new and two previously published localization of organelle proteins by isotope tagging experiments, we identified the subcellular localization of 1,110 proteins with high confidence. These include 197 Golgi apparatus proteins, 79 of which have not been localized previously by a high-confidence method, as well as the localization of 304 endoplasmic reticulum and 208 plasma membrane proteins. Comparison of the hydrophobic domains of the localized proteins showed that the single-span transmembrane domains have unique properties in each organelle. Many of the novel Golgi-localized proteins belong to uncharacterized protein families. Structure-based homology analysis identified 12 putative Golgi glycosyltransferase (GT) families that have no functionally characterized members and, therefore, are not yet assigned to a Carbohydrate-Active Enzymes database GT family. The substantial numbers of these putative GTs lead us to estimate that the true number of plant Golgi GTs might be one-third above those currently annotated. Other newly identified proteins are likely to be involved in the transport and interconversion of nucleotide sugar substrates as well as polysaccharide and protein modification.
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18
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Wang Y, Alonso AP, Wilkerson CG, Keegstra K. Deep EST profiling of developing fenugreek endosperm to investigate galactomannan biosynthesis and its regulation. PLANT MOLECULAR BIOLOGY 2012; 79:243-58. [PMID: 22527750 PMCID: PMC3349874 DOI: 10.1007/s11103-012-9909-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2012] [Accepted: 03/28/2012] [Indexed: 05/23/2023]
Abstract
Galactomannans are hemicellulosic polysaccharides composed of a (1 → 4)-linked β-D-mannan backbone substituted with single-unit (1 → 6)-α-linked D-galactosyl residues. Developing fenugreek (Trigonella foenum-graecum) seeds are known to accumulate large quantities of galactomannans in the endosperm, and were thus used here as a model system to better understand galactomannan biosynthesis and its regulation. We first verified the specific deposition of galactomannans in developing endosperms and determined that active accumulation occurred from 25 to 38 days post anthesis (DPA) under our growth conditions. We then examined the expression levels during seed development of ManS and GMGT, two genes encoding backbone and side chain synthetic enzymes. Based on transcript accumulation dynamics for ManS and GMGT, cDNA libraries were constructed using RNA isolated from endosperms at four ages corresponding to before, at the beginning of, and during active galactomannan deposition. DNA from these libraries was sequenced using the 454 sequencing technology to yield a total of 1.5 million expressed sequence tags (ESTs). Through analysis of the EST profiling data, we identified genes known to be involved in galactomannan biosynthesis, as well as new genes that may be involved in this process, and proposed a model for the flow of carbon from sucrose to galactomannans. Measurement of in vitro ManS and GMGT activities and analysis of sugar phosphate and nucleotide sugar levels in the endosperms of developing fenugreek seeds provided data consistent with this model. In vitro enzymatic assays also revealed that the ManS enzyme from fenugreek endosperm preferentially used GDP-mannose as the substrate for the backbone synthesis.
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Affiliation(s)
- Yan Wang
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
| | - Ana P. Alonso
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Present Address: Department of Molecular Genetics, Ohio State University, Columbus, OH 43210 USA
| | - Curtis G. Wilkerson
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
| | - Kenneth Keegstra
- DOE Great Lakes Bioenergy Research Center, Michigan State University, East Lansing, MI 48824 USA
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824 USA
- Department of Plant Biology, Michigan State University, East Lansing, MI 48824 USA
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI 48824 USA
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The glycosyltransferase repertoire of the spikemoss Selaginella moellendorffii and a comparative study of its cell wall. PLoS One 2012; 7:e35846. [PMID: 22567114 PMCID: PMC3342304 DOI: 10.1371/journal.pone.0035846] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2011] [Accepted: 03/26/2012] [Indexed: 01/28/2023] Open
Abstract
Spike mosses are among the most basal vascular plants, and one species, Selaginella moellendorffii, was recently selected for full genome sequencing by the Joint Genome Institute (JGI). Glycosyltransferases (GTs) are involved in many aspects of a plant life, including cell wall biosynthesis, protein glycosylation, primary and secondary metabolism. Here, we present a comparative study of the S. moellendorffii genome across 92 GT families and an additional family (DUF266) likely to include GTs. The study encompasses the moss Physcomitrella patens, a non-vascular land plant, while rice and Arabidopsis represent commelinid and non-commelinid seed plants. Analysis of the subset of GT-families particularly relevant to cell wall polysaccharide biosynthesis was complemented by a detailed analysis of S. moellendorffii cell walls. The S. moellendorffii cell wall contains many of the same components as seed plant cell walls, but appears to differ somewhat in its detailed architecture. The S. moellendorffii genome encodes fewer GTs (287 GTs including DUF266s) than the reference genomes. In a few families, notably GT51 and GT78, S. moellendorffii GTs have no higher plant orthologs, but in most families S. moellendorffii GTs have clear orthologies with Arabidopsis and rice. A gene naming convention of GTs is proposed which takes orthologies and GT-family membership into account. The evolutionary significance of apparently modern and ancient traits in S. moellendorffii is discussed, as is its use as a reference organism for functional annotation of GTs.
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20
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Parsons HT, Christiansen K, Knierim B, Carroll A, Ito J, Batth TS, Smith-Moritz AM, Morrison S, McInerney P, Hadi MZ, Auer M, Mukhopadhyay A, Petzold CJ, Scheller HV, Loqué D, Heazlewood JL. Isolation and proteomic characterization of the Arabidopsis Golgi defines functional and novel components involved in plant cell wall biosynthesis. PLANT PHYSIOLOGY 2012; 159:12-26. [PMID: 22430844 PMCID: PMC3375956 DOI: 10.1104/pp.111.193151] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2012] [Accepted: 03/04/2012] [Indexed: 05/17/2023]
Abstract
The plant Golgi plays a pivotal role in the biosynthesis of cell wall matrix polysaccharides, protein glycosylation, and vesicle trafficking. Golgi-localized proteins have become prospective targets for reengineering cell wall biosynthetic pathways for the efficient production of biofuels from plant cell walls. However, proteomic characterization of the Golgi has so far been limited, owing to the technical challenges inherent in Golgi purification. In this study, a combination of density centrifugation and surface charge separation techniques have allowed the reproducible isolation of Golgi membranes from Arabidopsis (Arabidopsis thaliana) at sufficiently high purity levels for in-depth proteomic analysis. Quantitative proteomic analysis, immunoblotting, enzyme activity assays, and electron microscopy all confirm high purity levels. A composition analysis indicated that approximately 19% of proteins were likely derived from contaminating compartments and ribosomes. The localization of 13 newly assigned proteins to the Golgi using transient fluorescent markers further validated the proteome. A collection of 371 proteins consistently identified in all replicates has been proposed to represent the Golgi proteome, marking an appreciable advancement in numbers of Golgi-localized proteins. A significant proportion of proteins likely involved in matrix polysaccharide biosynthesis were identified. The potential within this proteome for advances in understanding Golgi processes has been demonstrated by the identification and functional characterization of the first plant Golgi-resident nucleoside diphosphatase, using a yeast complementation assay. Overall, these data show key proteins involved in primary cell wall synthesis and include a mixture of well-characterized and unknown proteins whose biological roles and importance as targets for future research can now be realized.
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21
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Hansen SF, Harholt J, Oikawa A, Scheller HV. Plant Glycosyltransferases Beyond CAZy: A Perspective on DUF Families. FRONTIERS IN PLANT SCIENCE 2012; 3:59. [PMID: 22629278 PMCID: PMC3355507 DOI: 10.3389/fpls.2012.00059] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2012] [Accepted: 03/10/2012] [Indexed: 05/18/2023]
Abstract
The carbohydrate active enzyme (CAZy) database is an invaluable resource for glycobiology and currently contains 45 glycosyltransferase families that are represented in plants. Glycosyltransferases (GTs) have many functions in plants, but the majority are likely to be involved in biosynthesis of polysaccharides and glycoproteins in the plant cell wall. Bioinformatic approaches and structural modeling suggest that a number of protein families in plants include GTs that have not yet been identified as such and are therefore not included in CAZy. These families include proteins with domain of unknown function (DUF) DUF23, DUF246, and DUF266. The evidence for these proteins being GTs and their possible roles in cell wall biosynthesis is discussed.
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Affiliation(s)
- Sara Fasmer Hansen
- Feedstocks Division, Joint Bioenergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - Jesper Harholt
- Department of Plant Biology and Biotechnology, University of CopenhagenFrederiksberg, Denmark
| | - Ai Oikawa
- Feedstocks Division, Joint Bioenergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
| | - Henrik V. Scheller
- Feedstocks Division, Joint Bioenergy Institute, Physical Biosciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
- Department of Plant and Microbial Biology, University of CaliforniaBerkeley, CA, USA
- *Correspondence: Henrik V. Scheller, Feedstocks Division, Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, 5885 Hollis Street, Emeryville, CA 94608, USA. e-mail:
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22
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Ye CY, Li T, Tuskan GA, Tschaplinski TJ, Yang X. Comparative analysis of GT14/GT14-like gene family in Arabidopsis, Oryza, Populus, Sorghum and Vitis. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2011; 181:688-95. [PMID: 21958711 DOI: 10.1016/j.plantsci.2011.01.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2010] [Revised: 01/26/2011] [Accepted: 01/27/2011] [Indexed: 05/22/2023]
Abstract
Glycosyltransferase family14 (GT14) belongs to the glycosyltransferase (GT) superfamily that plays important roles in the biosynthesis of cell walls, the most abundant source of cellulosic biomass for bioethanol production. It has been hypothesized that DUF266 proteins are a new class of GTs related to GT14. In this study, we identified 62 GT14 and 106 DUF266 genes (named GT14-like herein) in Arabidopsis, Oryza, Populus, Sorghum and Vitis. Our phylogenetic analysis separated GT14 and GT14-like genes into two distinct clades, which were further divided into eight and five groups, respectively. Similarities in protein domain, 3D structure and gene expression were uncovered between the two phylogenetic clades, supporting the hypothesis that GT14 and GT14-like genes belong to one family. Therefore, we proposed a new family name, GT14/GT14-like family that combines both subfamilies. Variation in gene expression and protein subcellular localization within the GT14-like subfamily were greater than those within the GT14 subfamily. One-half of the Arabidopsis and Populus GT14/GT14-like genes were found to be preferentially expressed in stem/xylem, indicating that they are likely involved in cell wall biosynthesis. This study provided new insights into the evolution and functional diversification of the GT14/GT14-like family genes.
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Affiliation(s)
- Chu-Yu Ye
- Biosciences Division and BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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23
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Zhou C, Yin Y, Dam P, Xu Y. Identification of novel proteins involved in plant cell-wall synthesis based on protein-protein interaction data. J Proteome Res 2010; 9:5025-37. [PMID: 20687615 DOI: 10.1021/pr100249c] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The plant cell wall is mainly composed of polysaccharides, representing the richest source of biomass for future biofuel production. Currently, the majority of the cell-wall synthesis-related (CWSR) proteins are unknown even for model plant Arabidopsis thaliana. We report a computational framework for predicting CWSR proteins based on protein-protein interaction (PPI) data and known CWSR proteins. We predict a protein to be a CWSR protein if it interacts with known CWSR proteins (seeds) with high statistical significance. Using this technique, we predicted 100 candidate CWSR proteins in Arabidopsis thaliana, 8 of which were experimentally confirmed by previous reports. Forty-two candidates have either independent supporting evidence or strong functional relevance to cell-wall synthesis and, hence, are considered as the most reliable predictions. For 33 of the predicted CWSR proteins, we have predicted their detailed functional roles in CWS, based on analyses of their domain architectures, phylogeny, and current functional annotation in conjunction with a literature search. We present the constructed PPIs covering all the known and predicted CWSR proteins at http://csbl.bmb.uga.edu/∼zhouchan/CellWallProtein/. The 42 most reliable candidates provide useful targets to experimentalists for further investigation, and the PPI data constructed in this work provides new information for cell-wall research.
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Affiliation(s)
- Chan Zhou
- Computational Systems Biology Laboratory, Department of Biochemistry and Molecular Biology, and Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA
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24
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Hansen SF, Bettler E, Rinnan A, Engelsen SB, Breton C. Exploring genomes for glycosyltransferases. MOLECULAR BIOSYSTEMS 2010; 6:1773-81. [PMID: 20556308 DOI: 10.1039/c000238k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Glycosyltransferases are one of the largest and most diverse enzyme groups in Nature. They catalyse the synthesis of glycosidic linkages by the transfer of a sugar residue from a donor to an acceptor substrate. These enzymes have been classified into families on the basis of amino acid sequence similarity that are kept updated in the Carbohydrate Active enZyme database (CAZy, ). The repertoire of glycosyltransferases in genomes is believed to determine the diversity of cellular glycan structures, and current estimates suggest that for most genomes about 1% of the coding regions are glycosyltransferases. However, plants tend to have far more glycosyltransferase genes than any other organism sequenced to date, and this can be explained by the highly complex polysaccharide network that form the cell wall and also by the numerous glycosylated secondary metabolites. In recent years, various bioinformatics strategies have been used to search bacterial and plant genomes for new glycosyltransferase genes. These are based on the use of remote homology detection methods that act at the 1D, 2D, and 3D level. The combined use of methods such as profile Hidden Markov Model (HMM) and fold recognition appears to be appropriate for this class of enzyme. Chemometric tools are also particularly well suited for obtaining an overview of multivariate data and revealing hidden latent information when dealing with large and highly complex datasets.
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Harholt J, Suttangkakul A, Vibe Scheller H. Biosynthesis of pectin. PLANT PHYSIOLOGY 2010; 153:384-95. [PMID: 20427466 PMCID: PMC2879803 DOI: 10.1104/pp.110.156588] [Citation(s) in RCA: 335] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2010] [Accepted: 04/27/2010] [Indexed: 05/17/2023]
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Si JN, Yan RX, Wang C, Zhang Z, Su XD. TIM-Finder: a new method for identifying TIM-barrel proteins. BMC STRUCTURAL BIOLOGY 2009; 9:73. [PMID: 20003393 PMCID: PMC2803183 DOI: 10.1186/1472-6807-9-73] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Accepted: 12/14/2009] [Indexed: 11/28/2022]
Abstract
Background The triosephosphate isomerase (TIM)-barrel fold occurs frequently in the proteomes of different organisms, and the known TIM-barrel proteins have been found to play diverse functional roles. To accelerate the exploration of the sequence-structure protein landscape in the TIM-barrel fold, a computational tool that allows sensitive detection of TIM-barrel proteins is required. Results To develop a new TIM-barrel protein identification method in this work, we consider three descriptors: a sequence-alignment-based descriptor using PSI-BLAST e-values and bit scores, a descriptor based on secondary structure element alignment (SSEA), and a descriptor based on the occurrence of PROSITE functional motifs. With the assistance of Support Vector Machine (SVM), the three descriptors were combined to obtain a new method with improved performance, which we call TIM-Finder. When tested on the whole proteome of Bacillus subtilis, TIM-Finder is able to detect 194 TIM-barrel proteins at a 99% confidence level, outperforming the PSI-BLAST search as well as one existing fold recognition method. Conclusions TIM-Finder can serve as a competitive tool for proteome-wide TIM-barrel protein identification. The TIM-Finder web server is freely accessible at http://202.112.170.199/TIM-Finder/.
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Affiliation(s)
- Jing-Na Si
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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Titz A, Butschi A, Henrissat B, Fan YY, Hennet T, Razzazi-Fazeli E, Hengartner MO, Wilson IBH, Künzler M, Aebi M. Molecular basis for galactosylation of core fucose residues in invertebrates: identification of caenorhabditis elegans N-glycan core alpha1,6-fucoside beta1,4-galactosyltransferase GALT-1 as a member of a novel glycosyltransferase family. J Biol Chem 2009; 284:36223-36233. [PMID: 19858195 DOI: 10.1074/jbc.m109.058354] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Galectin CGL2 from the ink cap mushroom Coprinopsis cinerea displays toxicity toward the model nematode Caenorhabditis elegans. A mutation in a putative glycosyltransferase-encoding gene resulted in a CGL2-resistant C. elegans strain characterized by N-glycans lacking the beta1,4-galactoside linked to the alpha1,6-linked core fucose. Expression of the corresponding GALT-1 protein in insect cells was used to demonstrate a manganese-dependent galactosyltransferase activity. In vitro, the GALT-1 enzyme showed strong selectivity for acceptors with alpha1,6-linked N-glycan core fucosides and required Golgi- dependent modifications on the oligosaccharide antennae for optimal synthesis of the Gal-beta1,4-fucose structure. Phylogenetic analysis of the GALT-1 protein sequence identified a novel glycosyltransferase family (GT92) with members widespread among eukarya but absent in mammals.
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Affiliation(s)
- Alexander Titz
- Institute of Microbiology, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
| | - Alex Butschi
- Institute of Molecular Biology, University of Zürich, CH-8057 Zürich, Switzerland
| | - Bernard Henrissat
- Architecture et Fonction des Macromolécules Biologiques, UMR6098, CNRS and Universités Aix-Marseille I and II, 13288 Marseille, France
| | - Yao-Yun Fan
- Institute of Microbiology, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
| | - Thierry Hennet
- Institute of Physiology, University of Zürich, CH-8057 Zürich, Switzerland
| | - Ebrahim Razzazi-Fazeli
- VetOMICS Core Facility for Proteomics and Metabolomics Studies, University of Veterinary Medicine, A-1210 Vienna, Austria
| | - Michael O Hengartner
- Institute of Molecular Biology, University of Zürich, CH-8057 Zürich, Switzerland
| | - Iain B H Wilson
- Department für Chemie, Universität für Bodenkultur, A-1190 Vienna, Austria
| | - Markus Künzler
- Institute of Microbiology, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland
| | - Markus Aebi
- Institute of Microbiology, ETH Zürich, Wolfgang-Pauli-Strasse 10, CH-8093 Zürich, Switzerland.
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