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Boerjan W, Burlat V, Cosgrove DJ, Dunand C, Dupree P, Haas KT, Ingram G, Jamet E, Mohnen D, Moussu S, Peaucelle A, Persson S, Voiniciuc C, Höfte H. Top five unanswered questions in plant cell surface research. Cell Surf 2024; 11:100121. [PMID: 38405175 PMCID: PMC10885547 DOI: 10.1016/j.tcsw.2024.100121] [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: 12/20/2023] [Revised: 02/12/2024] [Accepted: 02/12/2024] [Indexed: 02/27/2024] Open
Abstract
Plant cell wall researchers were asked their view on what the major unanswered questions are in their field. This article summarises the feedback that was received from them in five questions. In this issue you can find equivalent syntheses for researchers working on bacterial, unicellular parasite and fungal systems.
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Affiliation(s)
- Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Gent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Gent, Belgium
| | - Vincent Burlat
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Daniel J. Cosgrove
- Department of Biology, Pennsylvania State University, University Park, PA 16870, the United States of America
| | - Christophe Dunand
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Kalina T. Haas
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Gwyneth Ingram
- Laboratoire Reproduction et Développement des Plantes, ENS de Lyon, CNRS, INRAE, UCBL, Lyon, France
| | - Elisabeth Jamet
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Debra Mohnen
- Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
| | - Steven Moussu
- Laboratoire de Recherche en Sciences Végétales, Université de Toulouse, CNRS, UPS, Toulouse INP, Auzeville-Tolosane, France
| | - Alexis Peaucelle
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
| | - Staffan Persson
- Copenhagen Plant Science Center (CPSC), Department of Plant & Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Cătălin Voiniciuc
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, the United States of America
| | - Herman Höfte
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000, Versailles, France
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Kankaanpää S, Väisänen E, Goeminne G, Soliymani R, Desmet S, Samoylenko A, Vainio S, Wingsle G, Boerjan W, Vanholme R, Kärkönen A. Extracellular vesicles of Norway spruce contain precursors and enzymes for lignin formation and salicylic acid. Plant Physiol 2024:kiae287. [PMID: 38771246 DOI: 10.1093/plphys/kiae287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 04/09/2024] [Accepted: 04/29/2024] [Indexed: 05/22/2024]
Abstract
Lignin is a phenolic polymer in plants that rigidifies the cell walls of water-conducting tracheary elements and support-providing fibers and stone cells. Different mechanisms have been suggested for the transport of lignin precursors to the site of lignification in the cell wall. Extracellular vesicle (EV)-enriched samples isolated from a lignin-forming cell suspension culture of Norway spruce (Picea abies L. Karst.) contained both phenolic metabolites and enzymes related to lignin biosynthesis. Metabolomic analysis revealed mono-, di- and oligolignols in the EV isolates, as well as carbohydrates and amino acids. In addition, salicylic acid (SA) and some proteins involved in SA signaling were detected in the EV-enriched samples. A proteomic analysis detected several laccases, peroxidases, β-glucosidases, putative dirigent proteins, and cell wall-modifying enzymes such as glycosyl hydrolases, transglucosylase/hydrolases, and expansins in EVs. Our findings suggest that EVs are involved in transporting enzymes required for lignin polymerization in Norway spruce, and that radical coupling of monolignols can occur in these vesicles.
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Affiliation(s)
- Santeri Kankaanpää
- Natural Resources Institute Finland (Luke), Production Systems, Jokioinen, Finland
| | - Enni Väisänen
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, Viikki Plant Science Centre, University of Helsinki, Finland
| | - Geert Goeminne
- VIB Metabolomics Core Ghent, VIB-UGent Center for Plant Systems Biology, Ghent University, Ghent, Belgium
| | - Rabah Soliymani
- Meilahti Clinical Proteomics Core Facility, Biochemistry & Developmental Biology, Faculty of Medicine, Biomedicum Helsinki, University of Helsinki, Finland
| | - Sandrien Desmet
- VIB Metabolomics Core Ghent, VIB-UGent Center for Plant Systems Biology, Ghent University, Ghent, Belgium
| | - Anatoliy Samoylenko
- Faculty of Biochemistry and Molecular Medicine, Disease Networks Research Unit, Kvantum Institute, Infotech Oulu, University of Oulu, Oulu, Finland
| | - Seppo Vainio
- Faculty of Biochemistry and Molecular Medicine, Disease Networks Research Unit, Kvantum Institute, Infotech Oulu, University of Oulu, Oulu, Finland
| | - Gunnar Wingsle
- Umeå Plant Science Centre, Swedish University of Agricultural Sciences, Department of Forest Genetics and Plant Physiology, Umeå, Sweden
| | - Wout Boerjan
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Ruben Vanholme
- VIB Center for Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Anna Kärkönen
- Natural Resources Institute Finland (Luke), Production Systems, Helsinki, Finland
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, Finland
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3
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Yoshioka K, Kim H, Lu F, De Ridder N, Vanholme R, Kajita S, Boerjan W, Ralph J. Hydroxycinnamaldehyde-derived benzofuran components in lignins. Plant Physiol 2024; 194:1370-1382. [PMID: 37773018 DOI: 10.1093/plphys/kiad514] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/11/2023] [Accepted: 09/11/2023] [Indexed: 09/30/2023]
Abstract
Lignin is an abundant polymer in plant secondary cell walls. Prototypical lignins derive from the polymerization of monolignols (hydroxycinnamyl alcohols), mainly coniferyl and sinapyl alcohol, via combinatorial radical coupling reactions and primarily via the endwise coupling of a monomer with the phenolic end of the growing polymer. Hydroxycinnamaldehyde units have long been recognized as minor components of lignins. In plants deficient in cinnamyl alcohol dehydrogenase, the last enzyme in the monolignol biosynthesis pathway that reduces hydroxycinnamaldehydes to monolignols, chain-incorporated aldehyde unit levels are elevated. The nature and relative levels of aldehyde components in lignins can be determined from their distinct and dispersed correlations in 2D 1H-13C-correlated nuclear magnetic resonance (NMR) spectra. We recently became aware of aldehyde NMR peaks, well resolved from others, that had been overlooked. NMR of isolated low-molecular-weight oligomers from biomimetic radical coupling reactions involving coniferaldehyde revealed that the correlation peaks belonged to hydroxycinnamaldehyde-derived benzofuran moieties. Coniferaldehyde 8-5-coupling initially produces the expected phenylcoumaran structures, but the derived phenolic radicals undergo preferential disproportionation rather than radical coupling to extend the growing polymer. As a result, the hydroxycinnamaldehyde-derived phenylcoumaran units are difficult to detect in lignins, but the benzofurans are now readily observed by their distinct and dispersed correlations in the aldehyde region of NMR spectra from any lignin or monolignol dehydrogenation polymer. Hydroxycinnamaldehydes that are coupled to coniferaldehyde can be distinguished from those coupled with a generic guaiacyl end-unit. These benzofuran peaks may now be annotated and reported and their structural ramifications further studied.
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Affiliation(s)
- Koichi Yoshioka
- The US Department of Energy's Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53726, USA
- The Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726, USA
| | - Hoon Kim
- The US Department of Energy's Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53726, USA
- The Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726, USA
| | - Fachuang Lu
- The US Department of Energy's Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53726, USA
- The Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726, USA
| | - Nette De Ridder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 71, Ghent 9052, Belgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 71, Ghent 9052, Belgium
| | - Shinya Kajita
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
- Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent 9052, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 71, Ghent 9052, Belgium
| | - John Ralph
- The US Department of Energy's Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI 53726, USA
- The Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726, USA
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
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4
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Carreno-Quintero N, Tohge T, Van Acker R, McKee LS, Zhou Q, Bolze A, Xing X, Özparpucu M, Rüggeberg M, Piofczyk T, Koram Y, Bulone V, Boerjan W, Fernie AR, Fraser PD. Non-targeted discovery of high-value bio-products in Nicotiana glauca L: a potential renewable plant feedstock. BIORESOUR BIOPROCESS 2024; 11:12. [PMID: 38647836 PMCID: PMC10991672 DOI: 10.1186/s40643-023-00726-4] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 12/28/2023] [Indexed: 04/25/2024] Open
Abstract
The evaluation of plant-based feedstocks is an important aspect of biorefining. Nicotiana glauca is a solanaceous, non-food crop that produces large amounts of biomass and is well adapted to grow in suboptimal conditions. In the present article, compatible sequential solvent extractions were applied to N. glauca leaves to enable the generation of enriched extracts containing higher metabolite content comparing to direct leaf extracts. Typically, between 60 to 100 metabolite components were identified within the fractions. The occurrence of plant fatty acids, fatty acid alcohols, alkanes, sterols and terpenoids was detected by gas liquid chromatography-mass spectrometry (GC-MS) and metabolite identification was confirmed by comparison of physico-chemical properties displayed by available authentic standards. Collectively, co-products such waxes, oils, fermentable sugars, and terpenoids were all identified and quantified. The enriched fractions of N. glauca revealed a high level of readily extractable hydrocarbons, oils and high value co-products. In addition, the saccharification yield and cell wall composition analyses in the stems revealed the potential of the residue material as a promising lignocellulosic substrate for the production of fermentable sugars. In conclusion a multifractional cascade for valuable compounds/commodities has been development, that uses N. glauca biomass. These data have enabled the evaluation of N. glauca material as a potential feedstock for biorefining.
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Affiliation(s)
- Natalia Carreno-Quintero
- Biochemistry Department, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
- Vegetable Crop Research Unit, Keygene N.V, Agro Business Park, 90 6708 PW, Wageningen, The Netherlands
| | - Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rebecca Van Acker
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
| | - Lauren S McKee
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91, Stockholm, Sweden
- Division of Glycoscience, School of Biotechnology, Wallenberg Wood Science Centre, KTH, Stockholm, Sweden
| | - Qi Zhou
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91, Stockholm, Sweden
- Division of Glycoscience, School of Biotechnology, Wallenberg Wood Science Centre, KTH, Stockholm, Sweden
| | - Antje Bolze
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Xiaohui Xing
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91, Stockholm, Sweden
| | - Merve Özparpucu
- Institute for Building Materials, Swiss Federal Institute of Technology Zürich (ETH Zürich), Zurich, Switzerland
- Applied Wood Materials, Swiss Federal Laboratories of Materials Science and Technology (EMPA), Dübendorf, Switzerland
| | - Markus Rüggeberg
- Institute for Building Materials, Swiss Federal Institute of Technology Zürich (ETH Zürich), Zurich, Switzerland
- Applied Wood Materials, Swiss Federal Laboratories of Materials Science and Technology (EMPA), Dübendorf, Switzerland
| | - Thomas Piofczyk
- Pilot Pflanzenöltechnologie Magdeburg e. V. (PPM e. V.), Berliner Chaussee 66, 39114, Magdeburg, Germany
| | - Yaw Koram
- Neutral Supply Chain Limited, 337 Bath Road, Slough, Berkshire, SL1 5PR, UK
| | - Vincent Bulone
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, 106 91, Stockholm, Sweden
- ARC Centre of Excellence in Plant Cell Walls and School of Agriculture, Food and Wine, The University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Paul D Fraser
- Biochemistry Department, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK.
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Li W, Lin YCJ, Chen YL, Zhou C, Li S, De Ridder N, Oliveira DM, Zhang L, Zhang B, Wang JP, Xu C, Fu X, Luo K, Wu AM, Demura T, Lu MZ, Zhou Y, Li L, Umezawa T, Boerjan W, Chiang VL. Woody plant cell walls: Fundamentals and utilization. Mol Plant 2024; 17:112-140. [PMID: 38102833 DOI: 10.1016/j.molp.2023.12.008] [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: 10/31/2023] [Revised: 12/12/2023] [Accepted: 12/12/2023] [Indexed: 12/17/2023]
Abstract
Cell walls in plants, particularly forest trees, are the major carbon sink of the terrestrial ecosystem. Chemical and biosynthetic features of plant cell walls were revealed early on, focusing mostly on herbaceous model species. Recent developments in genomics, transcriptomics, epigenomics, transgenesis, and associated analytical techniques are enabling novel insights into formation of woody cell walls. Here, we review multilevel regulation of cell wall biosynthesis in forest tree species. We highlight current approaches to engineering cell walls as potential feedstock for materials and energy and survey reported field tests of such engineered transgenic trees. We outline opportunities and challenges in future research to better understand cell type biogenesis for more efficient wood cell wall modification and utilization for biomaterials or for enhanced carbon capture and storage.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | | | - Ying-Lan Chen
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
| | - Nette De Ridder
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Dyoni M Oliveira
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Lanjun Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Baocai Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jack P Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Changzheng Xu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Xiaokang Fu
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation, School of Life Sciences, Southwest University, Chongqing 400715, China
| | - Ai-Min Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architectures, South China Agricultural University, Guangzhou 510642, China
| | - Taku Demura
- Center for Digital Green-innovation, Nara Institute of Science and Technology, Ikoma, Nara 630-0192, Japan
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou 311300, China
| | - Yihua Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Laigeng Li
- CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China
| | - Toshiaki Umezawa
- Laboratory of Metabolic Science of Forest Plants and Microorganisms, Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Vincent L Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA.
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6
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Hoengenaert L, Van Doorsselaere J, Vanholme R, Boerjan W. Microparticle-mediated CRISPR DNA delivery for genome editing in poplar. Front Plant Sci 2023; 14:1286663. [PMID: 38023888 PMCID: PMC10679337 DOI: 10.3389/fpls.2023.1286663] [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] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
The use of CRISPR/Cas9 is currently the method of choice for precise genome engineering in plants, including in the biomass crop poplar. The most commonly used method for delivering CRISPR/Cas9 and its components in poplar is via Agrobacterium-mediated transformation, that besides the desired gene-editing event also results in stable T-DNA integration. Here we explore the delivery of the gene-editing reagents via DNA-coated microparticle bombardment into the model tree Populus tremula x P. alba to evaluate its potential for developing transgene-free, gene-edited trees, as well as its potential for integrating donor DNA at specific target sites. Using an optimized transformation method, which favors the regeneration of plants that transiently express the genes on the delivered donor DNA, we regenerated gene-edited plants that are free of the Cas9 and the antibiotic resistance-encoding transgenes. In addition, we report the frequent integration of donor DNA fragments at the Cas9-induced double-strand break, opening opportunities toward targeted gene insertions.
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Affiliation(s)
- Lennart Hoengenaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | | | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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7
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Wouters M, Bastiaanse H, Rombauts S, de Vries L, De Pooter T, Strazisar M, Neutelings G, Vanholme R, Boerjan W. Suppression of the Arabidopsis cinnamoyl-CoA reductase 1-6 intronic T-DNA mutation by epigenetic modification. Plant Physiol 2023; 192:3001-3016. [PMID: 37139862 PMCID: PMC7614886 DOI: 10.1093/plphys/kiad261] [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: 03/24/2023] [Revised: 04/10/2023] [Accepted: 04/10/2023] [Indexed: 05/05/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) transfer DNA (T-DNA) insertion collections are popular resources for fundamental plant research. Cinnamoyl-CoA reductase 1 (CCR1) catalyzes an essential step in the biosynthesis of the cell wall polymer lignin. Accordingly, the intronic T-DNA insertion mutant ccr1-6 has reduced lignin levels and shows a stunted growth phenotype. Here, we report restoration of the ccr1-6 mutant phenotype and CCR1 expression levels after a genetic cross with a UDP-glucosyltransferase 72e1 (ugt72e1),-e2,-e3 T-DNA mutant. We discovered that the phenotypic recovery was not dependent on the UGT72E family loss of function but due to an epigenetic phenomenon called trans T-DNA suppression. Via trans T-DNA suppression, the gene function of an intronic T-DNA mutant was restored after the introduction of an additional T-DNA sharing identical sequences, leading to heterochromatinization and splicing out of the T-DNA-containing intron. Consequently, the suppressed ccr1-6 allele was named epiccr1-6. Long-read sequencing revealed that epiccr1-6, not ccr1-6, carries dense cytosine methylation over the full length of the T-DNA. We showed that the SAIL T-DNA in the UGT72E3 locus could trigger the trans T-DNA suppression of the GABI-Kat T-DNA in the CCR1 locus. Furthermore, we scanned the literature for other potential cases of trans T-DNA suppression in Arabidopsis and found that 22% of the publications matching our query report on double or higher-order T-DNA mutants that meet the minimal requirements for trans T-DNA suppression. These combined observations indicate that intronic T-DNA mutants need to be used with caution since methylation of intronic T-DNA might derepress gene expression and can thereby confound results.
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Affiliation(s)
- Marlies Wouters
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Héloïse Bastiaanse
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Stéphane Rombauts
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Lisanne de Vries
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Tim De Pooter
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Mojca Strazisar
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Godfrey Neutelings
- Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), UMR 8576, CNRS, Université de Lille, Lille, France
| | - Ruben Vanholme
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Wout Boerjan
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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8
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Brouckaert M, Peng M, Höfer R, El Houari I, Darrah C, Storme V, Saeys Y, Vanholme R, Goeminne G, Timokhin VI, Ralph J, Morreel K, Boerjan W. QT-GWAS: A novel method for unveiling biosynthetic loci affecting qualitative metabolic traits. Mol Plant 2023; 16:1212-1227. [PMID: 37349988 PMCID: PMC7614782 DOI: 10.1016/j.molp.2023.06.004] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 04/06/2023] [Accepted: 06/16/2023] [Indexed: 06/24/2023]
Abstract
Although the plant kingdom provides an enormous diversity of metabolites with potentially beneficial applications for humankind, a large fraction of these metabolites and their biosynthetic pathways remain unknown. Resolving metabolite structures and their biosynthetic pathways is key to gaining biological understanding and to allow metabolic engineering. In order to retrieve novel biosynthetic genes involved in specialized metabolism, we developed a novel untargeted method designated as qualitative trait GWAS (QT-GWAS) that subjects qualitative metabolic traits to a genome-wide association study, while the conventional metabolite GWAS (mGWAS) mainly considers the quantitative variation of metabolites. As a proof of the validity of QT-GWAS, 23 and 15 of the retrieved associations identified in Arabidopsis thaliana by QT-GWAS and mGWAS, respectively, were supported by previous research. Furthermore, seven gene-metabolite associations retrieved by QT-GWAS were confirmed in this study through reverse genetics combined with metabolomics and/or in vitro enzyme assays. As such, we established that CYTOCHROME P450 706A5 (CYP706A5) is involved in the biosynthesis of chroman derivatives, UDP-GLYCOSYLTRANSFERASE 76C3 (UGT76C3) is able to hexosylate guanine in vitro and in planta, and SULFOTRANSFERASE 202B1 (SULT202B1) catalyzes the sulfation of neolignans in vitro. Collectively, our study demonstrates that the untargeted QT-GWAS method can retrieve valid gene-metabolite associations at the level of enzyme-encoding genes, even new associations that cannot be found by the conventional mGWAS, providing a new approach for dissecting qualitative metabolic traits.
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Affiliation(s)
- Marlies Brouckaert
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Meng Peng
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - René Höfer
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Ilias El Houari
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Chiarina Darrah
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Véronique Storme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Yvan Saeys
- Ghent University, Department of Applied Mathematics, Computer Science and Statistics, 9000 Ghent, Belgium; VIB Center for Inflammation Research, 9052 Ghent, Belgium
| | - Ruben Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Geert Goeminne
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium; VIB Metabolomics Core, 9052 Ghent, Belgium
| | - Vitaliy I Timokhin
- Department of Biochemistry, and US Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - John Ralph
- Department of Biochemistry, and US Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Kris Morreel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, 9000 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
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9
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El Houari I, Klíma P, Baekelandt A, Staswick PE, Uzunova V, Del Genio CI, Steenackers W, Dobrev PI, Filepová R, Novák O, Napier R, Petrášek J, Inzé D, Boerjan W, Vanholme B. Non-specific effects of the CINNAMATE-4-HYDROXYLASE inhibitor piperonylic acid. Plant J 2023. [PMID: 37036146 DOI: 10.1111/tpj.16237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 03/25/2023] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
Chemical inhibitors are often implemented for the functional characterization of genes to overcome the limitations associated with genetic approaches. Although it is well established that the specificity of the compound is key to success of a pharmacological approach, off-target effects are often overlooked or simply neglected in a complex biological setting. Here we illustrate the cause and implications of such secondary effects by focusing on piperonylic acid (PA), an inhibitor of CINNAMATE-4-HYDROXYLASE (C4H) that is frequently used to investigate the involvement of lignin during plant growth and development. When supplied to plants, we found that PA is recognized as a substrate by GRETCHEN HAGEN 3.6 (GH3.6), an amido synthetase involved in the formation of the indole-3-acetic acid (IAA) conjugate IAA-Asp. By competing for the same enzyme, PA interferes with IAA conjugation, resulting in an increase in IAA concentrations in the plant. In line with the broad substrate specificity of the GH3 family of enzymes, treatment with PA increased not only IAA levels but also those of other GH3-conjugated phytohormones, namely jasmonic acid and salicylic acid. Finally, we found that interference with the endogenous function of GH3s potentially contributes to phenotypes previously observed upon PA treatment. We conclude that deregulation of phytohormone homeostasis by surrogate occupation of the conjugation machinery in the plant is likely a general phenomenon when using chemical inhibitors. Our results hereby provide a novel and important basis for future reference in studies using chemical inhibitors.
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Affiliation(s)
- Ilias El Houari
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Petr Klíma
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Alexandra Baekelandt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Paul E Staswick
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, Nebraska, USA
| | - Veselina Uzunova
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Charo I Del Genio
- Centre for Fluid and Complex Systems, School of Computing, Electronics and Mathematics, Coventry University, Prior Street, Coventry, CV1 5FB, UK
| | - Ward Steenackers
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Petre I Dobrev
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Roberta Filepová
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02, Prague 6, Czech Republic
| | - Ondrej Novák
- Laboratory of Growth Regulators, Faculty of Science of Palacký University & Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 27, CZ-78371, Olomouc, Czech Republic
| | - Richard Napier
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Jan Petrášek
- The Czech Academy of Sciences, Institute of Experimental Botany, Rozvojová 263, 165 02, Prague 6, Czech Republic
- Department of Experimental Plant Biology, Faculty of Science, Charles University, Viničná 5, 128 43, Prague 2, Czech Republic
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
| | - Bartel Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, B-9052, Ghent, Belgium
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10
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Witvrouw K, Kim H, Vanholme R, Goeminne G, Ralph J, Boerjan W, Vanholme B. Reassessing the claimed cytokinin-substituting activity of dehydrodiconiferyl alcohol glucoside. Proc Natl Acad Sci U S A 2023; 120:e2123301120. [PMID: 36827261 PMCID: PMC9992782 DOI: 10.1073/pnas.2123301120] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 01/14/2023] [Indexed: 02/25/2023] Open
Abstract
Dehydrodiconiferyl alcohol glucoside (DCG) is a phenylpropanoid-derived plant metabolite with reported cytokinin-substituting and cell-division-promoting activity. Despite its claimed activity, DCG did not trigger morphological changes in Arabidopsis seedlings nor did it alter transcriptional shifts in cell division and cytokinin-responsive genes. In reinvestigating the bioactivity of DCG in its original setting, the previously described stimulation of tobacco callus formation could not be confirmed. No evidence was found that DCG is actually taken up by plant cells, which could explain the absence of any observable activity in the performed experiments. The DCG content in plant tissue increased when feeding explants with the DCG aglycone dehydrodiconiferyl alcohol, which is readily taken up and converted to DCG by plant cells. Despite the increased DCG content, no activity for this metabolite could be demonstrated. Our results therefore demand a reevaluation of the often-quoted cytokinin-substituting and cell-division-promoting activity that has previously been attributed to this metabolite.
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Affiliation(s)
- Klaas Witvrouw
- Department of Plant Biotechnology and Bioinformatics, Ghent University, GhentB-9052, Belgium
- VIB Center for Plant Systems Biology, GhentB-9052, Belgium
| | - Hoon Kim
- Department of Biochemistry, University of Wisconsin, Madison, WI53706
- The U.S. Department of Energy's Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin, Madison, WI53726
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, GhentB-9052, Belgium
- VIB Center for Plant Systems Biology, GhentB-9052, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, GhentB-9052, Belgium
- VIB Center for Plant Systems Biology, GhentB-9052, Belgium
- VIB Metabolomics Core, GhentB-9052, Belgium
| | - John Ralph
- Department of Biochemistry, University of Wisconsin, Madison, WI53706
- The U.S. Department of Energy's Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin, Madison, WI53726
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, GhentB-9052, Belgium
- VIB Center for Plant Systems Biology, GhentB-9052, Belgium
| | - Bartel Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, GhentB-9052, Belgium
- VIB Center for Plant Systems Biology, GhentB-9052, Belgium
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11
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Baekelandt A, Saltenis VLR, Nacry P, Malyska A, Cornelissen M, Nanda AK, Nair A, Rogowsky P, Pauwels L, Muller B, Collén J, Blomme J, Pribil M, Scharff LB, Davies J, Wilhelm R, Rolland N, Harbinson J, Boerjan W, Murchie EH, Burgess AJ, Cohan J, Debaeke P, Thomine S, Inzé D, Lankhorst RK, Parry MAJ. Paving the way towards future‐proofing our crops. Food Energy Secur 2023. [DOI: 10.1002/fes3.441] [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] [Indexed: 02/06/2023] Open
Affiliation(s)
- Alexandra Baekelandt
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | - Vandasue L. R. Saltenis
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences University of Copenhagen Denmark
| | - Philippe Nacry
- BPMP, Univ. Montpellier, INRAE, CNRS, Institut Agro Montpellier France
| | | | | | - Amrit Kaur Nanda
- Plants for the Future' European Technology Platform Brussels Belgium
| | - Abhishek Nair
- Marketing and Consumer Behaviour Group Wageningen University Wageningen Gelderland Netherlands
| | - Peter Rogowsky
- INRAE, UMR Plant Reproduction and Development Lyon France
| | - Laurens Pauwels
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | - Bertrand Muller
- Université de Montpellier – LEPSE – INRAE – Institut Agro Montpellier France
| | - Jonas Collén
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff Sorbonne Université Roscoff France
| | - Jonas Blomme
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
- Phycology Research Group, Department of Biology Ghent University Ghent Belgium
| | - Mathias Pribil
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences University of Copenhagen Denmark
| | - Lars B. Scharff
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences University of Copenhagen Denmark
| | - Jessica Davies
- Lancaster Environment Centre Lancaster University Lancaster UK
| | - Ralf Wilhelm
- Institute for Biosafety in Plant Biotechnology Julius Kühn‐Institut – Federal Research Centre for Cultivated Plants Quedlinburg Germany
| | - Norbert Rolland
- Laboratoire de Physiologie Cellulaire et Végétale Univ. Grenoble Alpes, INRAE, CNRS, CEA Grenoble France
| | - Jeremy Harbinson
- Laboratory of Biophysics Wageningen University & Research Wageningen The Netherlands
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | - Erik H. Murchie
- School of Biosciences University of Nottingham, Sutton Bonington campus Loughborough UK
| | - Alexandra J. Burgess
- School of Biosciences University of Nottingham, Sutton Bonington campus Loughborough UK
| | | | | | - Sébastien Thomine
- Institute for Integrative Biology of the Cell (I2BC) Université Paris‐Saclay, CEA, CNRS Gif‐sur‐Yvette France
| | - Dirk Inzé
- Department of Plant Biotechnology and Bioinformatics Ghent University Ghent Belgium
- VIB Center for Plant Systems Biology Ghent Belgium
| | - René Klein Lankhorst
- Wageningen Plant Research Wageningen University & Research Wageningen The Netherlands
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12
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Anders C, Hoengenaert L, Boerjan W. Accelerating wood domestication in forest trees through genome editing: Advances and prospects. Curr Opin Plant Biol 2023; 71:102329. [PMID: 36586396 PMCID: PMC7614060 DOI: 10.1016/j.pbi.2022.102329] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [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: 09/12/2022] [Revised: 11/07/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
The high economic value of wood requires intensive breeding towards multipurpose biomass. However, long breeding cycles hamper the fast development of novel tree varieties that have improved biomass properties, are tolerant to biotic and abiotic stresses, and resilient to climate change. To speed up domestication, the integration of conventional breeding and new breeding techniques is needed. In this review, we discuss recent advances in genome editing and Cas-DNA-free genome engineering of forest trees, and briefly discuss how multiplex editing combined with multi-omics approaches can accelerate the genetic improvement of forest trees, with a focus on wood.
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Affiliation(s)
- Chantal Anders
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Lennart Hoengenaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, 9052 Ghent, Belgium.
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13
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Shafiei R, Hooper M, McClellan C, Oakey H, Stephens J, Lapierre C, Tsuji Y, Goeminne G, Vanholme R, Boerjan W, Ralph J, Halpin C. Downregulation of barley ferulate 5-hydroxylase dramatically alters straw lignin structure without impact on mechanical properties. Front Plant Sci 2023; 13:1125003. [PMID: 36726680 PMCID: PMC9886061 DOI: 10.3389/fpls.2022.1125003] [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: 12/15/2022] [Accepted: 12/22/2022] [Indexed: 06/18/2023]
Abstract
Barley is a major cereal crop for temperate climates, and a diploid genetic model for polyploid wheat. Cereal straw biomass is an attractive source of feedstock for green technologies but lignin, a key determinant of feedstock recalcitrance, complicates bio-conversion processes. However, manipulating lignin content to improve the conversion process could negatively affect agronomic traits. An alternative approach is to manipulate lignin composition which influences the physical and chemical properties of straw. This study validates the function of a barley ferulate 5-hydroxylase gene and demonstrates that its downregulation using the RNA-interference approach substantially impacts lignin composition. We identified five barley genes having putative ferulate 5-hydroxylase activity. Downregulation of HvF5H1 substantially reduced the lignin syringyl/guaiacyl (S/G) ratio in straw while the lignin content, straw mechanical properties, plant growth habit, and grain characteristics all remained unaffected. Metabolic profiling revealed significant changes in the abundance of 173 features in the HvF5H1-RNAi lines. The drastic changes in the lignin polymer of transgenic lines highlight the plasticity of barley lignification processes and the associated potential for manipulating and improving lignocellulosic biomass as a feedstock for green technologies. On the other hand, our results highlight some differences between the lignin biosynthetic pathway in barley, a temperate climate grass, and the warm climate grass, rice, and underscore potential diversity in the lignin biosynthetic pathways in grasses.
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Affiliation(s)
- Reza Shafiei
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
| | - Matthew Hooper
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
| | - Christopher McClellan
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
| | - Helena Oakey
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
- Faculty of Sciences, School of Agriculture, Food and Wine, University of Adelaide, Adelaide, SA, Australia
| | - Jennifer Stephens
- Cell And Molecular Sciences, James Hutton Institute, Dundee, United Kingdom
| | | | - Yukiko Tsuji
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, United States
- Department of Energy’s Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
| | | | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent, Center for Plant Systems Biology, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent, Center for Plant Systems Biology, Ghent, Belgium
| | - John Ralph
- Department of Energy’s Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Claire Halpin
- Division of Plant Sciences, School of Life Sciences, University of Dundee at the James Hutton Institute, Dundee, United Kingdom
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14
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De Meester B, Van Acker R, Wouters M, Traversari S, Steenackers M, Neukermans J, Van Breusegem F, Déjardin A, Pilate G, Boerjan W. Field and saccharification performances of poplars severely downregulated in CAD1. New Phytol 2022; 236:2075-2090. [PMID: 35808905 DOI: 10.1111/nph.18366] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 05/22/2022] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Lignin is one of the main factors causing lignocellulosic biomass recalcitrance to enzymatic hydrolysis. Glasshouse-grown poplars severely downregulated for CINNAMYL ALCOHOL DEHYDROGENASE 1 (CAD1), the enzyme catalysing the last step in the monolignol-specific branch of lignin biosynthesis, have increased saccharification yields and normal growth. Here, we assess the performance of these hpCAD poplars in the field under short rotation coppice culture for two consecutive rotations of 1 yr and 3 yr. While 1-yr-old hpCAD wood had 10% less lignin, 3-yr-old hpCAD wood had wild-type lignin levels. Because of their altered cell wall composition, including elevated levels of cinnamaldehydes, both 1-yr-old and 3-yr-old hpCAD wood showed enhanced saccharification yields upon harsh alkaline pretreatments (up to +85% and +77%, respectively). In contrast with previous field trials with poplars less severely downregulated for CINNAMYL ALCOHOL DEHYDROGENASE (CAD), the hpCAD poplars displayed leaning phenotypes, early bud set, early flowering and yield penalties. Moreover, hpCAD wood had enlarged vessels, decreased wood density and reduced relative and free water contents. Our data show that the phenotypes of CAD-deficient poplars are strongly dependent on the environment and underpin the importance of field trials in translating basic research towards applications.
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Affiliation(s)
- Barbara De Meester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Rebecca Van Acker
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Marlies Wouters
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Silvia Traversari
- BioLabs, Institute of Life Sciences, Scuola Superiore Sant'Anna, Piazza Martiri della Libertà 33, 56127, Pisa, Italy
- Research Institute on Terrestrial Ecosytems (IRET-CNR), Via Moruzzi 1, 56124, Pisa, Italy
| | - Marijke Steenackers
- Research Institute for Nature and Forest (INBO), Gaverstraat 4, 9500, Geraardsbergen, Belgium
| | - Jenny Neukermans
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Annabelle Déjardin
- INRAE, ONF, BioForA Orléans, 2163 Avenue de la pomme de pin, 45075, Ardon, France
| | - Gilles Pilate
- INRAE, ONF, BioForA Orléans, 2163 Avenue de la pomme de pin, 45075, Ardon, France
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
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15
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De Meester B, Vanholme R, Mota T, Boerjan W. Lignin engineering in forest trees: From gene discovery to field trials. Plant Commun 2022; 3:100465. [PMID: 36307984 PMCID: PMC9700206 DOI: 10.1016/j.xplc.2022.100465] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 10/10/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
Wood is an abundant and renewable feedstock for the production of pulp, fuels, and biobased materials. However, wood is recalcitrant toward deconstruction into cellulose and simple sugars, mainly because of the presence of lignin, an aromatic polymer that shields cell-wall polysaccharides. Hence, numerous research efforts have focused on engineering lignin amount and composition to improve wood processability. Here, we focus on results that have been obtained by engineering the lignin biosynthesis and branching pathways in forest trees to reduce cell-wall recalcitrance, including the introduction of exotic lignin monomers. In addition, we draw general conclusions from over 20 years of field trial research with trees engineered to produce less or altered lignin. We discuss possible causes and solutions for the yield penalty that is often associated with lignin engineering in trees. Finally, we discuss how conventional and new breeding strategies can be combined to develop elite clones with desired lignin properties. We conclude this review with priorities for the development of commercially relevant lignin-engineered trees.
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Affiliation(s)
- Barbara De Meester
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Ruben Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Thatiane Mota
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium.
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16
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Ferreira SS, Goeminne G, Simões MS, Pina AVDA, Lima LGAD, Pezard J, Gutiérrez A, Rencoret J, Mortimer JC, Del Río JC, Boerjan W, Cesarino I. Transcriptional and metabolic changes associated with internode development and reduced cinnamyl alcohol dehydrogenase activity in sorghum. J Exp Bot 2022; 73:6307-6333. [PMID: 35788296 DOI: 10.1093/jxb/erac300] [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: 02/03/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The molecular mechanisms associated with secondary cell wall (SCW) deposition in sorghum remain largely uncharacterized. Here, we employed untargeted metabolomics and large-scale transcriptomics to correlate changes in SCW deposition with variation in global gene expression profiles and metabolite abundance along an elongating internode of sorghum, with a major focus on lignin and phenolic metabolism. To gain deeper insight into the metabolic and transcriptional changes associated with pathway perturbations, a bmr6 mutant [with reduced cinnamyl alcohol dehydrogenase (CAD) activity] was analyzed. In the wild type, internode development was accompanied by an increase in the content of oligolignols, p-hydroxybenzaldehyde, hydroxycinnamate esters, and flavonoid glucosides, including tricin derivatives. We further identified modules of genes whose expression pattern correlated with SCW deposition and the accumulation of these target metabolites. Reduced CAD activity resulted in the accumulation of hexosylated forms of hydroxycinnamates (and their derivatives), hydroxycinnamaldehydes, and benzenoids. The expression of genes belonging to one specific module in our co-expression analysis correlated with the differential accumulation of these compounds and contributed to explaining this metabolic phenotype. Metabolomics and transcriptomics data further suggested that CAD perturbation activates distinct detoxification routes in sorghum internodes. Our systems biology approach provides a landscape of the metabolic and transcriptional changes associated with internode development and with reduced CAD activity in sorghum.
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Affiliation(s)
- Sávio Siqueira Ferreira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, São Paulo, Brazil
| | - Geert Goeminne
- VIB Center for Plant Systems Biology, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Marcella Siqueira Simões
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, São Paulo, Brazil
| | | | | | - Jade Pezard
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes, Seville, Spain
| | - Jorge Rencoret
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes, Seville, Spain
| | - Jenny C Mortimer
- Joint BioEnergy Institute, Emeryville, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - José C Del Río
- Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Avenida de la Reina Mercedes, Seville, Spain
| | - Wout Boerjan
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Igor Cesarino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, São Paulo, Brazil
- Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues, São Paulo, Brazil
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17
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Wouters M, Corneillie S, Dewitte A, Van Doorsselaere J, Van den Bulcke J, Van Acker J, Vanholme B, Boerjan W. Whole genome duplication of wild-type and CINNAMYL ALCOHOL DEHYDROGENASE1-downregulated hybrid poplar reduces biomass yield and causes a brittle apex phenotype in field-grown wild types. Front Plant Sci 2022; 13:995402. [PMID: 36160989 PMCID: PMC9504066 DOI: 10.3389/fpls.2022.995402] [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: 07/15/2022] [Accepted: 08/22/2022] [Indexed: 06/16/2023]
Abstract
The potential of whole genome duplication to increase plant biomass yield is well-known. In Arabidopsis tetraploids, an increase in biomass yield was accompanied by a reduction in lignin content and, as a result, a higher saccharification efficiency was achieved compared with diploid controls. Here, we evaluated whether the results obtained in Arabidopsis could be translated into poplar and whether the enhanced saccharification yield upon alkaline pretreatment of hairpin-downregulated CINNAMYL ALCOHOL DEHYDROGENASE1 (hpCAD) transgenic poplar could be further improved upon a whole genome duplication. Using a colchicine treatment, wild-type (WT) Populus tremula x P. alba cv. INRA 717-1B4, a commonly used model clone in tree biotechnology research, and hpCAD tetraploids were generated and grown in the greenhouse. In parallel, WT tetraploid poplars were grown in the field. In contrast to Arabidopsis, a whole genome duplication of poplar had a negative impact on the biomass yield of both greenhouse- and field-grown trees. Strikingly, field-grown WT tetraploids developed a brittle apex phenotype, i.e., their tip broke off just below the apex. In addition, the chromosome doubling altered the biomass composition of field-grown, but not of greenhouse-grown tetraploid poplars. More specifically, the lignin content of field-grown tetraploid poplars was increased at the expense of matrix polysaccharides. This increase in lignin deposition in biomass is likely the cause of the observed brittle apex phenotype, though no major differences in stem anatomy or in mechanical properties could be found between di- and tetraploid WT poplars grown in the field. Finally, without biomass pretreatment, the saccharification efficiency of greenhouse- and field-grown WT diploids was not different from that of tetraploids, whereas that of greenhouse-grown hpCAD tetraploids was higher than that of greenhouse-grown diploids. Upon alkaline pretreatment, the saccharification yield of diploids was similar to that of tetraploids for all genotypes and growth conditions tested. This study showed that a whole genome duplication in hybrid WT and hpCAD poplar did neither result in further improvements in biomass yield, nor in improved biomass composition and, hence, saccharification performance.
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Affiliation(s)
- Marlies Wouters
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Sander Corneillie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Angelo Dewitte
- Expertisecentrum Agro- en Biotechnologie, VIVES, Roeselare, Belgium
| | | | - Jan Van den Bulcke
- Laboratory of Wood Technology, Department of Environment, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Joris Van Acker
- Laboratory of Wood Technology, Department of Environment, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Bartel Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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18
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Hoengenaert L, Wouters M, Kim H, De Meester B, Morreel K, Vandersyppe S, Pollier J, Desmet S, Goeminne G, Ralph J, Boerjan W, Vanholme R. Overexpression of the scopoletin biosynthetic pathway enhances lignocellulosic biomass processing. Sci Adv 2022; 8:eabo5738. [PMID: 35857515 PMCID: PMC9278857 DOI: 10.1126/sciadv.abo5738] [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] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/03/2022] [Indexed: 06/15/2023]
Abstract
Lignin is the main factor limiting the enzymatic conversion of lignocellulosic biomass into fermentable sugars. To reduce the recalcitrance engendered by the lignin polymer, the coumarin scopoletin was incorporated into the lignin polymer through the simultaneous expression of FERULOYL-CoA 6'-HYDROXYLASE 1 (F6'H1) and COUMARIN SYNTHASE (COSY) in lignifying cells in Arabidopsis. The transgenic lines overproduced scopoletin and incorporated it into the lignin polymer, without adversely affecting plant growth. About 3.3% of the lignin units in the transgenic lines were derived from scopoletin, thereby exceeding the levels of the traditional p-hydroxyphenyl units. Saccharification efficiency of alkali-pretreated scopoletin-overproducing lines was 40% higher than for wild type.
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Affiliation(s)
- Lennart Hoengenaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Marlies Wouters
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Hoon Kim
- Department of Biochemistry and U.S. Department of Energy’s Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA
| | - Barbara De Meester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Steven Vandersyppe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Sandrien Desmet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - John Ralph
- Department of Biochemistry and U.S. Department of Energy’s Great Lakes Bioenergy Research Center, University of Wisconsin, Madison, WI, USA
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
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19
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De Meester B, Oyarce P, Vanholme R, Van Acker R, Tsuji Y, Vangeel T, Van den Bosch S, Van Doorsselaere J, Sels B, Ralph J, Boerjan W. Engineering Curcumin Biosynthesis in Poplar Affects Lignification and Biomass Yield. Front Plant Sci 2022; 13:943349. [PMID: 35860528 PMCID: PMC9289561 DOI: 10.3389/fpls.2022.943349] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 06/14/2022] [Indexed: 06/02/2023]
Abstract
Lignocellulosic biomass is recalcitrant toward deconstruction into simple sugars mainly due to the presence of lignin. By engineering plants to partially replace traditional lignin monomers with alternative ones, lignin degradability and extractability can be enhanced. Previously, the alternative monomer curcumin has been successfully produced and incorporated into lignified cell walls of Arabidopsis by the heterologous expression of DIKETIDE-CoA SYNTHASE (DCS) and CURCUMIN SYNTHASE2 (CURS2). The resulting transgenic plants did not suffer from yield penalties and had an increased saccharification yield after alkaline pretreatment. Here, we translated this strategy into the bio-energy crop poplar. Via the heterologous expression of DCS and CURS2 under the control of the secondary cell wall CELLULOSE SYNTHASE A8-B promoter (ProCesA8-B), curcumin was also produced and incorporated into the lignified cell walls of poplar. ProCesA8-B:DCS_CURS2 transgenic poplars, however, suffered from shoot-tip necrosis and yield penalties. Compared to that of the wild-type (WT), the wood of transgenic poplars had 21% less cellulose, 28% more matrix polysaccharides, 23% more lignin and a significantly altered lignin composition. More specifically, ProCesA8-B:DCS_CURS2 lignin had a reduced syringyl/guaiacyl unit (S/G) ratio, an increased frequency of p-hydroxyphenyl (H) units, a decreased frequency of p-hydroxybenzoates and a higher fraction of phenylcoumaran units. Without, or with alkaline or hot water pretreatment, the saccharification efficiency of the transgenic lines was equal to that of the WT. These differences in (growth) phenotype illustrate that translational research in crops is essential to assess the value of an engineering strategy for applications. Further fine-tuning of this research strategy (e.g., by using more specific promoters or by translating this strategy to other crops such as maize) might lead to transgenic bio-energy crops with cell walls more amenable to deconstruction without settling in yield.
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Affiliation(s)
- Barbara De Meester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Paula Oyarce
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Rebecca Van Acker
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yukiko Tsuji
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- US Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, United States
| | - Thijs Vangeel
- Center for Sustainable Catalysis and Engineering, KU Leuven, Leuven, Belgium
| | | | | | - Bert Sels
- Center for Sustainable Catalysis and Engineering, KU Leuven, Leuven, Belgium
| | - John Ralph
- Department of Biochemistry, University of Wisconsin, Madison, WI, United States
- US Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, United States
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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20
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Allen H, Zeef L, Morreel K, Goeminne G, Kumar M, Gomez LD, Dean AP, Eckmann A, Casiraghi C, McQueen-Mason SJ, Boerjan W, Turner SR. Flexible and digestible wood caused by viral-induced alteration of cell wall composition. Curr Biol 2022; 32:3398-3406.e6. [PMID: 35732179 PMCID: PMC9616729 DOI: 10.1016/j.cub.2022.06.005] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 03/29/2022] [Accepted: 06/01/2022] [Indexed: 11/16/2022]
Abstract
Woody plant material represents a vast renewable resource that has the potential to produce biofuels and other bio-based products with favorable net CO2 emissions.1,2 Its potential has been demonstrated in a recent study that generated novel structural materials from flexible moldable wood.3 Apple rubbery wood (ARW) disease is the result of a viral infection that causes woody stems to exhibit increased flexibility.4 Although ARW disease is associated with the presence of an RNA virus5 known as apple rubbery wood virus (ARWV), how the unique symptoms develop is unknown. We demonstrate that the symptoms of ARWV infections arise from reduced lignification within the secondary cell wall of xylem fibers and result in increased wood digestibility. In contrast, the mid-lamellae region and xylem ray cells are largely unaffected by the infection. Gene expression and proteomic data from symptomatic xylem clearly show the downregulation of phenylalanine ammonia lyase (PAL), the enzyme catalyzing the first committed step in the phenylpropanoid pathway leading to lignin biosynthesis. A large increase in soluble phenolics in symptomatic xylem, including the lignin precursor phenylalanine, is also consistent with PAL downregulation. ARWV infection results in the accumulation of many host-derived virus-activated small interfering RNAs (vasiRNAs). PAL-derived vasiRNAs are among the most abundant vasiRNAs in symptomatic xylem and are likely the cause of reduced PAL activity. Apparently, the mechanism used by the virus to alter lignin exhibits similarities to the RNAi strategy used to alter lignin in genetically modified trees to generate comparable improvements in wood properties.6, 7, 8 Video abstract
Apple rubbery wood (ARW) symptoms are caused by decreased lignin in woody tissue RNA-seq, proteomics, and metabolomics suggest phenylalanine levels decrease Virus-activated small interfering RNAs (vasiRNAs) are generated in response to ARWV infection VasiRNAs cause siRNA-based downregulation of phenylalanine ammonia
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Affiliation(s)
- Holly Allen
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Leo Zeef
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Metabolomics Core Gent, VIB, 9052 Zwijnaarde, Belgium
| | - Manoj Kumar
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Leonardo D Gomez
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, York YO10 5DD, UK
| | - Andrew P Dean
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Axel Eckmann
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Cinzia Casiraghi
- Department of Chemistry, University of Manchester, Oxford Road, Manchester M13 9PT, UK
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products (CNAP), Department of Biology, University of York, York YO10 5DD, UK
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Simon R Turner
- School of Biological Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK.
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21
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Hu S, Kamimura N, Sakamoto S, Nagano S, Takata N, Liu S, Goeminne G, Vanholme R, Uesugi M, Yamamoto M, Hishiyama S, Kim H, Boerjan W, Ralph J, Masai E, Mitsuda N, Kajita S. Rerouting of the lignin biosynthetic pathway by inhibition of cytosolic shikimate recycling in transgenic hybrid aspen. Plant J 2022; 110:358-376. [PMID: 35044002 DOI: 10.1111/tpj.15674] [Citation(s) in RCA: 7] [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: 09/12/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Lignin is a phenolic polymer deposited in the plant cell wall, and is mainly polymerized from three canonical monomers (monolignols), i.e. p-coumaryl, coniferyl and sinapyl alcohols. After polymerization, these alcohols form different lignin substructures. In dicotyledons, monolignols are biosynthesized from phenylalanine, an aromatic amino acid. Shikimate acts at two positions in the route to the lignin building blocks. It is part of the shikimate pathway that provides the precursor for the biosynthesis of phenylalanine, and is involved in the transesterification of p-coumaroyl-CoA to p-coumaroyl shikimate, one of the key steps in the biosynthesis of coniferyl and sinapyl alcohols. The shikimate residue in p-coumaroyl shikimate is released in later steps, and the resulting shikimate becomes available again for the biosynthesis of new p-coumaroyl shikimate molecules. In this study, we inhibited cytosolic shikimate recycling in transgenic hybrid aspen by accelerated phosphorylation of shikimate in the cytosol through expression of a bacterial shikimate kinase (SK). This expression elicited an increase in p-hydroxyphenyl units of lignin and, by contrast, a decrease in guaiacyl and syringyl units. Transgenic plants with high SK activity produced a lignin content comparable to that in wild-type plants, and had an increased processability via enzymatic saccharification. Although expression of many genes was altered in the transgenic plants, elevated SK activity did not exert a significant effect on the expression of the majority of genes responsible for lignin biosynthesis. The present results indicate that cytosolic shikimate recycling is crucial to the monomeric composition of lignin rather than for lignin content.
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Affiliation(s)
- Shi Hu
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Naofumi Kamimura
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Shingo Sakamoto
- Plant Gene Regulation Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Smart CO2 Utilization Research Team, Global Zero Emission Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Soichiro Nagano
- Forest Tree Breeding Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Naoki Takata
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Hitachi, Ibaraki, Japan
| | - Sarah Liu
- Department of Biochemistry, and US Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Metabolomics Core Ghent, VIB, Ghent, Belgium
| | - Mikiko Uesugi
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Masanobu Yamamoto
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
| | - Shojiro Hishiyama
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Tsukuba, Japan
| | - Hoon Kim
- Department of Biochemistry, and US Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - John Ralph
- Department of Biochemistry, and US Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, Wisconsin, USA
| | - Eiji Masai
- Department of Bioengineering, Nagaoka University of Technology, Nagaoka, Japan
| | - Nobutaka Mitsuda
- Plant Gene Regulation Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
- Smart CO2 Utilization Research Team, Global Zero Emission Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Japan
| | - Shinya Kajita
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Koganei, Tokyo, Japan
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22
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Feijao C, Morreel K, Anders N, Tryfona T, Busse-Wicher M, Kotake T, Boerjan W, Dupree P. Hydroxycinnamic acid-modified xylan side chains and their cross-linking products in rice cell walls are reduced in the Xylosyl arabinosyl substitution of xylan 1 mutant. Plant J 2022; 109:1152-1167. [PMID: 34862679 DOI: 10.1111/tpj.15620] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [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: 05/22/2021] [Revised: 11/13/2021] [Accepted: 11/29/2021] [Indexed: 06/13/2023]
Abstract
The intricate architecture of cell walls and the complex cross-linking of their components hinders some industrial and agricultural applications of plant biomass. Xylan is a key structural element of grass cell walls, closely interacting with other cell wall components such as cellulose and lignin. The main branching points of grass xylan, 3-linked l-arabinosyl substitutions, can be modified by ferulic acid (a hydroxycinnamic acid), which cross-links xylan to other xylan chains and lignin. XAX1 (Xylosyl arabinosyl substitution of xylan 1), a rice (Oryza sativa) member of the glycosyltransferase family GT61, has been described to add xylosyl residues to arabinosyl substitutions modified by ferulic acid. In this study, we characterize hydroxycinnamic acid-decorated arabinosyl substitutions present on rice xylan and their cross-linking, in order to decipher the role of XAX1 in xylan synthesis. Our results show a general reduction of hydroxycinnamic acid-modified 3-linked arabinosyl substitutions in xax1 mutant rice regardless of their modification with a xylosyl residue. Moreover, structures resembling the direct cross-link between xylan and lignin (ferulated arabinosyl substitutions bound to lignin monomers and dimers), together with diferulates known to cross-link xylan, are strongly reduced in xax1. Interestingly, apart from feruloyl and p-coumaroyl modifications on arabinose, putative caffeoyl and oxalyl modifications were characterized, which were also reduced in xax1. Our results suggest an alternative function of XAX1 in the transfer of hydroxycinnamic acid-modified arabinosyl substitutions to xylan, rather than xylosyl transfer to arabinosyl substitutions. Ultimately, XAX1 plays a fundamental role in cross-linking, providing a potential target for the improvement of use of grass biomass.
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Affiliation(s)
- Carolina Feijao
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Nadine Anders
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Theodora Tryfona
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Marta Busse-Wicher
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
| | - Toshihisa Kotake
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
- Saitama University, 255 Shimo-Okubo, Saitama, 338-8570, Japan
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, UK
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23
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De Meester B, Vanholme R, de Vries L, Wouters M, Van Doorsselaere J, Boerjan W. Vessel- and ray-specific monolignol biosynthesis as an approach to engineer fiber-hypolignification and enhanced saccharification in poplar. Plant J 2021; 108:752-765. [PMID: 34403547 DOI: 10.1111/tpj.15468] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 06/24/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
Lignin is one of the main factors determining recalcitrance to processing of lignocellulosic biomass towards bio-based materials and fuels. Consequently, wood of plants engineered for low lignin content is typically more amenable to processing. However, lignin-modified plants often exhibit collapsed vessels and associated growth defects. Vessel-specific reintroduction of lignin biosynthesis in dwarfed low-lignin cinnamoyl-CoA reductase1 (ccr1) Arabidopsis mutants using the ProSNBE:AtCCR1 construct overcame the yield penalty while maintaining high saccharification yields, and showed that monolignols can be transported between the different xylem cells acting as 'good neighbors' in Arabidopsis. Here, we translated this research into the bio-energy crop poplar. By expressing ProSNBE:AtCCR1 into CRISPR/Cas9-generated ccr2 poplars, we aimed for vessel-specific lignin biosynthesis to: (i) achieve growth restoration while maintaining high saccharification yields; and (ii) study the existence of 'good neighbors' in poplar wood. Analyzing the resulting ccr2 ProSNBE:AtCCR1 poplars showed that vessels and rays act as good neighbors for lignification in poplar. If sufficient monolignols are produced by these cells, monolignols migrate over multiple cell layers, resulting in a restoration of the lignin amount to wild-type levels. If the supply of monolignols is limited, the monolignols are incorporated into the cell walls of the vessels and rays producing them and their adjoining cells resulting in fiber hypolignification. One such fiber-hypolignified line had 18% less lignin and, despite its small yield penalty, had an increase of up to 71% in sugar release on a plant base upon saccharification.
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Affiliation(s)
- Barbara De Meester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Lisanne de Vries
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Marlies Wouters
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, 9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, 9052, Belgium
| | - Jan Van Doorsselaere
- Higher Institute for Nursing and Biotechnology, VIVES University College, Wilgenstraat 32, Roeselare, 8800, Belgium
| | - Wout Boerjan
- 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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24
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de Vries L, Brouckaert M, Chanoca A, Kim H, Regner MR, Timokhin VI, Sun Y, De Meester B, Van Doorsselaere J, Goeminne G, Chiang VL, Wang JP, Ralph J, Morreel K, Vanholme R, Boerjan W. CRISPR-Cas9 editing of CAFFEOYL SHIKIMATE ESTERASE 1 and 2 shows their importance and partial redundancy in lignification in Populus tremula × P. alba. Plant Biotechnol J 2021; 19:2221-2234. [PMID: 34160888 PMCID: PMC8541784 DOI: 10.1111/pbi.13651] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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: 04/10/2021] [Revised: 06/10/2021] [Accepted: 06/18/2021] [Indexed: 05/06/2023]
Abstract
Lignins are cell wall-located aromatic polymers that provide strength and hydrophobicity to woody tissues. Lignin monomers are synthesized via the phenylpropanoid pathway, wherein CAFFEOYL SHIKIMATE ESTERASE (CSE) converts caffeoyl shikimate into caffeic acid. Here, we explored the role of the two CSE homologs in poplar (Populus tremula × P. alba). Reporter lines showed that the expression conferred by both CSE1 and CSE2 promoters is similar. CRISPR-Cas9-generated cse1 and cse2 single mutants had a wild-type lignin level. Nevertheless, CSE1 and CSE2 are not completely redundant, as both single mutants accumulated caffeoyl shikimate. In contrast, the cse1 cse2 double mutants had a 35% reduction in lignin and associated growth penalty. The reduced-lignin content translated into a fourfold increase in cellulose-to-glucose conversion upon limited saccharification. Phenolic profiling of the double mutants revealed large metabolic shifts, including an accumulation of p-coumaroyl, 5-hydroxyferuloyl, feruloyl and sinapoyl shikimate, in addition to caffeoyl shikimate. This indicates that the CSEs have a broad substrate specificity, which was confirmed by in vitro enzyme kinetics. Taken together, our results suggest an alternative path within the phenylpropanoid pathway at the level of the hydroxycinnamoyl-shikimates, and show that CSE is a promising target to improve plants for the biorefinery.
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Affiliation(s)
- Lisanne de Vries
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Marlies Brouckaert
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Alexandra Chanoca
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Hoon Kim
- Department of Biochemistry, and U.S. Department of Energy Great Lakes Bioenergy Research CenterWisconsin Energy InstituteUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Matthew R. Regner
- Department of Biochemistry, and U.S. Department of Energy Great Lakes Bioenergy Research CenterWisconsin Energy InstituteUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Vitaliy I. Timokhin
- Department of Biochemistry, and U.S. Department of Energy Great Lakes Bioenergy Research CenterWisconsin Energy InstituteUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Yi Sun
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
| | - Barbara De Meester
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | | | - Geert Goeminne
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
- VIB Metabolomics CoreGhentBelgium
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
- Forest Biotechnology GroupDepartment of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNCUSA
- Department of Forest BiomaterialsNorth Carolina State UniversityRaleighNCUSA
| | - Jack P. Wang
- State Key Laboratory of Tree Genetics and BreedingNortheast Forestry UniversityHarbinChina
- Forest Biotechnology GroupDepartment of Forestry and Environmental ResourcesNorth Carolina State UniversityRaleighNCUSA
| | - John Ralph
- Department of Biochemistry, and U.S. Department of Energy Great Lakes Bioenergy Research CenterWisconsin Energy InstituteUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Kris Morreel
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Wout Boerjan
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
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25
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El Houari I, Van Beirs C, Arents HE, Han H, Chanoca A, Opdenacker D, Pollier J, Storme V, Steenackers W, Quareshy M, Napier R, Beeckman T, Friml J, De Rybel B, Boerjan W, Vanholme B. Seedling developmental defects upon blocking CINNAMATE-4-HYDROXYLASE are caused by perturbations in auxin transport. New Phytol 2021; 230:2275-2291. [PMID: 33728703 DOI: 10.1111/nph.17349] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 03/06/2021] [Indexed: 05/20/2023]
Abstract
The phenylpropanoid pathway serves a central role in plant metabolism, providing numerous compounds involved in diverse physiological processes. Most carbon entering the pathway is incorporated into lignin. Although several phenylpropanoid pathway mutants show seedling growth arrest, the role for lignin in seedling growth and development is unexplored. We use complementary pharmacological and genetic approaches to block CINNAMATE-4-HYDROXYLASE (C4H) functionality in Arabidopsis seedlings and a set of molecular and biochemical techniques to investigate the underlying phenotypes. Blocking C4H resulted in reduced lateral rooting and increased adventitious rooting apically in the hypocotyl. These phenotypes coincided with an inhibition in AUX transport. The upstream accumulation in cis-cinnamic acid was found to be likely to cause polar AUX transport inhibition. Conversely, a downstream depletion in lignin perturbed phloem-mediated AUX transport. Restoring lignin deposition effectively reestablished phloem transport and, accordingly, AUX homeostasis. Our results show that the accumulation of bioactive intermediates and depletion in lignin jointly cause the aberrant phenotypes upon blocking C4H, and demonstrate that proper deposition of lignin is essential for the establishment of AUX distribution in seedlings. Our data position the phenylpropanoid pathway and lignin in a new physiological framework, consolidating their importance in plant growth and development.
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Affiliation(s)
- Ilias El Houari
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Caroline Van Beirs
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Helena E Arents
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Huibin Han
- Institute of Science and Technology (IST) Austria, Klosterneuburg, 3400, Austria
| | - Alexandra Chanoca
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Davy Opdenacker
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Jacob Pollier
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Metabolomics Core, Ghent, 9052, Belgium
| | - Véronique Storme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Ward Steenackers
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Mussa Quareshy
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Richard Napier
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Jiří Friml
- Institute of Science and Technology (IST) Austria, Klosterneuburg, 3400, Austria
| | - Bert De Rybel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
| | - Bartel Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, Ghent, B-9052, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, Ghent, B-9052, Belgium
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26
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Liu X, Van Acker R, Voorend W, Pallidis A, Goeminne G, Pollier J, Morreel K, Kim H, Muylle H, Bosio M, Ralph J, Vanholme R, Boerjan W. Rewired phenolic metabolism and improved saccharification efficiency of a Zea mays cinnamyl alcohol dehydrogenase 2 (zmcad2) mutant. Plant J 2021; 105:1240-1257. [PMID: 33258151 DOI: 10.1111/tpj.15108] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 06/12/2023]
Abstract
Lignocellulosic biomass is an abundant byproduct from cereal crops that can potentially be valorized as a feedstock to produce biomaterials. Zea mays CINNAMYL ALCOHOL DEHYDROGENASE 2 (ZmCAD2) is involved in lignification, and is a promising target to improve the cellulose-to-glucose conversion of maize stover. Here, we analyzed a field-grown zmcad2 Mutator transposon insertional mutant. Zmcad2 mutant plants had an 18% lower Klason lignin content, whereas their cellulose content was similar to that of control lines. The lignin in zmcad2 mutants contained increased levels of hydroxycinnamaldehydes, i.e. the substrates of ZmCAD2, ferulic acid and tricin. Ferulates decorating hemicelluloses were not altered. Phenolic profiling further revealed that hydroxycinnamaldehydes are partly converted into (dihydro)ferulic acid and sinapic acid and their derivatives in zmcad2 mutants. Syringyl lactic acid hexoside, a metabolic sink in CAD-deficient dicot trees, appeared not to be a sink in zmcad2 maize. The enzymatic cellulose-to-glucose conversion efficiency was determined after 10 different thermochemical pre-treatments. Zmcad2 yielded significantly higher conversions compared with controls for almost every pre-treatment. However, the relative increase in glucose yields after alkaline pre-treatment was not higher than the relative increase when no pre-treatment was applied, suggesting that the positive effect of the incorporation of hydroxycinnamaldehydes was leveled off by the negative effect of reduced p-coumarate levels in the cell wall. Taken together, our results reveal how phenolic metabolism is affected in CAD-deficient maize, and further support mutating CAD genes in cereal crops as a promising strategy to improve lignocellulosic biomass for sugar-platform biorefineries.
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Affiliation(s)
- Xinyu Liu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Rebecca Van Acker
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wannes Voorend
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Andreas Pallidis
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Metabolomics Core, 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
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hoon Kim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, Wisconsin, 53726, USA
| | - Hilde Muylle
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - John Ralph
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
- Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, Wisconsin, 53726, USA
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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27
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Desmet S, Saeys Y, Verstaen K, Dauwe R, Kim H, Niculaes C, Fukushima A, Goeminne G, Vanholme R, Ralph J, Boerjan W, Morreel K. Maize specialized metabolome networks reveal organ-preferential mixed glycosides. Comput Struct Biotechnol J 2021; 19:1127-1144. [PMID: 33680356 PMCID: PMC7890092 DOI: 10.1016/j.csbj.2021.01.004] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/06/2021] [Accepted: 01/07/2021] [Indexed: 12/13/2022] Open
Abstract
Despite the scientific and economic importance of maize, little is known about its specialized metabolism. Here, five maize organs were profiled using different reversed-phase liquid chromatography-mass spectrometry methods. The resulting spectral metadata, combined with candidate substrate-product pair (CSPP) networks, allowed the structural characterization of 427 of the 5,420 profiled compounds, including phenylpropanoids, flavonoids, benzoxazinoids, and auxin-related compounds, among others. Only 75 of the 427 compounds were already described in maize. Analysis of the CSPP networks showed that phenylpropanoids are present in all organs, whereas other metabolic classes are rather organ-enriched. Frequently occurring CSPP mass differences often corresponded with glycosyl- and acyltransferase reactions. The interplay of glycosylations and acylations yields a wide variety of mixed glycosides, bearing substructures corresponding to the different biochemical classes. For example, in the tassel, many phenylpropanoid and flavonoid-bearing glycosides also contain auxin-derived moieties. The characterized compounds and mass differences are an important step forward in metabolic pathway discovery and systems biology research. The spectral metadata of the 5,420 compounds is publicly available (DynLib spectral database, https://bioit3.irc.ugent.be/dynlib/).
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Affiliation(s)
- Sandrien Desmet
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium.,Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
| | - Yvan Saeys
- Department of Applied Mathematics, Computer Science and Statistics, Ghent University, B-9052 Gent, Belgium.,Data Mining and Modelling for Biomedicine, Center for Inflammation Research, VIB, B-9052 Gent, Belgium
| | - Kevin Verstaen
- Data Mining and Modelling for Biomedicine, Center for Inflammation Research, VIB, B-9052 Gent, Belgium
| | - Rebecca Dauwe
- Unité de Recherche BIOPI EA3900, Université de Picardie Jules Verne, 80000 Amiens, France
| | - Hoon Kim
- Department of Biochemistry and the U.S. Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726, United States
| | - Claudiu Niculaes
- Plant Breeding, TUM School of Life Sciences Weihenstephan, Technical University of Munich, 85354 Freising, Germany
| | - Atsushi Fukushima
- RIKEN Center for Sustainable Resource Science, Yokohama, Kanagawa 230-0045, Japan
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium.,VIB Metabolomics Core Ghent, VIB, B-9052 Gent, Belgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium.,Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
| | - John Ralph
- Department of Biochemistry and the U.S. Department of Energy Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726, United States
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium.,Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Gent, Belgium.,Center for Plant Systems Biology, VIB, B-9052 Gent, Belgium
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28
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El Houari I, Boerjan W, Vanholme B. Behind the Scenes: The Impact of Bioactive Phenylpropanoids on the Growth Phenotypes of Arabidopsis Lignin Mutants. Front Plant Sci 2021; 12:734070. [PMID: 34567045 PMCID: PMC8458929 DOI: 10.3389/fpls.2021.734070] [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] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/02/2021] [Indexed: 05/20/2023]
Abstract
The phenylpropanoid pathway converts the aromatic amino acid phenylalanine into a wide range of secondary metabolites. Most of the carbon entering the pathway incorporates into the building blocks of lignin, an aromatic polymer providing mechanical strength to plants. Several intermediates in the phenylpropanoid pathway serve as precursors for distinct classes of metabolites that branch out from the core pathway. Untangling this metabolic network in Arabidopsis was largely done using phenylpropanoid pathway mutants, all with different degrees of lignin depletion and associated growth defects. The phenotypic defects of some phenylpropanoid pathway mutants have been attributed to differentially accumulating phenylpropanoids or phenylpropanoid-derived compounds. In this perspectives article, we summarize and discuss the reports describing an altered accumulation of these bioactive molecules as the causal factor for the phenotypes of lignin mutants in Arabidopsis.
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Affiliation(s)
- Ilias El Houari
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Bartel Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- *Correspondence: Bartel Vanholme,
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29
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Desmet S, Brouckaert M, Boerjan W, Morreel K. Seeing the forest for the trees: Retrieving plant secondary biochemical pathways from metabolome networks. Comput Struct Biotechnol J 2020; 19:72-85. [PMID: 33384856 PMCID: PMC7753198 DOI: 10.1016/j.csbj.2020.11.050] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 09/04/2020] [Revised: 11/26/2020] [Accepted: 11/28/2020] [Indexed: 02/06/2023] Open
Abstract
Over the last decade, a giant leap forward has been made in resolving the main bottleneck in metabolomics, i.e., the structural characterization of the many unknowns. This has led to the next challenge in this research field: retrieving biochemical pathway information from the various types of networks that can be constructed from metabolome data. Searching putative biochemical pathways, referred to as biotransformation paths, is complicated because several flaws occur during the construction of metabolome networks. Multiple network analysis tools have been developed to deal with these flaws, while in silico retrosynthesis is appearing as an alternative approach. In this review, the different types of metabolome networks, their flaws, and the various tools to trace these biotransformation paths are discussed.
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Affiliation(s)
- Sandrien Desmet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Marlies Brouckaert
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Kris Morreel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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30
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Bauters L, Kyndt T, De Meyer T, Morreel K, Boerjan W, Lefevere H, Gheysen G. Chorismate mutase and isochorismatase, two potential effectors of the migratory nematode Hirschmanniella oryzae, increase host susceptibility by manipulating secondary metabolite content of rice. Mol Plant Pathol 2020; 21:1634-1646. [PMID: 33084136 PMCID: PMC7694671 DOI: 10.1111/mpp.13003] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 09/07/2020] [Accepted: 09/07/2020] [Indexed: 05/11/2023]
Abstract
Hirschmanniella oryzae is one of the most devastating nematodes on rice, leading to substantial yield losses. Effector proteins aid the nematode during the infection process by subduing plant defence responses. In this research we characterized two potential H. oryzae effector proteins, chorismate mutase (HoCM) and isochorismatase (HoICM), and investigated their enzymatic activity and their role in plant immunity. Both HoCM and HoICM proved to be enzymatically active in complementation tests in mutant Escherichia coli strains. Infection success by the migratory nematode H. oryzae was significantly higher in transgenic rice lines constitutively expressing HoCM or HoICM. Expression of HoCM, but not HoICM, increased rice susceptibility against the sedentary nematode Meloidogyne graminicola also. Transcriptome and metabolome analyses indicated reductions in secondary metabolites in the transgenic rice plants expressing the potential nematode effectors. The results presented here demonstrate that both HoCM and HoICM suppress the host immune system and that this may be accomplished by lowering secondary metabolite levels in the plant.
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Affiliation(s)
- Lander Bauters
- Department of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Tina Kyndt
- Department of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Tim De Meyer
- Department of Data Analysis and Mathematical ModellingFaculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Kris Morreel
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
- Department of Plant Biotechnology and BioinformaticsFaculty of SciencesGhent UniversityGhentBelgium
| | - Wout Boerjan
- VIB‐UGent Center for Plant Systems BiologyGhentBelgium
- Department of Plant Biotechnology and BioinformaticsFaculty of SciencesGhent UniversityGhentBelgium
| | - Hannes Lefevere
- Department of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Godelieve Gheysen
- Department of BiotechnologyFaculty of Bioscience EngineeringGhent UniversityGhentBelgium
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31
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De Meester B, Madariaga Calderón B, de Vries L, Pollier J, Goeminne G, Van Doorsselaere J, Chen M, Ralph J, Vanholme R, Boerjan W. Tailoring poplar lignin without yield penalty by combining a null and haploinsufficient CINNAMOYL-CoA REDUCTASE2 allele. Nat Commun 2020; 11:5020. [PMID: 33024118 PMCID: PMC7538556 DOI: 10.1038/s41467-020-18822-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [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: 03/31/2020] [Accepted: 09/16/2020] [Indexed: 01/09/2023] Open
Abstract
Lignin causes lignocellulosic biomass recalcitrance to enzymatic hydrolysis. Engineered low-lignin plants have reduced recalcitrance but often exhibit yield penalties, offsetting their gains in fermentable sugar yield. Here, CRISPR/Cas9-generated CCR2(−/*) line 12 poplars have one knockout CCR2 allele while the other contains a 3-bp deletion, resulting in a 114I115A-to-114T conversion in the corresponding protein. Despite having 10% less lignin, CCR2(−/*) line 12 grows normally. On a plant basis, the saccharification efficiency of CCR2(−/*) line 12 is increased by 25–41%, depending on the pretreatment. Analysis of monoallelic CCR2 knockout lines shows that the reduced lignin amount in CCR2(−/*) line 12 is due to the combination of a null and the specific haploinsufficient CCR2 allele. Analysis of another CCR2(−/*) line shows that depending on the specific CCR2 amino-acid change, lignin amount and growth can be affected to different extents. Our findings open up new possibilities for stably fine-tuning residual gene function in planta. Plants with reduced amounts of lignin typically suffer from dwarfed growth, which offsets their gain in fermentable sugar yield. Here, the authors show that genome-edited poplar lines with a null and a haploinsufficient allele of CINNAMOYL-COA REDUCTASE2 (CCR2) can be obtained that have a reduced lignin level and normal growth.
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Affiliation(s)
- Barbara De Meester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Barbara Madariaga Calderón
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Lisanne de Vries
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Jacob Pollier
- VIB Metabolomics Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Geert Goeminne
- VIB Metabolomics Core, Technologiepark 71, 9052, Ghent, Belgium
| | - Jan Van Doorsselaere
- Higher Institute for Nursing and Biotechnology, VIVES University College, Wilgenstraat 32, 8800, Roeselare, Belgium
| | - Mingjie Chen
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.,US Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, 53726, USA
| | - John Ralph
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.,US Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, 53726, USA
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium. .,VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium.
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32
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Behr M, Baldacci-Cresp F, Kohler A, Morreel K, Goeminne G, Van Acker R, Veneault-Fourrey C, Mol A, Pilate G, Boerjan W, de Almeida Engler J, El Jaziri M, Baucher M. Alterations in the phenylpropanoid pathway affect poplar ability for ectomycorrhizal colonisation and susceptibility to root-knot nematodes. Mycorrhiza 2020; 30:555-566. [PMID: 32647969 DOI: 10.1007/s00572-020-00976-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [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: 03/11/2020] [Accepted: 07/06/2020] [Indexed: 06/11/2023]
Abstract
This study investigates the impact of the alteration of the monolignol biosynthesis pathway on the establishment of the in vitro interaction of poplar roots either with a mutualistic ectomycorrhizal fungus or with a pathogenic root-knot nematode. Overall, the five studied transgenic lines downregulated for caffeoyl-CoA O-methyltransferase (CCoAOMT), caffeic acid O-methyltransferase (COMT), cinnamoyl-CoA reductase (CCR), cinnamyl alcohol dehydrogenase (CAD) or both COMT and CAD displayed a lower mycorrhizal colonisation percentage, indicating a lower ability for establishing mutualistic interaction than the wild-type. The susceptibility to root-knot nematode infection was variable in the five lines, and the CAD-deficient line was found to be less susceptible than the wild-type. We discuss these phenotypic differences in the light of the large shifts in the metabolic profile and gene expression pattern occurring between roots of the CAD-deficient line and wild-type. A role of genes related to trehalose metabolism, phytohormones, and cell wall construction in the different mycorrhizal symbiosis efficiency and nematode sensitivity between these two lines is suggested. Overall, these results show that the alteration of plant metabolism caused by the repression of a single gene within phenylpropanoid pathway results in significant alterations, at the root level, in the response towards mutualistic and pathogenic associates. These changes may constrain plant fitness and biomass production, which are of economic importance for perennial industrial crops such as poplar.
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Affiliation(s)
- Marc Behr
- Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles (ULB), Rue des Professeurs Jeener et Brachet 12, B-6041, Gosselies, Belgium
| | - Fabien Baldacci-Cresp
- Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles (ULB), Rue des Professeurs Jeener et Brachet 12, B-6041, Gosselies, Belgium
| | - Annegret Kohler
- Unité Mixte de Recherche 1136, Interactions Arbres-Microorganismes, Laboratoire d'Excellence ARBRE, Centre INRAE Grand-Est-Nancy, INRAE-Université de Lorraine, 54280, Champenoux, France
| | - Kris Morreel
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Geert Goeminne
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
- VIB Metabolomics Core, 9052, Ghent, Belgium
| | - Rebecca Van Acker
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | - Claire Veneault-Fourrey
- Unité Mixte de Recherche 1136, Interactions Arbres-Microorganismes, Laboratoire d'Excellence ARBRE, Centre INRAE Grand-Est-Nancy, INRAE-Université de Lorraine, 54280, Champenoux, France
| | - Adeline Mol
- Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles (ULB), Rue des Professeurs Jeener et Brachet 12, B-6041, Gosselies, Belgium
| | | | - Wout Boerjan
- VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
| | | | - Mondher El Jaziri
- Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles (ULB), Rue des Professeurs Jeener et Brachet 12, B-6041, Gosselies, Belgium
| | - Marie Baucher
- Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles (ULB), Rue des Professeurs Jeener et Brachet 12, B-6041, Gosselies, Belgium.
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33
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Oliveira DM, Mota TR, Salatta FV, Sinzker RC, Končitíková R, Kopečný D, Simister R, Silva M, Goeminne G, Morreel K, Rencoret J, Gutiérrez A, Tryfona T, Marchiosi R, Dupree P, Del Río JC, Boerjan W, McQueen-Mason SJ, Gomez LD, Ferrarese-Filho O, Dos Santos WD. Cell wall remodeling under salt stress: Insights into changes in polysaccharides, feruloylation, lignification, and phenolic metabolism in maize. Plant Cell Environ 2020; 43:2172-2191. [PMID: 32441772 DOI: 10.1111/pce.13805] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [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: 03/21/2020] [Revised: 04/27/2020] [Accepted: 05/14/2020] [Indexed: 05/15/2023]
Abstract
Although cell wall polymers play important roles in the tolerance of plants to abiotic stress, the effects of salinity on cell wall composition and metabolism in grasses remain largely unexplored. Here, we conducted an in-depth study of changes in cell wall composition and phenolic metabolism induced upon salinity in maize seedlings and plants. Cell wall characterization revealed that salt stress modulated the deposition of cellulose, matrix polysaccharides and lignin in seedling roots, plant roots and stems. The extraction and analysis of arabinoxylans by size-exclusion chromatography, 2D-NMR spectroscopy and carbohydrate gel electrophoresis showed a reduction of arabinoxylan content in salt-stressed roots. Saponification and mild acid hydrolysis revealed that salinity also reduced the feruloylation of arabinoxylans in roots of seedlings and plants. Determination of lignin content and composition by nitrobenzene oxidation and 2D-NMR confirmed the increased incorporation of syringyl units in lignin of maize roots. Salt stress also induced the expression of genes and the activity of enzymes enrolled in phenylpropanoid biosynthesis. The UHPLC-MS-based metabolite profiling confirmed the modulation of phenolic profiling by salinity and the accumulation of ferulate and its derivatives 3- and 4-O-feruloyl quinate. In conclusion, we present a model for explaining cell wall remodeling in response to salinity.
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Affiliation(s)
- Dyoni M Oliveira
- Department of Biochemistry, State University of Maringá, Maringá, Brazil
| | - Thatiane R Mota
- Department of Biochemistry, State University of Maringá, Maringá, Brazil
| | - Fábio V Salatta
- Department of Biochemistry, State University of Maringá, Maringá, Brazil
| | - Renata C Sinzker
- Department of Biochemistry, State University of Maringá, Maringá, Brazil
| | - Radka Končitíková
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - David Kopečný
- Department of Protein Biochemistry and Proteomics, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, Czech Republic
| | - Rachael Simister
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Mariana Silva
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jorge Rencoret
- Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, Seville, Spain
| | - Ana Gutiérrez
- Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, Seville, Spain
| | - Theodora Tryfona
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Rogério Marchiosi
- Department of Biochemistry, State University of Maringá, Maringá, Brazil
| | - Paul Dupree
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - José C Del Río
- Instituto de Recursos Naturales y Agrobiología de Sevilla, CSIC, Seville, Spain
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Simon J McQueen-Mason
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
| | - Leonardo D Gomez
- Centre for Novel Agricultural Products, Department of Biology, University of York, York, UK
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34
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Tsai CJ, Xu P, Xue LJ, Hu H, Nyamdari B, Naran R, Zhou X, Goeminne G, Gao R, Gjersing E, Dahlen J, Pattathil S, Hahn MG, Davis MF, Ralph J, Boerjan W, Harding SA. Compensatory Guaiacyl Lignin Biosynthesis at the Expense of Syringyl Lignin in 4CL1-Knockout Poplar. Plant Physiol 2020; 183:123-136. [PMID: 32139476 PMCID: PMC7210618 DOI: 10.1104/pp.19.01550] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 02/26/2020] [Indexed: 05/22/2023]
Abstract
The lignin biosynthetic pathway is highly conserved in angiosperms, yet pathway manipulations give rise to a variety of taxon-specific outcomes. Knockout of lignin-associated 4-coumarate:CoA ligases (4CLs) in herbaceous species mainly reduces guaiacyl (G) lignin and enhances cell wall saccharification. Here we show that CRISPR-knockout of 4CL1 in poplar (Populus tremula × alba) preferentially reduced syringyl (S) lignin, with negligible effects on biomass recalcitrance. Concordant with reduced S-lignin was downregulation of ferulate 5-hydroxylases (F5Hs). Lignification was largely sustained by 4CL5, a low-affinity paralog of 4CL1 typically with only minor xylem expression or activity. Levels of caffeate, the preferred substrate of 4CL5, increased in line with significant upregulation of caffeoyl shikimate esterase1 Upregulation of caffeoyl-CoA O-methyltransferase1 and downregulation of F5Hs are consistent with preferential funneling of 4CL5 products toward G-lignin biosynthesis at the expense of S-lignin. Thus, transcriptional and metabolic adaptations to 4CL1-knockout appear to have enabled 4CL5 catalysis at a level sufficient to sustain lignification. Finally, genes involved in sulfur assimilation, the glutathione-ascorbate cycle, and various antioxidant systems were upregulated in the mutants, suggesting cascading responses to perturbed thioesterification in lignin biosynthesis.
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Affiliation(s)
- Chung-Jui Tsai
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602
- Department of Genetics, University of Georgia, Athens, Georgia 30602
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Peng Xu
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Liang-Jiao Xue
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602
- Department of Genetics, University of Georgia, Athens, Georgia 30602
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Hao Hu
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602
- Department of Genetics, University of Georgia, Athens, Georgia 30602
| | - Batbayar Nyamdari
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602
| | - Radnaa Naran
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602
| | - Xiaohong Zhou
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Vlaams Instituut voor Biotechnologie, UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Ruili Gao
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin 53726
| | - Erica Gjersing
- National Renewable Energy Laboratory, Golden, Colorado 80401
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - Joseph Dahlen
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602
| | - Sivakumar Pattathil
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Michael G Hahn
- Department of Plant Biology, University of Georgia, Athens, Georgia 30602
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Mark F Davis
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
- National Renewable Energy Laboratory, Golden, Colorado 80401
- BioEnergy Science Center, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831
| | - John Ralph
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706
- Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin 53726
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Vlaams Instituut voor Biotechnologie, UGent Center for Plant Systems Biology, 9052 Ghent, Belgium
| | - Scott A Harding
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, Georgia 30602
- Department of Genetics, University of Georgia, Athens, Georgia 30602
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35
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Yamamoto M, Tomiyama H, Koyama A, Okuizumi H, Liu S, Vanholme R, Goeminne G, Hirai Y, Shi H, Takata N, Ikeda T, Uesugi M, Kim H, Sakamoto S, Mitsuda N, Boerjan W, Ralph J, Kajita S. A Century-Old Mystery Unveiled: Sekizaisou is a Natural Lignin Mutant. Plant Physiol 2020; 182:1821-1828. [PMID: 32051179 PMCID: PMC7140961 DOI: 10.1104/pp.19.01467] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/31/2020] [Indexed: 05/23/2023]
Abstract
Sekizaisou, a red-wood mulberry variety used in traditional sericulture, is a naturally occurring lignin mutant.
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Affiliation(s)
- Masanobu Yamamoto
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Hirokazu Tomiyama
- Tsukuba Technical Support Center, Department of Planning and Coordination, National Agriculture and Food Research Organization, Ibaraki 305-8634, Japan
| | - Akio Koyama
- Division of Biotechnology, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Ibaraki 305-8634, Japan
| | - Hisato Okuizumi
- Genebank, National Agriculture and Food Research Organization, Ibaraki 305-0856, Japan
| | - Sarah Liu
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 and US Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, Wisconsin 53726
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium and Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium, Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium, and VIB Metabolomics Core, Technologiepark 71, 9052 Ghent, Belgium
| | - Yuta Hirai
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Hu Shi
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Naoki Takata
- Forest Bio-Research Center, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki 319-1301, Japan
| | - Tsutomu Ikeda
- Department of Forest Resource Chemistry, Forestry and Forest Products Research Institute, Forest Research and Management Organization, Ibaraki 305-8687, Japan
| | - Mikiko Uesugi
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
| | - Hoon Kim
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 and US Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, Wisconsin 53726
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki 305-8566, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Ibaraki 305-8566, Japan
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium and Center for Plant Systems Biology, VIB, Technologiepark 71, 9052 Ghent, Belgium
| | - John Ralph
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706 and US Department of Energy's Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, Wisconsin 53726
| | - Shinya Kajita
- Graduate School of Bio-Applications and Systems Engineering, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan and Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Tokyo 184-8588, Japan
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36
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Zhang B, Sztojka B, Escamez S, Vanholme R, Hedenström M, Wang Y, Turumtay H, Gorzsás A, Boerjan W, Tuominen H. PIRIN2 suppresses S-type lignin accumulation in a noncell-autonomous manner in Arabidopsis xylem elements. New Phytol 2020; 225:1923-1935. [PMID: 31625609 PMCID: PMC7027918 DOI: 10.1111/nph.16271] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [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: 06/27/2019] [Accepted: 10/10/2019] [Indexed: 05/21/2023]
Abstract
PIRIN (PRN) genes encode cupin domain-containing proteins that function as transcriptional co-regulators in humans but that are poorly described in plants. A previous study in xylogenic cell cultures of Zinnia elegans suggested a role for a PRN protein in lignification. This study aimed to identify the function of Arabidopsis (Arabidopsis thaliana) PRN proteins in lignification of xylem tissues. Chemical composition of the secondary cell walls was analysed in Arabidopsis stems and/or hypocotyls by pyrolysis-gas chromatography/mass spectrometry, 2D-nuclear magnetic resonance and phenolic profiling. Secondary cell walls of individual xylem elements were chemotyped by Fourier transform infrared and Raman microspectroscopy. Arabidopsis PRN2 suppressed accumulation of S-type lignin in Arabidopsis stems and hypocotyls. PRN2 promoter activity and PRN2:GFP fusion protein were localised specifically in cells next to the vessel elements, suggesting a role for PRN2 in noncell-autonomous lignification of xylem vessels. Accordingly, PRN2 modulated lignin chemistry in the secondary cell walls of the neighbouring vessel elements. These results indicate that PRN2 suppresses S-type lignin accumulation in the neighbourhood of xylem vessels to bestow G-type enriched lignin composition on the secondary cell walls of the vessel elements. Gene expression analyses suggested that PRN2 function is mediated by regulation of the expression of the lignin-biosynthetic genes.
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Affiliation(s)
- Bo Zhang
- Department of Plant PhysiologyUmeå Plant Science CentreUmeå UniversityS‐901 87UmeåSweden
| | - Bernadette Sztojka
- Department of Plant PhysiologyUmeå Plant Science CentreUmeå UniversityS‐901 87UmeåSweden
| | - Sacha Escamez
- Department of Plant PhysiologyUmeå Plant Science CentreUmeå UniversityS‐901 87UmeåSweden
| | - Ruben Vanholme
- Department of Plant Biotechnology and BioinformaticsGhent UniversityTechnologiepark 719052GhentBelgium
- VIB Center for Plant Systems BiologyTechnologiepark 719052GhentBelgium
| | | | - Yin Wang
- Department of Plant PhysiologyUmeå Plant Science CentreUmeå UniversityS‐901 87UmeåSweden
| | - Halbay Turumtay
- Department of Plant Biotechnology and BioinformaticsGhent UniversityTechnologiepark 719052GhentBelgium
- VIB Center for Plant Systems BiologyTechnologiepark 719052GhentBelgium
| | - András Gorzsás
- Department of ChemistryUmeå UniversityS‐901 87UmeåSweden
| | - Wout Boerjan
- Department of Plant Biotechnology and BioinformaticsGhent UniversityTechnologiepark 719052GhentBelgium
- VIB Center for Plant Systems BiologyTechnologiepark 719052GhentBelgium
| | - Hannele Tuominen
- Department of Plant PhysiologyUmeå Plant Science CentreUmeå UniversityS‐901 87UmeåSweden
- Present address:
Umeå Plant science Centre, Department of Forest Genetics and Plant PhysiologyThe Swedish University of Agricultural Sciences90183UmeåSweden
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37
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Perez-Fons L, Bohorquez-Chaux A, Irigoyen ML, Garceau DC, Morreel K, Boerjan W, Walling LL, Becerra Lopez-Lavalle LA, Fraser PD. A metabolomics characterisation of natural variation in the resistance of cassava to whitefly. BMC Plant Biol 2019; 19:518. [PMID: 31775619 PMCID: PMC6882011 DOI: 10.1186/s12870-019-2107-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [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: 07/20/2019] [Accepted: 10/28/2019] [Indexed: 05/13/2023]
Abstract
BACKGROUND Cassava whitefly outbreaks were initially reported in East and Central Africa cassava (Manihot esculenta Crantz) growing regions in the 1990's and have now spread to other geographical locations, becoming a global pest severely affecting farmers and smallholder income. Whiteflies impact plant yield via feeding and vectoring cassava mosaic and brown streak viruses, making roots unsuitable for food or trading. Deployment of virus resistant varieties has had little impact on whitefly populations and therefore development of whitefly resistant varieties is also necessary as part of integrated pest management strategies. Suitable sources of whitefly resistance exist in germplasm collections that require further characterization to facilitate and assist breeding programs. RESULTS In the present work, a hierarchical metabolomics approach has been employed to investigate the underlying biochemical mechanisms associated with whitefly resistance by comparing two naturally occurring accessions of cassava, one susceptible and one resistant to whitefly. Quantitative differences between genotypes detected at pre-infestation stages were consistently observed at each time point throughout the course of the whitefly infestation. This prevalent differential feature suggests that inherent genotypic differences override the response induced by the presence of whitefly and that they are directly linked with the phenotype observed. The most significant quantitative changes relating to whitefly susceptibility were linked to the phenylpropanoid super-pathway and its linked sub-pathways: monolignol, flavonoid and lignan biosynthesis. These findings suggest that the lignification process in the susceptible variety is less active, as the susceptible accession deposits less lignin and accumulates monolignol intermediates and derivatives thereof, differences that are maintained during the time-course of the infestation. CONCLUSIONS Resistance mechanism associated to the cassava whitefly-resistant accession ECU72 is an antixenosis strategy based on reinforcement of cell walls. Both resistant and susceptible accessions respond differently to whitefly attack at biochemical level, but the inherent metabolic differences are directly linked to the resistance phenotype rather than an induced response in the plant.
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Affiliation(s)
- Laura Perez-Fons
- School of Biological Sciences, Royal Holloway University of London, Egham, UK
| | | | - Maria L Irigoyen
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Danielle C Garceau
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | - Kris Morreel
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Linda L Walling
- Department of Botany and Plant Sciences, University of California, Riverside, California, USA
| | | | - Paul D Fraser
- School of Biological Sciences, Royal Holloway University of London, Egham, UK.
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Steenackers W, El Houari I, Baekelandt A, Witvrouw K, Dhondt S, Leroux O, Gonzalez N, Corneillie S, Cesarino I, Inzé D, Boerjan W, Vanholme B. cis-Cinnamic acid is a natural plant growth-promoting compound. J Exp Bot 2019; 70:6293-6304. [PMID: 31504728 PMCID: PMC6859716 DOI: 10.1093/jxb/erz392] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 04/01/2019] [Accepted: 08/19/2019] [Indexed: 05/20/2023]
Abstract
Agrochemicals provide vast potential to improve plant productivity, because they are easy to implement at low cost while not being restricted by species barriers as compared with breeding strategies. Despite the general interest, only a few compounds with growth-promoting activity have been described so far. Here, we add cis-cinnamic acid (c-CA) to the small portfolio of existing plant growth stimulators. When applied at low micromolar concentrations to Arabidopsis roots, c-CA stimulates both cell division and cell expansion in leaves. Our data support a model explaining the increase in shoot biomass as the consequence of a larger root system, which allows the plant to explore larger areas for resources. The requirement of the cis-configuration for the growth-promoting activity of CA was validated by implementing stable structural analogs of both cis- and trans-CA in this study. In a complementary approach, we used specific light conditions to prevent cis/trans-isomerization of CA during the experiment. In both cases, the cis-form stimulated plant growth, whereas the trans-form was inactive. Based on these data, we conclude that c-CA is an appealing lead compound representing a novel class of growth-promoting agrochemicals. Unraveling the underlying molecular mechanism could lead to the development of innovative strategies for boosting plant biomass.
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Affiliation(s)
- Ward Steenackers
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Gent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium
| | - Ilias El Houari
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Gent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium
| | - Alexandra Baekelandt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Gent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium
| | - Klaas Witvrouw
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Gent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium
| | - Stijn Dhondt
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Gent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium
| | | | - Nathalie Gonzalez
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Gent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium
| | - Sander Corneillie
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Gent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium
| | - Igor Cesarino
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Gent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium
| | - Dirk Inzé
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Gent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Gent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium
| | - Bartel Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Gent, Belgium
- VIB Center for Plant Systems Biology, VIB, Technologiepark 927, Gent, Belgium
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Allona I, Kirst M, Boerjan W, Strauss S, Sederoff R. Editorial: Forest Genomics and Biotechnology. Front Plant Sci 2019; 10:1187. [PMID: 31681350 PMCID: PMC6806019 DOI: 10.3389/fpls.2019.01187] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Accepted: 08/29/2019] [Indexed: 06/10/2023]
Affiliation(s)
- Isabel Allona
- Centro de Biotecnología y Genómica de Plantas (CBGP, UPM-INIA), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA), Campus de Montegancedo, Pozuelo de Alarcón, Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), Madrid, Spain
| | - Matias Kirst
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL, United States
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Steven Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR, United States
| | - Ronald Sederoff
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
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Vanholme R, Sundin L, Seetso KC, Kim H, Liu X, Li J, De Meester B, Hoengenaert L, Goeminne G, Morreel K, Haustraete J, Tsai HH, Schmidt W, Vanholme B, Ralph J, Boerjan W. COSY catalyses trans-cis isomerization and lactonization in the biosynthesis of coumarins. Nat Plants 2019; 5:1066-1075. [PMID: 31501530 DOI: 10.1038/s41477-019-0510-0] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 07/30/2019] [Indexed: 05/23/2023]
Abstract
Coumarins, also known as 1,2-benzopyrones, comprise a large class of secondary metabolites that are ubiquitously found throughout the plant kingdom. In many plant species, coumarins are particularly important for iron acquisition and plant defence. Here, we show that COUMARIN SYNTHASE (COSY) is a key enzyme in the biosynthesis of coumarins. Arabidopsis thaliana cosy mutants have strongly reduced levels of coumarin and accumulate o-hydroxyphenylpropanoids instead. Accordingly, cosy mutants have reduced iron content and show growth defects when grown under conditions in which there is a limited availability of iron. Recombinant COSY is able to produce umbelliferone, esculetin and scopoletin from their respective o-hydroxycinnamoyl-CoA thioesters by two reaction steps-a trans-cis isomerization followed by a lactonization. This conversion happens partially spontaneously and is catalysed by light, which explains why the need for an enzyme for this conversion has been overlooked. The combined results show that COSY has an essential function in the biosynthesis of coumarins in organs that are shielded from light, such as roots. These findings provide routes to improving coumarin production in crops or by microbial fermentation.
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Affiliation(s)
- Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Lisa Sundin
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Keletso Carol Seetso
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Hoon Kim
- Department of Biochemistry and the DOE Great Lakes Bioenergy Research Center, the Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA
| | - Xinyu Liu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jin Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Barbara De Meester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Lennart Hoengenaert
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
- Metabolomics Core, VIB, Ghent, Belgium
| | - Kris Morreel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - Jurgen Haustraete
- Protein Core, VIB-UGent Center for Inflammation Research, VIB, Ghent University, Ghent, Belgium
| | - Huei-Hsuan Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Wolfgang Schmidt
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung Hsing University and Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung, Taiwan
- Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University, Taipei, Taiwan
| | - Bartel Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Center for Plant Systems Biology, VIB, Ghent, Belgium
| | - John Ralph
- Department of Biochemistry and the DOE Great Lakes Bioenergy Research Center, the Wisconsin Energy Institute, University of Wisconsin, Madison, WI, USA
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- Center for Plant Systems Biology, VIB, Ghent, Belgium.
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Strauss SH, Boerjan W, Chiang V, Costanza A, Coleman H, Davis JM, Lu MZ, Mansfield SD, Merkle S, Myburg A, Nilsson O, Pilate G, Powell W, Seguin A, Valenzuela S. Certification for gene-edited forests. Science 2019; 365:767-768. [PMID: 31439790 DOI: 10.1126/science.aay6165] [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: 11/02/2022]
Affiliation(s)
- Steven H Strauss
- Department of Forest Ecosystems and Society, Oregon State University, Corvallis, OR 97331, USA.
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University and Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Vincent Chiang
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Heather Coleman
- Department of Biology, Syracuse University, Syracuse, NY 13244, USA
| | - John M Davis
- School of Forest Resources and Conservation, University of Florida, Gainesville, FL 32611, USA
| | - Meng-Zhu Lu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou 311300, China
| | - Shawn D Mansfield
- Forest Sciences Centre, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Scott Merkle
- Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA 30602, USA
| | - Alexander Myburg
- Department of Biochemistry, Genetics, and Microbiology, and Forestry and Agricultural Biotechnology Institute, University of Pretoria, Pretoria 0002, South Africa
| | - Ove Nilsson
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90183 Umeå, Sweden
| | | | - William Powell
- College of Environmental Science and Forestry, Syracuse, NY 13210, USA
| | - Armand Seguin
- Faculty of Forestry, Geography and Geomatics, Université Laval, Quebec, QC G1V 0A6, Canada
| | - Sofia Valenzuela
- Facultad Ciencias Forestales, Universidad de Concepción, Concepción, Chile
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42
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Özparpucu M, Gierlinger N, Cesarino I, Burgert I, Boerjan W, Rüggeberg M. Significant influence of lignin on axial elastic modulus of poplar wood at low microfibril angles under wet conditions. J Exp Bot 2019; 70:4039-4047. [PMID: 31187131 PMCID: PMC6685656 DOI: 10.1093/jxb/erz180] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [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: 11/13/2018] [Accepted: 04/02/2019] [Indexed: 05/20/2023]
Abstract
Wood is extensively used as a construction material. Despite increasing knowledge of its mechanical properties, the contribution of the cell-wall matrix polymers to wood mechanics is still not well understood. Previous studies have shown that axial stiffness correlates with lignin content only for cellulose microfibril angles larger than around 20°, while no influence is found for smaller angles. Here, by analysing the wood of poplar with reduced lignin content due to down-regulation of CAFFEOYL SHIKIMATE ESTERASE, we show that lignin content also influences axial stiffness at smaller angles. Micro-tensile tests of the xylem revealed that axial stiffness was strongly reduced in the low-lignin transgenic lines. Strikingly, microfibril angles were around 15° for both wild-type and transgenic poplars, suggesting that cellulose orientation is not responsible for the observed changes in mechanical behavior. Multiple linear regression analysis showed that the decrease in stiffness was almost completely related to the variation in both density and lignin content. We suggest that the influence of lignin content on axial stiffness may gradually increase as a function of the microfibril angle. Our results may help in building up comprehensive models of the cell wall that can unravel the individual roles of the matrix polymers.
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Affiliation(s)
- Merve Özparpucu
- Institute for Building Materials (IfB), ETH Zurich, Zurich, Switzerland
- School of Life Sciences Weihenstephan, Wood Research Munich, Technical University of Munich (TUM), Munich, Germany
| | - Notburga Gierlinger
- Institute for Biophysics, University of Natural Resources and Life Sciences Vienna (BOKU), Wien, Austria
| | - Igor Cesarino
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo – SP, Brazil
| | - Ingo Burgert
- Institute for Building Materials (IfB), ETH Zurich, Zurich, Switzerland
- Laboratory of Cellulose and Wood Materials, EMPA, Dübendorf, Switzerland
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Markus Rüggeberg
- Institute for Building Materials (IfB), ETH Zurich, Zurich, Switzerland
- Laboratory of Cellulose and Wood Materials, EMPA, Dübendorf, Switzerland
- Correspondence:
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Abstract
Wood is a renewable resource that is mainly composed of lignin and cell wall polysaccharides. The polysaccharide fraction is valuable as it can be converted into pulp and paper, or into fermentable sugars. On the other hand, the lignin fraction is increasingly being considered a valuable source of aromatic building blocks for the chemical industry. The presence of lignin in wood is one of the major recalcitrance factors in woody biomass processing, necessitating the need for harsh chemical treatments to degrade and extract it prior to the valorization of the cell wall polysaccharides, cellulose and hemicellulose. Over the past years, large research efforts have been devoted to engineering lignin amount and composition to reduce biomass recalcitrance toward chemical processing. We review the efforts made in forest trees, and compare results from greenhouse and field trials. Furthermore, we address the value and potential of CRISPR-based gene editing in lignin engineering and its integration in tree breeding programs.
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Affiliation(s)
- Alexandra Chanoca
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lisanne de Vries
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Wout Boerjan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
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44
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SriBala G, Toraman HE, Symoens S, Déjardin A, Pilate G, Boerjan W, Ronsse F, Van Geem KM, Marin GB. Analytical Py-GC/MS of Genetically Modified Poplar for the Increased Production of Bio-aromatics. Comput Struct Biotechnol J 2019; 17:599-610. [PMID: 31080566 PMCID: PMC6502739 DOI: 10.1016/j.csbj.2019.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 11/30/2022] Open
Abstract
Genetic engineering is a powerful tool to steer bio-oil composition towards the production of speciality chemicals such as guaiacols, syringols, phenols, and vanillin through well-defined biomass feedstocks. Our previous work demonstrated the effects of lignin biosynthesis gene modification on the pyrolysis vapour compositions obtained from wood derived from greenhouse-grown poplars. In this study, field-grown poplars downregulated in the genes encoding CINNAMYL ALCOHOL DEHYDROGENASE (CAD), CAFFEIC ACID O-METHYLTRANSFERASE (COMT) and CAFFEOYL-CoA O-METHYLTRANSFERASE (CCoAOMT), and their corresponding wild type were pyrolysed in a Py-GC/MS. This work aims at capturing the effects of downregulation of the three enzymes on bio-oil composition using principal component analysis (PCA). 3,5-methoxytoluene, vanillin, coniferyl alcohol, 4-vinyl guaiacol, syringol, syringaldehyde, and guaiacol are the determining factors in the PCA analysis that are the substantially affected by COMT, CAD and CCoAOMT enzyme downregulation. COMT and CAD downregulated transgenic lines proved to be statistically different from the wild type because of a substantial difference in S and G lignin units. The sCAD line lead to a significant drop (nearly 51%) in S-lignin derived compounds, while CCoAOMT downregulation affected the least (7–11%). Further, removal of extractives via pretreatment enhanced the statistical differences among the CAD transgenic lines and its wild type. On the other hand, COMT downregulation caused 2-fold reduction in S-derived compounds compared to G-derived compounds. This study manifests the applicability of PCA analysis in tracking the biological changes in biomass (poplar in this case) and their effects on pyrolysis-oil compositions.
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Key Words
- Analytical fast pyrolysis
- C, Holocellulose
- CAD, CINNAMYL ALCOHOL DEHYDROGENASE
- CCoAOMT, CAFFEOYL-CoA O-METHYLTRANSFERASE
- COMT, CAFFEIC ACID O-METHYLTRANSFERASE
- G, Guaiacyl units
- GC, Gas chromatography
- Genetically modified poplar
- H, p-hydroxyphenyl units
- L, Lignin-derived aromatic compounds
- L-G, Guaiacyl lignin-derived compounds
- L-H, p-Hydroxyphenyl lignin-derived compounds
- L-S, Syringyl lignin-derived compounds
- Lignin
- MD, Mahalanobis distance
- MS, Mass spectroscopy
- PC, Principal component
- Phenolic compounds
- Principal component analysis
- Py, Micropyrolysis or micropyrolyzer
- S, Syringyl units
- as, Antisense line
- s, Sense line
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Affiliation(s)
- Gorugantu SriBala
- Ghent University, Laboratory for Chemical Technology, Technologiepark 125, 9052 Ghent, Belgium
| | - Hilal Ezgi Toraman
- Ghent University, Laboratory for Chemical Technology, Technologiepark 125, 9052 Ghent, Belgium
| | - Steffen Symoens
- Ghent University, Laboratory for Chemical Technology, Technologiepark 125, 9052 Ghent, Belgium
| | - Annabelle Déjardin
- Institut National de la Recherche Agronomique (INRA), Unité de Recherche 0588, Amélioration, Génétique et Physiologie Forestières, 45075 Orléans, France
| | - Gilles Pilate
- Institut National de la Recherche Agronomique (INRA), Unité de Recherche 0588, Amélioration, Génétique et Physiologie Forestières, 45075 Orléans, France
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium.,VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Frederik Ronsse
- Ghent University, Department of Biosystems Engineering, Coupure Links 653, 9000 Ghent, Belgium
| | - Kevin M Van Geem
- Ghent University, Laboratory for Chemical Technology, Technologiepark 125, 9052 Ghent, Belgium
| | - Guy B Marin
- Ghent University, Laboratory for Chemical Technology, Technologiepark 125, 9052 Ghent, Belgium
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45
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Affiliation(s)
- Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, VIB-UGent Center for Plant Systems Biology, Technologiepark 71, B-9052 Ghent, Belgium.
| | - John Ralph
- Departments of Biochemistry and Biological Systems Engineering, and the Department of Energy's Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, The University of Wisconsin, Madison, WI 53726, USA
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Vanholme B, El Houari I, Boerjan W. Bioactivity: phenylpropanoids’ best kept secret. Curr Opin Biotechnol 2019; 56:156-162. [DOI: 10.1016/j.copbio.2018.11.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 11/10/2018] [Accepted: 11/14/2018] [Indexed: 11/24/2022]
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Ralph J, Lapierre C, Boerjan W. Lignin structure and its engineering. Curr Opin Biotechnol 2019; 56:240-249. [PMID: 30921563 DOI: 10.1016/j.copbio.2019.02.019] [Citation(s) in RCA: 256] [Impact Index Per Article: 51.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/02/2019] [Accepted: 02/22/2019] [Indexed: 02/06/2023]
Abstract
Studies on lignin structure and its engineering are inextricably and bidirectionally linked. Perturbations of genes on the lignin biosynthetic pathway may result in striking compositional and structural changes that in turn suggest novel approaches for altering lignin and even 'designing' the polymer to enhance its value or with a view toward its simpler removal from the cell wall polysaccharides. Basic structural studies on various native lignins increasingly refine our knowledge of lignin structure, and examining lignins in different species reveals the extent to which evolution and natural variation have resulted in the incorporation of 'non-traditional' phenolic monomers, including phenolics from beyond the monolignol biosynthetic pathway. As a result, the very definition of lignin continues to be expanded and refined.
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Affiliation(s)
- John Ralph
- Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA; Department of Energy Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726, USA.
| | - Catherine Lapierre
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000, Versailles, France
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, B-9052, Gent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 927, B-9052, Gent, Belgium
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Vanholme R, De Meester B, Ralph J, Boerjan W. Lignin biosynthesis and its integration into metabolism. Curr Opin Biotechnol 2019; 56:230-239. [PMID: 30913460 DOI: 10.1016/j.copbio.2019.02.018] [Citation(s) in RCA: 305] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 02/05/2019] [Accepted: 02/22/2019] [Indexed: 11/25/2022]
Abstract
Lignin is a principal structural component of cell walls in higher terrestrial plants. It reinforces the cell walls, facilitates water transport, and acts as a physical barrier to pathogens. Lignin is typically described as being composed of p-hydroxyphenyl (H), guaiacyl (G), and syringyl (S) units that derive from the polymerization of the hydroxycinnamyl alcohols, p-coumaryl, coniferyl, and sinapyl alcohol, respectively. However, lignin also derives from various other aromatic monomers. Here, we review the biosynthetic pathway to the lignin monomers, and how flux through the pathway is regulated. Upon perturbation of the phenylpropanoid pathway, pathway intermediates may successfully incorporate into the lignin polymer, thereby affecting its physicochemical properties, or may remain soluble as such or as derivatized molecules that might interfere with physiological processes.
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Affiliation(s)
- Ruben Vanholme
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - Barbara De Meester
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium
| | - John Ralph
- Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin, Madison, WI 53726, USA; Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Wout Boerjan
- Ghent University, Department of Plant Biotechnology and Bioinformatics, Technologiepark 71, 9052 Ghent, Belgium; VIB Center for Plant Systems Biology, Technologiepark 71, 9052 Ghent, Belgium.
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49
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Daly P, McClellan C, Maluk M, Oakey H, Lapierre C, Waugh R, Stephens J, Marshall D, Barakate A, Tsuji Y, Goeminne G, Vanholme R, Boerjan W, Ralph J, Halpin C. RNAi-suppression of barley caffeic acid O-methyltransferase modifies lignin despite redundancy in the gene family. Plant Biotechnol J 2019; 17:594-607. [PMID: 30133138 PMCID: PMC6381794 DOI: 10.1111/pbi.13001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 11/02/2017] [Accepted: 08/18/2018] [Indexed: 05/12/2023]
Abstract
Caffeic acid O-methyltransferase (COMT), the lignin biosynthesis gene modified in many brown-midrib high-digestibility mutants of maize and sorghum, was targeted for downregulation in the small grain temperate cereal, barley (Hordeum vulgare), to improve straw properties. Phylogenetic and expression analyses identified the barley COMT orthologue(s) expressed in stems, defining a larger gene family than in brachypodium or rice with three COMT genes expressed in lignifying tissues. RNAi significantly reduced stem COMT protein and enzyme activity, and modestly reduced stem lignin content while dramatically changing lignin structure. Lignin syringyl-to-guaiacyl ratio was reduced by ~50%, the 5-hydroxyguaiacyl (5-OH-G) unit incorporated into lignin at 10--15-fold higher levels than normal, and the amount of p-coumaric acid ester-linked to cell walls was reduced by ~50%. No brown-midrib phenotype was observed in any RNAi line despite significant COMT suppression and altered lignin. The novel COMT gene family structure in barley highlights the dynamic nature of grass genomes. Redundancy in barley COMTs may explain the absence of brown-midrib mutants in barley and wheat. The barley COMT RNAi lines nevertheless have the potential to be exploited for bioenergy applications and as animal feed.
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Affiliation(s)
- Paul Daly
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
- Present address:
Fungal PhysiologyWesterdijk Fungal Biodiversity Institute and Fungal Molecular PhysiologyUtrecht UniversityUtrechtThe Netherlands
| | - Christopher McClellan
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
| | - Marta Maluk
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
| | - Helena Oakey
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
- Faculty of SciencesSchool of Agriculture, Food and WineUniversity of AdelaideAdelaideAustralia
| | - Catherine Lapierre
- UMR1318 INRA‐AgroParistechIJPBUniversite Paris‐SaclayVersailles CedexFrance
| | - Robbie Waugh
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
- Cell and Molecular SciencesJames Hutton InstituteDundeeUK
| | | | - David Marshall
- Information and Computational SciencesJames Hutton InstituteDundeeUK
| | - Abdellah Barakate
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
| | - Yukiko Tsuji
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of Energy's Great Lakes Bioenergy Research CenterThe Wisconsin Energy InstituteUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Geert Goeminne
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Ruben Vanholme
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - Wout Boerjan
- Department of Plant Biotechnology and BioinformaticsGhent UniversityGhentBelgium
- VIB Center for Plant Systems BiologyGhentBelgium
| | - John Ralph
- Department of BiochemistryUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of Energy's Great Lakes Bioenergy Research CenterThe Wisconsin Energy InstituteUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Claire Halpin
- Division of Plant SciencesSchool of Life SciencesUniversity of Dundee at the James Hutton InstituteDundeeUK
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Oyarce P, De Meester B, Fonseca F, de Vries L, Goeminne G, Pallidis A, De Rycke R, Tsuji Y, Li Y, Van den Bosch S, Sels B, Ralph J, Vanholme R, Boerjan W. Introducing curcumin biosynthesis in Arabidopsis enhances lignocellulosic biomass processing. Nat Plants 2019; 5:225-237. [PMID: 30692678 DOI: 10.1038/s41477-018-0350-3] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Accepted: 12/14/2018] [Indexed: 05/19/2023]
Abstract
Lignin is the main cause of lignocellulosic biomass recalcitrance to industrial enzymatic hydrolysis. By partially replacing the traditional lignin monomers by alternative ones, lignin extractability can be enhanced. To design a lignin that is easier to degrade under alkaline conditions, curcumin (diferuloylmethane) was produced in the model plant Arabidopsis thaliana via simultaneous expression of the turmeric (Curcuma longa) genes DIKETIDE-CoA SYNTHASE (DCS) and CURCUMIN SYNTHASE 2 (CURS2). The transgenic plants produced a plethora of curcumin- and phenylpentanoid-derived compounds with no negative impact on growth. Catalytic hydrogenolysis gave evidence that both curcumin and phenylpentanoids were incorporated into the lignifying cell wall, thereby significantly increasing saccharification efficiency after alkaline pretreatment of the transgenic lines by 14-24% as compared with the wild type. These results demonstrate that non-native monomers can be synthesized and incorporated into the lignin polymer in plants to enhance their biomass processing efficiency.
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Affiliation(s)
- Paula Oyarce
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Barbara De Meester
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Fernando Fonseca
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Lisanne de Vries
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Geert Goeminne
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Andreas Pallidis
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Riet De Rycke
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
- Ghent University Expertise Centre for Transmission Electron Microscopy and VIB BioImaging Core, Ghent, Belgium
| | - Yukiko Tsuji
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- US Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, USA
| | - Yanding Li
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- US Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, USA
| | | | - Bert Sels
- Center for Surface Chemistry and Catalysis, KU Leuven, Heverlee, Belgium
| | - John Ralph
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
- US Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, Madison, WI, USA
| | - Ruben Vanholme
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- VIB Metabolomics Core, Ghent, Belgium
| | - Wout Boerjan
- 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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