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Knosp S, Kriegshauser L, Tatsumi K, Malherbe L, Erhardt M, Wiedemann G, Bakan B, Kohchi T, Reski R, Renault H. An ancient role for CYP73 monooxygenases in phenylpropanoid biosynthesis and embryophyte development. EMBO J 2024:10.1038/s44318-024-00181-7. [PMID: 39090438 DOI: 10.1038/s44318-024-00181-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 07/03/2024] [Accepted: 07/15/2024] [Indexed: 08/04/2024] Open
Abstract
The phenylpropanoid pathway is one of the plant metabolic pathways most prominently linked to the transition to terrestrial life, but its evolution and early functions remain elusive. Here, we show that activity of the t-cinnamic acid 4-hydroxylase (C4H), the first plant-specific step in the pathway, emerged concomitantly with the CYP73 gene family in a common ancestor of embryophytes. Through structural studies, we identify conserved CYP73 residues, including a crucial arginine, that have supported C4H activity since the early stages of its evolution. We further demonstrate that impairing C4H function via CYP73 gene inactivation or inhibitor treatment in three bryophyte species-the moss Physcomitrium patens, the liverwort Marchantia polymorpha and the hornwort Anthoceros agrestis-consistently resulted in a shortage of phenylpropanoids and abnormal plant development. The latter could be rescued in the moss by exogenous supply of p-coumaric acid, the product of C4H. Our findings establish the emergence of the CYP73 gene family as a foundational event in the development of the plant phenylpropanoid pathway, and underscore the deep-rooted function of the C4H enzyme in embryophyte biology.
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Affiliation(s)
- Samuel Knosp
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
| | - Lucie Kriegshauser
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
- Amatera Biosciences, Pépinière Genopole Entreprise, 91000, Evry, France
| | - Kanade Tatsumi
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
- Research Institute for Sustainable Humanosphere, Kyoto University, Kyoto, Japan
| | - Ludivine Malherbe
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
| | - Mathieu Erhardt
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France
| | - Gertrud Wiedemann
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Inselspital, University of Bern, 3010, Bern, Switzerland
| | - Bénédicte Bakan
- INRAE, Biopolymers, Interactions, Assemblies Research Unit, La Géraudière, Nantes, France
| | - Takayuki Kohchi
- Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Ralf Reski
- Plant Biotechnology, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, 79104, Freiburg, Germany
| | - Hugues Renault
- IBMP | Institut de biologie moléculaire des plantes, CNRS, University of Strasbourg, Strasbourg, France.
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Ren J, Li X, Dong C, Zheng P, Zhang N, Ji H, Yu J, Lu X, Li M, Chen C, Liang L. Effect of ozone treatment on phenylpropanoid metabolism in harvested cantaloupes. J Food Sci 2024; 89:4914-4925. [PMID: 38980985 DOI: 10.1111/1750-3841.17234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/12/2024] [Accepted: 06/19/2024] [Indexed: 07/11/2024]
Abstract
Phenylpropanoid metabolism plays an important role in cantaloupe ripening and senescence, but the mechanism of ozone regulation on phenylpropanoid metabolism remains unclear. This study investigated how ozone treatment modulates the levels of secondary metabolites associated with phenylpropanoid metabolism, the related enzyme activities, and gene expression in cantaloupe. Treating cantaloupes with 15 mg/m3 of ozone after precooling can help maintain postharvest hardness. This treatment also enhances the production and accumulation of secondary metabolites, such as total phenols, flavonoids, and lignin. These metabolites are essential components of the phenylpropanoid metabolic pathway, activating enzymes like phenylalanine ammonia-lyase, cinnamate 4-hydroxylase, 4CL, chalcone synthase, and chalcone isomerase. The results of the transcriptional expression patterns showed that differential gene expression related to phenylpropanoid metabolism in the peel of ozone-treated cantaloupes was primarily observed during the middle and late storage stages. In contrast, the pulp exhibited significant differential gene expression mainly during the early storage stage. Furthermore, it was observed that the level of gene expression in the peel was generally higher than that in the pulp. The correlation between the relative amount of gene changes in cantaloupe, activity of selected enzymes, and concentration of secondary metabolites could be accompanied by positive regulation of the phenylpropanoid metabolic pathway. Therefore, ozone stress induction positively enhances the biosynthesis of flavonoids in cantaloupes, leading to an increased accumulation of secondary metabolites. Additionally, it also improves the postharvest storage quality of cantaloupes.
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Affiliation(s)
- Jie Ren
- College of Food Science and Biological Engineering, Tianjin Agricultural University, Tianjin, China
| | - Xiaoxue Li
- Institute of Agricultural Products Preservation and Processing Technology, Tianjin Academy of Agricultural Sciences (National Engineering and Technology Research Center for Preservation of Agricultural Products (Tianjin)), Key Laboratory of Storage and Preservation of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Postharvest Physiology and Storage and Preservation of Agricultural Products, Tianjin, China
| | - Chenghu Dong
- Institute of Agricultural Products Preservation and Processing Technology, Tianjin Academy of Agricultural Sciences (National Engineering and Technology Research Center for Preservation of Agricultural Products (Tianjin)), Key Laboratory of Storage and Preservation of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Postharvest Physiology and Storage and Preservation of Agricultural Products, Tianjin, China
| | - Pufan Zheng
- Institute of Agricultural Products Preservation and Processing Technology, Tianjin Academy of Agricultural Sciences (National Engineering and Technology Research Center for Preservation of Agricultural Products (Tianjin)), Key Laboratory of Storage and Preservation of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Postharvest Physiology and Storage and Preservation of Agricultural Products, Tianjin, China
| | - Na Zhang
- Institute of Agricultural Products Preservation and Processing Technology, Tianjin Academy of Agricultural Sciences (National Engineering and Technology Research Center for Preservation of Agricultural Products (Tianjin)), Key Laboratory of Storage and Preservation of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Postharvest Physiology and Storage and Preservation of Agricultural Products, Tianjin, China
| | - Haipeng Ji
- Institute of Agricultural Products Preservation and Processing Technology, Tianjin Academy of Agricultural Sciences (National Engineering and Technology Research Center for Preservation of Agricultural Products (Tianjin)), Key Laboratory of Storage and Preservation of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Postharvest Physiology and Storage and Preservation of Agricultural Products, Tianjin, China
| | - Jinze Yu
- Institute of Agricultural Products Preservation and Processing Technology, Tianjin Academy of Agricultural Sciences (National Engineering and Technology Research Center for Preservation of Agricultural Products (Tianjin)), Key Laboratory of Storage and Preservation of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Postharvest Physiology and Storage and Preservation of Agricultural Products, Tianjin, China
| | - Xiaohui Lu
- College of Food Science and Engineering, Tianjin University of Science and Technology, Tianjin, China
| | - Mo Li
- School of Agriculture and Environment, College of Sciences, Massey University, Palmerston North, New Zealand
| | - Cunkun Chen
- Institute of Agricultural Products Preservation and Processing Technology, Tianjin Academy of Agricultural Sciences (National Engineering and Technology Research Center for Preservation of Agricultural Products (Tianjin)), Key Laboratory of Storage and Preservation of Agricultural Products, Ministry of Agriculture and Rural Affairs, Tianjin Key Laboratory of Postharvest Physiology and Storage and Preservation of Agricultural Products, Tianjin, China
| | - Liya Liang
- College of Food Science and Biological Engineering, Tianjin Agricultural University, Tianjin, China
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Unda F, de Vries L, Karlen SD, Rainbow J, Zhang C, Bartley LE, Kim H, Ralph J, Mansfield SD. Enhancing monolignol ferulate conjugate levels in poplar lignin via OsFMT1. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:97. [PMID: 39003470 PMCID: PMC11246582 DOI: 10.1186/s13068-024-02544-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 06/25/2024] [Indexed: 07/15/2024]
Abstract
BACKGROUND The phenolic polymer lignin is one of the primary chemical constituents of the plant secondary cell wall. Due to the inherent plasticity of lignin biosynthesis, several phenolic monomers have been shown to be incorporated into the polymer, as long as the monomer can undergo radicalization so it can participate in coupling reactions. In this study, we significantly enhance the level of incorporation of monolignol ferulate conjugates into the lignin polymer to improve the digestibility of lignocellulosic biomass. RESULTS Overexpression of a rice Feruloyl-CoA Monolignol Transferase (FMT), OsFMT1, in hybrid poplar (Populus alba x grandidentata) produced transgenic trees clearly displaying increased cell wall-bound ester-linked ferulate, p-hydroxybenzoate, and p-coumarate, all of which are in the lignin cell wall fraction, as shown by NMR and DFRC. We also demonstrate the use of a novel UV-Vis spectroscopic technique to rapidly screen plants for the presence of both ferulate and p-hydroxybenzoate esters. Lastly we show, via saccharification assays, that the OsFMT1 transgenic p oplars have significantly improved processing efficiency compared to wild-type and Angelica sinensis-FMT-expressing poplars. CONCLUSIONS The findings demonstrate that OsFMT1 has a broad substrate specificity and a higher catalytic efficiency compared to the previously published FMT from Angelica sinensis (AsFMT). Importantly, enhanced wood processability makes OsFMT1 a promising gene to optimize the composition of lignocellulosic biomass.
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Affiliation(s)
- Faride Unda
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- US Department of Energy (DOE) Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - Lisanne de Vries
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
- US Department of Energy (DOE) Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - Steven D Karlen
- US Department of Energy (DOE) Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Jordan Rainbow
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Chengcheng Zhang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, 73019, USA
| | - Laura E Bartley
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164, USA
| | - Hoon Kim
- US Department of Energy (DOE) Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726, USA
- US Department of Agriculture (USDA), Forest Service, Forest Products Laboratory (FPL), Madison, WI, 53726, USA
| | - John Ralph
- US Department of Energy (DOE) Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Shawn D Mansfield
- Department of Wood Science, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
- US Department of Energy (DOE) Great Lakes Bioenergy Research Center, The Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, WI, 53726, USA.
- Botany Department, Faculty of Science, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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Shin D, Cho KH, Tucker E, Yoo CY, Kim J. Identification of tomato F-box proteins functioning in phenylpropanoid metabolism. PLANT MOLECULAR BIOLOGY 2024; 114:85. [PMID: 38995464 DOI: 10.1007/s11103-024-01483-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Accepted: 06/26/2024] [Indexed: 07/13/2024]
Abstract
Phenylpropanoids, a class of specialized metabolites, play crucial roles in plant growth and stress adaptation and include diverse phenolic compounds such as flavonoids. Phenylalanine ammonia-lyase (PAL) and chalcone synthase (CHS) are essential enzymes functioning at the entry points of general phenylpropanoid biosynthesis and flavonoid biosynthesis, respectively. In Arabidopsis, PAL and CHS are turned over through ubiquitination-dependent proteasomal degradation. Specific kelch domain-containing F-Box (KFB) proteins as components of ubiquitin E3 ligase directly interact with PAL or CHS, leading to polyubiquitinated PAL and CHS, which in turn influences phenylpropanoid and flavonoid production. Although phenylpropanoids are vital for tomato nutritional value and stress responses, the post-translational regulation of PAL and CHS in tomato remains unknown. We identified 31 putative KFB-encoding genes in the tomato genome. Our homology analysis and phylogenetic study predicted four PAL-interacting SlKFBs, while SlKFB18 was identified as the sole candidate for the CHS-interacting KFB. Consistent with their homolog function, the predicted four PAL-interacting SlKFBs function in PAL degradation. Surprisingly, SlKFB18 did not interact with tomato CHS and the overexpression or knocking out of SlKFB18 did not affect phenylpropanoid contents in tomato transgenic lines, suggesting its irreverence with flavonoid metabolism. Our study successfully discovered the post-translational regulatory machinery of PALs in tomato while highlighting the limitation of relying solely on a homology-based approach to predict interacting partners of F-box proteins.
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Affiliation(s)
- Doosan Shin
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Keun Ho Cho
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ethan Tucker
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, USA
| | - Chan Yul Yoo
- School of Biological Sciences, University of Utah, Salt Lake City, UT, 84112, USA
| | - Jeongim Kim
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA.
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, USA.
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Wang C, Yang J, Pan Q, Zhu P, Li J. Integrated transcriptomic and proteomic analysis of exogenous abscisic acid regulation on tuberous root development in Pseudostellaria heterophylla. Front Nutr 2024; 11:1417526. [PMID: 39036490 PMCID: PMC11258014 DOI: 10.3389/fnut.2024.1417526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024] Open
Abstract
Abscisic acid (ABA) significantly regulates plant growth and development, promoting tuberous root formation in various plants. However, the molecular mechanisms of ABA in the tuberous root development of Pseudostellaria heterophylla are not yet fully understood. This study utilized Illumina sequencing and de novo assembly strategies to obtain a reference transcriptome associated with ABA treatment. Subsequently, integrated transcriptomic and proteomic analyses were used to determine gene expression profiles in P. heterophylla tuberous roots. ABA treatment significantly increases the diameter and shortens the length of tuberous roots. Clustering analysis identified 2,256 differentially expressed genes and 679 differentially abundant proteins regulated by ABA. Gene co-expression and protein interaction networks revealed ABA positively induced 30 vital regulators. Furthermore, we identified and assigned putative functions to transcription factors (PhMYB10, PhbZIP2, PhbZIP, PhSBP) that mediate ABA signaling involved in the regulation of tuberous root development, including those related to cell wall metabolism, cell division, starch synthesis, hormone metabolism. Our findings provide valuable insights into the complex signaling networks of tuberous root development modulated by ABA. It provided potential targets for genetic manipulation to improve the yield and quality of P. heterophylla, which could significantly impact its cultivation and medicinal value.
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Affiliation(s)
| | | | | | - Panpan Zhu
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Jun Li
- Guizhou University of Traditional Chinese Medicine, Guiyang, China
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Wang L, Li C, Luo K. Biosynthesis and metabolic engineering of isoflavonoids in model plants and crops: a review. FRONTIERS IN PLANT SCIENCE 2024; 15:1384091. [PMID: 38984160 PMCID: PMC11231381 DOI: 10.3389/fpls.2024.1384091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/10/2024] [Indexed: 07/11/2024]
Abstract
Isoflavonoids, the major secondary metabolites within the flavonoid biosynthetic pathway, play important roles in plant defense and exhibit free radical scavenging properties in mammals. Recent advancements in understanding the synthesis, transport, and regulation of isoflavonoids have identified their biosynthetic pathways as promising targets for metabolic engineering, offering potential benefits such as enhanced plant resistance, improved biomass, and restoration of soil fertility. This review provides an overview of recent breakthroughs in isoflavonoid biosynthesis, encompassing key enzymes in the biosynthetic pathway, transporters influencing their subcellular localization, molecular mechanisms regulating the metabolic pathway (including transcriptional and post-transcriptional regulation, as well as epigenetic modifications). Metabolic engineering strategies aimed at boosting isoflavonoid content in both leguminous and non-leguminous plants. Additionally, we discuss emerging technologies and resources for precise isoflavonoid regulation. This comprehensive review primarily focuses on model plants and crops, offering insights for more effective and sustainable metabolic engineering approaches to enhance nutritional quality and stress tolerance.
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Affiliation(s)
- Lijun Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Chaofeng Li
- Maize Research Institute, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
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Du T, Qu X, Wang Y, Li M, Qie X, Jin J, Gao Y, Wang Z, Lin K, Yang C, Sun J. Rhizosphere Mortierella strain of alfalfa exerted weed growth inhibition by inducing expression of plant hormone-related genes. Front Microbiol 2024; 15:1385992. [PMID: 38952443 PMCID: PMC11215053 DOI: 10.3389/fmicb.2024.1385992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Accepted: 05/31/2024] [Indexed: 07/03/2024] Open
Abstract
Introduction Weeds are significant factors that detrimentally affect crop health and hinder optimal herbage yield. Rhizosphere microorganisms play crucial roles in plant growth, development, and nutrient uptake. Therefore, research focusing on weed control through the lens of microorganisms has emerged as a prominent area of study. The oil-producing fungus Mortierella, which is known for its numerous agricultural benefits, has garnered significant attention in recent years. Methods In this study, we conducted inoculation experiments in a controlled artificial culture climate chamber to investigate the effects of differential hormones and differentially expressed genes in the stems and leaves of Digitaria sanguinalis using Liquid Chromatography Tandem Mass Spectrometry and RNA-seq techniques, respectively. Additionally, Pearson's correlation analysis was used to establish correlations between differential hormones and growth indicators of Digitaria sanguinalis. Results and discussion The results demonstrated that inoculation with Mortierella sp. MXBP304 effectively suppressed aboveground biomass and plant height in Digitaria sanguinalis. Furthermore, there was significant upregulation and downregulation in the expression of genes involved in the synthesis and metabolism of phenylalanine and L-phenylalanine. Conversely, the expression of genes related to tryptophan, L-tryptophan, and indole was significantly downregulated. The addition of Mortierella sp. MXBP304 can influence the gene expression associated with phenylalanine and tryptophan synthesis and metabolism during Digitaria sanguinalis growth, subsequently reducing the relative contents of phenylalanine and tryptophan, thereby directly inhibiting Digitaria sanguinalis growth.
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Affiliation(s)
- Taotao Du
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Xudong Qu
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yibo Wang
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Meixuan Li
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Xihu Qie
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Jing Jin
- College of Plant Health and Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Yuxuan Gao
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Zengyu Wang
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Kejian Lin
- Institute of Grassland Research of CAAS, Hohhot, Inner Mongolia, China
| | - Chao Yang
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Juan Sun
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, College of Grassland Science, Qingdao Agricultural University, Qingdao, Shandong, China
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Yan M, Yang D, He Y, Ma Y, Zhang X, Wang Q, Gao J. Alfalfa Responses to Intensive Soil Compaction: Effects on Plant and Root Growth, Phytohormones and Internal Gene Expression. PLANTS (BASEL, SWITZERLAND) 2024; 13:953. [PMID: 38611482 PMCID: PMC11013635 DOI: 10.3390/plants13070953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 03/04/2024] [Accepted: 03/15/2024] [Indexed: 04/14/2024]
Abstract
The perennial legume alfalfa (Medicago sativa L.) is of high value in providing cheap and high-nutritive forages. Due to a lack of tillage during the production period, the soil in which alfalfa grows prunes to become compacted through highly mechanized agriculture. Compaction deteriorates the soil's structure and fertility, leading to compromised alfalfa development and productivity. However, the way alfalfa responses to different levels of soil compaction and the underlying molecular mechanism are still unclear. In this study, we systematically evaluated the effects of gradient compacted soil on the growth of different cultivars of alfalfa, especially the root system architecture, phytohormones and internal gene expression profile alterations. The results showed that alfalfa growth was facilitated by moderate soil compaction, but drastically inhibited when compaction was intensified. The inhibition effect was universal across different cultivars, but with different severity. Transcriptomic and physiological studies revealed that the expression of a set of genes regulating the biosynthesis of lignin and flavonoids was significantly repressed in compaction treated alfalfa roots, and this might have resulted in a modified secondary cell wall and xylem vessel formation. Phytohormones, like ABA, are supposed to play pivotal roles in the regulation of the overall responses. These findings provide directions for the improvement of field soil management in alfalfa production and the molecular breeding of alfalfa germplasm with better soil compaction resilience.
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Affiliation(s)
- Mingke Yan
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
| | - Dongming Yang
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
| | - Yijun He
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yonglong Ma
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
- School of Agronomy, Ningxia University, Yinchuan 750021, China
| | - Xin Zhang
- College of Plant Protection, Northwest A&F University, Yangling 712100, China
| | - Quanzhen Wang
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
| | - Jinghui Gao
- College of Grassland Agriculture, Northwest A&F University, Yangling 712100, China
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9
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Liu Y, Song P, Yan M, Luo J, Wang Y, Fan F. Integrated Transcriptome and Proteome Analysis Reveals the Regulatory Mechanism of Root Growth by Protein Disulfide Isomerase in Arabidopsis. Int J Mol Sci 2024; 25:3596. [PMID: 38612408 PMCID: PMC11011405 DOI: 10.3390/ijms25073596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 04/14/2024] Open
Abstract
Protein disulfide isomerase (PDI, EC 5.3.4.1) is a thiol-disulfide oxidoreductase that plays a crucial role in catalyzing the oxidation and rearrangement of disulfides in substrate proteins. In plants, PDI is primarily involved in regulating seed germination and development, facilitating the oxidative folding of storage proteins in the endosperm, and also contributing to the formation of pollen. However, the role of PDI in root growth has not been previously studied. This research investigated the impact of PDI gene deficiency in plants by using 16F16 [2-(2-Chloroacetyl)-2,3,4,9-tetrahydro-1-methyl-1H-pyrido[3,4-b]indole-1-carboxylic acid methyl ester], a small-molecule inhibitor of PDI, to remove functional redundancy. The results showed that the growth of Arabidopsis roots was significantly inhibited when treated with 16F16. To further investigate the effects of 16F16 treatment, we conducted expression profiling of treated roots using RNA sequencing and a Tandem Mass Tag (TMT)-based quantitative proteomics approach at both the transcriptomic and proteomic levels. Our analysis revealed 994 differentially expressed genes (DEGs) at the transcript level, which were predominantly enriched in pathways associated with "phenylpropane biosynthesis", "plant hormone signal transduction", "plant-pathogen interaction" and "starch and sucrose metabolism" pathways. Additionally, we identified 120 differentially expressed proteins (DEPs) at the protein level. These proteins were mainly enriched in pathways such as "phenylpropanoid biosynthesis", "photosynthesis", "biosynthesis of various plant secondary metabolites", and "biosynthesis of secondary metabolites" pathways. The comprehensive transcriptome and proteome analyses revealed a regulatory network for root shortening in Arabidopsis seedlings under 16F16 treatment, mainly involving phenylpropane biosynthesis and plant hormone signal transduction pathways. This study enhances our understanding of the significant role of PDIs in Arabidopsis root growth and provides insights into the regulatory mechanisms of root shortening following 16F16 treatment.
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Affiliation(s)
| | | | | | | | - Yingjuan Wang
- State Key Laboratory of Biotechnology of Shannxi Province, College of Life Science, Northwest University, Xi’an 710069, China; (Y.L.); (P.S.); (M.Y.); (J.L.)
| | - Fenggui Fan
- State Key Laboratory of Biotechnology of Shannxi Province, College of Life Science, Northwest University, Xi’an 710069, China; (Y.L.); (P.S.); (M.Y.); (J.L.)
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Wang X, Yang J, Hu H, Yuan T, Zhao Y, Liu Y, Li W, Liu J. Genome-Wide Analysis and Identification of UDP Glycosyltransferases Responsive to Chinese Wheat Mosaic Virus Resistance in Nicotiana benthamiana. Viruses 2024; 16:489. [PMID: 38675832 PMCID: PMC11054786 DOI: 10.3390/v16040489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 04/28/2024] Open
Abstract
Glycosylation, a dynamic modification prevalent in viruses and higher eukaryotes, is principally regulated by uridine diphosphate (UDP)-glycosyltransferases (UGTs) in plants. Although UGTs are involved in plant defense responses, their responses to most pathogens, especially plant viruses, remain unclear. Here, we aimed to identify UGTs in the whole genome of Nicotiana benthamiana (N. benthamiana) and to analyze their function in Chinese wheat mosaic virus (CWMV) infection. A total of 147 NbUGTs were identified in N. benthamiana. To conduct a phylogenetic analysis, the UGT protein sequences of N. benthamiana and Arabidopsis thaliana were aligned. The gene structure and conserved motifs of the UGTs were also analyzed. Additionally, the physicochemical properties and predictable subcellular localization were examined in detail. Analysis of cis-acting elements in the putative promoter revealed that NbUGTs were involved in temperature, defense, and hormone responses. The expression levels of 20 NbUGTs containing defense-related cis-acting elements were assessed in CWMV-infected N. benthamiana, revealing a significant upregulation of 8 NbUGTs. Subcellular localization analysis of three NbUGTs (NbUGT12, NbUGT16 and NbUGT17) revealed their predominant localization in the cytoplasm of N. benthamiana leaves, and NbUGT12 was also distributed in the chloroplasts. CWMV infection did not alter the subcellular localization of NbUGT12, NbUGT16, and NbUGT17. Transient overexpression of NbUGT12, NbUGT16, and NbUGT17 enhanced CWMV infection, whereas the knockdown of NbUGT12, NbUGT16 and NbUGT17 inhibited CWMV infection in N. benthamiana. These NbUGTs could serve as potential susceptibility genes to facilitate CWMV infection. Overall, the findings throw light on the evolution and function of NbUGTs.
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Affiliation(s)
- Xia Wang
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (X.W.); (H.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.Y.); (Y.Z.); (Y.L.)
| | - Jin Yang
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.Y.); (Y.Z.); (Y.L.)
| | - Haichao Hu
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (X.W.); (H.H.)
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.Y.); (Y.Z.); (Y.L.)
| | - Tangyu Yuan
- Yantai Academy of Agricultural Science, No. 26 Gangcheng West Street, Fushan District, Yantai City 265500, China;
| | - Yingjie Zhao
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.Y.); (Y.Z.); (Y.L.)
| | - Ying Liu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.Y.); (Y.Z.); (Y.L.)
| | - Wei Li
- College of Plant Protection, Hunan Agricultural University, Changsha 410128, China; (X.W.); (H.H.)
| | - Jiaqian Liu
- State Key Laboratory for Quality and Safety of Agro-Products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China; (J.Y.); (Y.Z.); (Y.L.)
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11
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Xing F, Zhang L, Ge W, Fan H, Tian C, Meng F. Comparative transcriptome analysis reveals the importance of phenylpropanoid biosynthesis for the induced resistance of 84K poplar to anthracnose. BMC Genomics 2024; 25:306. [PMID: 38519923 PMCID: PMC10960379 DOI: 10.1186/s12864-024-10209-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 03/11/2024] [Indexed: 03/25/2024] Open
Abstract
BACKGROUND Poplar anthracnose, which is one of the most important tree diseases, is primarily caused by Colletotrichum gloeosporioides, which has been detected in poplar plantations in China and is responsible for serious economic losses. The characteristics of 84K poplar that have made it one of the typical woody model plants used for investigating stress resistance include its rapid growth, simple reproduction, and adaptability. RESULTS In this study, we found that the resistance of 84K poplar to anthracnose varied considerably depending on how the samples were inoculated of the two seedlings in each tissue culture bottle, one (84K-Cg) was inoculated for 6 days, whereas the 84K-DCg samples were another seedling inoculated at the 6th day and incubated for another 6 days under the same conditions. It was showed that the average anthracnose spot diameter on 84K-Cg and 84K-DCg leaves was 1.23 ± 0.0577 cm and 0.67 ± 0.1154 cm, respectively. Based on the transcriptome sequencing analysis, it was indicated that the upregulated phenylpropanoid biosynthesis-related genes in 84K poplar infected with C. gloeosporioides, including genes encoding PAL, C4H, 4CL, HCT, CCR, COMT, F5H, and CAD, are also involved in other KEGG pathways (i.e., flavonoid biosynthesis and phenylalanine metabolism). The expression levels of these genes were lowest in 84K-Cg and highest in 84K-DCg. CONCLUSIONS It was found that PAL-related genes may be crucial for the induced resistance of 84K poplar to anthracnose, which enriched in the phenylpropanoid biosynthesis. These results will provide the basis for future research conducted to verify the contribution of phenylpropanoid biosynthesis to induced resistance and explore plant immune resistance-related signals that may regulate plant defense capabilities, which may provide valuable insights relevant to the development of effective and environmentally friendly methods for controlling poplar anthracnose.
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Affiliation(s)
- Fei Xing
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, 100083, Beijing, China
| | - Linxuan Zhang
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, 100083, Beijing, China
| | - Wei Ge
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, 100083, Beijing, China
| | - Haixia Fan
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, 100083, Beijing, China
| | - Chengming Tian
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, 100083, Beijing, China
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, 100083, Beijing, China
| | - Fanli Meng
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, 100083, Beijing, China.
- Beijing Key Laboratory for Forest Pest Control, College of Forestry, Beijing Forestry University, 100083, Beijing, China.
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12
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Gong Q, Yu J, Guo Z, Fu K, Xu Y, Zou H, Li C, Si J, Cai S, Chen D, Han Z. Accumulation mechanism of metabolite markers identified by machine learning between Qingyuan and Xiushui counties in Polygonatum cyrtonema Hua. BMC PLANT BIOLOGY 2024; 24:173. [PMID: 38443808 PMCID: PMC10916035 DOI: 10.1186/s12870-024-04871-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 02/28/2024] [Indexed: 03/07/2024]
Abstract
Polygonatum cyrtonema Hua is a traditional Chinese medicinal plant acclaimed for its therapeutic potential in diabetes and various chronic diseases. Its rhizomes are the main functional parts rich in secondary metabolites, such as flavonoids and saponins. But their quality varies by region, posing challenges for industrial and medicinal application of P. cyrtonema. In this study, 482 metabolites were identified in P. cyrtonema rhizome from Qingyuan and Xiushui counties. Cluster analysis showed that samples between these two regions had distinct secondary metabolite profiles. Machine learning methods, specifically support vector machine-recursive feature elimination and random forest, were utilized to further identify metabolite markers including flavonoids, phenolic acids, and lignans. Comparative transcriptomics and weighted gene co-expression analysis were performed to uncover potential candidate genes including CHI, UGT1, and PcOMT10/11/12/13 associated with these compounds. Functional assays using tobacco transient expression system revealed that PcOMT10/11/12/13 indeed impacted metabolic fluxes of the phenylpropanoid pathway and phenylpropanoid-related metabolites such as chrysoeriol-6,8-di-C-glucoside, syringaresinol-4'-O-glucopyranosid, and 1-O-Sinapoyl-D-glucose. These findings identified metabolite markers between these two regions and provided valuable genetic insights for engineering the biosynthesis of these compounds.
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Affiliation(s)
- Qiqi Gong
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jianfeng Yu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Zhicheng Guo
- Shandong Marine Resource and Environment Research Institute, Shandong Provincial Key Laboratory of Restoration for Marine Ecology, Yantai, 264006, China
| | - Ke Fu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yi Xu
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Hui Zou
- Yipuyuan Huangjing Technology Co., Ltd, Xinhua, 417600, China
| | - Cong Li
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jinping Si
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China
| | - Shengguan Cai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310030, China
| | - Donghong Chen
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China.
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
| | - Zhigang Han
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou, 311300, China.
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, 311300, China.
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13
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Kong CH, Li Z, Li FL, Xia XX, Wang P. Chemically Mediated Plant-Plant Interactions: Allelopathy and Allelobiosis. PLANTS (BASEL, SWITZERLAND) 2024; 13:626. [PMID: 38475470 DOI: 10.3390/plants13050626] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024]
Abstract
Plant-plant interactions are a central driver for plant coexistence and community assembly. Chemically mediated plant-plant interactions are represented by allelopathy and allelobiosis. Both allelopathy and allelobiosis are achieved through specialized metabolites (allelochemicals or signaling chemicals) produced and released from neighboring plants. Allelopathy exerts mostly negative effects on the establishment and growth of neighboring plants by allelochemicals, while allelobiosis provides plant neighbor detection and identity recognition mediated by signaling chemicals. Therefore, plants can chemically affect the performance of neighboring plants through the allelopathy and allelobiosis that frequently occur in plant-plant intra-specific and inter-specific interactions. Allelopathy and allelobiosis are two probably inseparable processes that occur together in plant-plant chemical interactions. Here, we comprehensively review allelopathy and allelobiosis in plant-plant interactions, including allelopathy and allelochemicals and their application for sustainable agriculture and forestry, allelobiosis and plant identity recognition, chemically mediated root-soil interactions and plant-soil feedback, and biosynthesis and the molecular mechanisms of allelochemicals and signaling chemicals. Altogether, these efforts provide the recent advancements in the wide field of allelopathy and allelobiosis, and new insights into the chemically mediated plant-plant interactions.
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Affiliation(s)
- Chui-Hua Kong
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Zheng Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Feng-Li Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Xin-Xin Xia
- College of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Peng Wang
- Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang 110016, China
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14
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Dwivedi N, Yamamoto S, Zhao Y, Hou G, Bowling F, Tobimatsu Y, Liu C. Simultaneous suppression of lignin, tricin and wall-bound phenolic biosynthesis via the expression of monolignol 4-O-methyltransferases in rice. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:330-346. [PMID: 37795899 PMCID: PMC10826995 DOI: 10.1111/pbi.14186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/14/2023] [Accepted: 09/16/2023] [Indexed: 10/06/2023]
Abstract
Grass lignocelluloses feature complex compositions and structures. In addition to the presence of conventional lignin units from monolignols, acylated monolignols and flavonoid tricin also incorporate into lignin polymer; moreover, hydroxycinnamates, particularly ferulate, cross-link arabinoxylan chains with each other and/or with lignin polymers. These structural complexities make grass lignocellulosics difficult to optimize for effective agro-industrial applications. In the present study, we assess the applications of two engineered monolignol 4-O-methyltransferases (MOMTs) in modifying rice lignocellulosic properties. Two MOMTs confer regiospecific para-methylation of monolignols but with different catalytic preferences. The expression of MOMTs in rice resulted in differential but drastic suppression of lignin deposition, showing more than 50% decrease in guaiacyl lignin and up to an 90% reduction in syringyl lignin in transgenic lines. Moreover, the levels of arabinoxylan-bound ferulate were reduced by up to 50%, and the levels of tricin in lignin fraction were also substantially reduced. Concomitantly, up to 11 μmol/g of the methanol-extractable 4-O-methylated ferulic acid and 5-7 μmol/g 4-O-methylated sinapic acid were accumulated in MOMT transgenic lines. Both MOMTs in vitro displayed discernible substrate promiscuity towards a range of phenolics in addition to the dominant substrate monolignols, which partially explains their broad effects on grass phenolic biosynthesis. The cell wall structural and compositional changes resulted in up to 30% increase in saccharification yield of the de-starched rice straw biomass after diluted acid-pretreatment. These results demonstrate an effective strategy to tailor complex grass cell walls to generate improved cellulosic feedstocks for the fermentable sugar-based production of biofuel and bio-chemicals.
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Affiliation(s)
- Nidhi Dwivedi
- Biology DepartmentBrookhaven Nation LaboratoryUptonNew YorkUSA
- Feedstocks DivisionJoint BioEnergy InstituteEmeryvilleCAUSA
| | - Senri Yamamoto
- Research Institute for Sustainable HumanosphereKyoto UniversityGokasho, UjiKyotoJapan
| | - Yunjun Zhao
- Biology DepartmentBrookhaven Nation LaboratoryUptonNew YorkUSA
| | - Guichuan Hou
- Dewel Microscopy FacilityAppalachian State UniversityBooneNorth CarolinaUSA
| | - Forrest Bowling
- Biology DepartmentBrookhaven Nation LaboratoryUptonNew YorkUSA
| | - Yuki Tobimatsu
- Research Institute for Sustainable HumanosphereKyoto UniversityGokasho, UjiKyotoJapan
| | - Chang‐Jun Liu
- Biology DepartmentBrookhaven Nation LaboratoryUptonNew YorkUSA
- Feedstocks DivisionJoint BioEnergy InstituteEmeryvilleCAUSA
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15
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Qu D, Yan F, Zhang Y, Huang L. A 4D Proteome Investigation of the Potential Mechanisms of SA in Triggering Resistance in Kiwifruit to Pseudomonas syringae pv. actinidiae. Int J Mol Sci 2023; 24:17448. [PMID: 38139278 PMCID: PMC10744097 DOI: 10.3390/ijms242417448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/04/2023] [Accepted: 12/05/2023] [Indexed: 12/24/2023] Open
Abstract
Kiwifruit bacterial cankers caused by Pseudomonas syringae pv. actinidiae (Psa) are a serious threat to the kiwifruit industry. Salicylic acid (SA) regulates plant defense responses and was previously found to enhance kiwifruit's resistance to Psa. However, the underlying mechanisms of this process remain unclear. In this study, we used 4D proteomics to investigate how SA enhances kiwifruit's resistance to Psa and found that both SA treatment and Psa infection induced dramatic changes in the proteomic pattern of kiwifruit. Psa infection triggered the activation of numerous resistance events, including the MAPK cascade, phenylpropanoid biosynthesis, and hormone signaling transduction. In most cases, the differential expression of a number of genes involved in the SA signaling pathway played a significant role in kiwifruit's responses to Psa. Moreover, SA treatment upregulated numerous resistance-related proteins, which functioned in defense responses to Psa, including phenylpropanoid biosynthesis, the MAPK cascade, and the upregulation of pathogenesis-related proteins. We also found that SA treatment could facilitate timely defense responses to Psa infection and enhance the activation of defense responses that were downregulated in kiwifruit during infection with Psa. Thus, our research deciphered the potential mechanisms of SA in promoting Psa resistance in kiwifruit and can provide a basis for the use of SA to enhance kiwifruit resistance and effectively control the occurrence of kiwifruit bacterial cankers.
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Affiliation(s)
- Dong Qu
- College of Plant Protection, Northwest A&F University, Xianyang 712100, China;
- Shaanxi Provincial Bioresource Key Laboratory, College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, China; (F.Y.); (Y.Z.)
| | - Fei Yan
- Shaanxi Provincial Bioresource Key Laboratory, College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, China; (F.Y.); (Y.Z.)
| | - Yu Zhang
- Shaanxi Provincial Bioresource Key Laboratory, College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723000, China; (F.Y.); (Y.Z.)
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, Hanzhong 723001, China
| | - Lili Huang
- College of Plant Protection, Northwest A&F University, Xianyang 712100, China;
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16
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Shin J, Lee Y, Hahm S, Lee K, Park J. Effects of Exogenous Ethanol Treatment in Nutrient Solution on Growth and Secondary Metabolite Contents of Three Herb Species in an Indoor Vertical Farming System. PLANTS (BASEL, SWITZERLAND) 2023; 12:3842. [PMID: 38005739 PMCID: PMC10675256 DOI: 10.3390/plants12223842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 11/05/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023]
Abstract
This study aimed to explore the possibility of exogenous ethanol treatment as a technology to regulate the growth and the synthesis of secondary metabolites in herbaceous plants. After transplantation, sweet basil, Korean mint, and sweet wormwood were cultivated in a controlled vertical farming system and consistently exposed to exogenous ethanol at concentrations of 0, 0.5, 1, 2, 4, and 8 mM. Their growth parameters, antioxidant activity, and secondary metabolite contents were Everything is fine. measured to investigate the effects of the exogenous ethanol treatment on the three plants. The low-concentration ethanol treatments increased the shoot dry weight of the sweet basil and sweet wormwood compared to that of the control. As the ethanol concentration increased, the shoot fresh weight and leaf area in the sweet basil and Korean mint decreased compared to those of the control (0 mM). The DPPH (2,2-Diphenyl-1-picrylhydrazyl) radical scavenging activity and total phenolic content of the three plants increased with the ethanol concentration, while the total flavonoid content did not demonstrate a significant trend. The chlorophyll and carotenoids of the basil showed no apparent concentration-dependent trends; however, the chlorophyll and carotenoids of the Korean mint and sweet wormwood decreased with high ethanol concentrations. Moreover, the antioxidant enzyme activity increased with high ethanol concentrations, indicating that high ethanol concentrations induce oxidative stress in plants.
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Affiliation(s)
- Juhyung Shin
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of Korea; (J.S.); (Y.L.)
| | - YongJae Lee
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of Korea; (J.S.); (Y.L.)
| | - Seungyong Hahm
- Department of Horticultural Science, Chungnam National University, Daejeon 34134, Republic of Korea;
| | - Kwangya Lee
- Institute of Agricultural Science, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Jongseok Park
- Department of Bio-AI Convergence, Chungnam National University, Daejeon 34134, Republic of Korea; (J.S.); (Y.L.)
- Department of Horticultural Science, Chungnam National University, Daejeon 34134, Republic of Korea;
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17
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Shin D, Perez VC, Dickinson GK, Zhao H, Dai R, Tomiczek B, Cho KH, Zhu N, Koh J, Grenning A, Kim J. Altered methionine metabolism impacts phenylpropanoid production and plant development in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:187-200. [PMID: 37366635 DOI: 10.1111/tpj.16370] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 06/20/2023] [Indexed: 06/28/2023]
Abstract
Phenylpropanoids are specialized metabolites derived from phenylalanine. Glucosinolates are defense compounds derived mainly from methionine and tryptophan in Arabidopsis. It was previously shown that the phenylpropanoid pathway and glucosinolate production are metabolically linked. The accumulation of indole-3-acetaldoxime (IAOx), the precursor of tryptophan-derived glucosinolates, represses phenylpropanoid biosynthesis through accelerated degradation of phenylalanine ammonia lyase (PAL). As PAL functions at the entry point of the phenylpropanoid pathway, which produces indispensable specialized metabolites such as lignin, aldoxime-mediated phenylpropanoid repression is detrimental to plant survival. Although methionine-derived glucosinolates in Arabidopsis are abundant, any impact of aliphatic aldoximes (AAOx) derived from aliphatic amino acids such as methionine on phenylpropanoid production remains unclear. Here, we investigate the impact of AAOx accumulation on phenylpropanoid production using Arabidopsis aldoxime mutants, ref2 and ref5. REF2 and REF5 metabolize aldoximes to respective nitrile oxides redundantly, but with different substrate specificities. ref2 and ref5 mutants have decreased phenylpropanoid contents due to the accumulation of aldoximes. As REF2 and REF5 have high substrate specificity toward AAOx and IAOx, respectively, it was assumed that ref2 accumulates AAOx, not IAOx. Our study indicates that ref2 accumulates both AAOx and IAOx. Removing IAOx partially restored phenylpropanoid content in ref2, but not to the wild-type level. However, when AAOx biosynthesis was silenced, phenylpropanoid production and PAL activity in ref2 were completely restored, suggesting an inhibitory effect of AAOx on phenylpropanoid production. Further feeding studies revealed that the abnormal growth phenotype commonly observed in Arabidopsis mutants lacking AAOx production is a consequence of methionine accumulation.
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Affiliation(s)
- Doosan Shin
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Veronica C Perez
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, USA
| | - Gabriella K Dickinson
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, USA
| | - Haohao Zhao
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ru Dai
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Breanna Tomiczek
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Keun Ho Cho
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
| | - Ning Zhu
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32611, USA
| | - Jin Koh
- Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, FL, 32611, USA
| | - Alexander Grenning
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Jeongim Kim
- Horticultural Sciences Department, University of Florida, Gainesville, FL, 32611, USA
- Plant Molecular and Cellular Biology Graduate Program, University of Florida, Gainesville, FL, USA
- Genetic Institute, University of Florida, Gainesville, FL, USA
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18
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Liu S, Zenda T, Tian Z, Huang Z. Metabolic pathways engineering for drought or/and heat tolerance in cereals. FRONTIERS IN PLANT SCIENCE 2023; 14:1111875. [PMID: 37810398 PMCID: PMC10557149 DOI: 10.3389/fpls.2023.1111875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
Drought (D) and heat (H) are the two major abiotic stresses hindering cereal crop growth and productivity, either singly or in combination (D/+H), by imposing various negative impacts on plant physiological and biochemical processes. Consequently, this decreases overall cereal crop production and impacts global food availability and human nutrition. To achieve global food and nutrition security vis-a-vis global climate change, deployment of new strategies for enhancing crop D/+H stress tolerance and higher nutritive value in cereals is imperative. This depends on first gaining a mechanistic understanding of the mechanisms underlying D/+H stress response. Meanwhile, functional genomics has revealed several stress-related genes that have been successfully used in target-gene approach to generate stress-tolerant cultivars and sustain crop productivity over the past decades. However, the fast-changing climate, coupled with the complexity and multigenic nature of D/+H tolerance suggest that single-gene/trait targeting may not suffice in improving such traits. Hence, in this review-cum-perspective, we advance that targeted multiple-gene or metabolic pathway manipulation could represent the most effective approach for improving D/+H stress tolerance. First, we highlight the impact of D/+H stress on cereal crops, and the elaborate plant physiological and molecular responses. We then discuss how key primary metabolism- and secondary metabolism-related metabolic pathways, including carbon metabolism, starch metabolism, phenylpropanoid biosynthesis, γ-aminobutyric acid (GABA) biosynthesis, and phytohormone biosynthesis and signaling can be modified using modern molecular biotechnology approaches such as CRISPR-Cas9 system and synthetic biology (Synbio) to enhance D/+H tolerance in cereal crops. Understandably, several bottlenecks hinder metabolic pathway modification, including those related to feedback regulation, gene functional annotation, complex crosstalk between pathways, and metabolomics data and spatiotemporal gene expressions analyses. Nonetheless, recent advances in molecular biotechnology, genome-editing, single-cell metabolomics, and data annotation and analysis approaches, when integrated, offer unprecedented opportunities for pathway engineering for enhancing crop D/+H stress tolerance and improved yield. Especially, Synbio-based strategies will accelerate the development of climate resilient and nutrient-dense cereals, critical for achieving global food security and combating malnutrition.
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Affiliation(s)
- Songtao Liu
- Hebei Key Laboratory of Quality & Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Tinashe Zenda
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Agricultural University, Baoding, China
| | - Zaimin Tian
- Hebei Key Laboratory of Quality & Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
| | - Zhihong Huang
- Hebei Key Laboratory of Quality & Safety Analysis-Testing for Agro-Products and Food, Hebei North University, Zhangjiakou, China
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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 PHYSIOLOGY 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] [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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20
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Zang X, Liu J, Zhao J, Liu J, Ren J, Li L, Li X, Yang D. Uncovering mechanisms governing stem growth in peanut (Arachis hypogaea L.) with varying plant heights through integrated transcriptome and metabolomics analyses. JOURNAL OF PLANT PHYSIOLOGY 2023; 287:154052. [PMID: 37454530 DOI: 10.1016/j.jplph.2023.154052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/18/2023] [Accepted: 07/08/2023] [Indexed: 07/18/2023]
Abstract
The mechanisms responsible for stem growth in peanut (Arachis hypogaea L.) cultivars with varying plant heights remain unclear, despite the significant impact of plant height on peanut yield. Therefore, this study aimed to investigate the underlying mechanisms of peanut stem growth using phenotypic, physiological, transcriptomic, and metabolomic analyses. The findings revealed that the tallest cultivar, HY33, exhibited the highest rate of stem growth and accumulated the most stem dry matter, followed by the intermediate cultivar, SH108, while the dwarf cultivar, Df216, displayed the lowest values. Furthermore, SH108 exhibited a higher harvest index, as well as superior pod and kernel yields compared to both HY33 and Df216. Transcriptome and metabolome analyses identified differentially expressed genes (DEGs) and differentially expressed metabolites (DEMs) associated with phenylpropanoid and flavonoid biosynthesis. Notably, downregulated DEGs in Df216/HY33 and Df216/SH108 included phenylalanine ammonia-lyase (PAL), caffeoyl-CoA O-methyltransferase (COMT), and ferulate-5-hydroxylase (F5H), while downregulated DEMs included p-coumaryl alcohol, chlorogenic acid, and L-epicatechin. Compared to HY33, the reduced activities of PAL, COMT, and F5H resulted in a decreased stem lignin content in Df216. Additionally, downregulated DEGs involved in gibberellin (GA) and brassinosteroid (BR) biosynthesis were identified in Df216/HY33, which contributed to the lowest levels of GA1, GA3, and BR contents in Df216. The results suggest that the dwarf phenotype arises from impaired GA and BR biosynthesis and signaling, resulting in a slower stem growth rate and reduced lignin accumulation.
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Affiliation(s)
- Xiuzhi Zang
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Juan Liu
- Industrial Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China.
| | - Jihao Zhao
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Jianbo Liu
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Jinfeng Ren
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Liuyin Li
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Xiangdong Li
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Dongqing Yang
- College of Agronomy, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
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21
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Shin D, Perez VC, Dickinson GK, Zhao H, Dai R, Tomiczek B, Cho KH, Zhu N, Koh J, Grenning A, Kim J. Altered methionine metabolism impacts phenylpropanoid production and plant development in Arabidopsis thaliana. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.29.542770. [PMID: 37398371 PMCID: PMC10312446 DOI: 10.1101/2023.05.29.542770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Phenylpropanoids are specialized metabolites derived from phenylalanine. Glucosinolates are defense compounds derived mainly from methionine and tryptophan in Arabidopsis. It was previously shown that the phenylpropanoid pathway and glucosinolate production are metabolically linked. The accumulation of indole-3-acetaldoxime (IAOx), the precursor of tryptophan-derived glucosinolates, represses phenylpropanoid biosynthesis through accelerated degradation of phenylalanine-ammonia lyase (PAL). As PAL functions at the entry point of the phenylpropanoid pathway which produces indispensable specialized metabolites such as lignin, aldoxime-mediated phenylpropanoid repression is detrimental to plant survival. Although methionine-derived glucosinolates in Arabidopsis are abundant, any impact of aliphatic aldoximes (AAOx) derived from aliphatic amino acids such as methionine on phenylpropanoid production remains unclear. Here, we investigate the impact of AAOx accumulation on phenylpropanoid production using Arabidopsis aldoxime mutants, ref2 and ref5 . REF2 and REF5 metabolize aldoximes to respective nitrile oxides redundantly, but with different substrate specificities. ref2 and ref5 mutants have decreased phenylpropanoid contents due to the accumulation of aldoximes. As REF2 and REF5 have high substrate specificity toward AAOx and IAOx respectively, it was assumed that ref2 accumulates AAOx, not IAOx. Our study indicates that ref2 accumulates both AAOx and IAOx. Removing IAOx partially restored phenylpropanoid production in ref2 , but not to the wild-type level. However, when AAOx biosynthesis was silenced, phenylpropanoid production and PAL activity in ref2 were completely restored, suggesting an inhibitory effect of AAOx on phenylpropanoid production. Further feeding studies revealed that the abnormal growth phenotype commonly observed in Arabidopsis mutants lacking AAOx production is a consequence of methionine accumulation. Significance Statement Aliphatic aldoximes are precursors of various specialized metabolites including defense compounds. This study reveals that aliphatic aldoximes repress phenylpropanoid production and that altered methionine metabolism affects plant growth and development. As phenylpropanoids include vital metabolites such as lignin, a major sink of fixed carbon, this metabolic link may contribute to available resource allocation during defense.
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22
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Xiao S, Li D, Tang Z, Wei H, Zhang Y, Yang J, Zhao C, Liu Y, Wang W. Supplementary UV-B Radiation Effects on Photosynthetic Characteristics and Important Secondary Metabolites in Eucommia ulmoides Leaves. Int J Mol Sci 2023; 24:ijms24098168. [PMID: 37175879 PMCID: PMC10178938 DOI: 10.3390/ijms24098168] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/15/2023] Open
Abstract
To explore the effects of ultraviolet light supplementation on the photosynthetic characteristics and content of secondary metabolites in the leaves of Eucommia ulmoides Oliver (E. ulmoides), the effects of supplementary UV-B (sUV-B) radiation on the medicinally active components of E. ulmoides were comprehensively evaluated. In our study, we selected leaves of five-year-old E. ulmoides seedlings as experimental materials and studied the effect of supplemental ultraviolet-B (sUV-B) radiation on growth, photosynthetic parameters, photosynthetic pigments, fluorescence parameters, and secondary metabolites of E. ulmoides using multivariate analysis. The results showed that the leaf area and the number of branches increased after sUV-B radiation, which indicated that sUV-B radiation was beneficial to the growth of E. ulmoides. The contents of chlorophyll a and chlorophyll b increased by 2.25% and 4.25%, respectively; the net photosynthetic rate increased by 5.17%; the transpiration rate decreased by 35.32%; the actual photosynthetic efficiency increased by 10.64%; the content of the secondary metabolite genipin increased by 12.9%; and the content of chlorogenic acid increased by 75.03%. To identify the genes that may be related to the effects of sUV-B radiation on the growth and development of E. ulmoides leaves and important secondary metabolites, six cDNA libraries were prepared from natural sunlight radiation and sUV-B radiation in E. ulmoides leaves. Comparative analysis of both transcriptome databases revealed a total of 3698 differential expression genes (DEGs), including 1826 up-regulated and 1872 down-regulated genes. According to the KOG database, the up-regulated unigenes were mainly involved in signal transduction mechanisms [T] and cell wall/membrane biogenesis [M]. It is also involved in plant hormone signal transduction and phenylpropanoid biosynthesis metabolic pathways by the KEGG pathway, which might further affect the physiological indices and the content of chlorogenic acid, a secondary metabolite of E. ulmoides. Furthermore, 10 candidate unigenes were randomly selected to examine gene expression using qRT-PCR, and the six libraries exhibited differential expression and were identical to those obtained by sequencing. Thus, the data in this study were helpful in clarifying the reasons for leaf growth after sUV-B radiation. And it was beneficial to improve the active components and utilization rate of E. ulmoides after sUV-B radiation.
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Affiliation(s)
- Siqiu Xiao
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Dewen Li
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Zhonghua Tang
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Hongling Wei
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Ying Zhang
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Jing Yang
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Chunjian Zhao
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Ying Liu
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, China
| | - Wei Wang
- College of Chemistry, Chemical Engineering and Resource Utilization, Northeast Forestry University, Harbin 150040, China
- Key Laboratory of Forest Plant Ecology, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Engineering Research Center of Forest Bio-Preparation, Ministry of Education, Northeast Forestry University, Harbin 150040, China
- Institute of Advance Carbon Conversion Technology, Huaqiao University, Xiamen 361021, China
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23
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Zhao XW, Wang Q, Wang D, Guo W, Hu MX, Liu YL, Zhou GK, Chai GH, Zhao ST, Lu MZ. PagERF81 regulates lignin biosynthesis and xylem cell differentiation in poplar. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1134-1146. [PMID: 36647609 DOI: 10.1111/jipb.13453] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 01/15/2023] [Indexed: 05/13/2023]
Abstract
Lignin is a major component of plant cell walls and is essential for plant growth and development. Lignin biosynthesis is controlled by a hierarchical regulatory network involving multiple transcription factors. In this study, we showed that the gene encoding an APETALA 2/ethylene-responsive element binding factor (AP2/ERF) transcription factor, PagERF81, from poplar 84 K (Populus alba × P. glandulosa) is highly expressed in expanding secondary xylem cells. Two independent homozygous Pagerf81 mutant lines created by gene editing, produced significantly more but smaller vessel cells and longer fiber cells with more lignin in cell walls, while PagERF81 overexpression lines had less lignin, compared to non-transgenic controls. Transcriptome and reverse transcription quantitative PCR data revealed that multiple lignin biosynthesis genes including Cinnamoyl CoA reductase 1 (PagCCR1), Cinnamyl alcohol dehydrogenase 6 (PagCAD6), and 4-Coumarate-CoA ligase-like 9 (Pag4CLL9) were up-regulated in Pagerf81 mutants, but down-regulated in PagERF81 overexpression lines. In addition, a transient transactivation assay revealed that PagERF81 repressed the transcription of these three genes. Furthermore, yeast one hybrid and electrophoretic mobility shift assays showed that PagERF81 directly bound to a GCC sequence in the PagCCR1 promoter. No known vessel or fiber cell differentiation related genes were differentially expressed, so the smaller vessel cells and longer fiber cells observed in the Pagerf81 lines might be caused by abnormal lignin deposition in the secondary cell walls. This study provides insight into the regulation of lignin biosynthesis, and a molecular tool to engineer wood with high lignin content, which would contribute to the lignin-related chemical industry and carbon sequestration.
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Affiliation(s)
- Xin-Wei Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Qiao Wang
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Dian Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wei Guo
- Taishan Academy of Forestry Sciences, Taian, 271000, China
| | - Meng-Xuan Hu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Ying-Li Liu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Gong-Ke Zhou
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, 266109, China
| | - Guo-Hua Chai
- College of Resources and Environment, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shu-Tang Zhao
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
| | - Meng-Zhu Lu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, 100091, China
- State Key Laboratory of Subtropical Silviculture, College of Forestry and Biotechnology, Zhejiang A & F University, Hangzhou, 311300, China
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24
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Li L, Wang K, Zhou Y, Liu X. Review: A silent concert in developing plants: Dynamic assembly of cullin-RING ubiquitin ligases. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111662. [PMID: 36822503 PMCID: PMC10065934 DOI: 10.1016/j.plantsci.2023.111662] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/27/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Plants appear quiet: quietly, they break the ground, expand leaves, search for resources, alert each other to invaders, and heal their own wounds. In contrast to the stationary appearance, the inside world of a plant is full of movements: cells divide to increase the body mass and form new organs; signaling molecules migrate among cells and tissues to drive transcriptional cascades and developmental programs; macromolecules, such as RNAs and proteins, collaborate with different partners to maintain optimal organismal function under changing cellular and environmental conditions. All these activities require a dynamic yet appropriately controlled molecular network in plant cells. In this short review, we used the regulation of cullin-RING ubiquitin ligases (CRLs) as an example to discuss how dynamic biochemical processes contribute to plant development. CRLs comprise a large family of modular multi-unit enzymes that determine the activity and stability of diverse regulatory proteins playing crucial roles in plant growth and development. The mechanism governing the dynamic assembly of CRLs is essential for CRL activity and biological function, and it may provide insights and implications for the regulation of other dynamic multi-unit complexes involved in fundamental processes such as transcription, translation, and protein sorting in plants.
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Affiliation(s)
- Lihong Li
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Kankan Wang
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Yun Zhou
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Xing Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States; Center for Plant Biology, Purdue University, West Lafayette, IN, United States.
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25
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Liu C, Yu H, Voxeur A, Rao X, Dixon RA. FERONIA and wall-associated kinases coordinate defense induced by lignin modification in plant cell walls. SCIENCE ADVANCES 2023; 9:eadf7714. [PMID: 36897948 PMCID: PMC10005186 DOI: 10.1126/sciadv.adf7714] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/03/2023] [Indexed: 06/17/2023]
Abstract
Altering the content or composition of the cell wall polymer lignin is a favored approach to valorize lignin toward biomaterial and chemical production in the biorefinery. However, modifying lignin or cellulose in transgenic plants can induce expression of defense responses and negatively affect growth. Through genetic screening for suppressors of defense gene induction in the low lignin ccr1-3 mutant of Arabidopsis thaliana, we found that loss of function of the receptor-like kinase FERONIA, although not restoring growth, affected cell wall remodeling and blocked release of elicitor-active pectic polysaccharides as a result of the ccr1-3 mutation. Loss of function of multiple wall-associated kinases prevented perception of these elicitors. The elicitors are likely heterogeneous, with tri-galacturonic acid the smallest but not necessarily the most active component. Engineering of plant cell walls will require development of ways to bypass endogenous pectin signaling pathways.
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Affiliation(s)
- Chang Liu
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
| | - Hasi Yu
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
| | - Aline Voxeur
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France
| | - Xiaolan Rao
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, No.368, Friendship Avenue, Wuchang District, Wuhan, Hubei Province 430062, China
| | - Richard A. Dixon
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203, USA
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26
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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] [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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27
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Anders C, Hoengenaert L, Boerjan W. Accelerating wood domestication in forest trees through genome editing: Advances and prospects. CURRENT OPINION IN PLANT BIOLOGY 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] [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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Li W, Sun Y, Li K, Tian H, Jia J, Zhang H, Wang Y, Wang H, Bi B, Guo J, Tran LSP, Miao Y. Sinapate Esters Mediate UV-B-Induced Stomatal Closure by Regulating Nitric Oxide, Hydrogen Peroxide, and Malate Accumulation in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2023; 63:1890-1899. [PMID: 35475535 DOI: 10.1093/pcp/pcac059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 04/11/2022] [Accepted: 04/26/2022] [Indexed: 06/14/2023]
Abstract
Sinapate esters, which are induced in plants under ultraviolet-B (UV-B) irradiation, have important roles not only in the protection against UV-B irradiation but also in the regulation of stomatal closure. Here, we speculated that sinapate esters would function in the stomatal closure of Arabidopsis thaliana in response to UV-B. We measured the stomatal aperture size of the wild-type (WT) and bright trichomes 1 (brt1) and sinapoylglucose accumulator 1 (sng1) mutants under UV-B irradiation; the latter two mutants are deficient in the conversion of sinapic acid to sinapoylglucose (SG) and SG to sinapoylmalate (SM), respectively. Both the brt1 and sng1 plants showed smaller stomatal apertures than the WT under normal light and UV-B irradiation conditions. The accumulation of SM and malate were induced by UV-B irradiation in WT and brt1 plants but not in sng1 plants. Consistently, exogenous malate application reduced UV-B-induced stomatal closure in WT, brt1 and sng1 plants. Nonetheless, levels of reactive oxygen species (ROS), nitric oxide (NO) and cytosolic Ca2+ were higher in guard cells of the sng1 mutant than in those of the WT under normal white light and UV-B irradiation, suggesting that disturbance of sinapate metabolism induced the accumulation of these signaling molecules that promote stomatal closure. Unexpectedly, exogenous sinapic acid application prevented stomatal closure of WT, brt1 and sng1 plants. In summary, we hypothesize that SG or other sinapate esters may promote the UV-B-induced malate accumulation and stomatal closure, whereas sinapic acid inhibits the ROS-NO pathway that regulates UV-B-induced cytosolic Ca2+ accumulation and stomatal closure.
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Affiliation(s)
- Weiqiang Li
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
| | - Yaru Sun
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
| | - Kun Li
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
| | - Hongtao Tian
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
| | - Jiangtao Jia
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
| | - Hongyu Zhang
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
| | - Yaping Wang
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
| | - Hong Wang
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
| | - Baodi Bi
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
| | - Jinggong Guo
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, 03 Quang Trung, Da Nang 550000, Vietnam
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, 1006 Canton Ave, Lubbock, TX 79409, USA
| | - Yuchen Miao
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, No. 85 Jinming Road, Kaifeng 475004, China
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Gu Q, Wei Q, Hu Y, Chen M, Chen Z, Zheng S, Ma Q, Luo Z. Physiological and Full-Length Transcriptome Analyses Reveal the Dwarfing Regulation in Trifoliate Orange ( Poncirus trifoliata L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:271. [PMID: 36678984 PMCID: PMC9860739 DOI: 10.3390/plants12020271] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/01/2023] [Accepted: 01/03/2023] [Indexed: 06/17/2023]
Abstract
Dwarfing rootstocks are capable of high-density planting and are therefore urgently needed in the modern citrus cultivation system. However, little is known about the physiological relevance and molecular basis underlying citrus height. This study aimed to comprehensively analyze phytohormone, carbohydrate, and associated transcriptome changes in the stem of two weak growth rootstocks ('TO' and 'FD') relative to the vigorous 'CC' rootstock. The phenotypic observation revealed that the plant height, plant weight, and internode length were reduced in dwarfing rootstocks. Moreover, the contents of indole-3-acetic acid (IAA), trans-zeatin (tZ), and abscisic acid (ABA), were higher in TO and FD rootstocks, whereas the gibberellin 3 (GA3) content was higher in the CC rootstocks. The carbohydrate contents, including sucrose, fructose, glucose, starch, and lignin significantly decreased in both the TO and FD rootstocks. The full-length transcriptome analysis revealed a potential mechanism regulating dwarfing phenotype that was mainly related to the phytohormone signaling transduction, sugar and starch degradation, lignin synthesis, and cellulose and hemicellulose degradation processes. In addition, many transcription factors (TFs), long non-coding RNAs (lncRNAs), and alternative splicing (AS) events were identified, which might act as important contributors to control the stem elongation and development in the weak growth rootstocks. These findings might deepen the understanding of the complex mechanisms of the stem development responsible for citrus dwarfing and provide a series of candidate genes for the application in breeding new rootstocks with intensive dwarfing.
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Affiliation(s)
- Qingqing Gu
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, China
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qingjiang Wei
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Yongwei Hu
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Mengru Chen
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Ziwen Chen
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Shuang Zheng
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Qiaoli Ma
- College of Agronomy, Jiangxi Agricultural University, Nanchang 330045, China
| | - Zhengrong Luo
- Key Laboratory of Horticultural Plant Biology, Huazhong Agricultural University, Wuhan 430070, China
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Miranda S, Piazza S, Nuzzo F, Li M, Lagrèze J, Mithöfer A, Cestaro A, Tarkowska D, Espley R, Dare A, Malnoy M, Martens S. CRISPR/Cas9 genome-editing applied to MdPGT1 in apple results in reduced foliar phloridzin without impacting plant growth. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:92-105. [PMID: 36401738 DOI: 10.1111/tpj.16036] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 11/05/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Phloridzin is the most abundant polyphenolic compound in apple (Malus × domestica Borkh.), which results from the action of a key phloretin-specific UDP-2'-O-glucosyltransferase (MdPGT1). Here, we simultaneously assessed the effects of targeting MdPGT1 by conventional transgenesis and clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated genome editing. To this end, we conducted transcriptomic and metabolic analyses of MdPGT1 RNA interference knockdown and genome-edited lines. Knockdown lines exhibited characteristic impairment of plant growth and leaf morphology, whereas genome-edited lines exhibited normal growth despite reduced foliar phloridzin. RNA-sequencing analysis identified a common core of regulated genes, involved in phenylpropanoid and flavonoid pathways. However, we identified genes and processes differentially modulated in stunted and genome-edited lines, including key transcription factors and genes involved in phytohormone signalling. Therefore, we conducted a phytohormone profiling to obtain insight into their role in the phenotypes observed. We found that salicylic and jasmonic acid were increased in dwarf lines, whereas auxin and ABA showed no correlation with the growth phenotype. Furthermore, bioactive brassinosteroids were commonly up-regulated, whereas gibberellin GA4 was distinctively altered, showing a sharp decrease in RNA interference knockdown lines. Expression analysis by reverse transcriptase-quantitative polymerase chain reaction expression analysis further confirmed transcriptional regulation of key factors involved in brassinosteroid and gibberellin interaction. These findings suggest that a differential modulation of phytohormones may be involved in the contrasting effects on growth following phloridzin reduction. The present study also illustrates how CRISPR/Cas9 genome editing can be applied to dissect the contribution of genes involved in phloridzin biosynthesis in apple.
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Affiliation(s)
- Simón Miranda
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
- C3A Center Agriculture Food Environment, University of Trento, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
- The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland, 1025, New Zealand
| | - Stefano Piazza
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
| | - Floriana Nuzzo
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
| | - Mingai Li
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
| | - Jorge Lagrèze
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
- C3A Center Agriculture Food Environment, University of Trento, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
| | - Axel Mithöfer
- Research Group Plant Defense Physiology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, Jena, 07745, Germany
| | - Alessandro Cestaro
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
| | - Danuše Tarkowska
- Laboratory of Growth Regulators, Institute of Experimental Botany, The Czech Academy of Sciences and Palacky University, Slechtitelu 19, Olomouc, CZ-783 71, Czech Republic
| | - Richard Espley
- The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland, 1025, New Zealand
| | - Andrew Dare
- The New Zealand Institute for Plant and Food Research Limited, 120 Mt Albert Road, Auckland, 1025, New Zealand
| | - Mickael Malnoy
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
| | - Stefan Martens
- Research and Innovation Centre, Edmund Mach Foundation, Via Edmund Mach 1, San Michele all'Adige, 38098, Italy
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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. THE NEW PHYTOLOGIST 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] [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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Liu A, Yuan K, Li Q, Liu S, Li Y, Tao M, Xu H, Tian J, Guan S, Zhu W. Metabolomics and proteomics revealed the synthesis difference of aroma precursors in tobacco leaves at various growth stages. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 192:308-319. [PMID: 36288661 DOI: 10.1016/j.plaphy.2022.10.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 09/29/2022] [Accepted: 10/13/2022] [Indexed: 06/16/2023]
Abstract
Tobacco has a high economic value as the largest cash crop worldwide. The quality of flue-cured tobacco is closely related to the overall status of compounds in fresh tobacco leaves, and the aroma precursor plays a key role in the aroma quality of flue-cured tobacco. The untargeted metabolomics and label-free quantitative proteomics analysis of tobacco leaves in three growth stages (root stretching, prosperous growth, and maturation) retrieved 243 metabolites and 4313 proteins (944 differentially expressed proteins), which showed that carbohydrate, amino acid, and fatty acid metabolism varies among the three growth stages. Also, the most of amino acids, organic acids, fatty acids, and polyphenols reduced in the vegetative growth stage, while increased in the reproductive growth stage. On the other hand, alkaloids such as nicotine, nornicotine, and anatabine increased continuously in tobacco leaves during the three growth stages. This study helps us understand the growth and development characteristics of Yun87 flue-cured tobacco in the field before harvest, and it provides a certain omics basis for the industrial crop flue-cured tobacco.
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Affiliation(s)
- Amin Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027, PR China
| | - Kailong Yuan
- China Tobacco Zhejiang Industrial Co.,Ltd., Hangzhou, 310008, PR, China
| | - Qi Li
- China Tobacco Zhejiang Industrial Co.,Ltd., Hangzhou, 310008, PR, China
| | - Shengzhi Liu
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027, PR China
| | - Yaohan Li
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027, PR China
| | - Minglei Tao
- College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027, PR China
| | - Haiqing Xu
- Anhui Wannan Tobacco Co., Ltd., Xuancheng, 242000, PR, China
| | - Jingkui Tian
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310002, PR, China
| | - Shishuan Guan
- China Tobacco Shandong Industrial Co., Ltd., Jinan, 250014, PR, China.
| | - Wei Zhu
- The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, 310002, PR, China.
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Wang P, Guo L, Morgan J, Dudareva N, Chapple C. Transcript and metabolite network perturbations in lignin biosynthetic mutants of Arabidopsis. PLANT PHYSIOLOGY 2022; 190:2828-2846. [PMID: 35880844 PMCID: PMC9706439 DOI: 10.1093/plphys/kiac344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/24/2022] [Indexed: 06/01/2023]
Abstract
Lignin, one of the most abundant polymers in plants, is derived from the phenylpropanoid pathway, which also gives rise to an array of metabolites that are essential for plant fitness. Genetic engineering of lignification can cause drastic changes in transcription and metabolite accumulation with or without an accompanying development phenotype. To understand the impact of lignin perturbation, we analyzed transcriptome and metabolite data from the rapidly lignifying stem tissue in 13 selected phenylpropanoid mutants and wild-type Arabidopsis (Arabidopsis thaliana). Our dataset contains 20,974 expressed genes, of which over 26% had altered transcript levels in at least one mutant, and 18 targeted metabolites, all of which displayed altered accumulation in at least one mutant. We found that lignin biosynthesis and phenylalanine supply via the shikimate pathway are tightly co-regulated at the transcriptional level. The hierarchical clustering analysis of differentially expressed genes (DEGs) grouped the 13 mutants into 5 subgroups with similar profiles of mis-regulated genes. Functional analysis of the DEGs in these mutants and correlation between gene expression and metabolite accumulation revealed system-wide effects on transcripts involved in multiple biological processes.
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Affiliation(s)
- Peng Wang
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Longyun Guo
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - John Morgan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
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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 COMMUNICATIONS 2022; 3:100465. [PMID: 36307984 PMCID: PMC9700206 DOI: 10.1016/j.xplc.2022.100465] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [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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Liu J, Zhi L, Zhang N, Zhang W, Meng D, Batool A, Ren X, Ji J, Niu Y, Li R, Li J, Song L. Transcriptomic analysis reveals the contribution of QMrl-7B to wheat root growth and development. FRONTIERS IN PLANT SCIENCE 2022; 13:1062575. [PMID: 36457528 PMCID: PMC9706392 DOI: 10.3389/fpls.2022.1062575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 10/24/2022] [Indexed: 06/17/2023]
Abstract
Roots are the major organs for water and nutrient acquisition and substantially affect plant growth, development and reproduction. Improvements to root system architecture are highly important for the increased yield potential of bread wheat. QMrl-7B, a major stable quantitative trait locus (QTL) that controls maximum root length (MRL), essentially contributes to an improved root system in wheat. To further analyze the biological functions of QMrl-7B in root development, two sets of Triticum aestivum near-isogenic lines (NILs), one with superior QMrl-7B alleles from cultivar Kenong 9204 (KN9204) named NILKN9204 and another with inferior QMrl-7B alleles from cultivar Jing 411 (J411) named NILJ411, were subjected to transcriptomic analysis. Among all the mapped genes analyzed, 4871 genes were identified as being differentially expressed between the pairwise NILs under different nitrogen (N) conditions, with 3543 genes expressed under normal-nitrogen (NN) condition and 2689 genes expressed under low-nitrogen (LN) condition. These genes encode proteins that mainly include N O 3 - transporters, phytohormone signaling components and transcription factors (TFs), indicating the presence of a complex regulatory network involved in root determination. In addition, among the 13524 LN-induced differentially expressed genes (DEGs) detected in this study, 4308 and 2463 were specifically expressed in the NILKN9204 and NILJ411, respectively. These DEGs reflect different responses of the two sets of NILs to varying N supplies, which likely involve LN-induced root growth. These results explain the better-developed root system and increased root vitality conferred by the superior alleles of QMrl-7B and provide a deeper understanding of the genetic underpinnings of root traits, pointing to a valuable locus suitable for future breeding efforts for sustainable agriculture.
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Affiliation(s)
- Jiajia Liu
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- The College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Liya Zhi
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- The College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Na Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Wei Zhang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Deyuan Meng
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- The College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Aamana Batool
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- The College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoli Ren
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- The College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Jun Ji
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
| | - Yanxiao Niu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Ruiqi Li
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
| | - Junming Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
| | - Liqiang Song
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, Hebei, China
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Schneider HM. Functional implications of multiseriate cortical sclerenchyma for soil resource capture and crop improvement. AOB PLANTS 2022; 14:plac050. [PMID: 36545297 PMCID: PMC9762723 DOI: 10.1093/aobpla/plac050] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 10/17/2022] [Indexed: 06/09/2023]
Abstract
Suboptimal nutrient and water availability are primary constraints to crop growth. Global agriculture requires crops with greater nutrient and water efficiency. Multiseriate cortical sclerenchyma (MCS), a root anatomical trait characterized by small cells with thick cell walls encrusted with lignin in the outer cortex, has been shown to be an important trait for adaptation in maize and wheat in mechanically impeded soils. However, MCS has the potential to improve edaphic stress tolerance in a number of different crop taxa and in a number of different environments. This review explores the functional implications of MCS as an adaptive trait for water and nutrient acquisition and discusses future research perspectives on this trait for incorporation into crop breeding programs. For example, MCS may influence water and nutrient uptake, resistance to pests, symbiotic interactions, microbial interactions in the rhizosphere and soil carbon deposition. Root anatomical phenotypes are underutilized; however, important breeding targets for the development of efficient, productive and resilient crops urgently needed in global agriculture.
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Sipari N, Lihavainen J, Keinänen M. Metabolite Profiling of Paraquat Tolerant Arabidopsis thaliana Radical-induced Cell Death1 ( rcd1)-A Mediator of Antioxidant Defence Mechanisms. Antioxidants (Basel) 2022; 11:antiox11102034. [PMID: 36290757 PMCID: PMC9598866 DOI: 10.3390/antiox11102034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/06/2022] [Accepted: 10/13/2022] [Indexed: 11/16/2022] Open
Abstract
RADICAL-INDUCED CELL DEATH1 (RCD1) is an Arabidopsis thaliana nuclear protein that is disrupted during oxidative stress. RCD1 is considered an important integrative node in development and stress responses, and the rcd1 plants have several phenotypes and altered resistance to a variety of abiotic and biotic stresses. One of the phenotypes of rcd1 is resistance to the herbicide paraquat, but the mechanisms behind it are unknown. Paraquat causes a rapid burst of reactive oxygen species (ROS) initially in the chloroplast. We performed multi-platform metabolomic analyses in wild type Col-0 and paraquat resistant rcd1 plants to identify pathways conveying resistance and the function of RCD1 in this respect. Wild type and rcd1 plants were clearly distinguished by their abundance of antioxidants and specialized metabolites and their responses to paraquat. The lack of response in rcd1 suggested constitutively active defense against ROS via elevated flavonoid, glutathione, β-carotene, and tocopherol levels, whereas its ascorbic acid levels were compromised under non-stressed control conditions when compared to Col-0. We propose that RCD1 acts as a hub that maintains basal antioxidant system, and its inactivation induces defense responses by enhancing the biosynthesis and redox cycling of low molecular weight antioxidants and specialized metabolites with profound antioxidant activities alleviating oxidative stress.
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Affiliation(s)
- Nina Sipari
- Viikki Metabolomics Unit, Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, P.O. Box 65, FI-00014 Helsinki, Finland
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
- Correspondence: (N.S.); (M.K.)
| | - Jenna Lihavainen
- Umeå Plant Science Center, Department of Plant Physiology, Umeå Universitet, 90 187 Umeå, Sweden
| | - Markku Keinänen
- Department of Environmental and Biological Sciences, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
- Institute of Photonics, University of Eastern Finland, P.O. Box 111, FI-80101 Joensuu, Finland
- Correspondence: (N.S.); (M.K.)
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Shrestha HK, Fichman Y, Engle NL, Tschaplinski TJ, Mittler R, Dixon RA, Hettich RL, Barros J, Abraham PE. Multi-omic characterization of bifunctional peroxidase 4-coumarate 3-hydroxylase knockdown in Brachypodium distachyon provides insights into lignin modification-associated pleiotropic effects. FRONTIERS IN PLANT SCIENCE 2022; 13:908649. [PMID: 36247563 PMCID: PMC9554711 DOI: 10.3389/fpls.2022.908649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
A bifunctional peroxidase enzyme, 4-coumarate 3-hydroxylase (C3H/APX), provides a parallel route to the shikimate shunt pathway for the conversion of 4-coumarate to caffeate in the early steps of lignin biosynthesis. Knockdown of C3H/APX (C3H/APX-KD) expression has been shown to reduce the lignin content in Brachypodium distachyon. However, like many other lignin-modified plants, C3H/APX-KDs show unpredictable pleiotropic phenotypes, including stunted growth, delayed senescence, and reduced seed yield. A system-wide level understanding of altered biological processes in lignin-modified plants can help pinpoint the lignin-modification associated growth defects to benefit future studies aiming to negate the yield penalty. Here, a multi-omic approach was used to characterize molecular changes resulting from C3H/APX-KD associated lignin modification and negative growth phenotype in Brachypodium distachyon. Our findings demonstrate that C3H/APX knockdown in Brachypodium stems substantially alters the abundance of enzymes implicated in the phenylpropanoid biosynthetic pathway and disrupt cellular redox homeostasis. Moreover, it elicits plant defense responses associated with intracellular kinases and phytohormone-based signaling to facilitate growth-defense trade-offs. A deeper understanding along with potential targets to mitigate the pleiotropic phenotypes identified in this study could aid to increase the economic feasibility of lignocellulosic biofuel production.
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Affiliation(s)
- Him K. Shrestha
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Genome Science and Technology, University of Tennessee-Knoxville, Knoxville, TN, United States
| | - Yosef Fichman
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | | | - Ron Mittler
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Robert L. Hettich
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Jaime Barros
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO, United States
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX, United States
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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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. FRONTIERS IN PLANT SCIENCE 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] [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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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. FRONTIERS IN PLANT SCIENCE 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] [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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Mendes GGM, Mota TR, Bossoni GEB, Marchiosi R, Oliveira DMD, Constantin RP, Dos Santos WD, Ferrarese-Filho O. Inhibiting tricin biosynthesis improves maize lignocellulose saccharification. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 178:12-19. [PMID: 35247693 DOI: 10.1016/j.plaphy.2022.02.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/14/2022] [Accepted: 02/19/2022] [Indexed: 06/14/2023]
Abstract
Lignin is a technological bottleneck to convert polysaccharides into fermentable sugars, and different strategies of genetic-based metabolic engineering have been applied to improve biomass saccharification. Using maize seedlings grown hydroponically for 24 h, we conducted a quick non-transgenic approach with five enzyme inhibitors of the lignin and tricin pathways. Two compounds [3,4-(methylenedioxy)cinnamic acid: MDCA and 2,4-pyridinedicarboxylic acid: PDCA] revealed interesting findings on root growth, lignin composition, and saccharification. By inhibiting hydroxycinnamoyl-CoA ligase, a key enzyme of phenylpropanoid pathway, MDCA decreased the lignin content and improved saccharification, but it decreased root growth. By inhibiting flavone synthase, a key enzyme of tricin biosynthesis, PDCA decreased total lignin content and improved saccharification without affecting root growth. PDCA was three-fold more effective than MDCA, suggesting that controlling lignin biosynthesis with enzymatic inhibitors may be an attractive strategy to improve biomass saccharification.
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Affiliation(s)
| | - Thatiane Rodrigues Mota
- Ghent University, Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent, Belgium
| | | | - Rogério Marchiosi
- Laboratory of Plant Biochemistry, State University of Maringá, Av. Colombo, 5790, 87020-900, Maringá, PR, Brazil
| | - Dyoni Matias de Oliveira
- Ghent University, Department of Plant Biotechnology and Bioinformatics and VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Rodrigo Polimeni Constantin
- Laboratory of Plant Biochemistry, State University of Maringá, Av. Colombo, 5790, 87020-900, Maringá, PR, Brazil
| | - Wanderley Dantas Dos Santos
- Laboratory of Plant Biochemistry, State University of Maringá, Av. Colombo, 5790, 87020-900, Maringá, PR, Brazil
| | - Osvaldo Ferrarese-Filho
- Laboratory of Plant Biochemistry, State University of Maringá, Av. Colombo, 5790, 87020-900, Maringá, PR, Brazil.
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Zhao X, Niu Y, Bai X, Mao T. Transcriptomic and Metabolic Profiling Reveals a Lignin Metabolism Network Involved in Mesocotyl Elongation during Maize Seed Germination. PLANTS 2022; 11:plants11081034. [PMID: 35448762 PMCID: PMC9027596 DOI: 10.3390/plants11081034] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/03/2022] [Accepted: 04/04/2022] [Indexed: 11/18/2022]
Abstract
Lignin is an important factor affecting agricultural traits. The mechanism of lignin metabolism in maize (Zea mays) mesocotyl elongation was investigated during seed germination. Maize seeds were treated with 24-epibrassinolide (EBR) and brassinazole stimulation under 3 and 20 cm deep-seeding stress. Mesocotyl transcriptome sequencing together with targeted metabolomics analysis and physiological measurements were employed in two contrasting genotypes. Our results revealed differentially expressed genes (DEGs) were significantly enriched in phenylpropanoid biosynthesis, plant hormone signal transduction, flavonoid biosynthesis, and alpha-linolenic acid metabolism. There were 153 DEGs for lignin biosynthesis pathway, 70 DEGs for peroxisome pathway, and 325 differentially expressed transcription factors (TFs) of MYB, NAC, WRKY, and LIM were identified in all comparisons, and highly interconnected network maps were generated among multiple TFs (MYB and WRKY) and DEGs for lignin biosynthesis and peroxisome biogenesis. This caused p-coumaraldehyde, p-coumaryl alcohol, and sinapaldehyde down-accumulation,
however, caffeyl aldehyde and caffeyl alcohol up-accumulation. The sum/ratios of H-, S-, and G-lignin monomers was also altered, which decreased total lignin formation and accumulation, resulting in cell wall rigidity decreasing. As a result, a significant elongation of maize mesocotyl was detected under deep-seeding stress and EBR signaling. These findings provide information on the molecular mechanisms controlling maize seedling emergence under deep-seeding stress and will aid in the breeding of deep-seeding maize cultivars.
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Affiliation(s)
- Xiaoqiang Zhao
- Correspondence: (X.Z.); (Y.N.); Tel.: +86-183-9415-8662 (X.Z.); +86-139-1913-0638 (Y.N.)
| | - Yining Niu
- Correspondence: (X.Z.); (Y.N.); Tel.: +86-183-9415-8662 (X.Z.); +86-139-1913-0638 (Y.N.)
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Martínez-Camacho JE, Guevara-González RG, Rico-García E, Tovar-Pérez EG, Torres-Pacheco I. Delayed Senescence and Marketability Index Preservation of Blackberry Fruit by Preharvest Application of Chitosan and Salicylic Acid. FRONTIERS IN PLANT SCIENCE 2022; 13:796393. [PMID: 35310627 PMCID: PMC8931713 DOI: 10.3389/fpls.2022.796393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 01/27/2022] [Indexed: 06/14/2023]
Abstract
Blackberry fruits are appreciated as a source of nutrients and compounds related to benefit human health. However, they are highly perishable and very susceptible to decay factors. Current methods to improve and maintain blackberry quality are limited in use because of the fruit's fragile physical properties. Regarding these properties, it has been reported that the activities of certain enzymes are linked to senescence and fruit softening processes. This study was aimed to assess the effect of salicylic acid (SA) and chitosan (COS) as preharvest treatments on the physiology related to improving fruit conservation and preserving the marketability index of blackberry fruit. The preharvest treatments were foliar sprayed on blackberry plants at different concentrations. The activities of enzymes superoxide dismutase (SOD), catalase (CAT), phenylalanine ammonia-lyase (PAL), and polygalacturonase (PG) were measured. Total soluble solids (TSS), titratable acidity (TA), TSS/TA ratio, and marketability index (MI) were analyzed after 144 h of storage. The application of 3 mM of SA and 0.25% of COS treatments preserved the MI of blackberries by reducing leakage, red drupelet reversion (RDR), and mycelium presence in the fruit. SA application increased SOD, CAT, and PAL activities. Our results also showed that SA and COS preharvest treatments modified the activity of the cell wall degrading enzyme PG, which might play a role in improving the shelf life and resistance to decay factors of blackberry fruit without any significant effects on physicochemical properties like TSS, TA, and the TSS/TA ratio.
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Computational approach in lignin structural models: Influence of non-covalent intramolecular interactions on βO4 bond properties. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2021.131938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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González-Gordo S, Palma JM, Corpas FJ. Peroxisomal Proteome Mining of Sweet Pepper ( Capsicum annuum L.) Fruit Ripening Through Whole Isobaric Tags for Relative and Absolute Quantitation Analysis. FRONTIERS IN PLANT SCIENCE 2022; 13:893376. [PMID: 35615143 PMCID: PMC9125320 DOI: 10.3389/fpls.2022.893376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/21/2022] [Indexed: 05/05/2023]
Abstract
Peroxisomes are ubiquitous organelles from eukaryotic cells characterized by an active nitro-oxidative metabolism. They have a relevant metabolic plasticity depending on the organism, tissue, developmental stage, or physiological/stress/environmental conditions. Our knowledge of peroxisomal metabolism from fruits is very limited but its proteome is even less known. Using sweet pepper (Capsicum annuum L.) fruits at two ripening stages (immature green and ripe red), it was analyzed the proteomic peroxisomal composition by quantitative isobaric tags for relative and absolute quantitation (iTRAQ)-based protein profiling. For this aim, it was accomplished a comparative analysis of the pepper fruit whole proteome obtained by iTRAQ versus the identified peroxisomal protein profile from Arabidopsis thaliana. This allowed identifying 57 peroxisomal proteins. Among these proteins, 49 were located in the peroxisomal matrix, 36 proteins had a peroxisomal targeting signal type 1 (PTS1), 8 had a PTS type 2, 5 lacked this type of peptide signal, and 8 proteins were associated with the membrane of this organelle. Furthermore, 34 proteins showed significant differences during the ripening of the fruits, 19 being overexpressed and 15 repressed. Based on previous biochemical studies using purified peroxisomes from pepper fruits, it could be said that some of the identified peroxisomal proteins were corroborated as part of the pepper fruit antioxidant metabolism (catalase, superoxide dismutase, ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductaseglutathione reductase, 6-phosphogluconate dehydrogenase and NADP-isocitrate dehydrogenase), the β-oxidation pathway (acyl-coenzyme A oxidase, 3-hydroxyacyl-CoA dehydrogenase, enoyl-CoA hydratase), while other identified proteins could be considered "new" or "unexpected" in fruit peroxisomes like urate oxidase (UO), sulfite oxidase (SO), 5-methyltetrahydropteroyltriglutamate-homocysteine methyltransferase (METE1), 12-oxophytodienoate reductase 3 (OPR3) or 4-coumarate-CoA ligase (4CL), which participate in different metabolic pathways such as purine, sulfur, L-methionine, jasmonic acid (JA) or phenylpropanoid metabolisms. In summary, the present data provide new insights into the complex metabolic machinery of peroxisomes in fruit and open new windows of research into the peroxisomal functions during fruit ripening.
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Li L, Garsamo M, Yuan J, Wang X, Lam SH, Varala K, Boavida LC, Zhou Y, Liu X. CAND1 is required for pollen viability in Arabidopsis thaliana-a test of the adaptive exchange hypothesis. FRONTIERS IN PLANT SCIENCE 2022; 13:866086. [PMID: 35968124 PMCID: PMC9366119 DOI: 10.3389/fpls.2022.866086] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/04/2022] [Indexed: 05/11/2023]
Abstract
The dynamic assembly of SKP1•CUL1•F-box protein (SCF) ubiquitin ligases is important for protein ubiquitination and degradation. This process is enabled by CAND1, which exchanges F-box proteins associated with the common CUL1 scaffold, and thereby, recycles the limited CUL1 core and allows diverse F-box proteins to assemble active SCFs. Previous human cell biological and computational studies have led to the adaptive exchange hypothesis, which suggests that the CAND1-mediated exchange confers plasticity on the SCF system, allowing cells to tolerate large variations in F-box protein expression. Here, we tested this hypothesis using Arabidopsis thaliana, a multicellular organism expressing hundreds of F-box protein genes at variable levels in different tissues. The cand1 null mutant in Arabidopsis is viable but produce almost no seeds. Bioinformatic, cell biological, and developmental analyses revealed that the low fertility in the cand1 mutant is associated with cell death in pollen, where the net expression of F-box protein genes is significantly higher than any other Arabidopsis tissue. In addition, we show that the transmission efficiency of the cand1 null allele was reduced through the male but not the female gametophyte. Our results suggest that CAND1 activity is essential in cells or tissues expressing high levels of F-box proteins. This finding is consistent with the proposed adaptive exchange hypothesis, demonstrating the necessity of the evolutionarily conserved CAND1-mediated exchange system in the development of a multicellular organism.
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Affiliation(s)
- Lihong Li
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Melaku Garsamo
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Jing Yuan
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Xiaojin Wang
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Susan H. Lam
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
| | - Kranthi Varala
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, United States
| | - Leonor C. Boavida
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Yun Zhou
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, United States
| | - Xing Liu
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Center for Plant Biology, Purdue University, West Lafayette, IN, United States
- *Correspondence: Xing Liu,
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Yoshida K, Sakamoto S, Mitsuda N. In Planta Cell Wall Engineering: From Mutants to Artificial Cell Walls. PLANT & CELL PHYSIOLOGY 2021; 62:1813-1827. [PMID: 34718770 DOI: 10.1093/pcp/pcab157] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 10/03/2021] [Accepted: 10/26/2021] [Indexed: 06/13/2023]
Abstract
To mitigate the effects of global warming and to preserve the limited fossil fuel resources, an increased exploitation of plant-based materials and fuels is required, which would be one of the most important innovations related to sustainable development. Cell walls account for the majority of plant dry biomass and so is the target of such innovations. In this review, we discuss recent advances in in planta cell wall engineering through genetic manipulations, with a focus on wild-type-based and mutant-based approaches. The long history of using a wild-type-based approach has resulted in the development of many strategies for manipulating lignin, hemicellulose and pectin to decrease cell wall recalcitrance. In addition to enzyme-encoding genes, many transcription factor genes important for changing relevant cell wall characteristics have been identified. Although mutant-based cell wall engineering is relatively new, it has become feasible due to the rapid development of genome-editing technologies and systems biology-related research; we will soon enter an age of designed artificial wood production via complex genetic manipulations of many industrially important trees and crops.
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Affiliation(s)
- Kouki Yoshida
- Technology Center, Taisei Corporation, Nase-cho 344-1, Totsuka-ku, Yokohama, Kanagawa, 245-0051 Japan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566 Japan
- Global Zero Emission Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566 Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566 Japan
- Global Zero Emission Research Center, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8566 Japan
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Paolo D, Locatelli F, Cominelli E, Pirona R, Pozzo S, Graziani G, Ritieni A, De Palma M, Docimo T, Tucci M, Sparvoli F. Towards a Cardoon ( Cynara cardunculus var. altilis)-Based Biorefinery: A Case Study of Improved Cell Cultures via Genetic Modulation of the Phenylpropanoid Pathway. Int J Mol Sci 2021; 22:ijms222111978. [PMID: 34769407 PMCID: PMC8584892 DOI: 10.3390/ijms222111978] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/02/2021] [Accepted: 11/03/2021] [Indexed: 12/13/2022] Open
Abstract
Cultivated cardoon (Cynara cardunculus var. altilis L.) is a promising candidate species for the development of plant cell cultures suitable for large-scale biomass production and recovery of nutraceuticals. We set up a protocol for Agrobacterium tumefaciens-mediated transformation, which can be used for the improvement of cardoon cell cultures in a frame of biorefinery. As high lignin content determines lower saccharification yields for the biomass, we opted for a biotechnological approach, with the purpose of reducing lignin content; we generated transgenic lines overexpressing the Arabidopsis thaliana MYB4 transcription factor, a known repressor of lignin/flavonoid biosynthesis. Here, we report a comprehensive characterization, including metabolic and transcriptomic analyses of AtMYB4 overexpression cardoon lines, in comparison to wild type, underlining favorable traits for their use in biorefinery. Among these, the improved accessibility of the lignocellulosic biomass to degrading enzymes due to depletion of lignin content, the unexpected increased growth rates, and the valuable nutraceutical profiles, in particular for hydroxycinnamic/caffeoylquinic and fatty acids profiles.
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Affiliation(s)
- Dario Paolo
- National Research Council—Institute of Agricultural Biology and Biotechnology (CNR-IBBA), Via Edoardo Bassini 15, 20133 Milano, Italy; (F.L.); (E.C.); (R.P.); (S.P.)
- Correspondence: (D.P.); (F.S.); Tel.: +39-0223699407 (D.P.); +39-0223699435 (F.S.)
| | - Franca Locatelli
- National Research Council—Institute of Agricultural Biology and Biotechnology (CNR-IBBA), Via Edoardo Bassini 15, 20133 Milano, Italy; (F.L.); (E.C.); (R.P.); (S.P.)
| | - Eleonora Cominelli
- National Research Council—Institute of Agricultural Biology and Biotechnology (CNR-IBBA), Via Edoardo Bassini 15, 20133 Milano, Italy; (F.L.); (E.C.); (R.P.); (S.P.)
| | - Raul Pirona
- National Research Council—Institute of Agricultural Biology and Biotechnology (CNR-IBBA), Via Edoardo Bassini 15, 20133 Milano, Italy; (F.L.); (E.C.); (R.P.); (S.P.)
| | - Sara Pozzo
- National Research Council—Institute of Agricultural Biology and Biotechnology (CNR-IBBA), Via Edoardo Bassini 15, 20133 Milano, Italy; (F.L.); (E.C.); (R.P.); (S.P.)
| | - Giulia Graziani
- Department of Pharmacy—University of Naples Federico II (UNINA), Via Domenico Montesano 49, 80131 Naples, Italy; (G.G.); (A.R.)
| | - Alberto Ritieni
- Department of Pharmacy—University of Naples Federico II (UNINA), Via Domenico Montesano 49, 80131 Naples, Italy; (G.G.); (A.R.)
| | - Monica De Palma
- National Research Council—Institute of Bioscience and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy; (M.D.P.); (T.D.); (M.T.)
| | - Teresa Docimo
- National Research Council—Institute of Bioscience and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy; (M.D.P.); (T.D.); (M.T.)
| | - Marina Tucci
- National Research Council—Institute of Bioscience and Bioresources (CNR-IBBR), Via Università 133, 80055 Portici, Italy; (M.D.P.); (T.D.); (M.T.)
| | - Francesca Sparvoli
- National Research Council—Institute of Agricultural Biology and Biotechnology (CNR-IBBA), Via Edoardo Bassini 15, 20133 Milano, Italy; (F.L.); (E.C.); (R.P.); (S.P.)
- Correspondence: (D.P.); (F.S.); Tel.: +39-0223699407 (D.P.); +39-0223699435 (F.S.)
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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. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:752-765. [PMID: 34403547 DOI: 10.1111/tpj.15468] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [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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50
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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 BIOTECHNOLOGY JOURNAL 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] [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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