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Shiose L, Dos Reis Moreira J, Lira BS, Ponciano G, Gomez Ocampo G, Wu RTA, Dos Santos Júnior JL, Ntelkis N, Clicque E, Oliveira MJ, Lubini G, Floh EIS, Botto JF, Ferreira MJP, Goossens A, Freschi L, Rossi M. A tomato B-box protein regulates plant development and fruit quality through the interaction with PIF4, HY5 and RIN transcription factors. J Exp Bot 2024:erae119. [PMID: 38492237 DOI: 10.1093/jxb/erae119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Indexed: 03/18/2024]
Abstract
During the last decade, the knowledge about BBX proteins has abruptly increased. Genome-wide studies identified BBX gene family in several ornamental, industry and food crops; however, the reports regarding the role of these genes as regulators of agronomically important traits are scarce. Here, by phenotyping a knockout mutant, we performed a comprehensive functional characterization of the tomato locus Solyc12g089240, hereafter called SlBBX20. The data revealed the encoded protein as a positive regulator of light signaling affecting several physiological processes during plant lifespan. By the inhibition of PHYTOCHROME INTERACTING FACTOR 4 (SlPIF4)-auxin crosstalk, SlBBX20 regulates photomorphogenesis. Later, it controls the balance between cell division and expansion to guarantee the correct vegetative and reproductive development. In fruits, SlBBX20 is transcriptionally induced by the master transcription factor RIPENING INHIBITOR (SlRIN) and, together with ELONGATED HYPOCOTYL 5 (SlHY5), upregulates flavonoids biosynthetic genes. Finally, SlBBX20 promotes the accumulation of steroidal glycoalkaloids and attenuates Botrytis cinerea infection. This work clearly demonstrates that BBX proteins are multilayer regulators of plant physiology, not only because they affect multiple processes along plant development but also regulate other genes at the transcriptional and post-translational levels.
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Affiliation(s)
- Lumi Shiose
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brasil
| | - Juliene Dos Reis Moreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brasil
| | - Bruno Silvestre Lira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brasil
| | - Gabriel Ponciano
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brasil
| | - Gabriel Gomez Ocampo
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida San Martín 4453, Buenos Aires C1417DSE, Argentina
| | - Raquel Tsu Ay Wu
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brasil
| | - José Laurindo Dos Santos Júnior
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brasil
| | - Nikolaos Ntelkis
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark-Zwijnaarde 71, Ghent, Belgium
| | - Elke Clicque
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark-Zwijnaarde 71, Ghent, Belgium
| | - Maria José Oliveira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brasil
| | - Greice Lubini
- Departamento de Biologia, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida Bandeirantes 3900, 14040-901, Ribeirão Preto, Brasil
| | - Eny Iochevet Segal Floh
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brasil
| | - Javier Francisco Botto
- IFEVA, Facultad de Agronomía, Universidad de Buenos Aires y Consejo Nacional de Investigaciones Científicas y Técnicas, Avenida San Martín 4453, Buenos Aires C1417DSE, Argentina
| | - Marcelo José Pena Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brasil
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark-Zwijnaarde 71, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark-Zwijnaarde 71, Ghent, Belgium
| | - Luciano Freschi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brasil
| | - Magdalena Rossi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brasil
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Lacchini E, Venegas-Molina J, Goossens A. Structural and functional diversity in plant specialized metabolism signals and products: The case of oxylipins and triterpenes. Curr Opin Plant Biol 2023; 74:102371. [PMID: 37148672 DOI: 10.1016/j.pbi.2023.102371] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 05/08/2023]
Abstract
Metabolic enzymes tend to evolve towards catalytic efficacy, precision and speed. This seems particularly true for ancient and conserved enzymes involved in fundamental cellular processes that are present virtually in every cell and organism and converting and producing relatively limited metabolite numbers. Nevertheless, sessile organisms like plants have an astonishing repertoire of specific (specialized) metabolites that, by numbers and chemical complexity, by far exceed primary metabolites. Most theories agree that early gene duplication, subsequent positive selection and diversifying evolution have allowed relaxed selection of duplicated metabolic genes, thus facilitating the accumulation of mutations that could broaden substrate/product specificity and lower activation barriers and kinetics. Here, we use oxylipins, oxygenated fatty acids of plastidial origin to which the phytohormone jasmonate belongs, and triterpenes, a large group of specialized metabolites whose biosynthesis is often elicited by jasmonates, to showcase the structural and functional diversity of chemical signals and products in plant metabolism.
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Affiliation(s)
- Elia Lacchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Jhon Venegas-Molina
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium.
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3
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Lacchini E, Erffelinck ML, Mertens J, Marcou S, Molina-Hidalgo FJ, Tzfadia O, Venegas-Molina J, Cárdenas PD, Pollier J, Tava A, Bak S, Höfte M, Goossens A. The saponin bomb: a nucleolar-localized β-glucosidase hydrolyzes triterpene saponins in Medicago truncatula. New Phytol 2023; 239:705-719. [PMID: 36683446 DOI: 10.1111/nph.18763] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 01/09/2023] [Indexed: 06/15/2023]
Abstract
Plants often protect themselves from their own bioactive defense metabolites by storing them in less active forms. Consequently, plants also need systems allowing correct spatiotemporal reactivation of such metabolites, for instance under pathogen or herbivore attack. Via co-expression analysis with public transcriptomes, we determined that the model legume Medicago truncatula has evolved a two-component system composed of a β-glucosidase, denominated G1, and triterpene saponins, which are physically separated from each other in intact cells. G1 expression is root-specific, stress-inducible, and coregulated with that of the genes encoding the triterpene saponin biosynthetic enzymes. However, the G1 protein is stored in the nucleolus and is released and united with its typically vacuolar-stored substrates only upon tissue damage, partly mediated by the surfactant action of the saponins themselves. Subsequently, enzymatic removal of carbohydrate groups from the saponins creates a pool of metabolites with an increased broad-spectrum antimicrobial activity. The evolution of this defense system benefited from both the intrinsic condensation abilities of the enzyme and the bioactivity properties of its substrates. We dub this two-component system the saponin bomb, in analogy with the mustard oil and cyanide bombs, commonly used to describe the renowned β-glucosidase-dependent defense systems for glucosinolates and cyanogenic glucosides.
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Affiliation(s)
- Elia Lacchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Marie-Laure Erffelinck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Jan Mertens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Shirley Marcou
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, B-9000, Belgium
| | - Francisco Javier Molina-Hidalgo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Oren Tzfadia
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Jhon Venegas-Molina
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Pablo D Cárdenas
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, DK-1871, Denmark
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
| | - Aldo Tava
- CREA Research Centre for Animal Production and Aquaculture, Lodi, 26900, Italy
| | - Søren Bak
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, DK-1871, Denmark
| | - Monica Höfte
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, B-9000, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Ghent, B-9052, Belgium
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4
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De Bruyn C, Ruttink T, Lacchini E, Rombauts S, Haegeman A, De Keyser E, Van Poucke C, Desmet S, Jacobs TB, Eeckhaut T, Goossens A, Van Laere K. Identification and characterization of CYP71 subclade cytochrome P450 enzymes involved in the biosynthesis of bitterness compounds in Cichorium intybus. Front Plant Sci 2023; 14:1200253. [PMID: 37426959 PMCID: PMC10324620 DOI: 10.3389/fpls.2023.1200253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/06/2023] [Indexed: 07/11/2023]
Abstract
Industrial chicory (Cichorium intybus var. sativum) and witloof (C. intybus var. foliosum) are crops with an important economic value, mainly cultivated for inulin production and as a leafy vegetable, respectively. Both crops are rich in nutritionally relevant specialized metabolites with beneficial effects for human health. However, their bitter taste, caused by the sesquiterpene lactones (SLs) produced in leaves and taproot, limits wider applications in the food industry. Changing the bitterness would thus create new opportunities with a great economic impact. Known genes encoding enzymes involved in the SL biosynthetic pathway are GERMACRENE A SYNTHASE (GAS), GERMACRENE A OXIDASE (GAO), COSTUNOLIDE SYNTHASE (COS) and KAUNIOLIDE SYNTHASE (KLS). In this study, we integrated genome and transcriptome mining to further unravel SL biosynthesis. We found that C. intybus SL biosynthesis is controlled by the phytohormone methyl jasmonate (MeJA). Gene family annotation and MeJA inducibility enabled the pinpointing of candidate genes related with the SL biosynthetic pathway. We specifically focused on members of subclade CYP71 of the cytochrome P450 family. We verified the biochemical activity of 14 C. intybus CYP71 enzymes transiently produced in Nicotiana benthamiana and identified several functional paralogs for each of the GAO, COS and KLS genes, pointing to redundancy in and robustness of the SL biosynthetic pathway. Gene functionality was further analyzed using CRISPR/Cas9 genome editing in C. intybus. Metabolite profiling of mutant C. intybus lines demonstrated a successful reduction in SL metabolite production. Together, this study increases our insights into the C. intybus SL biosynthetic pathway and paves the way for the engineering of C. intybus bitterness.
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Affiliation(s)
- Charlotte De Bruyn
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Elia Lacchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Annelies Haegeman
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Ellen De Keyser
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Christof Van Poucke
- Technology and Food Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | | | - Thomas B. Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Tom Eeckhaut
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Katrijn Van Laere
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
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5
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Selma S, Ntelkis N, Nguyen TH, Goossens A. Engineering the plant metabolic system by exploiting metabolic regulation. Plant J 2023; 114:1149-1163. [PMID: 36799285 DOI: 10.1111/tpj.16157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/10/2023] [Accepted: 02/15/2023] [Indexed: 05/31/2023]
Abstract
Plants are the most sophisticated biofactories and sources of food and biofuels present in nature. By engineering plant metabolism, the production of desired compounds can be increased and the nutritional or commercial value of the plant species can be improved. However, this can be challenging because of the complexity of the regulation of multiple genes and the involvement of different protein interactions. To improve metabolic engineering (ME) capabilities, different tools and strategies for rerouting the metabolic pathways have been developed, including genome editing and transcriptional regulation approaches. In addition, cutting-edge technologies have provided new methods for understanding uncharacterized biosynthetic pathways, protein degradation mechanisms, protein-protein interactions, or allosteric feedback, enabling the design of novel ME approaches.
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Affiliation(s)
- Sara Selma
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Nikolaos Ntelkis
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Trang Hieu Nguyen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Nguyen TH, Thiers L, Van Moerkercke A, Bai Y, Fernández-Calvo P, Minne M, Depuydt T, Colinas M, Verstaen K, Van Isterdael G, Nützmann HW, Osbourn A, Saeys Y, De Rybel B, Vandepoele K, Ritter A, Goossens A. A redundant transcription factor network steers spatiotemporal Arabidopsis triterpene synthesis. Nat Plants 2023; 9:926-937. [PMID: 37188853 DOI: 10.1038/s41477-023-01419-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/14/2023] [Indexed: 05/17/2023]
Abstract
Plant specialized metabolites modulate developmental and ecological functions and comprise many therapeutic and other high-value compounds. However, the mechanisms determining their cell-specific expression remain unknown. Here we describe the transcriptional regulatory network that underlies cell-specific biosynthesis of triterpenes in Arabidopsis thaliana root tips. Expression of thalianol and marneral biosynthesis pathway genes depends on the phytohormone jasmonate and is limited to outer tissues. We show that this is promoted by the activity of redundant bHLH-type transcription factors from two distinct clades and coactivated by homeodomain factors. Conversely, the DOF-type transcription factor DAG1 and other regulators prevent expression of the triterpene pathway genes in inner tissues. We thus show how precise expression of triterpene biosynthesis genes is determined by a robust network of transactivators, coactivators and counteracting repressors.
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Affiliation(s)
- Trang Hieu Nguyen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Louis Thiers
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Alex Van Moerkercke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yuechen Bai
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- School of Life Sciences, Fudan University, Shanghai, P.R. China
| | - Patricia Fernández-Calvo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Misión Biolóxica de Galicia, CSIC, Pontevedra, Spain
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)-Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus Montegancedo UPM, Madrid, Spain
| | - Max Minne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Thomas Depuydt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Maite Colinas
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany
| | - Kevin Verstaen
- VIB Single Cell Core, Ghent-Leuven, Belgium
- VIB Center for Inflammation Research, Data Mining and Modelling for Biomedicine, Ghent, Belgium
| | - Gert Van Isterdael
- VIB Flow Core, VIB Center for Inflammation Research, Ghent, Belgium
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Hans-Wilhelm Nützmann
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, UK
- Department of Biology and Biochemistry, The Milner Centre for Evolution, University of Bath, Bath, UK
| | - Anne Osbourn
- Department of Biochemistry and Metabolism, John Innes Centre, Norwich, UK
| | - Yvan Saeys
- VIB Center for Inflammation Research, Data Mining and Modelling for Biomedicine, Ghent, Belgium
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, Belgium
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Bioinformatics Institute Ghent, Ghent University, Ghent, Belgium
| | - Andrés Ritter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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Gryffroy L, De Ryck J, Jonckheere V, Goormachtig S, Goossens A, Van Damme P. Cataloguing Protein Complexes In Planta Using TurboID-Catalyzed Proximity Labeling. Methods Mol Biol 2023; 2690:311-334. [PMID: 37450157 DOI: 10.1007/978-1-0716-3327-4_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/18/2023]
Abstract
Mapping protein-protein interactions is crucial to understand protein function. Recent advances in proximity-dependent biotinylation (BioID) coupled to mass spectrometry (MS) allow the characterization of protein complexes in diverse plant models. Here, we describe the use of BioID in hairy root cultures of tomato and provide detailed information on how to analyze the data obtained by MS.
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Affiliation(s)
- Lore Gryffroy
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Ghent, Belgium
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Joren De Ryck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Ghent, Belgium
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Veronique Jonckheere
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Sofie Goormachtig
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Ghent, Belgium
| | - Petra Van Damme
- iRIP Unit, Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium.
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Venegas-Molina J, Van Damme P, Goossens A. Identification of Plant Protein-Metabolite Interactions by Limited Proteolysis-Coupled Mass Spectrometry (LiP-MS). Methods Mol Biol 2023; 2554:47-67. [PMID: 36178620 DOI: 10.1007/978-1-0716-2624-5_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
The interactions between metabolites and proteins constitute crucial events in cell signaling and metabolism. In recent years, large-scale proteomics techniques have emerged to identify and characterize protein-metabolite interactions. However, their implementation in plants is generally lagging behind, preventing a complete understanding of the regulatory mechanisms governing plant physiology. Recently, a novel approach to identify metabolite-binding proteins, namely, limited proteolysis-coupled mass spectrometry (LiP-MS), was developed originally for microbial proteomes. Here, we present an adapted and accessible version of the LiP-MS protocol for use in plants. Plant proteomes are extracted and incubated with the metabolite of interest or control treatment, followed by a limited digestion by a nonspecific/promiscuous protease. Subsequently, a conventional shotgun proteomics sample preparation is performed including a complete digestion with the sequence-specific protease trypsin. Finally, label-free proteomics analysis is applied to identify structure-dependent proteolytic patterns corresponding to protein targets of the specific metabolite and their binding sites. Given its amenability to relatively high throughput, the LiP-MS approach may open a potent avenue for the discovery of novel regulatory mechanisms in plant species.
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Affiliation(s)
- Jhon Venegas-Molina
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Petra Van Damme
- Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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9
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Tuytens B, Goossens A, Yperzeele L, Van Diermen L, Cras P, Sabbe BGC, Schrijvers D, Van Den Eede F. [Does ECT raise the risk of a recurrent stroke?]. Tijdschr Psychiatr 2023; 65:430-436. [PMID: 37756028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 09/28/2023]
Abstract
BACKGROUND As the guidelines and evidence for the use of electroconvulsive therapy (ECT) in patients with a recent or past history of stroke are unclear, ECT tends to be avoided in this population. AIM To give a systematic review the literature on the risk and incidence of cerebrovascular accidents after ECT in these patients. METHOD A systematic literature search was performed according to the PRISMA guidelines in PubMed and in the Cochrane Library. Publications in which ECT was applied in patients with a history of stroke were included by using specific MeSH terms. RESULTS The following 19 articles met the criteria for review: 1 wide-scale prospective study, 1 small-scale prospective study with a control group, 3 small-scale retrospective studies, and 14 case reports. In the vast longitudinal Danish study, ECT was not associated with an elevated risk of recurrent stroke. Similarly, none of the other studies found the risk to be raised. CONCLUSION Despite the limited number of prospective studies and the methodological discrepancies in the reports, ECT does not seem to be associated with an elevated risk of recurrent stroke. This review supports the safe use of ECT in patients with a recent or past history of stroke, if prior neurologic and cardiovascular assessments are being performed, as well as monitoring during the treatment.
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10
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Ribeiro B, Erffelinck ML, Lacchini E, Ceulemans E, Colinas M, Williams C, Van Hamme E, De Clercq R, Perassolo M, Goossens A. Corrigendum: Interference between ER stress-related bZIP-type and jasmonate-inducible bHLH-type transcription factors in the regulation of triterpene saponin biosynthesis in Medicago truncatula. Front Plant Sci 2022; 13:1103943. [PMID: 36561454 PMCID: PMC9767438 DOI: 10.3389/fpls.2022.1103943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 06/17/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2022.903793.].
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Affiliation(s)
- Bianca Ribeiro
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marie-Laure Erffelinck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Elia Lacchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Evi Ceulemans
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Maite Colinas
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Clara Williams
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - Rebecca De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Maria Perassolo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Cátedra de Biotecnología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Nanobiotecnolog´ıa (NANOBIOTEC), Consejo Nacional de Investigaciones Científicas y TécnicasUniversidad de Buenos Aires, Buenos Aires, Argentina
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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11
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Swinnen G, De Meyer M, Pollier J, Molina-Hidalgo FJ, Ceulemans E, Venegas-Molina J, De Milde L, Fernández-Calvo P, Ron M, Pauwels L, Goossens A. The basic helix-loop-helix transcription factors MYC1 and MYC2 have a dual role in the regulation of constitutive and stress-inducible specialized metabolism in tomato. New Phytol 2022; 236:911-928. [PMID: 35838067 DOI: 10.1111/nph.18379] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
Plants produce specialized metabolites to protect themselves from biotic enemies. Members of the Solanaceae family accumulate phenylpropanoid-polyamine conjugates (PPCs) in response to attackers while also maintaining a chemical barrier of steroidal glycoalkaloids (SGAs). Across the plant kingdom, biosynthesis of such defense compounds is promoted by jasmonate signaling in which clade IIIe basic helix-loop-helix (bHLH) transcription factors play a central role. By characterizing hairy root mutants obtained through Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated protein 9 (CRISPR-Cas9) genome editing, we show that the tomato clade IIIe bHLH transcription factors, MYC1 and MYC2, redundantly control jasmonate-inducible PPC and SGA production, and are also essential for constitutive SGA biosynthesis. Double myc1 myc2 loss-of-function tomato hairy roots displayed suppressed constitutive expression of SGA biosynthesis genes, and severely reduced levels of the main tomato SGAs α-tomatine and dehydrotomatine. In contrast, basal expression of genes involved in PPC biosynthesis was not affected. CRISPR-Cas9(VQR) genome editing of a specific cis-regulatory element, targeted by MYC1/2, in the promoter of a SGA precursor biosynthesis gene led to decreased constitutive expression of this gene, but did not affect its jasmonate inducibility. Our results demonstrate that clade IIIe bHLH transcriptional regulators have evolved under the control of distinct regulatory cues to specifically steer constitutive and stress-inducible specialized metabolism.
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Affiliation(s)
- Gwen Swinnen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Margaux De Meyer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
- VIB Metabolomics Core, 9052, Ghent, Belgium
| | - Francisco Javier Molina-Hidalgo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Evi Ceulemans
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Jhon Venegas-Molina
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Liesbeth De Milde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Patricia Fernández-Calvo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Mily Ron
- Department of Plant Biology, University of California, Davis, Davis, CA, 95616, USA
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
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12
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Hu X, Garcia E, Goossens A, Gozo M, Lee T, Liu X, Le B, Taylor Meadows K, Eto D, Yusuf I, Lu K, Michels T, Kasem M, Marby K, Rowbottom M, Osterhout R, Carter L. An orally bioavailable ENPP1-selective inhibitor demonstrates superior immune preservation effects over STING agonists and confers antitumor efficacy in combination with other therapies in syngeneic tumor models. Eur J Cancer 2022. [DOI: 10.1016/s0959-8049(22)01133-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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13
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Ribeiro B, Erffelinck ML, Lacchini E, Ceulemans E, Colinas M, Williams C, Van Hamme E, De Clercq R, Perassolo M, Goossens A. Interference between ER stress-related bZIP-type and jasmonate-inducible bHLH-type transcription factors in the regulation of triterpene saponin biosynthesis in Medicago truncatula. Front Plant Sci 2022; 13:903793. [PMID: 36247618 PMCID: PMC9562455 DOI: 10.3389/fpls.2022.903793] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 09/07/2022] [Indexed: 06/01/2023]
Abstract
Triterpene saponins (TS) are a structurally diverse group of metabolites that are widely distributed in plants. They primarily serve as defense compounds and their production is often triggered by biotic stresses through signaling cascades that are modulated by phytohormones such as the jasmonates (JA). Two JA-modulated basic helix-loop-helix (bHLH) transcription factors (TFs), triterpene saponin biosynthesis activating regulator 1 (TSAR1) and TSAR2, have previously been identified as direct activators of TS biosynthesis in the model legume Medicago truncatula. Here, we report on the involvement of the core endoplasmic reticulum (ER) stress-related basic leucine zipper (bZIP) TFs bZIP17 and bZIP60 in the regulation of TS biosynthesis. Expression and processing of M. truncatula bZIP17 and bZIP60 proteins were altered in roots with perturbed TS biosynthesis or treated with JA. Accordingly, such roots displayed an altered ER network structure. M. truncatula bZIP17 and bZIP60 proteins were shown to localize in the nucleus and appeared to be capable of interfering with the TSAR-mediated transactivation of TS biosynthesis genes. Furthermore, interference between ER stress-related bZIP and JA-modulated bHLH TFs in the regulation of JA-dependent terpene biosynthetic pathways may be widespread in the plant kingdom, as we demonstrate that it also occurs in the regulation of monoterpene indole alkaloid biosynthesis in the medicinal plant Catharanthus roseus.
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Affiliation(s)
- Bianca Ribeiro
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marie-Laure Erffelinck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Elia Lacchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Evi Ceulemans
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Maite Colinas
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Clara Williams
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - Rebecca De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Maria Perassolo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Cátedra de Biotecnología, Departamento de Microbiología, Inmunología y Biotecnología, Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Nanobiotecnología (NANOBIOTEC), Consejo Nacional de Investigaciones Científicas y Técnicas-Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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14
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An C, Deng L, Zhai H, You Y, Wu F, Zhai Q, Goossens A, Li C. Regulation of jasmonate signaling by reversible acetylation of TOPLESS in Arabidopsis. Mol Plant 2022; 15:1329-1346. [PMID: 35780296 DOI: 10.1016/j.molp.2022.06.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 04/28/2022] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
The plant hormone jasmonate (JA) regulates plant immunity and adaptive growth by orchestrating a genome-wide transcriptional program. Key regulators of JA-responsive gene expression include the master transcription factor MYC2, which is repressed by the conserved Groucho/Tup1-like corepressor TOPLESS (TPL) in the resting state. However, the mechanisms underlying TPL-mediated transcriptional repression of MYC2 activity and hormone-dependent switching between repression and de-repression remain enigmatic. Here, we report the regulation of TPL activity and JA signaling by reversible acetylation of TPL. We found that the histone acetyltransferase GCN5 could mediate TPL acetylation, which enhances its interaction with the NOVEL-INTERACTOR-OF-JAZ (NINJA) adaptor and promotes its recruitment to MYC2 target promoters, facilitating transcriptional repression. Conversely, TPL deacetylation by the histone deacetylase HDA6 weakens TPL-NINJA interaction and inhibits TPL recruitment to MYC2 target promoters, facilitating transcriptional activation. In the resting state, the opposing activities of GCN5 and HDA6 maintain TPL acetylation homeostasis, promoting transcriptional repression activity of TPL. In response to JA elicitation, HDA6 expression is transiently induced, resulted in decreased TPL acetylation and repressor activity, thereby transcriptional activation of MYC2 target genes. Thus, the GCN5-TPL-HDA6 module maintains the homeostasis of acetylated TPL, thereby determining the transcriptional state of JA-responsive genes. Our findings uncovered a mechanism by which the TPL corepressor activity in JA signaling is actively tuned in a rapid and reversible manner.
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Affiliation(s)
- Chunpeng An
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Deng
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huawei Zhai
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China
| | - Yanrong You
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangming Wu
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingzhe Zhai
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Chuanyou Li
- State Key Laboratory of Plant Genomics, National Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Innovation Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai'an 271018, China.
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15
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Arora D, Abel NB, Liu C, Van Damme P, Yperman K, Eeckhout D, Vu LD, Wang J, Tornkvist A, Impens F, Korbei B, Van Leene J, Goossens A, De Jaeger G, Ott T, Moschou PN, Van Damme D. Correction to: Establishment of Proximity-Dependent Biotinylation Approaches in Different Plant Model Systems. Plant Cell 2022; 34:2806. [PMID: 35357494 PMCID: PMC9252476 DOI: 10.1093/plcell/koac101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Affiliation(s)
- Deepanksha Arora
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Nikolaj B Abel
- Faculty of Biology, Cell Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Chen Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
| | - Petra Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Klaas Yperman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jie Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Anna Tornkvist
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
| | - Francis Impens
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
- VIB Center for Medical Biotechnology, 9052 Ghent, Belgium
- VIB Proteomics Core, 9052 Ghent, Belgium
| | - Barbara Korbei
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Thomas Ott
- Faculty of Biology, Cell Biology, University of Freiburg, 79104 Freiburg, Germany
- Centre for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Panagiotis Nikolaou Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
- Department of Biology, University of Crete, 70013 Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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16
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Kim SW, Alci K, Van Gaever F, Driege Y, Bicalho K, Goeminne G, Libert C, Goossens A, Beyaert R, Staal J. Engineering a highly sensitive biosensor for abscisic acid in mammalian cells. FEBS Lett 2022; 596:2576-2590. [PMID: 35727199 DOI: 10.1002/1873-3468.14431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/21/2022] [Accepted: 05/24/2022] [Indexed: 11/10/2022]
Abstract
Abscisic acid (ABA) is a signaling molecule conserved in plants, bacteria, fungi and animals. Recently, ABA has gained attention for its pharmacological activities and its potential as a biomarker for the severity of chronic obstructive pulmonary disease (COPD) and glioma. This prompts the development of a reliable, sensitive, rapid, and cost-effective method to quantify ABA levels in mammalian cells and tissues. The previously described ABA biosensor system based on the ABA-dependent interaction between the plant ABA receptor PYL1 and co-receptor ABI1 is not sensitive enough for the low ABA levels seen in mammals. Therefore, we optimized this system by replacing PYL1 with other high-affinity plant PYL proteins. The optimized biosensor system engineered with the PYL8 receptor enabled the quantification of ABA at low concentrations in HEK293T cells.
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Affiliation(s)
- Seo Woo Kim
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Center for Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Kübra Alci
- Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,BCCM/GeneCorner, Ghent University, Ghent, Belgium
| | - Femke Van Gaever
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Yasmine Driege
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | | | | | - Claude Libert
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Alain Goossens
- Center for Plant Systems Biology, VIB, Ghent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Rudi Beyaert
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Jens Staal
- Center for Inflammation Research, VIB, Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent, Belgium
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17
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Nguyen TH, Goossens A, Lacchini E. Jasmonate: A hormone of primary importance for plant metabolism. Curr Opin Plant Biol 2022; 67:102197. [PMID: 35248983 DOI: 10.1016/j.pbi.2022.102197] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/26/2022] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Over the years, jasmonates (JAs) have become recognized as one of the main plant hormones that regulate stress responses by activating defense programs and the production of specialized metabolites. High JA levels have been associated with reduced plant growth, supposedly as a result of the reallocation of carbon sources from primary growth to the biosynthesis of defense compounds. Recent advances suggest however that tight regulatory networks integrate several sensing pathways to steer plant metabolism, and thereby drive the trade-off between growth and defense. In this review, we discuss how JA influences primary metabolism and how it is connected to light-regulated processes, nutrient sensing and energy metabolism. Finally, we speculate that JA, in a conceptual parallelism with adrenaline for humans, overall boosts cellular processes to keep up with an increased metabolic demand during harsh times.
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Affiliation(s)
- Trang Hieu Nguyen
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium.
| | - Elia Lacchini
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium
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18
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Darwish E, Ghosh R, Ontiveros-Cisneros A, Tran HC, Petersson M, De Milde L, Broda M, Goossens A, Van Moerkercke A, Khan K, Van Aken O. Touch signaling and thigmomorphogenesis are regulated by complementary CAMTA3- and JA-dependent pathways. Sci Adv 2022; 8:eabm2091. [PMID: 35594358 PMCID: PMC9122320 DOI: 10.1126/sciadv.abm2091] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Plants respond to mechanical stimuli to direct their growth and counteract environmental threats. Mechanical stimulation triggers rapid gene expression changes and affects plant appearance (thigmomorphogenesis) and flowering. Previous studies reported the importance of jasmonic acid (JA) in touch signaling. Here, we used reverse genetics to further characterize the molecular mechanisms underlying touch signaling. We show that Piezo mechanosensitive ion channels have no major role in touch-induced gene expression and thigmomorphogenesis. In contrast, the receptor-like kinase Feronia acts as a strong negative regulator of the JA-dependent branch of touch signaling. Last, we show that calmodulin-binding transcriptional activators CAMTA1/2/3 are key regulators of JA-independent touch signaling. CAMTA1/2/3 cooperate to directly bind the promoters and activate gene expression of JA-independent touch marker genes like TCH2 and TCH4. In agreement, camta3 mutants show a near complete loss of thigmomorphogenesis and touch-induced delay of flowering. In conclusion, we have now identified key regulators of two independent touch-signaling pathways.
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Affiliation(s)
- Essam Darwish
- Department of Biology, Lund University, Lund, Sweden
- Plant Physiology Section, Agricultural Botany Department, Faculty of Agriculture, Cairo University, Egypt
| | - Ritesh Ghosh
- Department of Biology, Lund University, Lund, Sweden
| | | | | | | | - Liesbeth De Milde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Gent, Belgium
| | - Martyna Broda
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Perth, Australia
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Gent, Belgium
- VIB Center for Plant Systems Biology, Gent, Belgium
| | | | - Kasim Khan
- Department of Biology, Lund University, Lund, Sweden
| | - Olivier Van Aken
- Department of Biology, Lund University, Lund, Sweden
- Corresponding author.
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19
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De Jaegere I, Cornelis Y, De Clercq T, Goossens A, Van de Poel B. Overview of Witloof Chicory ( Cichorium intybus L.) Discolorations and Their Underlying Physiological and Biochemical Causes. Front Plant Sci 2022; 13:843004. [PMID: 35283895 PMCID: PMC8905253 DOI: 10.3389/fpls.2022.843004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 01/31/2022] [Indexed: 06/14/2023]
Abstract
Many fruits and vegetables suffer from unwanted discolorations that reduce product quality, leading to substantial losses along the supply chain. Witloof chicory (Cichorium intybus L. var. foliosum), a specialty crop characterized by its unique bitter taste and crunchiness, is particularly sensitive to various types of red and brown discolorations. The etiolated vegetable suffers from three predominant color disorders, i.e., core browning, internal leaf reddening, and leaf edge browning. Additionally, several less frequently observed color disorders such as hollow pith, external red, and point noir can also negatively affect crop quality. In this article, we bring together fragmented literature and present a comprehensive overview of the different discoloration types in chicory, and discuss their potential underlying physiological causes, including laticifer rupture, calcium deficiency, and a disturbed water distribution. We also describe the role of environmental cues that influence discoloration incidence, including cultivation and postharvest storage conditions such as forcing and storage temperature, root ripeness and the duration of the forcing process. Finally, we zoom in on the underlying biochemical pathways that govern color disorders in witloof chicory, with a strong emphasis on polyphenol oxidase.
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Affiliation(s)
- Isabel De Jaegere
- Laboratory of Molecular Plant Hormone Physiology, Division of Crop Biotechnics, Department of Biosystems, University of Leuven, Leuven, Belgium
| | | | - Tim De Clercq
- Praktijkpunt Landbouw Vlaams-Brabant, Herent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Bram Van de Poel
- Laboratory of Molecular Plant Hormone Physiology, Division of Crop Biotechnics, Department of Biosystems, University of Leuven, Leuven, Belgium
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20
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Swinnen G, Mauxion JP, Baekelandt A, De Clercq R, Van Doorsselaere J, Inzé D, Gonzalez N, Goossens A, Pauwels L. SlKIX8 and SlKIX9 are negative regulators of leaf and fruit growth in tomato. Plant Physiol 2022; 188:382-396. [PMID: 34601614 PMCID: PMC8774823 DOI: 10.1093/plphys/kiab464] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/26/2021] [Indexed: 05/21/2023]
Abstract
Plant organ size and shape are major agronomic traits that depend on cell division and expansion, which are both regulated by complex gene networks. In several eudicot species belonging to the rosid clade, organ growth is controlled by a repressor complex consisting of PEAPOD (PPD) and KINASE-INDUCIBLE DOMAIN INTERACTING (KIX) proteins. The role of these proteins in asterids, which together with the rosids constitute most of the core eudicot species, is unknown. We used Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated protein 9 genome editing to target SlKIX8 and SlKIX9 in the asterid model species tomato (Solanum lycopersicum) and analyzed loss-of-function phenotypes. Loss-of-function of SlKIX8 and SlKIX9 led to the production of enlarged, dome-shaped leaves and these leaves exhibited increased expression of putative Solanum lycopersicum PPD (SlPPD target genes. Unexpectedly, kix8 kix9 mutants carried enlarged fruits with increased pericarp thickness due to cell expansion. At the molecular level, protein interaction assays indicated that SlKIX8 and SlKIX9 act as adaptors between the SlPPD and SlTOPLESS co-repressor proteins. Our results show that KIX8 and KIX9 are regulators of organ growth in asterids and can be used in strategies to improve important traits in produce such as thickness of the fruit flesh.
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Affiliation(s)
- Gwen Swinnen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | | | - Alexandra Baekelandt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Rebecca De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | | | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | | | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Author for communication:
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21
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Colinas M, Goossens A. Transient Gene Expression in Catharanthus roseus Flower Petals Using Agroinfiltration. Methods Mol Biol 2022; 2505:281-291. [PMID: 35732952 DOI: 10.1007/978-1-0716-2349-7_20] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Transient transformation methods are frequently used to determine gene function. However, until recently only a few methods have been available in the model medicinal plant Catharanthus roseus. Here, we describe a rapid and highly reproducible protocol for the overexpression of genes of interest by agroinfiltration of C. roseus flower petals. This high throughput method is particularly suitable for screening purposes, for instance, target gene screening of transcription factor candidates, and complements other available methods.
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Affiliation(s)
- Maite Colinas
- Department of Natural Product Biosynthesis, Max Planck Institute for Chemical Ecology, Jena, Germany.
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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22
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Agner T, Goossens A. Time for a change. Br J Dermatol 2021; 186:212-213. [PMID: 34818433 DOI: 10.1111/bjd.20867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/07/2021] [Indexed: 11/28/2022]
Affiliation(s)
- T Agner
- University of Copenhagen, Bispebjerg Hospital, Copenhagen, NV, 2400, Denmark
| | - A Goossens
- Department of Dermatology, University Hospital KU Leuven, Leuven, 3000, Belgium
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23
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Rigal A, Doyle SM, Ritter A, Raggi S, Vain T, O’Brien JA, Goossens A, Pauwels L, Robert S. A network of stress-related genes regulates hypocotyl elongation downstream of selective auxin perception. Plant Physiol 2021; 187:430-445. [PMID: 34618142 PMCID: PMC8418399 DOI: 10.1093/plphys/kiab269] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 05/06/2021] [Indexed: 06/13/2023]
Abstract
The plant hormone auxin, a master coordinator of development, regulates hypocotyl elongation during seedling growth. We previously identified the synthetic molecule RubNeddin 1 (RN1), which induces degradation of the AUXIN/INDOLE-3-ACETIC ACID (AUX/IAA) transcriptional repressors INDOLE-3-ACETIC ACID-INDUCIBLE3 (IAA3) and IAA7 in planta and strongly promotes hypocotyl elongation. In the present study, we show that despite the structural similarity of RN1 to the synthetic auxin 2,4-dichlorophenoxyacetic-acid (2,4-D), direct treatments with these compounds in Arabidopsis (Arabidopsis thaliana) result in distinct effects, possibly due to enhanced uptake of RN1 and low-level, chronic release of 2,4-D from RN1 in planta. We confirm RN1-induced hypocotyl elongation occurs via specific TRANSPORT INHIBITOR RESISTANT1 (TIR1)/AUXIN SIGNALING F-BOX (AFB) receptor-mediated auxin signaling involving TIR1, AFB2, and AFB5. Using a transcriptome profiling strategy and candidate gene approach, we identify the genes ZINC FINGER OF ARABIDOPSIS THALIANA10 (ZAT10), ARABIDOPSIS TOXICOS EN LEVADURA31 (ATL31), and WRKY DNA-BINDING PROTEIN33 (WRKY33) as being rapidly upregulated by RN1, despite being downregulated by 2,4-D treatment. RN1-induced expression of these genes also occurs via TIR1/AFB-mediated auxin signaling. Our results suggest both hypocotyl elongation and transcription of these genes are induced by RN1 via the promoted degradation of the AUX/IAA transcriptional repressor IAA7. Moreover, these three genes, which are known to be stress-related, act in an inter-dependent transcriptional regulatory network controlling hypocotyl elongation. Together, our results suggest ZAT10, ATL31, and WRKY33 take part in a common gene network regulating hypocotyl elongation in Arabidopsis downstream of a selective auxin perception module likely involving TIR1, AFB2, and AFB5 and inducing the degradation of IAA7.
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Affiliation(s)
- Adeline Rigal
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Siamsa M. Doyle
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Andrés Ritter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Sara Raggi
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - Thomas Vain
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | - José Antonio O’Brien
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Santiago, 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Avenida Libertador Bernardo O’Higgins 340, Santiago, 8331150, Chile
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Stéphanie Robert
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
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24
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Molina-Hidalgo FJ, Vazquez-Vilar M, D'Andrea L, Demurtas OC, Fraser P, Giuliano G, Bock R, Orzáez D, Goossens A. Engineering Metabolism in Nicotiana Species: A Promising Future. Trends Biotechnol 2021; 39:901-913. [PMID: 33341279 DOI: 10.1016/j.tibtech.2020.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Revised: 11/19/2020] [Accepted: 11/20/2020] [Indexed: 12/31/2022]
Abstract
Molecular farming intends to use crop plants as biofactories for high value-added compounds following application of a wide range of biotechnological tools. In particular, the conversion of nonfood crops into efficient biofactories is expected to be a strong asset in the development of a sustainable bioeconomy. The 'nonfood' status combined with the high metabolic versatility and the capacity of high-yield cultivation highlight the plant genus Nicotiana as one of the most appropriate 'chassis' for molecular farming. Nicotiana species are a rich source of valuable industrial, active pharmaceutical ingredients and nutritional compounds, synthesized from highly complex biosynthetic networks. Here, we review and discuss approaches currently used to design enriched Nicotiana species for molecular farming using new plant breeding techniques (NPBTs).
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Affiliation(s)
- Francisco Javier Molina-Hidalgo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marta Vazquez-Vilar
- Instituto de Biología Molecular y Celular de Plantas (IBMCP-UPV-CSIC), Valencia, Spain
| | - Lucio D'Andrea
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Olivia C Demurtas
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Paul Fraser
- School of Biological Sciences, Royal Holloway, University of London, London, UK
| | - Giovanni Giuliano
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Ralph Bock
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Diego Orzáez
- Instituto de Biología Molecular y Celular de Plantas (IBMCP-UPV-CSIC), Valencia, Spain
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium.
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25
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Zhu T, Herrfurth C, Xin M, Savchenko T, Feussner I, Goossens A, De Smet I. Warm temperature triggers JOX and ST2A-mediated jasmonate catabolism to promote plant growth. Nat Commun 2021; 12:4804. [PMID: 34376671 PMCID: PMC8355256 DOI: 10.1038/s41467-021-24883-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 07/13/2021] [Indexed: 11/12/2022] Open
Abstract
Plants respond to warm temperature by increased elongation growth of organs to enhance cooling capacity. Phytohormones, such as auxin and brassinosteroids, regulate this growth process. However, our view on the players involved in warm temperature-mediated growth remains fragmentary. Here, we show that warm temperature leads to an increased expression of JOXs and ST2A, genes controlling jasmonate catabolism. This leads to an elevated 12HSO4-JA level and consequently to a reduced level of bioactive jasmonates. Ultimately this results in more JAZ proteins, which facilitates plant growth under warm temperature conditions. Taken together, understanding the conserved role of jasmonate signalling during thermomorphogenesis contributes to ensuring food security under a changing climate. Plants undergo morphological changes to enhance cooling at warm temperatures. Here Zhu et al. show that JOXs and ST2A enzymes, which mediate jasmonate catabolism, contribute to this process by reducing the level of bioactive jasmonate facilitating growth responses.
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Affiliation(s)
- Tingting Zhu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Cornelia Herrfurth
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany.,Goettingen Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Mingming Xin
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genomics and Genetic Improvement (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, China
| | - Tatyana Savchenko
- Institute of Basic Biological Problems, Pushchino Scientific Center for Biological Research RAS, Pushchino, Russia
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences and Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany.,Goettingen Service Unit for Metabolomics and Lipidomics, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, Goettingen, Germany
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.,VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ive De Smet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium. .,VIB Center for Plant Systems Biology, Ghent, Belgium.
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26
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Ceulemans E, Ibrahim HMM, De Coninck B, Goossens A. Pathogen Effectors: Exploiting the Promiscuity of Plant Signaling Hubs. Trends Plant Sci 2021; 26:780-795. [PMID: 33674173 DOI: 10.1016/j.tplants.2021.01.005] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 01/21/2021] [Accepted: 01/29/2021] [Indexed: 05/27/2023]
Abstract
Pathogens produce effectors to overcome plant immunity, thereby threatening crop yields and global food security. Large-scale interactomic studies have revealed that pathogens from different kingdoms of life target common plant proteins during infection, the so-called effector hubs. These hubs often play central roles in numerous plant processes through their ability to interact with multiple plant proteins. This ability arises partly from the presence of intrinsically disordered domains (IDDs) in their structure. Here, we highlight the role of the TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP) and JASMONATE-ZIM DOMAIN (JAZ) transcription regulator families as plant signaling and effector hubs. We consider different evolutionary hypotheses to rationalize the existence of diverse effectors sharing common targets and the possible role of IDDs in this interaction.
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Affiliation(s)
- Evi Ceulemans
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB, Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Heba M M Ibrahim
- Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit (KU) Leuven, 3001 Leuven, Belgium
| | - Barbara De Coninck
- Division of Crop Biotechnics, Department of Biosystems, Katholieke Universiteit (KU) Leuven, 3001 Leuven, Belgium.
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium; VIB, Center for Plant Systems Biology, 9052 Ghent, Belgium.
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27
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Dong L, Almeida A, Pollier J, Khakimov B, Bassard JE, Miettinen K, Stærk D, Mehran R, Olsen CE, Motawia MS, Goossens A, Bak S. An independent evolutionary origin for insect deterrent cucurbitacins in Iberis amara. Mol Biol Evol 2021; 38:4659-4673. [PMID: 34264303 PMCID: PMC8557398 DOI: 10.1093/molbev/msab213] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Pieris rapae and Phyllotreta nemorum are Brassicaceae specialists, but do not feed on Iberis amara spp. that contain cucurbitacins. The cucurbitacins are highly oxygenated triterpenoid, occurring widespread in cucurbitaceous species and in a few other plant families. Using de-novo assembled transcriptomics from I. amara, gene co-expression analysis and comparative genomics, we unraveled the evolutionary origin of the insect deterrent cucurbitacins in I. amara. Phylogenetic analysis of five oxidosqualene cyclases and heterologous expression allowed us to identify the first committed enzyme in cucurbitacin biosynthesis in I. amara, cucurbitadienol synthase (IaCPQ). In addition, two species-specific cytochrome P450s (CYP708A16 and CYP708A15) were identified that catalyse the unique C16 and C22 hydroxylation of the cucurbitadienol backbone, enzymatic steps that have not been reported before. Furthermore, the draft genome assembly of I. amara showed that the IaCPQ was localized to the same scaffold together with CYP708A15 but spanning over 100 kb, this contrasts with the highly organized cucurbitacin gene cluster in the cucurbits. These results reveal that cucurbitacin biosynthesis has evolved convergently via different biosynthetic routes in different families rather than through divergence from an ancestral pathway. This study thus provides new insight into the mechanism of recurrent evolution and diversification of a plant defensive chemical.
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Affiliation(s)
- Lemeng Dong
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark.,Plant Hormone Biology group, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Aldo Almeida
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Jacob Pollier
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Bekzod Khakimov
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1958 Frederiksberg C, Denmark
| | - Jean-Etienne Bassard
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Karel Miettinen
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Dan Stærk
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Rahimi Mehran
- Plant Hormone Biology group, Swammerdam Institute for Life Science, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, the Netherlands
| | - Carl Erik Olsen
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Mohammed Saddik Motawia
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Søren Bak
- Department of Plant and Environmental Science, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Denmark
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28
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Colinas M, Pollier J, Vaneechoutte D, Malat DG, Schweizer F, De Milde L, De Clercq R, Guedes JG, Martínez-Cortés T, Molina-Hidalgo FJ, Sottomayor M, Vandepoele K, Goossens A. Subfunctionalization of Paralog Transcription Factors Contributes to Regulation of Alkaloid Pathway Branch Choice in Catharanthus roseus. Front Plant Sci 2021; 12:687406. [PMID: 34113373 PMCID: PMC8186833 DOI: 10.3389/fpls.2021.687406] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 04/27/2021] [Indexed: 06/12/2023]
Abstract
Catharanthus roseus produces a diverse range of specialized metabolites of the monoterpenoid indole alkaloid (MIA) class in a heavily branched pathway. Recent great progress in identification of MIA biosynthesis genes revealed that the different pathway branch genes are expressed in a highly cell type- and organ-specific and stress-dependent manner. This implies a complex control by specific transcription factors (TFs), only partly revealed today. We generated and mined a comprehensive compendium of publicly available C. roseus transcriptome data for MIA pathway branch-specific TFs. Functional analysis was performed through extensive comparative gene expression analysis and profiling of over 40 MIA metabolites in the C. roseus flower petal expression system. We identified additional members of the known BIS and ORCA regulators. Further detailed study of the ORCA TFs suggests subfunctionalization of ORCA paralogs in terms of target gene-specific regulation and synergistic activity with the central jasmonate response regulator MYC2. Moreover, we identified specific amino acid residues within the ORCA DNA-binding domains that contribute to the differential regulation of some MIA pathway branches. Our results advance our understanding of TF paralog specificity for which, despite the common occurrence of closely related paralogs in many species, comparative studies are scarce.
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Affiliation(s)
- Maite Colinas
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Dries Vaneechoutte
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Deniz G. Malat
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Fabian Schweizer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Liesbeth De Milde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Rebecca De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Joana G. Guedes
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairaão, Portugal
- I3S-Instituto de Investigação e Inovação em Saúde, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Porto, Portugal
- ICBAS–Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Teresa Martínez-Cortés
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairaão, Portugal
| | - Francisco J. Molina-Hidalgo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Mariana Sottomayor
- CIBIO/InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Vairaão, Portugal
- Faculdade de Ciências, Universidade do Porto, Porto, Portugal
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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Herman A, Uter W, Rustemeyer T, Matura M, Aalto-Korte K, Duus Johansen J, Gonçalo M, White IR, Balato A, Giménez Arnau AM, Brockow K, Mortz CG, Mahler V, Goossens A. Position statement: The need for EU legislation to require disclosure and labelling of the composition of medical devices. J Eur Acad Dermatol Venereol 2021; 35:1444-1448. [PMID: 33955077 PMCID: PMC8251888 DOI: 10.1111/jdv.17238] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 03/08/2021] [Indexed: 11/30/2022]
Abstract
BACKGROUND In recent years, skin reactions secondary to the use of medical devices (MD), such as allergic contact dermatitis have increasingly been observed (e.g. to continuous blood sugar monitoring systems, insulin pumps, wound dressings, medical gloves, etc.): this is regarded as a developing epidemic. Lack of labelling of the composition of MD, as well as frequent lack of cooperation of manufacturers to disclose this relevant information, even when contacted by the clinician for the individual case of an established adverse reaction, significantly impede patient care. OBJECTIVES To advocate for full ingredient labelling in the implementation of EU regulation for MD. METHODS This position paper reviews the scientific literature, the current regulatory framework adopted for MD to date, and the likely impact, including some costs data in case of the absence of such labelling. RESULTS Efforts made by several scientific teams, who are trying to identify the culprit of such adverse effects, either via asking for cooperation from companies, or using costly chemical analyses of MD, can only partly, and with considerable delay, compensate for the absence of meaningful information on the composition of MD; hence, patient management is compromised. Indeed, without knowing the chemical substances present, physicians are unable to inform patients about which substances they should avoid, and which alternative MD may be suitable/tolerated. CONCLUSION There is an urgent need for full and accurate labelling of the chemical composition of MD in contact with the human body.
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Affiliation(s)
- A Herman
- Department of Dermatology, Cliniques universitaires Saint-Luc, Université catholique de Louvain (UCLouvain), Brussels, Belgium
| | - W Uter
- Department of Medical Informatics, Biometry and Epidemiology, Univ. Erlangen/Nürnberg, Erlangen, Germany
| | - T Rustemeyer
- Department of Dermatology and Allergology, Amsterdam University Medical Centres, Amsterdam, The Netherlands
| | - M Matura
- Dermatology Unit, Skaraborgs Hospital Skövde, Skövde, Sweden
| | - K Aalto-Korte
- Occupational Health Unit, Finnish Institute of Occupational Heath, Helsinki, Finland
| | - J Duus Johansen
- Department of Dermatology and Allergy, National Allergy Research Centre, Herlev-Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - M Gonçalo
- Department of Dermatology, Coimbra University Hospital and Faculty of Medicine, University of Coimbra, Coimbra, Portugal
| | - I R White
- Cutaneous Allergy Team, St. John's Institute of Dermatology, Guy's Hospital, London, UK
| | - A Balato
- Department of Advanced Biomedical Sciences, University of Naples Federico II, Napoli, Italy
| | - A M Giménez Arnau
- Department of Dermatology, Hospital del Mar. Universitat Autònoma de Barcelona, Barcelona, Spain
| | - K Brockow
- Department of Dermatology and Allergy Biederstein, School of Medicine, Technical University of Munich, Munich, Germany
| | - C G Mortz
- Department of Dermatology and Allergy Center, Odense Research Center for Anaphylaxis (ORCA), Odense University Hospital, Odense, Denmark
| | - V Mahler
- Med. Faculty, Univ. Erlangen/Nuremberg, Erlangen, Germany
| | - A Goossens
- Contact Allergy Unit, Department of Dermatology, University Hospital KU Leuven, Leuven, Belgium
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Venegas-Molina J, Molina-Hidalgo FJ, Clicque E, Goossens A. Why and How to Dig into Plant Metabolite-Protein Interactions. Trends Plant Sci 2021; 26:472-483. [PMID: 33478816 DOI: 10.1016/j.tplants.2020.12.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 12/08/2020] [Accepted: 12/14/2020] [Indexed: 06/12/2023]
Abstract
Interaction between metabolites and proteins drives cellular regulatory processes within and between organisms. Recent reports highlight that numerous plant metabolites embrace multiple biological activities, beyond a sole role as substrates, products, or cofactors of enzymes, or as defense or growth-regulatory compounds. Though several technologies have been developed to identify and characterize metabolite-protein interactions, the systematic implementation of such methods in the plant field remains limited. Here, we discuss the plant metabolic space, with a specific focus on specialized metabolites and their roles, and review the technologies to study their interaction with proteins. We approach it both from a plant's perspective, to increase our understanding of plant metabolite-dependent regulatory networks, and from a human perspective, to empower agrochemical and drug discoveries.
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Affiliation(s)
- Jhon Venegas-Molina
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Francisco J Molina-Hidalgo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Elke Clicque
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium; VIB Center for Plant Systems Biology, Ghent, Belgium.
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31
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Bai Y, Fernández-Calvo P, Ritter A, Huang AC, Morales-Herrera S, Bicalho KU, Karady M, Pauwels L, Buyst D, Njo M, Ljung K, Martins JC, Vanneste S, Beeckman T, Osbourn A, Goossens A, Pollier J. Modulation of Arabidopsis root growth by specialized triterpenes. New Phytol 2021; 230:228-243. [PMID: 33616937 DOI: 10.1111/nph.17144] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/01/2020] [Indexed: 05/21/2023]
Abstract
Plant roots are specialized belowground organs that spatiotemporally shape their development in function of varying soil conditions. This root plasticity relies on intricate molecular networks driven by phytohormones, such as auxin and jasmonate (JA). Loss-of-function of the NOVEL INTERACTOR OF JAZ (NINJA), a core component of the JA signaling pathway, leads to enhanced triterpene biosynthesis, in particular of the thalianol gene cluster, in Arabidopsis thaliana roots. We have investigated the biological role of thalianol and its derivatives by focusing on Thalianol Synthase (THAS) and Thalianol Acyltransferase 2 (THAA2), two thalianol cluster genes that are upregulated in the roots of ninja mutant plants. THAS and THAA2 activity was investigated in yeast, and metabolite and phenotype profiling of thas and thaa2 loss-of-function plants was carried out. THAA2 was shown to be responsible for the acetylation of thalianol and its derivatives, both in yeast and in planta. In addition, THAS and THAA2 activity was shown to modulate root development. Our results indicate that the thalianol pathway is not only controlled by phytohormonal cues, but also may modulate phytohormonal action itself, thereby affecting root development and interaction with the environment.
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Affiliation(s)
- Yuechen Bai
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Patricia Fernández-Calvo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Andrés Ritter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Ancheng C Huang
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich,, NR4 7UH, UK
| | - Stefania Morales-Herrera
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
- Laboratory of Molecular Cell Biology, KU Leuven, Kasteelpark Arenberg 31, Leuven, 3000, Belgium
- VIB Center for Microbiology, Kasteelpark Arenberg 31, Leuven, 3000, Belgium
| | - Keylla U Bicalho
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
- Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, São Paulo, 14800-060, Brazil
| | - Michal Karady
- Laboratory of Growth Regulators, Institute of Experimental Botany of the Czech Academy of Sciences and Faculty of Science of Palacký University, Šlechtitelů 27, Olomouc, CZ-78371, Czech Republic
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Dieter Buyst
- Department of Organic Chemistry, Ghent University, Ghent, 9000, Belgium
| | - Maria Njo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Karen Ljung
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Umeå, SE-901 83, Sweden
| | - José C Martins
- Department of Organic Chemistry, Ghent University, Ghent, 9000, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
- Lab of Plant Growth Analysis, Ghent University Global Campus, Incheon, 21985, Korea
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Anne Osbourn
- Department of Metabolic Biology, John Innes Centre, Norwich Research Park, Colney Lane, Norwich,, NR4 7UH, UK
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
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Erffelinck ML, Ribeiro B, Gryffroy L, Rai A, Pollier J, Goossens A. The Heat Shock Protein 40-Type Chaperone MASH Supports the Endoplasmic Reticulum-Associated Degradation E3 Ubiquitin Ligase MAKIBISHI1 in Medicago truncatula. Front Plant Sci 2021; 12:639625. [PMID: 33708234 PMCID: PMC7940691 DOI: 10.3389/fpls.2021.639625] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/19/2021] [Indexed: 06/02/2023]
Abstract
Jasmonates (JA) are oxylipin-derived phytohormones that trigger the production of specialized metabolites that often serve in defense against biotic stresses. In Medicago truncatula, a JA-induced endoplasmic reticulum-associated degradation (ERAD)-type machinery manages the production of bioactive triterpenes and thereby secures correct plant metabolism, growth, and development. This machinery involves the conserved RING membrane-anchor (RMA)-type E3 ubiquitin ligase MAKIBISHI1 (MKB1). Here, we discovered two additional members of this protein control apparatus via a yeast-based protein-protein interaction screen and characterized their function. First, a cognate E2 ubiquitin-conjugating enzyme was identified that interacts with MKB1 to deliver activated ubiquitin and to mediate its ubiquitination activity. Second, we identified a heat shock protein 40 (HSP40) that interacts with MKB1 to support its activity and was therefore designated MKB1-supporting HSP40 (MASH). MASH expression was found to be co-regulated with that of MKB1. The presence of MASH is critical for MKB1 and ERAD functioning because the dramatic morphological, transcriptional, and metabolic phenotype of MKB1 knock-down M. truncatula hairy roots was phenocopied by silencing of MASH. Interaction was also observed between the Arabidopsis thaliana (Arabidopsis) homologs of MASH and MKB1, suggesting that MASH represents an essential and plant-specific component of this vital and conserved eukaryotic protein quality control machinery.
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Affiliation(s)
- Marie-Laure Erffelinck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Bianca Ribeiro
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lore Gryffroy
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Avanish Rai
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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33
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De Vriese K, Pollier J, Goossens A, Beeckman T, Vanneste S. Dissecting cholesterol and phytosterol biosynthesis via mutants and inhibitors. J Exp Bot 2021; 72:241-253. [PMID: 32929492 DOI: 10.1093/jxb/eraa429] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/11/2020] [Indexed: 06/11/2023]
Abstract
Plants stand out among eukaryotes due to the large variety of sterols and sterol derivatives that they can produce. These metabolites not only serve as critical determinants of membrane structures, but also act as signaling molecules, as growth-regulating hormones, or as modulators of enzyme activities. Therefore, it is critical to understand the wiring of the biosynthetic pathways by which plants generate these distinct sterols, to allow their manipulation and to dissect their precise physiological roles. Here, we review the complexity and variation of the biosynthetic routes of the most abundant phytosterols and cholesterol in the green lineage and how different enzymes in these pathways are conserved and diverged from humans, yeast, and even bacteria. Many enzymatic steps show a deep evolutionary conservation, while others are executed by completely different enzymes. This has important implications for the use and specificity of available human and yeast sterol biosynthesis inhibitors in plants, and argues for the development of plant-tailored inhibitors of sterol biosynthesis.
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Affiliation(s)
- Kjell De Vriese
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark, Ghent, Belgium
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark, Ghent, Belgium
- VIB Metabolomics Core, Technologiepark, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark, Ghent, Belgium
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark, Ghent, Belgium
| | - Steffen Vanneste
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark, Ghent, Belgium
- Laboratory of Plant Growth Analysis, Ghent University Global Campus, Songdomunhwa-Ro, Yeonsu-gu, Incheon, Republic of Korea
- Department of Plants and Crops, Ghent University, Ghent, Belgium
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De Bruyn C, Ruttink T, Eeckhaut T, Jacobs T, De Keyser E, Goossens A, Van Laere K. Establishment of CRISPR/Cas9 Genome Editing in Witloof (Cichorium intybus var. foliosum). Front Genome Ed 2020; 2:604876. [PMID: 34713228 PMCID: PMC8525355 DOI: 10.3389/fgeed.2020.604876] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 11/24/2020] [Indexed: 01/09/2023] Open
Abstract
Cichorium intybus var. foliosum (witloof) is an economically important crop with a high nutritional value thanks to many specialized metabolites, such as polyphenols and terpenoids. However, witloof plants are rich in sesquiterpene lactones (SL) which are important for plant defense but also impart a bitter taste, thus limiting industrial applications. Inactivating specific genes in the SL biosynthesis pathway could lead to changes in the SL metabolite content and result in altered bitterness. In this study, a CRISPR/Cas9 genome editing workflow was implemented for witloof, starting with polyethylene glycol (PEG) mediated protoplast transfection for CRISPR/Cas9 vector delivery, followed by whole plant regeneration and mutation analysis. Protoplast transfection efficiencies ranged from 20 to 26 %. A CRISPR/Cas9 vector targeting the first exon of the phytoene desaturase (CiPDS) gene was transfected into witloof protoplasts and resulted in the knockout of CiPDS, giving rise to an albino phenotype in 23% of the regenerated plants. Further implementing our protocol, the SL biosynthesis pathway genes germacrene A synthase (GAS), germacrene A oxidase (GAO), and costunolide synthase (COS) were targeted in independent experiments. Highly multiplex (HiPlex) amplicon sequencing of the genomic target loci revealed plant mutation frequencies of 27.3, 42.7, and 98.3% in regenerated plants transfected with a CRISPR/Cas9 vector targeting CiGAS, CiGAO, and CiCOS, respectively. We observed different mutation spectra across the loci, ranging from consistently the same +1 nucleotide insertion in CiCOS across independent mutated lines, to a complex set of 20 mutation types in CiGAO across independent mutated lines. These results demonstrate a straightforward workflow for genome editing based on transfection and regeneration of witloof protoplasts and subsequent HiPlex amplicon sequencing. Our CRISPR/Cas9 workflow can enable gene functional research and faster incorporation of novel traits in elite witloof lines in the future, thus facilitating the development of novel industrial applications for witloof.
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Affiliation(s)
- Charlotte De Bruyn
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Ghent, Belgium
- *Correspondence: Charlotte De Bruyn
| | - Tom Ruttink
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Tom Eeckhaut
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Thomas Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Ghent, Belgium
| | - Ellen De Keyser
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, Flanders Institute for Biotechnology (VIB), Ghent, Belgium
| | - Katrijn Van Laere
- Plant Sciences Unit, Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
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Affiliation(s)
- E. Debing
- Departments of Vascular Surgery, Academic Hospital, Vrije Universiteit Brussel, Brussels, Belgium
| | - P. Van Der Niepen
- Departments of Nephrology, Academic Hospital, Vrije Universiteit Brussel, Brussels, Belgium
| | - A. Goossens
- Departments of Pathology, Academic Hospital, Vrije Universiteit Brussel, Brussels, Belgium
| | - P. Van den Brande
- Departments of Vascular Surgery, Academic Hospital, Vrije Universiteit Brussel, Brussels, Belgium
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36
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Arora D, Abel NB, Liu C, Van Damme P, Yperman K, Eeckhout D, Vu LD, Wang J, Tornkvist A, Impens F, Korbei B, Van Leene J, Goossens A, De Jaeger G, Ott T, Moschou PN, Van Damme D. Establishment of Proximity-Dependent Biotinylation Approaches in Different Plant Model Systems. Plant Cell 2020; 32:3388-3407. [PMID: 32843435 PMCID: PMC7610282 DOI: 10.1105/tpc.20.00235] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 06/22/2020] [Accepted: 08/21/2020] [Indexed: 05/19/2023]
Abstract
Proximity labeling is a powerful approach for detecting protein-protein interactions. Most proximity labeling techniques use a promiscuous biotin ligase or a peroxidase fused to a protein of interest, enabling the covalent biotin labeling of proteins and subsequent capture and identification of interacting and neighboring proteins without the need for the protein complex to remain intact. To date, only a few studies have reported on the use of proximity labeling in plants. Here, we present the results of a systematic study applying a variety of biotin-based proximity labeling approaches in several plant systems using various conditions and bait proteins. We show that TurboID is the most promiscuous variant in several plant model systems and establish protocols that combine mass spectrometry-based analysis with harsh extraction and washing conditions. We demonstrate the applicability of TurboID in capturing membrane-associated protein interactomes using Lotus japonicus symbiotically active receptor kinases as a test case. We further benchmark the efficiency of various promiscuous biotin ligases in comparison with one-step affinity purification approaches. We identified both known and novel interactors of the endocytic TPLATE complex. We furthermore present a straightforward strategy to identify both nonbiotinylated and biotinylated peptides in a single experimental setup. Finally, we provide initial evidence that our approach has the potential to suggest structural information of protein complexes.
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Affiliation(s)
- Deepanksha Arora
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Nikolaj B Abel
- Faculty of Biology, Cell Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Chen Liu
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
| | - Petra Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University, 9000 Ghent, Belgium
| | - Klaas Yperman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lam Dai Vu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jie Wang
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Anna Tornkvist
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
| | - Francis Impens
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
- VIB Center for Medical Biotechnology, 9052 Ghent, Belgium
- VIB Proteomics Core, 9052 Ghent, Belgium
| | - Barbara Korbei
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, 1190 Vienna, Austria
| | - Jelle Van Leene
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Thomas Ott
- Faculty of Biology, Cell Biology, University of Freiburg, 79104 Freiburg, Germany
- Centre for Integrative Biological Signaling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Panagiotis Nikolaou Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala SE-75007, Sweden
- Department of Biology, University of Crete, 70013 Heraklion, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, 70013 Heraklion, Greece
| | - Daniël Van Damme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
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Garagounis C, Beritza K, Georgopoulou ME, Sonawane P, Haralampidis K, Goossens A, Aharoni A, Papadopoulou KK. A hairy-root transformation protocol for Trigonella foenum-graecum L. as a tool for metabolic engineering and specialised metabolite pathway elucidation. Plant Physiol Biochem 2020; 154:451-462. [PMID: 32659648 DOI: 10.1016/j.plaphy.2020.06.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/04/2020] [Accepted: 06/06/2020] [Indexed: 06/11/2023]
Abstract
The development of genetic transformation methods is critical for enabling the thorough characterization of an organism and is a key step in exploiting any species as a platform for synthetic biology and metabolic engineering approaches. In this work we describe the development of an Agrobacterium rhizogenes-mediated hairy root transformation protocol for the crop and medicinal legume fenugreek (Trigonella foenum-graecum). Fenugreek has a rich and diverse content in bioactive specialised metabolites, notably diosgenin, which is a common precursor for synthetic human hormone production. This makes fenugreek a prime target for identification and engineering of specific biosynthetic pathways for the production of triterpene and steroidal saponins, phenolics, and galactomanans. Through this transformation protocol, we identified a suitable promoter for robust transgene expression in fenugreek. Finally, we establish the proof of principle for the utility of the fenugreek system for metabolic engineering programs, by heterologous expression of known triterpene saponin biosynthesis regulators from the related legume Medicago truncatula in fenugreek hairy roots.
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Affiliation(s)
- Constantine Garagounis
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece.
| | - Konstantina Beritza
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece
| | - Maria-Eleni Georgopoulou
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece
| | - Prashant Sonawane
- Faculty of Biochemistry, Department of Plant Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Kosmas Haralampidis
- Faculty of Botany, Department of Biology, National and Kapodistrian University of Athens, 15701, Athens, Greece
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052, Ghent, Belgium; VIB-UGent Center for Plant Systems Biology, 9052, Ghent, Belgium
| | - Asaph Aharoni
- Faculty of Biochemistry, Department of Plant Sciences, Weizmann Institute of Science, 7610001, Rehovot, Israel
| | - Kalliope K Papadopoulou
- Department of Biochemistry and Biotechnology, Laboratory of Plant and Environmental Biotechnology, University of Thessaly, Biopolis, 41500, Larissa, Greece
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Oña Chuquimarca S, Ayala-Ruano S, Goossens J, Pauwels L, Goossens A, Leon-Reyes A, Ángel Méndez M. The Molecular Basis of JAZ-MYC Coupling, a Protein-Protein Interface Essential for Plant Response to Stressors. Front Plant Sci 2020; 11:1139. [PMID: 32973821 PMCID: PMC7468482 DOI: 10.3389/fpls.2020.01139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/14/2020] [Indexed: 05/29/2023]
Abstract
The jasmonic acid (JA) signaling pathway is one of the primary mechanisms that allow plants to respond to a variety of biotic and abiotic stressors. Within this pathway, the JAZ repressor proteins and the basic helix-loop-helix (bHLH) transcription factor MYC3 play a critical role. JA is a volatile organic compound with an essential role in plant immunity. The increase in the concentration of JA leads to the decoupling of the JAZ repressor proteins and the bHLH transcription factor MYC3 causing the induction of genes of interest. The primary goal of this study was to identify the molecular basis of JAZ-MYC coupling. For this purpose, we modeled and validated 12 JAZ-MYC3 3D in silico structures and developed a molecular dynamics/machine learning pipeline to obtain two outcomes. First, we calculated the average free binding energy of JAZ-MYC3 complexes, which was predicted to be -10.94 +/-2.67 kJ/mol. Second, we predicted which ones should be the interface residues that make the predominant contribution to the free energy of binding (molecular hotspots). The predicted protein hotspots matched a conserved linear motif SL••FL•••R, which may have a crucial role during MYC3 recognition of JAZ proteins. As a proof of concept, we tested, both in silico and in vitro, the importance of this motif on PEAPOD (PPD) proteins, which also belong to the TIFY protein family, like the JAZ proteins, but cannot bind to MYC3. By mutating these proteins to match the SL••FL•••R motif, we could force PPDs to bind the MYC3 transcription factor. Taken together, modeling protein-protein interactions and using machine learning will help to find essential motifs and molecular mechanisms in the JA pathway.
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Affiliation(s)
- Samara Oña Chuquimarca
- Grupo de Química Computacional y Teórica, Departamento de Ingeniería Química, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Instituto de Simulación Computacional (ISC-USFQ), Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Sebastián Ayala-Ruano
- Grupo de Química Computacional y Teórica, Departamento de Ingeniería Química, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Instituto de Simulación Computacional (ISC-USFQ), Universidad San Francisco de Quito USFQ, Quito, Ecuador
| | - Jonas Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Antonio Leon-Reyes
- Laboratorio de Biotecnología Agrícola y de Alimentos, Ingeniería en Agronomía, Colegio de Ciencias e Ingenierías, Universidad San Francisco de Quito, Campus Cumbayá, Quito, Ecuador
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto de Microbiología, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Colegio de Ciencias Biológicas y Ambientales COCIBA, Instituto de Investigaciones Biológicas y Ambientales BIÓSFERA, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Department of Biology, The University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Miguel Ángel Méndez
- Grupo de Química Computacional y Teórica, Departamento de Ingeniería Química, Universidad San Francisco de Quito USFQ, Campus Cumbayá, Quito, Ecuador
- Instituto de Simulación Computacional (ISC-USFQ), Universidad San Francisco de Quito USFQ, Quito, Ecuador
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Fernández-Calvo P, Iñigo S, Glauser G, Vanden Bossche R, Tang M, Li B, De Clercq R, Nagels Durand A, Eeckhout D, Gevaert K, De Jaeger G, Brady SM, Kliebenstein DJ, Pauwels L, Goossens A, Ritter A. FRS7 and FRS12 recruit NINJA to regulate expression of glucosinolate biosynthesis genes. New Phytol 2020; 227:1124-1137. [PMID: 32266972 DOI: 10.1111/nph.16586] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 03/25/2020] [Indexed: 05/24/2023]
Abstract
The sessile lifestyle of plants requires accurate physiology adjustments to be able to thrive in a changing environment. Plants integrate environmental timing signals to control developmental and stress responses. Here, we identified Far1 Related Sequence (FRS) 7 and FRS12, two transcriptional repressors that accumulate in short-day conditions, as regulators of Arabidopsis glucosinolate (GSL) biosynthesis. Loss of function of FRS7 and FRS12 results in plants with increased amplitudes of diurnal expression of GSL pathway genes. Protein interaction analyses revealed that FRS7 and FRS12 recruit the NOVEL INTERACTOR OF JAZ (NINJA) to assemble a transcriptional repressor complex. Genetic and molecular evidence demonstrated that FRS7, FRS12 and NINJA jointly regulate the expression of GSL biosynthetic genes, and thus constitute a molecular mechanism that modulates specialized metabolite accumulation.
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Affiliation(s)
- Patricia Fernández-Calvo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Sabrina Iñigo
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Gaétan Glauser
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, Avenue de Bellevaux 51, 2000, Neuchâtel, Switzerland
| | - Robin Vanden Bossche
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Michelle Tang
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Graduate Group in Plant Biology, University of California, Davis, CA, 95616, USA
| | - Baohua Li
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Rebecca De Clercq
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Astrid Nagels Durand
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Dominique Eeckhout
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, Albert Baertsoenkaai 3, B-9000, Ghent, Belgium
- VIB Center for Medical Biotechnology, Albert Baertsoenkaai 3, B-9000, Ghent, Belgium
| | - Geert De Jaeger
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Siobhan M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, One Shields Avenue, Davis, CA, 95616, USA
| | - Daniel J Kliebenstein
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- DynaMo Center of Excellence, University of Copenhagen, DK-1871, Frederiksberg C, Denmark
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Andrés Ritter
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
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40
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Abstract
Plants constantly perceive internal and external cues, many of which they need to address to safeguard their proper development and survival. They respond to these cues by selective activation of specific metabolic pathways involving a plethora of molecular players that act and interact in complex networks. In this review, we illustrate and discuss the complexity in the combinatorial control of plant specialized metabolism. We hereby go beyond the intuitive concept of combinatorial control as exerted by modular-acting complexes of transcription factors that govern expression of specialized metabolism genes. To extend this discussion, we also consider all known hierarchical levels of regulation of plant specialized metabolism and their interfaces by referring to reported regulatory concepts from the plant field. Finally, we speculate on possible yet-to-be-discovered regulatory principles of plant specialized metabolism that are inspired by knowledge from other kingdoms of life and areas of biological research.
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Affiliation(s)
- Elia Lacchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; , .,Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; , .,Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
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41
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Ribeiro B, Lacchini E, Bicalho KU, Mertens J, Arendt P, Vanden Bossche R, Calegario G, Gryffroy L, Ceulemans E, Buitink J, Goossens A, Pollier J. A Seed-Specific Regulator of Triterpene Saponin Biosynthesis in Medicago truncatula. Plant Cell 2020; 32:2020-2042. [PMID: 32303662 PMCID: PMC7268793 DOI: 10.1105/tpc.19.00609] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 03/27/2020] [Accepted: 04/10/2020] [Indexed: 05/06/2023]
Abstract
Plants produce a vast array of defense compounds to protect themselves from pathogen attack or herbivore predation. Saponins are a specific class of defense compounds comprising bioactive glycosides with a steroidal or triterpenoid aglycone backbone. The model legume Medicago truncatula synthesizes two types of saponins, hemolytic saponins and nonhemolytic soyasaponins, which accumulate as specific blends in different plant organs. Here, we report the identification of the seed-specific transcription factor TRITERPENE SAPONIN ACTIVATION REGULATOR3 (TSAR3), which controls hemolytic saponin biosynthesis in developing M. truncatula seeds. Analysis of genes that are coexpressed with TSAR3 in transcriptome data sets from developing M. truncatula seeds led to the identification of CYP88A13, a cytochrome P450 that catalyzes the C-16α hydroxylation of medicagenic acid toward zanhic acid, the final oxidation step of the hemolytic saponin biosynthesis branch in M. truncatula In addition, two uridine diphosphate glycosyltransferases, UGT73F18 and UGT73F19, which glucosylate hemolytic sapogenins at the C-3 position, were identified. The genes encoding the identified biosynthetic enzymes are present in clusters of duplicated genes in the M. truncatula genome. This appears to be a common theme among saponin biosynthesis genes, especially glycosyltransferases, and may be the driving force of the metabolic evolution of saponins.
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Affiliation(s)
- Bianca Ribeiro
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Elia Lacchini
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Keylla U Bicalho
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- Department of Organic Chemistry, Institute of Chemistry, São Paulo State University (UNESP), Araraquara, São Paulo 14800-900, Brazil
| | - Jan Mertens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Philipp Arendt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Robin Vanden Bossche
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Gabriela Calegario
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lore Gryffroy
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Evi Ceulemans
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Julia Buitink
- Institut de Recherche en Horticulture et Semences-Unités Mixtes de Recherche, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Jacob Pollier
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
- VIB Metabolomics Core, 9052 Ghent, Belgium
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42
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Fernandez MA, Belda-Palazon B, Julian J, Coego A, Lozano-Juste J, Iñigo S, Rodriguez L, Bueso E, Goossens A, Rodriguez PL. RBR-Type E3 Ligases and the Ubiquitin-Conjugating Enzyme UBC26 Regulate Abscisic Acid Receptor Levels and Signaling. Plant Physiol 2020; 182:1723-1742. [PMID: 31699847 PMCID: PMC7140949 DOI: 10.1104/pp.19.00898] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 10/21/2019] [Indexed: 05/06/2023]
Abstract
The turnover of abscisic acid (ABA) signaling core components modulates the plant's response to ABA and is regulated by ubiquitination. We show that Arabidopsis (Arabidopsis thaliana) RING Finger ABA-Related1 (RFA1) and RFA4 E3 ubiquitin ligases, members of the RING between RING fingers (RBR)-type RSL1/RFA family, are key regulators of ABA receptor stability in root and leaf tissues, targeting ABA receptors for degradation in different subcellular locations. RFA1 is localized both in the nucleus and cytosol, whereas RFA4 shows specific nuclear localization and promotes nuclear degradation of ABA receptors. Therefore, members of the RSL1/RFA family interact with ABA receptors at plasma membrane, cytosol, and nucleus, targeting them for degradation via the endosomal/vacuolar RSL1-dependent pathway or 26S proteasome. Additionally, we provide insight into the physiological function of the relatively unexplored plant RBR-type E3 ligases, and through mutagenesis and biochemical assays we identified cysteine-361 in RFA4 as the putative active site cysteine, which is a distinctive feature of RBR-type E3 ligases. Endogenous levels of PYR1 and PYL4 ABA receptors were higher in the rfa1 rfa4 double mutant than in wild-type plants. UBC26 was identified as the cognate nuclear E2 enzyme that interacts with the RFA4 E3 ligase and forms UBC26-RFA4-receptor complexes in nuclear speckles. Loss-of-function ubc26 alleles and the rfa1 rfa4 double mutant showed enhanced sensitivity to ABA and accumulation of ABA receptors compared with the wild type. Together, our results reveal a sophisticated mechanism by which ABA receptors are targeted by ubiquitin at different subcellular locations, in which the complexity of the ABA receptor family is mirrored in the partner RBR-type E3 ligases.
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Affiliation(s)
- Maria Angeles Fernandez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Borja Belda-Palazon
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Jose Julian
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Alberto Coego
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Jorge Lozano-Juste
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Sabrina Iñigo
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lesia Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Eduardo Bueso
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
| | - Alain Goossens
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Pedro L Rodriguez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Uiversidad Politécnica de Valencia, 46022 Valencia, Spain
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43
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Kim SW, Goossens A, Libert C, Van Immerseel F, Staal J, Beyaert R. Phytohormones: Multifunctional nutraceuticals against metabolic syndrome and comorbid diseases. Biochem Pharmacol 2020; 175:113866. [PMID: 32088261 DOI: 10.1016/j.bcp.2020.113866] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 02/18/2020] [Indexed: 12/12/2022]
Abstract
Metabolic syndrome is characterized by the co-occurrence of diverse symptoms initiating the development of type 2 diabetes, cardiovascular diseases, and a variety of comorbid diseases. The complex constellation of numerous comorbidities makes it difficult to develop common therapeutic approaches that ameliorate these pathological features simultaneously. The plant hormones abscisic acid, salicylic acid, auxin, and cytokinins, have shown promising anti-inflammatory and pro-metabolic effects that could mitigate several disorders relevant to metabolic syndrome. Intriguingly, besides plants, human cells and gut microbes also endogenously produce these molecules, indicating a role in the complex interplay between inflammatory responses associated with metabolic syndrome, the gut microbiome, and nutrition. Here, we introduce how bioactive phytohormones can be generated endogenously and through the gut microbiome. These molecules subsequently influence immune responses and metabolism. We also elaborate on how phytohormones can beneficially modulate metabolic syndrome comorbidities, and propose them as nutraceuticals.
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Affiliation(s)
- Seo Woo Kim
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium; VIB-UGent Center for Plant Systems Biology, VIB, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Alain Goossens
- VIB-UGent Center for Plant Systems Biology, VIB, Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Claude Libert
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium
| | - Filip Van Immerseel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Jens Staal
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
| | - Rudi Beyaert
- VIB-UGent Center for Inflammation Research, VIB, Ghent, Belgium; Department of Biomedical Molecular Biology, Ghent University, Ghent, Belgium.
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44
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Vaccaro MC, Alfieri M, De Tommasi N, Moses T, Goossens A, Leone A. Boosting the Synthesis of Pharmaceutically Active Abietane Diterpenes in S. sclarea Hairy Roots by Engineering the GGPPS and CPPS Genes. Front Plant Sci 2020; 11:924. [PMID: 32625231 PMCID: PMC7315395 DOI: 10.3389/fpls.2020.00924] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 06/05/2020] [Indexed: 05/02/2023]
Abstract
Abietane diterpenoids (ADs), synthesized in the roots of different Salvia species, such as aethiopinone, 1-oxoaethiopinone, salvipisone, and ferruginol, have a variety of known biological activities. We have shown that aethiopinone has promising cytotoxic activity against several human tumor cell lines, including the breast adenocarcinoma MCF7, HeLa, epithelial carcinoma, prostate adenocarcinoma PC3, and human melanoma A375. The low content of these compounds in natural sources, and the limited possibility to synthesize them chemically at low cost, prompted us to optimize the production of abietane diterpenoids by targeting genes of the methylerythritol phosphate (MEP) pathway, from which they are derived. Here, we report our current and ongoing efforts to boost the metabolic flux towards this interesting class of compounds in Salvia sclarea hairy roots (HRs). Silencing the gene encoding the ent-copalyl-diphosphate synthase gene (entCPPS), acting at the lateral geranylgeranyl pyrophosphate (GGPP) competitive gibberellin route, enhanced the content of aethiopinone and other ADs in S. sclarea HRs, indicating indirectly that the GGPP pool is a metabolic constraint to the accumulation of ADs. This was confirmed by overexpressing the GGPPS gene (geranyl-geranyl diphosphate synthase) which triggered also a significant 8-fold increase of abietane diterpene content above the basal constitutive level, with a major boosting effect on aethiopinone accumulation in S. sclarea HRs. A significant accumulation of aethiopinone and other AD compounds was also achieved by overexpressing the CPPS gene (copalyl diphosphate synthase) pointing to this biosynthetic step as another potential metabolic target for optimizing the biosynthesis of this class of compounds. However, by co-expressing of GGPPS and CPPS genes, albeit significant, the increase of abietane diterpenoids was less effective than that obtained by overexpressing the two genes individually. Taken together, the results presented here add novel and instrumental knowledge to a rational design of a hairy root-based platform to yield reliable amounts of aethiopinone and other ADs for a deeper understanding of their molecular pharmacological targets and potential future commercialization.
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Affiliation(s)
| | | | | | - Tessa Moses
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Antonietta Leone
- Department of Pharmacy, University of Salerno, Fisciano, Italy
- *Correspondence: Antonietta Leone,
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45
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Abstract
Loss-of-function mutants are crucial for plant functional genomics studies. With the advent of CRISPR-Cas genome editing, generating null alleles for one or multiple specific gene(s) has become feasible for many plant species including tomato (Solanum lycopersicum). An easily programmable RNA-guided Cas endonuclease efficiently creates DNA double-strand breaks (DSBs) at targeted genomic sites that can be repaired by nonhomologous end joining (NHEJ) typically leading to small insertions or deletions that can produce null mutations. Here, we describe how to utilize CRISPR-Cas genome editing to obtain stable tomato gene knockout lines.
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Affiliation(s)
- Gwen Swinnen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Thomas Jacobs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
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46
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Goossens A, Farmer EE. Regulatory Oxylipins Anno 2019: Jasmonates Galore in the Plant Oxylipin Research Community. Plant Cell Physiol 2019; 60:2609-2612. [PMID: 31626278 DOI: 10.1093/pcp/pcz197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/10/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Edward E Farmer
- Department of Plant Molecular Biology, University of Lausanne, Lausanne, Switzerland
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47
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Dendooven E, Darrigade A, Foubert K, Pieters L, Lambert J, Goossens A, Aerts O. The presence of sulfites in ‘natural rubber latex’ and ‘synthetic’ rubber gloves: an experimental pilot study. Br J Dermatol 2019; 182:1054-1055. [DOI: 10.1111/bjd.18608] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- E. Dendooven
- Department of Dermatology Contact Allergy Unit University Hospital Antwerp (UZA) and University of Antwerp (UA) Wilrijkstraat 10 B‐2650 Antwerp Belgium
| | - A.‐S. Darrigade
- Department of Dermatology Contact Allergy Unit University Hospital Antwerp (UZA) and University of Antwerp (UA) Wilrijkstraat 10 B‐2650 Antwerp Belgium
| | - K. Foubert
- Research Group Natural Products and Food – Research and Analysis (NatuRA) Department of Pharmaceutical Sciences University of Antwerp B‐2610 Wilrijk Belgium
| | - L. Pieters
- Research Group Natural Products and Food – Research and Analysis (NatuRA) Department of Pharmaceutical Sciences University of Antwerp B‐2610 Wilrijk Belgium
| | - J. Lambert
- Department of Dermatology Contact Allergy Unit University Hospital Antwerp (UZA) and University of Antwerp (UA) Wilrijkstraat 10 B‐2650 Antwerp Belgium
| | - A. Goossens
- Department of Dermatology Contact Allergy Unit University Hospitals KU Leuven Herestraat 49 B‐3000 Leuven Belgium
| | - O. Aerts
- Department of Dermatology Contact Allergy Unit University Hospital Antwerp (UZA) and University of Antwerp (UA) Wilrijkstraat 10 B‐2650 Antwerp Belgium
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48
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Bicalho KU, Santoni MM, Arendt P, Zanelli CF, Furlan M, Goossens A, Pollier J. CYP712K4 Catalyzes the C-29 Oxidation of Friedelin in the Maytenus ilicifolia Quinone Methide Triterpenoid Biosynthesis Pathway. Plant Cell Physiol 2019; 60:2510-2522. [PMID: 31350564 DOI: 10.1093/pcp/pcz144] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 07/13/2019] [Indexed: 06/10/2023]
Abstract
The native Brazilian plant Maytenus ilicifolia accumulates a set of quinone methide triterpenoids with important pharmacological properties, of which maytenin, pristimerin and celastrol accumulate exclusively in the root bark of this medicinal plant. The first committed step in the quinone methide triterpenoid biosynthesis is the cyclization of 2,3-oxidosqualene to friedelin, catalyzed by the oxidosqualene cyclase friedelin synthase (FRS). In this study, we produced heterologous friedelin by the expression of M. ilicifolia FRS in Nicotiana benthamiana leaves and in a Saccharomyces cerevisiae strain engineered using CRISPR/Cas9. Furthermore, friedelin-producing N. benthamiana leaves and S. cerevisiae cells were used for the characterization of CYP712K4, a cytochrome P450 from M. ilicifolia that catalyzes the oxidation of friedelin at the C-29 position, leading to maytenoic acid, an intermediate of the quinone methide triterpenoid biosynthesis pathway. Maytenoic acid produced in N. benthamiana leaves was purified and its structure was confirmed using high-resolution mass spectrometry and nuclear magnetic resonance analysis. The three-step oxidation of friedelin to maytenoic acid by CYP712K4 can be considered as the second step of the quinone methide triterpenoid biosynthesis pathway, and may form the basis for further discovery of the pathway and heterologous production of friedelanes and ultimately quinone methide triterpenoids.
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Affiliation(s)
- Keylla U Bicalho
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Organic Chemistry, Institute of Chemistry, S�o Paulo State University (UNESP), Araraquara, S�o Paulo, Brazil
- Department of Biological Sciences, School of Pharmaceutical Sciences, S�o Paulo State University (UNESP), Araraquara, S�o Paulo, Brazil
| | - Mariana M Santoni
- Department of Organic Chemistry, Institute of Chemistry, S�o Paulo State University (UNESP), Araraquara, S�o Paulo, Brazil
- Department of Biological Sciences, School of Pharmaceutical Sciences, S�o Paulo State University (UNESP), Araraquara, S�o Paulo, Brazil
| | - Philipp Arendt
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Cleslei F Zanelli
- Department of Biological Sciences, School of Pharmaceutical Sciences, S�o Paulo State University (UNESP), Araraquara, S�o Paulo, Brazil
| | - Maysa Furlan
- Department of Organic Chemistry, Institute of Chemistry, S�o Paulo State University (UNESP), Araraquara, S�o Paulo, Brazil
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
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49
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Swinnen G, Goossens A, Pauwels L. Lessons from Domestication: Targeting Cis-Regulatory Elements for Crop Improvement. Trends Plant Sci 2019; 24:1065. [PMID: 31623994 DOI: 10.1016/j.tplants.2019.09.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
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50
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Swinnen G, Goossens A, Colinas M. Metabolic editing: small measures, great impact. Curr Opin Biotechnol 2019; 59:16-23. [DOI: 10.1016/j.copbio.2019.02.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 01/25/2019] [Accepted: 02/04/2019] [Indexed: 12/23/2022]
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