1
|
Choudhary N, Pucker B. Conserved amino acid residues and gene expression patterns associated with the substrate preferences of the competing enzymes FLS and DFR. PLoS One 2024; 19:e0305837. [PMID: 39196921 PMCID: PMC11356453 DOI: 10.1371/journal.pone.0305837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 06/05/2024] [Indexed: 08/30/2024] Open
Abstract
BACKGROUND Flavonoids, an important class of specialized metabolites, are synthesized from phenylalanine and present in almost all plant species. Different branches of flavonoid biosynthesis lead to products like flavones, flavonols, anthocyanins, and proanthocyanidins. Dihydroflavonols form the branching point towards the production of non-colored flavonols via flavonol synthase (FLS) and colored anthocyanins via dihydroflavonol 4-reductase (DFR). Despite the wealth of publicly accessible data, there remains a gap in understanding the mechanisms that mitigate competition between FLS and DFR for the shared substrate, dihydroflavonols. RESULTS An angiosperm-wide comparison of FLS and DFR sequences revealed the amino acids at positions associated with the substrate specificity in both enzymes. A global analysis of the phylogenetic distribution of these amino acid residues revealed that monocots generally possess FLS with Y132 (FLSY) and DFR with N133 (DFRN). In contrast, dicots generally possess FLSH and DFRN, DFRD, and DFRA. DFRA, which restricts substrate preference to dihydrokaempferol, previously believed to be unique to strawberry species, is found to be more widespread in angiosperms and has evolved independently multiple times. Generally, angiosperm FLS appears to prefer dihydrokaempferol, whereas DFR appears to favor dihydroquercetin or dihydromyricetin. Moreover, in the FLS-DFR competition, the dominance of one over the other is observed, with typically only one gene being expressed at any given time. CONCLUSION This study illustrates how almost mutually exclusive gene expression and substrate-preference determining residues could mitigate competition between FLS and DFR, delineates the evolution of these enzymes, and provides insights into mechanisms directing the metabolic flux of the flavonoid biosynthesis, with potential implications for ornamental plants and molecular breeding strategies.
Collapse
Affiliation(s)
- Nancy Choudhary
- Institute of Plant Biology & BRICS, Plant Biotechnology and Bioinformatics, TU Braunschweig, Braunschweig, Germany
| | - Boas Pucker
- Institute of Plant Biology & BRICS, Plant Biotechnology and Bioinformatics, TU Braunschweig, Braunschweig, Germany
| |
Collapse
|
2
|
Ruan H, Gao L, Fang Z, Lei T, Xing D, Ding Y, Rashid A, Zhuang J, Zhang Q, Gu C, Qian W, Zhang N, Qian T, Li K, Xia T, Wang Y. A flavonoid metabolon: cytochrome b 5 enhances B-ring trihydroxylated flavan-3-ols synthesis in tea plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1793-1814. [PMID: 38461478 DOI: 10.1111/tpj.16710] [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: 12/17/2023] [Revised: 02/02/2024] [Accepted: 02/14/2024] [Indexed: 03/12/2024]
Abstract
Flavan-3-ols are prominent phenolic compounds found abundantly in the young leaves of tea plants. The enzymes involved in flavan-3-ol biosynthesis in tea plants have been extensively investigated. However, the localization and associations of these numerous functional enzymes within cells have been largely neglected. In this study, we aimed to investigate the synthesis of flavan-3-ols in tea plants, particularly focusing on epigallocatechin gallate. Our analysis involving the DESI-MSI method to reveal a distinct distribution pattern of B-ring trihydroxylated flavonoids, primarily concentrated in the outer layer of buds. Subcellular localization showed that CsC4H, CsF3'H, and CsF3'5'H localizes endoplasmic reticulum. Protein-protein interaction studies demonstrated direct associations between CsC4H, CsF3'H, and cytoplasmic enzymes (CHS, CHI, F3H, DFR, FLS, and ANR), highlighting their interactions within the biosynthetic pathway. Notably, CsF3'5'H, the enzyme for B-ring trihydroxylation, did not directly interact with other enzymes. We identified cytochrome b5 isoform C serving as an essential redox partner, ensuring the proper functioning of CsF3'5'H. Our findings suggest the existence of distinct modules governing the synthesis of different B-ring hydroxylation compounds. This study provides valuable insights into the mechanisms underlying flavonoid diversity and efficient synthesis and enhances our understanding of the substantial accumulation of B-ring trihydroxylated flavan-3-ols in tea plants.
Collapse
Affiliation(s)
- Haixiang Ruan
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Liping Gao
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Zhou Fang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Ting Lei
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Dawei Xing
- School of Biological and Environmental Engineering, Chaohu University, Chaohu, Anhui, 238024, China
| | - Yan Ding
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Arif Rashid
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Juhua Zhuang
- College of Tea Science, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Qiang Zhang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Chunyang Gu
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Wei Qian
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Niuniu Zhang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Tao Qian
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Kongqing Li
- College of Humanities and Social Development, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Yunsheng Wang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
| |
Collapse
|
3
|
Dixon RA, Dickinson AJ. A century of studying plant secondary metabolism-From "what?" to "where, how, and why?". PLANT PHYSIOLOGY 2024; 195:48-66. [PMID: 38163637 PMCID: PMC11060662 DOI: 10.1093/plphys/kiad596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/15/2023] [Indexed: 01/03/2024]
Abstract
Over the past century, early advances in understanding the identity of the chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why they are synthesized in the first place. Many small molecules are specific to the plant kingdom and have been termed plant secondary metabolites, despite the fact that they can play primary and essential roles in plant structure, development, and response to the environment. The past 100 yr have witnessed elucidation of the structure, function, localization, and biosynthesis of selected plant secondary metabolites. Nevertheless, many mysteries remain about the vast diversity of chemicals produced by plants and their roles in plant biology. From early work characterizing unpurified plant extracts, to modern integration of 'omics technology to discover genes in metabolite biosynthesis and perception, research in plant (bio)chemistry has produced knowledge with substantial benefits for society, including human medicine and agricultural biotechnology. Here, we review the history of this work and offer suggestions for future areas of exploration. We also highlight some of the recently developed technologies that are leading to ongoing research advances.
Collapse
Affiliation(s)
- Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Alexandra Jazz Dickinson
- Department of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093, USA
| |
Collapse
|
4
|
Maruyama K, Yamada H, Doi M, Ohno S. Identification of two 6'-deoxychalcone 4'-glucosyltransferase genes in dahlia (Dahlia variabilis). PLANTA 2024; 259:114. [PMID: 38587670 DOI: 10.1007/s00425-024-04395-1] [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: 08/07/2023] [Accepted: 03/19/2024] [Indexed: 04/09/2024]
Abstract
MAIN CONCLUSION Two glycosyltransferase genes belonging to UGT88 family were identified to have 6'-deoxychalcone 4'-glucosyltransferase activity in dahlia. 6'-Deoxychalcones (isoliquiritigenin and butein) are important pigments for yellow and orange to red flower color. 6'-Deoxychalcones are glucosylated at the 4'-position in vivo, but the genes encoding 6'-deoxychalcone 4'-glucosyltransferase have not yet been identified. In our previous study, it was indicated that snapdragon (Antirrhinum majus) chalcone 4'-O-glucosyltransferase (Am4'CGT) has isoliquiritigenin 4'-glucosylation activity. Therefore, to identify genes encoding 6'-deoxychalcone 4'-glucosyltransferase in dahlia (Dahlia variabilis), genes expressed in ray florets that shared high homology with Am4'CGT were explored. As a result, c34671_g1_i1 and c35662_g1_i1 were selected as candidate genes for 6'-deoxychalcone 4'-glucosyltransferases in dahlia. We conducted transient co-overexpression of three genes (c34671_g1_i1 or c35662_g1_i1, dahlia aldo-keto reductase1 (DvAKR1) or soybean (Glycine max) chalcone reductase5 (GmCHR5), and chili pepper (Capsicum annuum) MYB transcription factor (CaMYBA)) in Nicotiana benthamiana by agroinfiltration. Transient overexpression of c34671_g1_i1, DvAKR1, and CaMYBA resulted in increase in the accumulation of isoliquiritigenin 4'-glucosides, isoliquiritigenin 4'-O-glucoside, and isoliquiritigenin 4'-O-[6-O-(malonyl)-glucoside]. However, transient overexpression of c35662_g1_i1, DvAKR1, and CaMYBA did not increase accumulation of isoliquiritigenin 4'-glucosides. Using GmCHR5 instead of DvAKR1 showed similar results suggesting that c34671_g1_i1 has isoliquiritigenin 4'-glucosyltransferase activity. In addition, we conducted co-overexpression of four genes (c34671_g1_i1, c35662_g1_i1 or Am4'CGT, DvAKR1 or GmCHR5, CaMYBA, and chalcone 3-hydroxylase from dahlia). Accumulation of butein 4'-O-glucoside and butein 4'-O-[6-O-(malonyl)-glucoside] was detected for c35662_g1_i1, suggesting that c35662_g1_i1 has butein 4'-glucosyltransferase activity. Recombinant enzyme analysis also supported butein 4'-glucosyltransferases activity of c35662_g1_i1. Therefore, our results suggested that both c34671_g1_i1 and c35662_g1_i1 are 6'-deoxychalcone 4'-glucosyltransferases but with different substrate preference.
Collapse
Affiliation(s)
- Kei Maruyama
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Haruka Yamada
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Motoaki Doi
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto, 606-8502, Japan
| | - Sho Ohno
- Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto, 606-8502, Japan.
| |
Collapse
|
5
|
Yang Q, Wang G. Isoflavonoid metabolism in leguminous plants: an update and perspectives. FRONTIERS IN PLANT SCIENCE 2024; 15:1368870. [PMID: 38405585 PMCID: PMC10884283 DOI: 10.3389/fpls.2024.1368870] [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: 01/11/2024] [Accepted: 01/29/2024] [Indexed: 02/27/2024]
Abstract
Isoflavonoids constitute a well-investigated category of phenylpropanoid-derived specialized metabolites primarily found in leguminous plants. They play a crucial role in legume development and interactions with the environment. Isoflavonoids usually function as phytoalexins, acting against pathogenic microbes in nature. Additionally, they serve as signaling molecules in rhizobial symbiosis. Notably, owing to their molecular structure resembling human estrogen, they are recognized as phytoestrogens, imparting positive effects on human health. This review comprehensively outlines recent advancements in research pertaining to isoflavonoid biosynthesis, transcriptional regulation, transport, and physiological functions, with a particular emphasis on soybean plants. Additionally, we pose several questions to encourage exploration into novel contributors to isoflavonoid metabolism and their potential roles in plant-microbe interactions.
Collapse
Affiliation(s)
- Qilin Yang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing, China
| | - Guodong Wang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing, China
| |
Collapse
|
6
|
Clayton EJ, Islam NS, Pannunzio K, Kuflu K, Sirjani R, Kohalmi SE, Dhaubhadel S. Soybean AROGENATE DEHYDRATASES (GmADTs): involvement in the cytosolic isoflavonoid metabolon or trans-organelle continuity? FRONTIERS IN PLANT SCIENCE 2024; 15:1307489. [PMID: 38322824 PMCID: PMC10845154 DOI: 10.3389/fpls.2024.1307489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024]
Abstract
Soybean (Glycine max) produces a class of phenylalanine (Phe) derived specialized metabolites, isoflavonoids. Isoflavonoids are unique to legumes and are involved in defense responses in planta, and they are also necessary for nodule formation with nitrogen-fixing bacteria. Since Phe is a precursor of isoflavonoids, it stands to reason that the synthesis of Phe is coordinated with isoflavonoid production. Two putative AROGENATE DEHYDRATASE (ADT) isoforms were previously co-purified with the soybean isoflavonoid metabolon anchor ISOFLAVONE SYNTHASE2 (GmIFS2), however the GmADT family had not been characterized. Here, we present the identification of the nine member GmADT family. We determined that the GmADTs share sequences required for enzymatic activity and allosteric regulation with other characterized plant ADTs. Furthermore, the GmADTs are differentially expressed, and multiple members have dual substrate specificity, also acting as PREPHENATE DEHYDRATASES. All GmADT isoforms were detected in the stromules of chloroplasts, and they all interact with GmIFS2 in the cytosol. In addition, GmADT12A interacts with multiple other isoflavonoid metabolon members. These data substantiate the involvement of GmADT isoforms in the isoflavonoid metabolon.
Collapse
Affiliation(s)
- Emily J. Clayton
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Nishat S. Islam
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Kelsey Pannunzio
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Kuflom Kuflu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Ramtin Sirjani
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Susanne E. Kohalmi
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| |
Collapse
|
7
|
Kriechbaumer V, Botchway SW. Immunoprecipitation and FRET-FLIM to Determine Metabolons on the Plant ER. Methods Mol Biol 2024; 2772:169-177. [PMID: 38411813 DOI: 10.1007/978-1-0716-3710-4_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Metabolons are protein complexes that contain all the enzymes necessary for a metabolic pathway but also scaffolding proteins. Such a structure allows efficient channeling of intermediate metabolites form one active site to the next and is highly advantageous for labile or toxic intermediates. Here we describe two methods currently used to identify metabolons via protein-protein interaction methodology: immunoprecipitations using GFP-Trap®_A beads to find novel interaction partners and potential metabolon components and FRET-FLIM to test for and quantify protein-protein interactions in planta.
Collapse
Affiliation(s)
- Verena Kriechbaumer
- Endomembrane Structure and Function Research Group, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK.
| | - Stanley W Botchway
- Central Laser Facility, Science and Technology Facilities Council (STFC) Rutherford Appleton Laboratory, Research Complex at Harwell, Didcot, UK
| |
Collapse
|
8
|
Rates ADB, Cesarino I. Pour some sugar on me: The diverse functions of phenylpropanoid glycosylation. JOURNAL OF PLANT PHYSIOLOGY 2023; 291:154138. [PMID: 38006622 DOI: 10.1016/j.jplph.2023.154138] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/06/2023] [Indexed: 11/27/2023]
Abstract
The phenylpropanoid metabolism is the source of a vast array of specialized metabolites that play diverse functions in plant growth and development and contribute to all aspects of plant interactions with their surrounding environment. These compounds protect plants from damaging ultraviolet radiation and reactive oxygen species, provide mechanical support for the plants to stand upright, and mediate plant-plant and plant-microorganism communications. The enormous metabolic diversity of phenylpropanoids is further expanded by chemical modifications known as "decorative reactions", including hydroxylation, methylation, glycosylation, and acylation. Among these modifications, glycosylation is the major driving force of phenylpropanoid structural diversification, also contributing to the expansion of their properties. Phenylpropanoid glycosylation is catalyzed by regioselective uridine diphosphate (UDP)-dependent glycosyltransferases (UGTs), whereas glycosyl hydrolases known as β-glucosidases are the major players in deglycosylation. In this article, we review how the glycosylation process affects key physicochemical properties of phenylpropanoids, such as molecular stability and solubility, as well as metabolite compartmentalization/storage and biological activity/toxicity. We also summarize the recent knowledge on the functional implications of glycosylation of different classes of phenylpropanoid compounds. A balance of glycosylation/deglycosylation might represent an essential molecular mechanism to regulate phenylpropanoid homeostasis, allowing plants to dynamically respond to diverse environmental signals.
Collapse
Affiliation(s)
- Arthur de Barros Rates
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brazil
| | - Igor Cesarino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brazil; Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues 370, 05508-020, São Paulo, Brazil.
| |
Collapse
|
9
|
Yao L, Wu X, Jiang X, Shan M, Zhang Z, Li Y, Yang A, Li Y, Yang C. Subcellular compartmentalization in the biosynthesis and engineering of plant natural products. Biotechnol Adv 2023; 69:108258. [PMID: 37722606 DOI: 10.1016/j.biotechadv.2023.108258] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Plant natural products (PNPs) are specialized metabolites with diverse bioactivities. They are extensively used in the pharmaceutical, cosmeceutical and food industries. PNPs are synthesized in plant cells by enzymes that are distributed in different subcellular compartments with unique microenvironments, such as ions, co-factors and substrates. Plant metabolic engineering is an emerging and promising approach for the sustainable production of PNPs, for which the knowledge of the subcellular compartmentalization of their biosynthesis is instrumental. In this review we describe the state of the art on the role of subcellular compartments in the biosynthesis of major types of PNPs, including terpenoids, phenylpropanoids, alkaloids and glucosinolates, and highlight the efforts to target biosynthetic pathways to subcellular compartments in plants. In addition, we will discuss the challenges and strategies in the field of plant synthetic biology and subcellular engineering. We expect that newly developed methods and tools, together with the knowledge gained from the microbial chassis, will greatly advance plant metabolic engineering.
Collapse
Affiliation(s)
- Lu Yao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Xiuming Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Xun Jiang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Muhammad Shan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Zhuoxiang Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Yiting Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Aiguo Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Changqing Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China.
| |
Collapse
|
10
|
Xia Y, Su Q, Li X, Yan S, Liu J, He C, Huang H, Jiang W, Pang Y. Two CYP93A enzymes play a dual role in isoflavonoid biosynthesis in Glycine max L. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108073. [PMID: 37839274 DOI: 10.1016/j.plaphy.2023.108073] [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: 03/26/2023] [Revised: 09/08/2023] [Accepted: 09/29/2023] [Indexed: 10/17/2023]
Abstract
Glycine max L. is rich in isoflavonoids with diverse biological activities. However, isoflavonoid biosynthetic pathway is not fully elucidated in soybean. In the present study, we investigated characteristics of all the thirteen CYP93 subfamily members, and found GmCYP93A1, GmCYP93A2, and GmCYP93A3 are closely clustered, preferentially expressed in roots, and highly inducible by elicitor. When expressed in yeast, GmCYP93A1 was active towards liquiritigenin, naringenin, and 3,9-dihydroxyptercarpan, GmCYP93A2 towards 3,9-dihydroxyptercarpan with strict substrate specificity, whereas GmCYP93A3 did not show any activity towards all the tested substrates. Both GmCYP93A1 and GmCYP93A2 could catalyze 3,9-dihydroxyptercarpan into daidzein and glycinol, with both hydroxylation and aryl migration activity. Site-directed mutagenesis assays revealed that mutation in Thr446 to Ser446 in heme-binding domain increased the enzyme activity of GmCYP93A1 towards 3,9-dihydroxyptercarpan, which highlights its key amino acid residues as shown with its molecular docking with 3,9-dihydroxyptercarpan and HEM. Overexpression of GmCYP93A1 and GmCYP93A2 in the soybean hairy roots reduced the content of daidzein, whereas knockdown of these two genes increased genistein content, indicating changes in expression level of GmCYP93A1 and GmCYP93A2 altered isoflavonoid flux in soybean. Our studies on the activity of GmCYP93A1 and GmCYP93A2 enriched diverse functions of CYP93 subfamily in soybean isoflavonoid pathway, which is valuable for further understanding and bioengineering of isoflavonoid pathway in soybean.
Collapse
Affiliation(s)
- Yaying Xia
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Qian Su
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xue Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Su Yan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Jinyue Liu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Chunfeng He
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Haijun Huang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Wenbo Jiang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yongzhen Pang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| |
Collapse
|
11
|
Wu Y, Liu C, Koganitsky A, Gong FL, Li S. Discovering Dynamic Plant Enzyme Complexes in Yeast for Kratom Alkaloid Pathway Identification. Angew Chem Int Ed Engl 2023; 62:e202307995. [PMID: 37549372 PMCID: PMC10530425 DOI: 10.1002/anie.202307995] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 07/24/2023] [Accepted: 08/07/2023] [Indexed: 08/09/2023]
Abstract
Discovering natural product biosynthetic pathways of medicinal plants is challenging and laborious. Capturing the coregulation patterns of pathway enzymes, particularly transcriptomic regulation, has proven an effective method to accelerate pathway identification. In this study, we developed a yeast-based screening method to capture the protein-protein interactions (PPI) between plant enzymes, which is another useful pattern to complement the prevalent approach. Combining this method with plant multiomics analysis, we discovered four enzyme complexes and their organized pathways from kratom, an alkaloid-producing plant. The four pathway branches involved six enzymes, including a strictosidine synthase, a strictosidine β-D-glucosidase (MsSGD), and four medium-chain dehydrogenase/reductases (MsMDRs). PPI screening selected six MsMDRs interacting with MsSGD from 20 candidates predicted by multiomics analysis. Four of the six MsMDRs were then characterized as functional, indicating the high selectivity of the PPI screening method. This study highlights the opportunity of leveraging post-translational regulation features to discover novel plant natural product biosynthetic pathways.
Collapse
Affiliation(s)
- Yinan Wu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Chang Liu
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Anna Koganitsky
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Franklin L Gong
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| | - Sijin Li
- Robert F. Smith School of Chemical and Biomolecular Engineering, Cornell University, 14853, Ithaca, NY, USA
| |
Collapse
|
12
|
Wolf-Saxon ER, Moorman CC, Castro A, Ruiz A, Mallari JP, Burke JR. Regulatory ligand binding in plant chalcone isomerase-like (CHIL) proteins. J Biol Chem 2023:104804. [PMID: 37172720 DOI: 10.1016/j.jbc.2023.104804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 04/19/2023] [Accepted: 04/29/2023] [Indexed: 05/15/2023] Open
Abstract
Chalcone isomerase-like (CHIL) is a noncatalytic protein that enhances flavonoid content in green plants by serving as a metabolite binder and a rectifier of chalcone synthase (CHS). Rectification of CHS catalysis occurs through direct protein-protein interactions between CHIL and CHS, which alter CHS kinetics and product profiles, favoring naringenin chalcone production. These discoveries raise questions about how CHIL proteins interact structurally with metabolites and how CHIL-ligand interactions affect interactions with CHS. Using differential scanning fluorimetry (DSF) on a CHIL protein from Vitis Vinifera (VvCHIL), we report positive thermostability effects are induced by the binding of naringenin chalcone and negative thermostability effects are induced by the binding of naringenin. Naringenin chalcone further causes positive changes to CHIL-CHS binding, while naringenin causes negative changes to CHIL-CHS binding. These results suggest that CHILs may act as sensors for ligand-mediated pathway feedback by influencing CHS function. The protein X-ray crystal structure of VvCHIL compared with the protein X-ray crystal structure of a CHIL from Physcomitrella patens, reveals key amino acid differences at a ligand binding site of VvCHIL that can be substituted to nullify the destabilizing effect caused by naringenin. Together these results support a role for CHIL proteins as metabolite sensors that modulate the committed step of the flavonoid pathway.
Collapse
Affiliation(s)
- Emma R Wolf-Saxon
- Department of Chemistry and Biochemistry, California State University San Bernardino, San Bernardino, California 92407, USA
| | - Chad C Moorman
- Department of Chemistry and Biochemistry, California State University San Bernardino, San Bernardino, California 92407, USA
| | - Anthony Castro
- Department of Chemistry and Biochemistry, California State University San Bernardino, San Bernardino, California 92407, USA
| | - Alfredo Ruiz
- Department of Chemistry and Biochemistry, California State University San Bernardino, San Bernardino, California 92407, USA
| | - Jeremy P Mallari
- Department of Chemistry and Biochemistry, California State University San Bernardino, San Bernardino, California 92407, USA
| | - Jason R Burke
- Department of Chemistry and Biochemistry, California State University San Bernardino, San Bernardino, California 92407, USA.
| |
Collapse
|
13
|
Yu B, Gao P, Song J, Yang H, Qin L, Yu X, Song H, Coulson J, Bekkaoui Y, Akhov L, Han X, Cram D, Wei Y, Zaharia LI, Zou J, Konkin D, Quilichini TD, Fobert P, Patterson N, Datla R, Xiang D. Spatiotemporal transcriptomics and metabolic profiling provide insights into gene regulatory networks during lentil seed development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 36965062 DOI: 10.1111/tpj.16205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 06/18/2023]
Abstract
Lentil (Lens culinaris Medik.) is a nutritious legume with seeds rich in protein, minerals and an array of diverse specialized metabolites. The formation of a seed requires regulation and tight coordination of developmental programs to form the embryo, endosperm and seed coat compartments, which determines the structure and composition of mature seed and thus its end-use quality. Understanding the molecular and cellular events and metabolic processes of seed development is essential for improving lentil yield and seed nutritional value. However, such information remains largely unknown, especially at the seed compartment level. In this study, we generated high-resolution spatiotemporal gene expression profiles in lentil embryo, seed coat and whole seeds from fertilization through maturation. Apart from anatomic differences between the embryo and seed coat, comparative transcriptomics and weighted gene co-expression network analysis revealed embryo- and seed coat-specific genes and gene modules predominant in specific tissues and stages, which highlights distinct genetic programming. Furthermore, we investigated the dynamic profiles of flavonoid, isoflavone, phytic acid and saponin in seed compartments across seed development. Coupled with transcriptome data, we identified sets of candidate genes involved in the biosynthesis of these metabolites. The global view of the transcriptional and metabolic changes of lentil seed tissues throughout development provides a valuable resource for dissecting the genetic control of secondary metabolism and development of molecular tools for improving seed nutritional quality.
Collapse
Affiliation(s)
- Bianyun Yu
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Peng Gao
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK, S7N 0X2, Canada
| | - Jingpu Song
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Hui Yang
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Li Qin
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Xiaoyu Yu
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Halim Song
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Justin Coulson
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Yasmina Bekkaoui
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Leonid Akhov
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Xiumei Han
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Dustin Cram
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Yangdou Wei
- College of Art & Science, University of Saskatchewan, 9 Campus Drive, Saskatoon, SK, S7N 5A5, Canada
| | - L Irina Zaharia
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Jitao Zou
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - David Konkin
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Teagen D Quilichini
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Pierre Fobert
- Aquatic and Crop Resource Development, National Research Council Canada, Ottawa, Ontario, K1A 0R6, Canada
| | - Nii Patterson
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| | - Raju Datla
- Global Institute for Food Security, University of Saskatchewan, Saskatoon, SK, S7N 4L8, Canada
| | - Daoquan Xiang
- Aquatic and Crop Resource Development, National Research Council Canada, Saskatoon, Saskatchewan, S7N 0W9, Canada
| |
Collapse
|
14
|
Yu K, Song Y, Lin J, Dixon RA. The complexities of proanthocyanidin biosynthesis and its regulation in plants. PLANT COMMUNICATIONS 2023; 4:100498. [PMID: 36435967 PMCID: PMC10030370 DOI: 10.1016/j.xplc.2022.100498] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/07/2022] [Accepted: 11/23/2022] [Indexed: 05/04/2023]
Abstract
Proanthocyanidins (PAs) are natural flavan-3-ol polymers that contribute protection to plants under biotic and abiotic stress, benefits to human health, and bitterness and astringency to food products. They are also potential targets for carbon sequestration for climate mitigation. In recent years, from model species to commercial crops, research has moved closer to elucidating the flux control and channeling, subunit biosynthesis and polymerization, transport mechanisms, and regulatory networks involved in plant PA metabolism. This review extends the conventional understanding with recent findings that provide new insights to address lingering questions and focus strategies for manipulating PA traits in plants.
Collapse
Affiliation(s)
- Keji Yu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Yushuang Song
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jinxing Lin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
| |
Collapse
|
15
|
Suntichaikamolkul N, Akashi T, Mahalapbutr P, Sanachai K, Rungrotmongkol T, Bassard JE, Schaller H, De-Eknamkul W, Vimolmangkang S, Yamazaki M, Sirikantaramas S. Daidzein Hydroxylation by CYP81E63 Is Involved in the Biosynthesis of Miroestrol in Pueraria mirifica. PLANT & CELL PHYSIOLOGY 2023; 64:64-79. [PMID: 36218384 DOI: 10.1093/pcp/pcac140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
White Kwao Krua (Pueraria candollei var. mirifica), a Thai medicinal plant, is a rich source of phytoestrogens, especially isoflavonoids and chromenes. These phytoestrogens are well known; however, their biosynthetic genes remain largely uncharacterized. Cytochrome P450 (P450) is a large protein family that plays a crucial role in the biosynthesis of various compounds in plants, including phytoestrogens. Thus, we focused on P450s involved in the isoflavone hydroxylation that potentially participates in the biosynthesis of miroestrol. Three candidate P450s were isolated from the transcriptome libraries by considering the phylogenetic and expression data of each tissue of P. mirifica. The candidate P450s were functionally characterized both in vitro and in planta. Accordingly, the yeast microsome harboring PmCYP81E63 regiospecifically exhibited either 2' or 3' daidzein hydroxylation and genistein hydroxylation. Based on in silico calculation, PmCYP81E63 had higher binding energy with daidzein than with genistein, which supported the in vitro result of the isoflavone specificity. To confirm in planta function, the candidate P450s were then transiently co-expressed with isoflavone-related genes in Nicotiana benthamiana. Despite no daidzein in the infiltrated N. benthamiana leaves, genistein and hydroxygenistein biosynthesis were detectable by liquid Chromatography with tandem mass spectrometry (LC-MS/MS). Additionally, we demonstrated that PmCYP81E63 interacted with several enzymes related to isoflavone biosynthesis using bimolecular fluorescence complementation studies and a yeast two-hybrid analysis, suggesting a scheme of metabolon formation in the pathway. Our findings provide compelling evidence regarding the involvement of PmCYP81E63 in the early step of the proposed miroestrol biosynthesis in P. mirifica.
Collapse
Affiliation(s)
- Nithiwat Suntichaikamolkul
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
| | - Tomoyoshi Akashi
- Department of Applied Biological Sciences, College of Bioresource Sciences, Nihon University, 1866 Kameino, Fujisawa, Kanagawa 252-0880, Japan
| | - Panupong Mahalapbutr
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, 123 Muang District, Khon Kaen 40002, Thailand
| | - Kamonpan Sanachai
- Department of Biochemistry, Faculty of Science, Khon Kaen University, 123 Muang District, Khon Kaen 40002, Thailand
| | - Thanyada Rungrotmongkol
- Center of Excellence in Biocatalyst and Sustainable Biotechnology, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
| | - Jean-Etienne Bassard
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, Strasbourg 67084, France
| | - Hubert Schaller
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, Strasbourg 67084, France
| | - Wanchai De-Eknamkul
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
| | - Sornkanok Vimolmangkang
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
- Center of Excellence in Plant-Produced Pharmaceuticals, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
| | - Mami Yamazaki
- Laboratory of Molecular Biology and Biotechnology, Graduate School of Pharmaceutical Science, Chiba University, 1-8-1 Inohana, Chuo-ku, Chiba 260-8675, Japan
- Plant Molecular Science Center, Chiba University, 1-8-1 Inohana, Chuo-ku Chiba 260-8675, Japan
| | - Supaart Sirikantaramas
- Center of Excellence in Molecular Crop, Department of Biochemistry, Faculty of Science, Chulalongkorn University, 254 Pathumwan, Bangkok 10330, Thailand
| |
Collapse
|
16
|
Du H, Fang C, Li Y, Kong F, Liu B. Understandings and future challenges in soybean functional genomics and molecular breeding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:468-495. [PMID: 36511121 DOI: 10.1111/jipb.13433] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
Soybean (Glycine max) is a major source of plant protein and oil. Soybean breeding has benefited from advances in functional genomics. In particular, the release of soybean reference genomes has advanced our understanding of soybean adaptation to soil nutrient deficiencies, the molecular mechanism of symbiotic nitrogen (N) fixation, biotic and abiotic stress tolerance, and the roles of flowering time in regional adaptation, plant architecture, and seed yield and quality. Nevertheless, many challenges remain for soybean functional genomics and molecular breeding, mainly related to improving grain yield through high-density planting, maize-soybean intercropping, taking advantage of wild resources, utilization of heterosis, genomic prediction and selection breeding, and precise breeding through genome editing. This review summarizes the current progress in soybean functional genomics and directs future challenges for molecular breeding of soybean.
Collapse
Affiliation(s)
- Haiping Du
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Yaru Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| |
Collapse
|
17
|
Lin J, Monsalvo I, Ly M, Jahan MA, Wi D, Martirosyan I, Kovinich N. RNA-Seq Dissects Incomplete Activation of Phytoalexin Biosynthesis by the Soybean Transcription Factors GmMYB29A2 and GmNAC42-1. PLANTS (BASEL, SWITZERLAND) 2023; 12:545. [PMID: 36771629 PMCID: PMC9921300 DOI: 10.3390/plants12030545] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Glyceollins, isoflavonoid-derived antimicrobial metabolites, are the major phytoalexins in soybean (Glycine max). They play essential roles in providing resistance to the soil-borne pathogen Phytophthora sojae and have unconventional anticancer and neuroprotective activities that render them desirable for pharmaceutical development. Our previous studies revealed that the transcription factors GmMYB29A2 and GmNAC42-1 have essential roles in activating glyceollin biosynthesis, yet each cannot activate the transcription of all biosynthesis genes in the absence of a pathogen elicitor treatment. Here, we report that co-overexpressing both transcription factors is also insufficient to activate glyceollin biosynthesis. To understand this insufficiency, we compared the transcriptome profiles of hairy roots overexpressing each transcription factor with glyceollin-synthesizing roots treated with wall glucan elicitor (WGE) from P. sojae. GmMYB29A2 upregulated most of the WGE-regulated genes that encode enzymatic steps spanning from primary metabolism to the last step of glyceollin biosynthesis. By contrast, GmNAC42-1 upregulated glyceollin biosynthesis genes only when overexpressed in the presence of WGE treatment. This is consistent with our recent discovery that, in the absence of WGE, GmNAC42-1 is bound by GmJAZ1 proteins that inhibit its transactivation activity. WGE, and not GmMYB29A2 or GmNAC42-1, upregulated the heat shock family gene GmHSF6-1, the homolog of Arabidopsis HSFB2a that directly activated the transcription of several glyceollin biosynthesis genes. Our results provide important insights into what biosynthesis genes will need to be upregulated to activate the entire glyceollin biosynthetic pathway.
Collapse
Affiliation(s)
- Jie Lin
- Department of Biology, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
| | - Ivan Monsalvo
- Department of Biology, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
| | - Melissa Ly
- Department of Biology, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
| | - Md Asraful Jahan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Dasol Wi
- Department of Biology, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
| | - Izabella Martirosyan
- Department of Biology, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
| | - Nik Kovinich
- Department of Biology, Faculty of Science, York University, Toronto, ON M3J 1P3, Canada
| |
Collapse
|
18
|
New dual functional CYP450 gene involves in isoflavone biosynthesis in Glycine max L. Synth Syst Biotechnol 2023; 8:157-167. [PMID: 36714060 PMCID: PMC9860299 DOI: 10.1016/j.synbio.2023.01.002] [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: 08/17/2022] [Revised: 01/02/2023] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Glycine max L. accumulates a large amount of isoflavonoid compounds, which is beneficial for plant defense, plant-microbe symbiotic interactions, and human health. Several CYP450 subfamily genes are involved in the flavonoid biosynthetic pathway in plants. In the present study, we found 24 CYP82 subfamily genes were differentially expressed in various tissues of soybean, in Phytophthora sojae-infected soybean varieties and in soybean hairy roots treated with cell wall glucan elicitor. Six of them (GmCYP82A2, GmCYP82A3, GmCYP82A4, GmCYP82A23, GmCYP82C20 and GmCYP82D26) were co-expressed with other known isoflavonoid pathway genes in soybean. Their enzymatic activity in yeast feeding assays showed that only GmCYP82D26 was able to convert naringenin to daidzein with both aryl migration and dehydration function. When GmCYP82D26 was over-expressed in soybean hairy roots, the contents of the two major isoflavonoid aglycones in soybean (daidzein and genistein) were reduced, but total flavonoids were not affected. When GmCYP82D26 was suppressed by RNAi in the hairy roots, daidzein content was decreased but genistein content was increased, with unchanged total flavonoid content. GmCYP82D26 was found to be localized in the endoplasmic reticulum at subcellular level when transiently expressed in tobacco leaf epidermis. GmCYP82D26 gene was preferentially expressed in roots, with low expression level in other tissues in soybean. Homology modeling and molecular docking showed that GmCYP82D26 could form hydrogen bond with both HEM and naringenin at C5-OH and C4 carbonyl. All these results indicated that GmCYP82D26 possesses new and dual enzymatic activity, which bridges the two branches (daidzein and genistein branch) of isoflavonoid pathway in soybean.
Collapse
|
19
|
Khatri P, Chen L, Rajcan I, Dhaubhadel S. Functional characterization of Cinnamate 4-hydroxylase gene family in soybean (Glycine max). PLoS One 2023; 18:e0285698. [PMID: 37186600 PMCID: PMC10184913 DOI: 10.1371/journal.pone.0285698] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/28/2023] [Indexed: 05/17/2023] Open
Abstract
Cinnamate 4-hydroxylase (C4H) is the first key cytochrome P450 monooxygenase (P450) enzyme in the phenylpropanoid pathway. It belongs to the CYP73 family of P450 superfamily, and catalyzes the conversion of trans-cinnamic acid to p-coumaric acid. Since p-coumaric acid serves as the precursor for the synthesis of a wide variety of metabolites involved in plant development and stress resistance, alteration in the expression of soybean C4H genes is expected to affect the downstream metabolite levels, and its ability to respond to stress. In this study, we identified four C4H genes in the soybean genome that are distributed into both class I and class II CYP73 family. GmC4H2, GmC4H14 and GmC4H20 displayed tissue- and developmental stage-specific gene expression patterns with their transcript accumulation at the highest level in root tissues. GmC4H10 appears to be a pseudogene as its transcript was not detected in any soybean tissues. Furthermore, protein homology modelling revealed substrate docking only for GmC4H2, GmC4H14 and GmC4H20. To demonstrate the function of GmC4Hs, we modified a cloning vector for the heterologous expression of P450s in yeast, and used it for microsomal protein production and enzyme assay. Our results confirmed that GmC4H2, GmC4H14 and GmC4H20 contain the ability to hydroxylate trans-cinnamic acid with varying efficiencies.
Collapse
Affiliation(s)
- Praveen Khatri
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Ling Chen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| |
Collapse
|
20
|
Islam NS, Duwadi K, Chen L, Pajak A, McDowell T, Marsolais F, Dhaubhadel S. Global analysis of common bean multidrug and toxic compound extrusion transporters (PvMATEs): PvMATE8 and pinto bean seed coat darkening. FRONTIERS IN PLANT SCIENCE 2022; 13:1046597. [PMID: 36438155 PMCID: PMC9686396 DOI: 10.3389/fpls.2022.1046597] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
In common bean (Phaseolus vulgaris L.), postharvest seed coat darkening is an undesirable trait that affects crop value. The increased accumulation of proanthocyanidins (PAs) in the seed coat results in darker seeds in many market classes of colored beans after harvest. The precursors of PAs are synthesized in the cytoplasm, and subsequently get glycosylated and then transported to the vacuoles where polymerization occurs. Thus, vacuolar transporters play an important role in the accumulation of PAs. Here, we report that common bean genome contains 59 multidrug and toxic compound extrusion genes (PvMATEs). Phylogenetic analysis of putative PvMATEs with functionally characterized MATEs from other plant species categorized them into substrate-specific clades. Our data demonstrate that a vacuolar transporter PvMATE8 is expressed at a higher level in the pinto bean cultivar CDC Pintium (regular darkening) compared to 1533-15 (slow darkening). PvMATE8 localizes in the vacuolar membrane and rescues the PA deficient (tt12) mutant phenotype in Arabidopsis thaliana. Analysis of PA monomers in transgenic seeds together with wild-type and mutants suggests a possible feedback regulation of PA biosynthesis and accumulation. Identification of PvMATE8 will help better understand the mechanism of PA accumulation in common bean.
Collapse
Affiliation(s)
- Nishat S. Islam
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Kishor Duwadi
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Ling Chen
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Aga Pajak
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Tim McDowell
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Frédéric Marsolais
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| |
Collapse
|
21
|
Tang D, Shen Y, Li F, Yue R, Duan J, Ye Z, Lin Y, Zhou W, Yang Y, Chen L, Wang H, Zhao J, Li P. Integrating metabolite and transcriptome analysis revealed the different mechanisms of characteristic compound biosynthesis and transcriptional regulation in tea flowers. FRONTIERS IN PLANT SCIENCE 2022; 13:1016692. [PMID: 36247612 PMCID: PMC9557745 DOI: 10.3389/fpls.2022.1016692] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
The flowers of tea plants (Camellia sinensis), as well as tea leaves, contain abundant secondary metabolites and are big potential resources for the extraction of bioactive compounds or preparation of functional foods. However, little is known about the biosynthesis and transcriptional regulation mechanisms of those metabolites in tea flowers, such as terpenoid, flavonol, catechins, caffeine, and theanine. This study finely integrated target and nontarget metabolism analyses to explore the metabolic feature of developing tea flowers. Tea flowers accumulated more abundant terpenoid compounds than young leaves. The transcriptome data of developing flowers and leaves showed that a higher expression level of later genes of terpenoid biosynthesis pathway, such as Terpene synthases gene family, in tea flowers was the candidate reason of the more abundant terpenoid compounds than in tea leaves. Differently, even though flavonol and catechin profiling between tea flowers and leaves was similar, the gene family members of flavonoid biosynthesis were selectively expressed by tea flowers and tea leaves. Transcriptome and phylogenetic analyses indicated that the regulatory mechanism of flavonol biosynthesis was perhaps different between tea flowers and leaves. However, the regulatory mechanism of catechin biosynthesis was perhaps similar between tea flowers and leaves. This study not only provides a global vision of metabolism and transcriptome in tea flowers but also uncovered the different mechanisms of biosynthesis and transcriptional regulation of those important compounds.
Collapse
Affiliation(s)
- Dingkun Tang
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yihua Shen
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Fangdong Li
- College of Science, Anhui Agricultural University, Hefei, China
| | - Rui Yue
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Jianwei Duan
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Zhili Ye
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Ying Lin
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Wei Zhou
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Yilin Yang
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Lixiao Chen
- Municipal Research Institute for Processing of Agricultural and Featured Products, Shiyan Academy of Agricultural Science, Shiyan, China
| | - Hongyan Wang
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Jian Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| | - Penghui Li
- State Key Laboratory of Tea Plant Biology and Utilization, College of Tea and Food Science and Technology, Anhui Agricultural University, Hefei, China
| |
Collapse
|
22
|
Gong FL, Han J, Li S. MULTI-SCULPT: Multiplex Integration via Selective, CRISPR-Mediated, Ultralong Pathway Transformation in Yeast for Plant Natural Product Synthesis. ACS Synth Biol 2022; 11:2484-2495. [PMID: 35737816 DOI: 10.1021/acssynbio.2c00135] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Yeast has been a versatile model host for complex and valuable natural product biosynthesis via the reconstruction of heterologous biosynthetic pathways. Recent advances in natural product pathway elucidation have uncovered many large and complicated plant pathways that contain 10-30 genes for the biosynthesis of structurally complex, valuable natural products. However, the ability to reconstruct ultralong pathways efficiently in yeast does not match the increasing demand for valuable plant natural product biomanufacturing. Here, we developed a one-pot, multigene pathway integration method in yeast, named MULTI-SCULPT for multiplex integration via selective, CRISPR-mediated, ultralong pathway transformation. Leveraging multilocus genomic disruption via CRISPR/Cas9, newly developed native and synthetic genetic parts, and fine-tuned gene integration and characterization methods, we managed to integrate 21 DNA inserts that contain a 12-gene plant isoflavone biosynthetic pathway into yeast with a 90-100% success rate in 12 days. This method enables fast and efficient ultralong biosynthetic pathway integration and can allow for the fast iterative integration of even longer pathways in the future. Ultimately, this method will accelerate combinatorial optimization of elucidated plant natural product pathways and accelerate putative pathway characterization heterologously.
Collapse
Affiliation(s)
- Franklin Leyang Gong
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Jianing Han
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| | - Sijin Li
- Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, United States
| |
Collapse
|
23
|
Qu Y, Guan R, Yu L, Berkowitz O, David R, Whelan J, Ford M, Wege S, Qiu L, Gilliham M. Enhanced reactive oxygen detoxification occurs in salt-stressed soybean roots expressing GmSALT3. PHYSIOLOGIA PLANTARUM 2022; 174:e13709. [PMID: 35580210 PMCID: PMC9327525 DOI: 10.1111/ppl.13709] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
Soybean (Glycine max) is an important crop globally for food and edible oil production. Soybean plants are sensitive to salinity (NaCl), with significant yield decreases reported under saline conditions. GmSALT3 is the dominant gene underlying a major QTL for salt tolerance in soybean. GmSALT3 encodes a transmembrane protein belonging to the plant cation/proton exchanger (CHX) family, and is predominately expressed in root phloem and xylem associated cells under both saline and non-saline conditions. It is currently unknown through which molecular mechanism(s) the ER-localised GmSALT3 contributes to salinity tolerance, as its localisation excludes direct involvement in ion exclusion. In order to gain insights into potential molecular mechanism(s), we used RNA-seq analysis of roots from two soybean NILs (near isogenic lines); NIL-S (salt-sensitive, Gmsalt3), and NIL-T (salt-tolerant, GmSALT3), grown under control and saline conditions (200 mM NaCl) at three time points (0 h, 6 h, and 3 days). Gene ontology (GO) analysis showed that NIL-T has greater responses aligned to oxidation reduction. ROS were less abundant and scavenging enzyme activity was greater in NIL-T, consistent with the RNA-seq data. Further analysis indicated that genes related to calcium signalling, vesicle trafficking and Casparian strip (CS) development were upregulated in NIL-T following salt treatment. We propose that GmSALT3 improves the ability of NIL-T to cope with saline stress through preventing ROS overaccumulation in roots, and potentially modulating Ca2+ signalling, vesicle trafficking and formation of diffusion barriers.
Collapse
Affiliation(s)
- Yue Qu
- ARC Centre of Excellence in Plant Energy BiologyWaite Research Institute & School of Agriculture, Food and Wine, University of AdelaideGlen OsmondSouth AustraliaAustralia
| | - Rongxia Guan
- The National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop Science, Chinese Academy of Agricultural SciencesBeijingChina
| | - Lili Yu
- The National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop Science, Chinese Academy of Agricultural SciencesBeijingChina
| | - Oliver Berkowitz
- Department of Animal, Plant and Soil ScienceSchool of Life Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe UniversityBundooraVictoriaAustralia
| | - Rakesh David
- ARC Centre of Excellence in Plant Energy BiologyWaite Research Institute & School of Agriculture, Food and Wine, University of AdelaideGlen OsmondSouth AustraliaAustralia
| | - James Whelan
- Department of Animal, Plant and Soil ScienceSchool of Life Science, Australian Research Council Centre of Excellence in Plant Energy Biology, La Trobe UniversityBundooraVictoriaAustralia
| | - Melanie Ford
- ARC Centre of Excellence in Plant Energy BiologyWaite Research Institute & School of Agriculture, Food and Wine, University of AdelaideGlen OsmondSouth AustraliaAustralia
| | - Stefanie Wege
- ARC Centre of Excellence in Plant Energy BiologyWaite Research Institute & School of Agriculture, Food and Wine, University of AdelaideGlen OsmondSouth AustraliaAustralia
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic ImprovementInstitute of Crop Science, Chinese Academy of Agricultural SciencesBeijingChina
| | - Matthew Gilliham
- ARC Centre of Excellence in Plant Energy BiologyWaite Research Institute & School of Agriculture, Food and Wine, University of AdelaideGlen OsmondSouth AustraliaAustralia
| |
Collapse
|
24
|
Ozber N, Facchini PJ. Phloem-specific localization of benzylisoquinoline alkaloid metabolism in opium poppy. JOURNAL OF PLANT PHYSIOLOGY 2022; 271:153641. [PMID: 35240512 DOI: 10.1016/j.jplph.2022.153641] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/31/2022] [Accepted: 02/07/2022] [Indexed: 05/28/2023]
Abstract
Opium poppy is the only commercial source of the narcotic analgesics morphine and codeine, and semi-synthetic derivatives of the natural opiate precursor thebaine, including oxycodone and the opioid antagonist naloxone. The plant also accumulates the vasodilator and antitussive agents papaverine and noscapine, respectively, which together with morphine, codeine and thebaine comprise the major benzylisoquinoline alkaloids (BIAs) in opium poppy. A majority of enzymes involved in the highly branched BIA metabolism in opium poppy have now been discovered, with many specifically localized to sieve elements of the phloem based on immunofluorescence labeling techniques. Transcripts corresponding to sieve element-localized biosynthetic enzymes were detected in companion cells, as expected. The more recent application of shotgun proteomics has shown that several enzymes operating late in the morphine and noscapine biosynthetic pathways occur primarily in laticifers that are adjacent or proximal to sieve elements. BIA biosynthesis and accumulation in opium poppy involves three phloem cell types and implicates the translocation of key pathway intermediates between sieve elements and laticifers. The recent isolation of uptake transporters associated with laticifers supports an apoplastic rather than a symplastic route for translocation. In spite of the extensive elucidation of BIA biosynthetic enzymes in opium poppy, additional transporters and other auxiliary proteins are clearly necessary to support the complex spatial organization and dynamics involved in product formation and sequestration. In this review, we provide an update of BIA metabolism in opium poppy with a focus on the role of phloem in the biosynthesis of the major alkaloids.
Collapse
Affiliation(s)
- Natali Ozber
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada
| | - Peter J Facchini
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, T2N 1N4, Canada.
| |
Collapse
|
25
|
Zhang M, Liu S, Wang Z, Yuan Y, Zhang Z, Liang Q, Yang X, Duan Z, Liu Y, Kong F, Liu B, Ren B, Tian Z. Progress in soybean functional genomics over the past decade. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:256-282. [PMID: 34388296 PMCID: PMC8753368 DOI: 10.1111/pbi.13682] [Citation(s) in RCA: 58] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Revised: 08/04/2021] [Accepted: 08/09/2021] [Indexed: 05/24/2023]
Abstract
Soybean is one of the most important oilseed and fodder crops. Benefiting from the efforts of soybean breeders and the development of breeding technology, large number of germplasm has been generated over the last 100 years. Nevertheless, soybean breeding needs to be accelerated to meet the needs of a growing world population, to promote sustainable agriculture and to address future environmental changes. The acceleration is highly reliant on the discoveries in gene functional studies. The release of the reference soybean genome in 2010 has significantly facilitated the advance in soybean functional genomics. Here, we review the research progress in soybean omics (genomics, transcriptomics, epigenomics and proteomics), germplasm development (germplasm resources and databases), gene discovery (genes that are responsible for important soybean traits including yield, flowering and maturity, seed quality, stress resistance, nodulation and domestication) and transformation technology during the past decade. At the end, we also briefly discuss current challenges and future directions.
Collapse
Affiliation(s)
- Min Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Zhao Wang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yaqin Yuan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhifang Zhang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Qianjin Liang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xia Yang
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zongbiao Duan
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Yucheng Liu
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
| | - Fanjiang Kong
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Baohui Liu
- Innovative Center of Molecular Genetics and EvolutionSchool of Life SciencesGuangzhou UniversityGuangzhouChina
| | - Bo Ren
- State Key Laboratory of Plant GenomicsInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome EngineeringInstitute of Genetics and Developmental BiologyInnovative Academy for Seed DesignChinese Academy of SciencesBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| |
Collapse
|
26
|
Banasiak J, Jasiński M. ATP-binding cassette transporters in nonmodel plants. THE NEW PHYTOLOGIST 2022; 233:1597-1612. [PMID: 34614235 DOI: 10.1111/nph.17779] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 09/21/2021] [Indexed: 06/13/2023]
Abstract
Knowledge about plant ATP-binding cassette (ABC) proteins is of great value for sustainable agriculture, economic yield, and the generation of high-quality products, especially under unfavorable growth conditions. We have learned much about ABC proteins in model organisms, notably Arabidopsis thaliana; however, the importance of research dedicated to these transporters extends far beyond Arabidopsis biology. Recent progress in genomic and transcriptomic approaches for nonmodel and noncanonical model plants allows us to look at ABC transporters from a wider perspective and consider chemodiversity and functionally driven adaptation as distinctive mechanisms during their evolution. Here, by considering several representatives from agriculturally important families and recent progress in functional characterization of nonArabidopsis ABC proteins, we aim to bring attention to understanding the evolutionary background, distribution among lineages and possible mechanisms underlying the adaptation of this versatile transport system for plant needs. Increasing the knowledge of ABC proteins in nonmodel plants will facilitate breeding and development of new varieties based on, for example, genetic variations of endogenous genes and/or genome editing, representing an alternative to transgenic approaches.
Collapse
Affiliation(s)
- Joanna Banasiak
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
| | - Michał Jasiński
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Z. Noskowskiego 12/14, 61-704, Poznań, Poland
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632, Poznań, Poland
| |
Collapse
|
27
|
Tian S, Yang Y, Wu T, Luo C, Li X, Zhao X, Xi W, Liu X, Zeng M. Functional Characterization of a Flavone Synthase That Participates in a Kumquat Flavone Metabolon. FRONTIERS IN PLANT SCIENCE 2022; 13:826780. [PMID: 35310637 PMCID: PMC8924551 DOI: 10.3389/fpls.2022.826780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 02/07/2022] [Indexed: 05/17/2023]
Abstract
Flavones predominantly accumulate as O- and C-glycosides in kumquat plants. Two catalytic mechanisms of flavone synthase II (FNSII) support the biosynthesis of glycosyl flavones, one involving flavanone 2-hydroxylase (which generates 2-hydroxyflavanones for C-glycosylation) and another involving the direct catalysis of flavanones to flavones for O-glycosylation. However, FNSII has not yet been characterized in kumquats. In this study, we identified two kumquat FNSII genes (FcFNSII-1 and FcFNSII-2), based on transcriptome and bioinformatics analysis. Data from in vivo and in vitro assays showed that FcFNSII-2 directly synthesized apigenin and acacetin from naringenin and isosakuranetin, respectively, whereas FcFNSII-1 showed no detectable catalytic activities with flavanones. In agreement, transient overexpression of FcFNSII-2 in kumquat peels significantly enhanced the transcription of structural genes of the flavonoid-biosynthesis pathway and the accumulation of several O-glycosyl flavones. Moreover, studying the subcellular localizations of FcFNSII-1 and FcFNSII-2 demonstrated that N-terminal membrane-spanning domains were necessary to ensure endoplasmic reticulum localization and anchoring. Protein-protein interaction analyses, using the split-ubiquitin yeast two-hybrid system and bimolecular fluorescence-complementation assays, revealed that FcFNSII-2 interacted with chalcone synthase 1, chalcone synthase 2, and chalcone isomerase-like proteins. The results provide strong evidence that FcFNSII-2 serves as a nucleation site for an O-glycosyl flavone metabolon that channels flavanones for O-glycosyl flavone biosynthesis in kumquat fruits. They have implications for guiding genetic engineering efforts aimed at enhancing the composition of bioactive flavonoids in kumquat fruits.
Collapse
Affiliation(s)
- Shulin Tian
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
| | - Yuyan Yang
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
| | - Tao Wu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Chuan Luo
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Xin Li
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
| | - Xijuan Zhao
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
| | - Wanpeng Xi
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
| | - Xiaogang Liu
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
- *Correspondence: Xiaogang Liu,
| | - Ming Zeng
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China
- Ming Zeng, ;
| |
Collapse
|
28
|
Lin CY, Sun Y, Song J, Chen HC, Shi R, Yang C, Liu J, Tunlaya-Anukit S, Liu B, Loziuk PL, Williams CM, Muddiman DC, Lin YCJ, Sederoff RR, Wang JP, Chiang VL. Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa. FRONTIERS IN PLANT SCIENCE 2021; 12:727932. [PMID: 34691108 PMCID: PMC8527181 DOI: 10.3389/fpls.2021.727932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Co-enzyme A (CoA) ligation of hydroxycinnamic acids by 4-coumaric acid:CoA ligase (4CL) is a critical step in the biosynthesis of monolignols. Perturbation of 4CL activity significantly impacts the lignin content of diverse plant species. In Populus trichocarpa, two well-studied xylem-specific Ptr4CLs (Ptr4CL3 and Ptr4CL5) catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. Subsequently, two 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) mediate the conversion of 4-coumaroyl-CoA to caffeoyl-CoA. Here, we show that the CoA ligation of 4-coumaric and caffeic acids is modulated by Ptr4CL/PtrHCT protein complexes. Downregulation of PtrHCTs reduced Ptr4CL activities in the stem-differentiating xylem (SDX) of transgenic P. trichocarpa. The Ptr4CL/PtrHCT interactions were then validated in vivo using biomolecular fluorescence complementation (BiFC) and protein pull-down assays in P. trichocarpa SDX extracts. Enzyme activity assays using recombinant proteins of Ptr4CL and PtrHCT showed elevated CoA ligation activity for Ptr4CL when supplemented with PtrHCT. Numerical analyses based on an evolutionary computation of the CoA ligation activity estimated the stoichiometry of the protein complex to consist of one Ptr4CL and two PtrHCTs, which was experimentally confirmed by chemical cross-linking using SDX plant protein extracts and recombinant proteins. Based on these results, we propose that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa.
Collapse
Affiliation(s)
- Chien-Yuan Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jina Song
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - Hsi-Chuan Chen
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Rui Shi
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Chenmin Yang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Jie Liu
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Sermsawat Tunlaya-Anukit
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Department of Forestry, Beihua University, Jilin, China
| | - Philip L. Loziuk
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Cranos M. Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - David C. Muddiman
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Ying-Chung Jimmy Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Jack P. Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Vincent L. Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| |
Collapse
|
29
|
Dastmalchi M. Elusive partners: a review of the auxiliary proteins guiding metabolic flux in flavonoid biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:314-329. [PMID: 34318549 DOI: 10.1111/tpj.15446] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 07/20/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Flavonoids are specialized metabolites widely distributed across the plant kingdom. They are involved in the growth and survival of plants, conferring the ability to filter ultra-violet rays, conduct symbiotic partnerships, and respond to stress. While many branches of flavonoid biosynthesis have been resolved, recent discoveries suggest missing auxiliary components. These overlooked elements can guide metabolic flux, enhance production, mediate stereoselectivity, transport intermediates, and exert regulatory functions. This review describes several families of auxiliary proteins from across the plant kingdom, including examples from specialized metabolism. In flavonoid biosynthesis, we discuss the example of chalcone isomerase-like (CHIL) proteins and their non-catalytic role. CHILs mediate the cyclization of tetraketides, forming the chalcone scaffold by interacting with chalcone synthase (CHS). Loss of CHIL activity leads to derailment of the CHS-catalyzed reaction and a loss of pigmentation in fruits and flowers. Similarly, members of the pathogenesis-related 10 (PR10) protein family have been found to differentially bind flavonoid intermediates, guiding the composition of anthocyanins. This role comes within a larger body of PR10 involvement in specialized metabolism, from outright catalysis (e.g., (S)-norcoclaurine synthesis) to controlling stereochemistry (e.g., enhancing cis-trans cyclization in catnip). Both CHILs and PR10s hail from larger families of ligand-binding proteins with a spectrum of activity, complicating the characterization of their enigmatic roles. Strategies for the discovery of auxiliary proteins are discussed, as well as mechanistic models for their function. Targeting such unanticipated components will be crucial in manipulating plants or engineering microbial systems for natural product synthesis.
Collapse
Affiliation(s)
- Mehran Dastmalchi
- Department of Plant Science, McGill University, Sainte-Anne-de-Bellevue, Québec, H9X 3V9, Canada
| |
Collapse
|
30
|
Sørensen M, Møller BL. Metabolic Engineering of Photosynthetic Cells – in Collaboration with Nature. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
31
|
Chao N, Wang RF, Hou C, Yu T, Miao K, Cao FY, Fang RJ, Liu L. Functional characterization of two chalcone isomerase (CHI) revealing their responsibility for anthocyanins accumulation in mulberry. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 161:65-73. [PMID: 33578286 DOI: 10.1016/j.plaphy.2021.01.044] [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: 11/11/2020] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
Mulberry (Morus sp., Moraceae) is an important economic crop plant and mulberry fruits are rich in anthocyanidins. Chalcone isomerase (CHI) catalyzes the conversion of chalcones to flavanones providing precursors for biosynthesis of anthocyanidins. In this study, bona fide CHIs were cloned and characterized from different Morus species with differently colored fruits (Morus multicaulis, Mm and Morus alba variety LvShenZi, LSZ). Enzymatic assay of MmCHI1 and MmCHI2 showed that they can utilize naringenin chalcone as substrate. The catalytic efficiency of MmCHI2 and LSZCHI2 are approximately 200 and 120-fold greater than that of MmCHI1 respectively. Phylogenetic analysis showed the two mulberry CHIs belonged to different sub-clade of Type I CHI1 named type IA (CHI2) and type IB (CHI1). Type IB CHIs are mulberry specific. MmCHI1 and MmCHI2 had similar expression profiles and showed preferred expression in fruits. In addition, both mulberry CHI1 and CHI2 played roles in the response to excess zinc stress and sclerotiniose pathogen infection. Both MmCHI1 and MmCHI2 expression levels showed positive close relationship with anthocyanins content during fruit ripening process. The co-expression of MmCHI1 and MmCHI2 was observed during fruit ripening process and in transgenic mulberry. VIGS (virus induced gene silence) targeting on MmCHI1 and MmCHI2 showed significant down-regulation of MmCHI2 instead of MmCHI1 would result in significant (about 50%) decrease in anthocyanins content. MmCHI2 is the dominant CHI for anthocyanins accumulation in mulberry. The results presented in this work provided insight on bona fide CHIs in mulberry and reveal their roles in anthocyanins accumulation.
Collapse
Affiliation(s)
- Nan Chao
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, 212018, China
| | - Ru-Feng Wang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Chong Hou
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Ting Yu
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Ke Miao
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Fang-Yuan Cao
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China
| | - Rong-Jun Fang
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, 212018, China
| | - Li Liu
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, 212018, China; Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, Jiangsu, 212018, China.
| |
Collapse
|
32
|
Anguraj Vadivel AK, McDowell T, Renaud JB, Dhaubhadel S. A combinatorial action of GmMYB176 and GmbZIP5 controls isoflavonoid biosynthesis in soybean (Glycine max). Commun Biol 2021; 4:356. [PMID: 33742087 PMCID: PMC7979867 DOI: 10.1038/s42003-021-01889-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/19/2021] [Indexed: 02/08/2023] Open
Abstract
GmMYB176 is an R1 MYB transcription factor that regulates multiple genes in the isoflavonoid biosynthetic pathway, thereby affecting their levels in soybean roots. While GmMYB176 is important for isoflavonoid synthesis, it is not sufficient for the function and requires additional cofactor(s). The aim of this study was to identify the GmMYB176 interactome for the regulation of isoflavonoid biosynthesis in soybean. Here, we demonstrate that a bZIP transcription factor GmbZIP5 co-immunoprecipitates with GmMYB176 and shows protein-protein interaction in planta. RNAi silencing of GmbZIP5 reduced the isoflavonoid level in soybean hairy roots. Furthermore, co-overexpression of GmMYB176 and GmbZIP5 enhanced the level of multiple isoflavonoid phytoallexins including glyceollin, isowighteone and a unique O-methylhydroxy isoflavone in soybean hairy roots. These findings could be utilized to develop biotechnological strategies to manipulate the metabolite levels either to enhance plant defense mechanisms or for human health benefits in soybean or other economically important crops.
Collapse
Affiliation(s)
- Arun Kumaran Anguraj Vadivel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Tim McDowell
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Justin B Renaud
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.
- Department of Biology, University of Western Ontario, London, ON, Canada.
| |
Collapse
|
33
|
Anguraj Vadivel AK, McDowell T, Renaud JB, Dhaubhadel S. A combinatorial action of GmMYB176 and GmbZIP5 controls isoflavonoid biosynthesis in soybean (Glycine max). Commun Biol 2021; 4:356. [PMID: 33742087 DOI: 10.1038/s42003-021-01889-1886] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 02/19/2021] [Indexed: 05/25/2023] Open
Abstract
GmMYB176 is an R1 MYB transcription factor that regulates multiple genes in the isoflavonoid biosynthetic pathway, thereby affecting their levels in soybean roots. While GmMYB176 is important for isoflavonoid synthesis, it is not sufficient for the function and requires additional cofactor(s). The aim of this study was to identify the GmMYB176 interactome for the regulation of isoflavonoid biosynthesis in soybean. Here, we demonstrate that a bZIP transcription factor GmbZIP5 co-immunoprecipitates with GmMYB176 and shows protein-protein interaction in planta. RNAi silencing of GmbZIP5 reduced the isoflavonoid level in soybean hairy roots. Furthermore, co-overexpression of GmMYB176 and GmbZIP5 enhanced the level of multiple isoflavonoid phytoallexins including glyceollin, isowighteone and a unique O-methylhydroxy isoflavone in soybean hairy roots. These findings could be utilized to develop biotechnological strategies to manipulate the metabolite levels either to enhance plant defense mechanisms or for human health benefits in soybean or other economically important crops.
Collapse
Affiliation(s)
- Arun Kumaran Anguraj Vadivel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Tim McDowell
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Justin B Renaud
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.
- Department of Biology, University of Western Ontario, London, ON, Canada.
| |
Collapse
|
34
|
Zhang Y, Fernie AR. Metabolons, enzyme-enzyme assemblies that mediate substrate channeling, and their roles in plant metabolism. PLANT COMMUNICATIONS 2021; 2:100081. [PMID: 33511342 PMCID: PMC7816073 DOI: 10.1016/j.xplc.2020.100081] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 05/05/2023]
Abstract
Metabolons are transient multi-protein complexes of sequential enzymes that mediate substrate channeling. They differ from multi-enzyme complexes in that they are dynamic, rather than permanent, and as such have considerably lower dissociation constants. Despite the fact that a huge number of metabolons have been suggested to exist in plants, most of these claims are erroneous as only a handful of these have been proven to channel metabolites. We believe that physical protein-protein interactions between consecutive enzymes of a pathway should rather be called enzyme-enzyme assemblies. In this review, we describe how metabolons are generally assembled by transient interactions and held together by both structural elements and non-covalent interactions. Experimental evidence for their existence comes from protein-protein interaction studies, which indicate that the enzymes physically interact, and direct substrate channeling measurements, which indicate that they functionally interact. Unfortunately, advances in cell biology and proteomics have far outstripped those in classical enzymology and flux measurements, rendering most reports reliant purely on interactome studies. Recent developments in co-fractionation mass spectrometry will likely further exacerbate this bias. Given this, only dynamic enzyme-enzyme assemblies in which both physical and functional interactions have been demonstrated should be termed metabolons. We discuss the level of evidence for the manifold plant pathways that have been postulated to contain metabolons and then list examples in both primary and secondary metabolism for which strong evidence has been provided to support these claims. In doing so, we pay particular attention to experimental and mathematical approaches to study metabolons as well as complexities that arise in attempting to follow them. Finally, we discuss perspectives for improving our understanding of these fascinating but enigmatic interactions.
Collapse
Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| |
Collapse
|
35
|
Kriechbaumer V, Brandizzi F. The plant endoplasmic reticulum: an organized chaos of tubules and sheets with multiple functions. J Microsc 2020; 280:122-133. [PMID: 32426862 PMCID: PMC10895883 DOI: 10.1111/jmi.12909] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/08/2020] [Accepted: 05/14/2020] [Indexed: 12/14/2022]
Abstract
The endoplasmic reticulum is a fascinating organelle at the core of the secretory pathway. It is responsible for the synthesis of one third of the cellular proteome and, in plant cells, it produces receptors and transporters of hormones as well as the proteins responsible for the biosynthesis of critical components of a cellulosic cell wall. The endoplasmic reticulum structure resembles a spider-web network of interconnected tubules and cisternae that pervades the cell. The study of the dynamics and interaction of this organelles with other cellular structures such as the plasma membrane, the Golgi apparatus and the cytoskeleton, have been permitted by the implementation of fluorescent protein and advanced confocal imaging. In this review, we report on the findings that contributed towards the understanding of the endoplasmic reticulum morphology and function with the aid of fluorescent proteins, focusing on the contributions provided by pioneering work from the lab of the late Professor Chris Hawes.
Collapse
Affiliation(s)
- V Kriechbaumer
- Plant Cell Biology, Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, U.K
| | - F Brandizzi
- MSU-DOE Plant Research Laboratory, Department of Plant Biology, Michigan State University, East Lansing, Michigan, U.S.A
| |
Collapse
|
36
|
García-Calderón M, Pérez-Delgado CM, Palove-Balang P, Betti M, Márquez AJ. Flavonoids and Isoflavonoids Biosynthesis in the Model Legume Lotus japonicus; Connections to Nitrogen Metabolism and Photorespiration. PLANTS 2020; 9:plants9060774. [PMID: 32575698 PMCID: PMC7357106 DOI: 10.3390/plants9060774] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/11/2022]
Abstract
Phenylpropanoid metabolism represents an important metabolic pathway from which originates a wide number of secondary metabolites derived from phenylalanine or tyrosine, such as flavonoids and isoflavonoids, crucial molecules in plants implicated in a large number of biological processes. Therefore, various types of interconnection exist between different aspects of nitrogen metabolism and the biosynthesis of these compounds. For legumes, flavonoids and isoflavonoids are postulated to play pivotal roles in adaptation to their biological environments, both as defensive compounds (phytoalexins) and as chemical signals in symbiotic nitrogen fixation with rhizobia. In this paper, we summarize the recent progress made in the characterization of flavonoid and isoflavonoid biosynthetic pathways in the model legume Lotus japonicus (Regel) Larsen under different abiotic stress situations, such as drought, the impairment of photorespiration and UV-B irradiation. Emphasis is placed on results obtained using photorespiratory mutants deficient in glutamine synthetase. The results provide different types of evidence showing that an enhancement of isoflavonoid compared to standard flavonol metabolism frequently occurs in Lotus under abiotic stress conditions. The advance produced in the analysis of isoflavonoid regulatory proteins by the use of co-expression networks, particularly MYB transcription factors, is also described. The results obtained in Lotus japonicus plants can be also extrapolated to other cultivated legume species, such as soybean, of extraordinary agronomic importance with a high impact in feeding, oil production and human health.
Collapse
Affiliation(s)
- Margarita García-Calderón
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Calle Profesor García González, 1, 41012-Sevilla, Spain; (M.G.-C.); (C.M.P.-D.); (M.B.)
| | - Carmen M. Pérez-Delgado
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Calle Profesor García González, 1, 41012-Sevilla, Spain; (M.G.-C.); (C.M.P.-D.); (M.B.)
| | - Peter Palove-Balang
- Institute of Biology and Ecology, Faculty of Science, P.J. Šafárik University in Košice, Mánesova 23, SK-04001 Košice, Slovakia;
| | - Marco Betti
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Calle Profesor García González, 1, 41012-Sevilla, Spain; (M.G.-C.); (C.M.P.-D.); (M.B.)
| | - Antonio J. Márquez
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Calle Profesor García González, 1, 41012-Sevilla, Spain; (M.G.-C.); (C.M.P.-D.); (M.B.)
- Correspondence: ; Tel.: +34-954557145
| |
Collapse
|
37
|
Jacobowitz JR, Weng JK. Exploring Uncharted Territories of Plant Specialized Metabolism in the Postgenomic Era. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:631-658. [PMID: 32176525 DOI: 10.1146/annurev-arplant-081519-035634] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
For millennia, humans have used plants for food, raw materials, and medicines, but only within the past two centuries have we begun to connect particular plant metabolites with specific properties and utilities. Since the utility of classical molecular genetics beyond model species is limited, the vast specialized metabolic systems present in the Earth's flora remain largely unstudied. With an explosion in genomics resources and a rapidly expanding toolbox over the past decade, exploration of plant specialized metabolism in nonmodel species is becoming more feasible than ever before. We review the state-of-the-art tools that have enabled this rapid progress. We present recent examples of de novo biosynthetic pathway discovery that employ various innovative approaches. We also draw attention to the higher-order organization of plant specialized metabolism at subcellular, cellular, tissue, interorgan, and interspecies levels, which will have important implications for the future design of comprehensive metabolic engineering strategies.
Collapse
Affiliation(s)
- Joseph R Jacobowitz
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| |
Collapse
|
38
|
Ni R, Zhu TT, Zhang XS, Wang PY, Sun CJ, Qiao YN, Lou HX, Cheng AX. Identification and evolutionary analysis of chalcone isomerase-fold proteins in ferns. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:290-304. [PMID: 31557291 PMCID: PMC6913697 DOI: 10.1093/jxb/erz425] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/12/2019] [Indexed: 05/07/2023]
Abstract
The distribution of type I and II chalcone isomerases (CHIs) in plants is highly family specific. We have previously reported that ancient land plants, such as the liverworts and Selaginella moellendorffii, harbor type II CHIs. To better understand the function and evolution of CHI-fold proteins, transcriptomic data obtained from 52 pteridophyte species were subjected to sequence alignment and phylogenetic analysis. The residues determining type I/II CHI identity in the pteridophyte CHIs were identical to those of type I CHIs. The enzymatic characterization of a sample of 24 CHIs, representing all the key pteridophyte lineages, demonstrated that 19 of them were type I enzymes and that five exhibited some type II activity due to an amino acid mutation. Two pteridophyte chalcone synthases (CHSs) were also characterized, and a type IV CHI (CHIL) was demonstrated to interact physically with CHSs and CHI, and to increase CHS activity by decreasing derailment products, thus enhancing flavonoid production. These findings suggest that the emergence of type I CHIs may have coincided with the divergence of the pteridophytes. This study deepens our understanding of the molecular mechanism of CHIL as an enhancer in the flavonoid biosynthesis pathway.
Collapse
Affiliation(s)
- Rong Ni
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Ting-Ting Zhu
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Xiao-Shuang Zhang
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Piao-Yi Wang
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Chun-Jing Sun
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Ya-Nan Qiao
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Hong-Xiang Lou
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Ai-Xia Cheng
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
- Correspondence:
| |
Collapse
|
39
|
Synthetic Protein Scaffolding at Biological Membranes. Trends Biotechnol 2019; 38:432-446. [PMID: 31718802 DOI: 10.1016/j.tibtech.2019.10.009] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 10/18/2019] [Accepted: 10/21/2019] [Indexed: 02/07/2023]
Abstract
Protein scaffolding is a natural phenomenon whereby proteins colocalize into macromolecular complexes via specific protein-protein interactions. In the case of metabolic enzymes, protein scaffolding drives metabolic flux through specific pathways by colocalizing enzyme active sites. Synthetic protein scaffolding is increasingly used as a mechanism to improve product specificity and yields in metabolic engineering projects. To date, synthetic scaffolding has focused primarily on soluble enzyme systems, but many metabolic pathways for high-value secondary metabolites depend on membrane-bound enzymes. The compositional diversity of biological membranes and general challenges associated with modifying membrane proteins complicate scaffolding with membrane-requiring enzymes. Several recent studies have introduced new approaches to protein scaffolding at membrane surfaces, with notable success in improving product yields from specific metabolic pathways.
Collapse
|
40
|
Blakeslee JJ, Spatola Rossi T, Kriechbaumer V. Auxin biosynthesis: spatial regulation and adaptation to stress. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:5041-5049. [PMID: 31198972 DOI: 10.1093/jxb/erz283] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 06/03/2019] [Indexed: 05/25/2023]
Abstract
The plant hormone auxin is essential for plant growth and development, controlling both organ development and overall plant architecture. Auxin homeostasis is regulated by coordination of biosynthesis, transport, conjugation, sequestration/storage, and catabolism to optimize concentration-dependent growth responses and adaptive responses to temperature, water stress, herbivory, and pathogens. At present, the best defined pathway of auxin biosynthesis is the TAA/YUC route, in which the tryptophan aminotransferases TAA and TAR and YUCCA flavin-dependent monooxygenases produce the auxin indole-3-acetic acid from tryptophan. This review highlights recent advances in our knowledge of TAA/YUC-dependent auxin biosynthesis focusing on membrane localization of auxin biosynthetic enzymes, differential regulation in root and shoot tissue, and auxin biosynthesis during abiotic stress.
Collapse
Affiliation(s)
- Joshua J Blakeslee
- Department of Horticulture and Crop Science, The Ohio State University, Wooster, OH, USA
| | - Tatiana Spatola Rossi
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Verena Kriechbaumer
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| |
Collapse
|
41
|
Pontiggia D, Spinelli F, Fabbri C, Licursi V, Negri R, De Lorenzo G, Mattei B. Changes in the microsomal proteome of tomato fruit during ripening. Sci Rep 2019; 9:14350. [PMID: 31586085 PMCID: PMC6778153 DOI: 10.1038/s41598-019-50575-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Accepted: 08/23/2019] [Indexed: 11/09/2022] Open
Abstract
The variations in the membrane proteome of tomato fruit pericarp during ripening have been investigated by mass spectrometry-based label-free proteomics. Mature green (MG30) and red ripe (R45) stages were chosen because they are pivotal in the ripening process: MG30 corresponds to the end of cellular expansion, when fruit growth has stopped and fruit starts ripening, whereas R45 corresponds to the mature fruit. Protein patterns were markedly different: among the 1315 proteins identified with at least two unique peptides, 145 significantly varied in abundance in the process of fruit ripening. The subcellular and biochemical fractionation resulted in GO term enrichment for organelle proteins in our dataset, and allowed the detection of low-abundance proteins that were not detected in previous proteomic studies on tomato fruits. Functional annotation showed that the largest proportion of identified proteins were involved in cell wall metabolism, vesicle-mediated transport, hormone biosynthesis, secondary metabolism, lipid metabolism, protein synthesis and degradation, carbohydrate metabolic processes, signalling and response to stress.
Collapse
Affiliation(s)
- Daniela Pontiggia
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Francesco Spinelli
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Claudia Fabbri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy
| | - Valerio Licursi
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.,Institute for Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Rome, Italy
| | - Rodolfo Negri
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy.,Foundation Cenci Bolognetti-Institut Pasteur, Rome, Italy
| | - Giulia De Lorenzo
- Department of Biology and Biotechnology "C. Darwin", Sapienza University of Rome, Rome, Italy. .,Foundation Cenci Bolognetti-Institut Pasteur, Rome, Italy.
| | - Benedetta Mattei
- Department of Life, Health and Environmental Sciences, University of L'Aquila, L'Aquila, Italy
| |
Collapse
|
42
|
Plant Fibers and Phenolics: A Review on Their Synthesis, Analysis and Combined Use for Biomaterials with New Properties. FIBERS 2019. [DOI: 10.3390/fib7090080] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Devising environmental-friendly processes in biotechnology is a priority in the current economic scenario. We are witnessing a constant and steady push towards finding sustainable solutions to societal challenges by promoting innovation-driven activities minimizing the environmental impact and valorizing natural resources. In bioeconomy, plants are among the most important renewable sources of both fibers (woody and cellulosic) and phytochemicals, which find applications in many industrial sectors, spanning from the textile, to the biocomposite, medical, nutraceutical, and pharma sectors. Given the key role of plants as natural sources of (macro)molecules, we here provide a compendium on the use of plant fibers functionalized/impregnated with phytochemicals (in particular phenolic extracts). The goal is to review the various applications of natural fibers functionalized with plant phenolics and to valorize those plants that are source of both fibers and phytochemicals.
Collapse
|
43
|
Knudsen C, Gallage NJ, Hansen CC, Møller BL, Laursen T. Dynamic metabolic solutions to the sessile life style of plants. Nat Prod Rep 2019; 35:1140-1155. [PMID: 30324199 PMCID: PMC6254060 DOI: 10.1039/c8np00037a] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Plants are sessile organisms. To compensate for not being able to escape when challenged by unfavorable growth conditions, pests or herbivores, plants have perfected their metabolic plasticity by having developed the capacity for on demand dynamic biosynthesis and storage of a plethora of phytochemicals.
Covering: up to 2018 Plants are sessile organisms. To compensate for not being able to escape when challenged by unfavorable growth conditions, pests or herbivores, plants have perfected their metabolic plasticity by having developed the capacity for on demand synthesis of a plethora of phytochemicals to specifically respond to the challenges arising during plant ontogeny. Key steps in the biosynthesis of phytochemicals are catalyzed by membrane-bound cytochrome P450 enzymes which in plants constitute a superfamily. In planta, the P450s may be organized in dynamic enzyme clusters (metabolons) and the genes encoding the P450s and other enzymes in a specific pathway may be clustered. Metabolon formation facilitates transfer of substrates between sequential enzymes and therefore enables the plant to channel the flux of general metabolites towards biosynthesis of specific phytochemicals. In the plant cell, compartmentalization of the operation of specific biosynthetic pathways in specialized plastids serves to avoid undesired metabolic cross-talk and offers distinct storage sites for molar concentrations of specific phytochemicals. Liquid–liquid phase separation may lead to formation of dense biomolecular condensates within the cytoplasm or vacuole allowing swift activation of the stored phytochemicals as required upon pest or herbivore attack. The molecular grid behind plant plasticity offers an endless reservoir of functional modules, which may be utilized as a synthetic biology tool-box for engineering of novel biological systems based on rational design principles. In this review, we highlight some of the concepts used by plants to coordinate biosynthesis and storage of phytochemicals.
Collapse
Affiliation(s)
- Camilla Knudsen
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark.
| | | | | | | | | |
Collapse
|
44
|
Matern A, Böttcher C, Eschen-Lippold L, Westermann B, Smolka U, Döll S, Trempel F, Aryal B, Scheel D, Geisler M, Rosahl S. A substrate of the ABC transporter PEN3 stimulates bacterial flagellin (flg22)-induced callose deposition in Arabidopsis thaliana. J Biol Chem 2019; 294:6857-6870. [PMID: 30833326 DOI: 10.1074/jbc.ra119.007676] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/20/2019] [Indexed: 12/28/2022] Open
Abstract
Nonhost resistance of Arabidopsis thaliana against Phytophthora infestans, a filamentous eukaryotic microbe and the causal agent of potato late blight, is based on a multilayered defense system. Arabidopsis thaliana controls pathogen entry through the penetration-resistance genes PEN2 and PEN3, encoding an atypical myrosinase and an ABC transporter, respectively, required for synthesis and export of unknown indole compounds. To identify pathogen-elicited leaf surface metabolites and further unravel nonhost resistance in Arabidopsis, we performed untargeted metabolite profiling by incubating a P. infestans zoospore suspension on leaves of WT or pen3 mutant Arabidopsis plants. Among the plant-secreted metabolites, 4-methoxyindol-3-yl-methanol and S-(4-methoxy-indol-3-yl-methyl) cysteine were detected in spore suspensions recollected from WT plants, but at reduced levels from the pen3 mutant plants. In both whole-cell and microsome-based assays, 4-methoxyindol-3-yl-methanol was transported in a PEN3-dependent manner, suggesting that this compound is a PEN3 substrate. The syntheses of both compounds were dependent on functional PEN2 and phytochelatin synthase 1. None of these compounds inhibited mycelial growth of P. infestans in vitro Of note, exogenous application of 4-methoxyindol-3-yl methanol slightly elevated cytosolic Ca2+ levels and enhanced callose deposition in hydathodes of seedlings treated with a bacterial pathogen-associated molecular pattern (PAMP), flagellin (flg22). Loss of flg22-induced callose deposition in leaves of pen3 seedlings was partially reverted by the addition of 4-methoxyindol-3-yl methanol. In conclusion, we have identified a specific indole compound that is a substrate for PEN3 and contributes to the plant defense response against microbial pathogens.
Collapse
Affiliation(s)
- Andreas Matern
- From the Department of Stress and Developmental Biology and
| | | | | | - Bernhard Westermann
- Department of Bioorganic Chemistry, Leibniz Institute of Plant Biochemistry, Weinberg 3, D-06120 Halle (Saale), Germany and
| | - Ulrike Smolka
- From the Department of Stress and Developmental Biology and
| | - Stefanie Döll
- From the Department of Stress and Developmental Biology and
| | - Fabian Trempel
- From the Department of Stress and Developmental Biology and
| | - Bibek Aryal
- the Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Dierk Scheel
- From the Department of Stress and Developmental Biology and
| | - Markus Geisler
- the Department of Biology, University of Fribourg, Chemin du Musée 10, CH-1700 Fribourg, Switzerland
| | - Sabine Rosahl
- From the Department of Stress and Developmental Biology and
| |
Collapse
|
45
|
Ha J, Kang YG, Lee T, Kim M, Yoon MY, Lee E, Yang X, Kim D, Kim YJ, Lee TR, Kim MY, Lee SH. Comprehensive RNA sequencing and co-expression network analysis to complete the biosynthetic pathway of coumestrol, a phytoestrogen. Sci Rep 2019; 9:1934. [PMID: 30760815 PMCID: PMC6374408 DOI: 10.1038/s41598-018-38219-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 12/17/2018] [Indexed: 01/22/2023] Open
Abstract
Coumestrol (CMS), a coumestan isoflavone, plays key roles in nodulation through communication with rhizobia, and has been used as phytoestrogens for hormone replacement therapy in humans. Because CMS content is controlled by multiple genetic factors, the genetic basis of CMS biosynthesis has remained unclear. We identified soybean genotypes with consistently high (Daewonkong) or low (SS0903-2B-21-1-2) CMS content over 2 years. We performed RNA sequencing of leaf samples from both genotypes at developmental stage R7, when CMS levels are highest. Within the phenylpropanoid biosynthetic pathway, 41 genes were tightly connected in a functional co-expression gene network; seven of these genes were differentially expressed between two genotypes. We identified 14 candidate genes involved in CMS biosynthesis. Among them, seven were annotated as encoding oxidoreductases that may catalyze the transfer of electrons from daidzein, a precursor of CMS. Two of the other genes, annotated as encoding a MYB domain protein and a MLP-like protein, may increase CMS accumulation in response to stress conditions. Our results will help to complete our understanding of the CMS biosynthetic pathway, and should facilitate development of soybean cultivars with high CMS content that could be used to promote the fitness of plants and human beings.
Collapse
Affiliation(s)
- Jungmin Ha
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Young-Gyu Kang
- Basic Research & Innovation Division, R&D Center, AmorePacific Corporation, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Taeyoung Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Myoyeon Kim
- Basic Research & Innovation Division, R&D Center, AmorePacific Corporation, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Min Young Yoon
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Eunsoo Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Xuefei Yang
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Donghyun Kim
- Basic Research & Innovation Division, R&D Center, AmorePacific Corporation, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Yong-Jin Kim
- Basic Research & Innovation Division, R&D Center, AmorePacific Corporation, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Tae Ryong Lee
- Basic Research & Innovation Division, R&D Center, AmorePacific Corporation, Yongin-si, Gyeonggi-do, Republic of Korea
| | - Moon Young Kim
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea
| | - Suk-Ha Lee
- Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea.
| |
Collapse
|
46
|
Nakayama T, Takahashi S, Waki T. Formation of Flavonoid Metabolons: Functional Significance of Protein-Protein Interactions and Impact on Flavonoid Chemodiversity. FRONTIERS IN PLANT SCIENCE 2019; 10:821. [PMID: 31338097 PMCID: PMC6629762 DOI: 10.3389/fpls.2019.00821] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/07/2019] [Indexed: 05/21/2023]
Abstract
Flavonoids are a class of plant specialized metabolites with more than 6,900 known structures and play important roles in plant survival and reproduction. These metabolites are derived from p-coumaroyl-CoA via the sequential actions of a variety of flavonoid enzymes, which have been proposed to form weakly bound, ordered protein complexes termed flavonoid metabolons. This review discusses the impacts of the formation of flavonoid metabolons on the chemodiversity of flavonoids. Specific protein-protein interactions in the metabolons of Arabidopsis thaliana and other plant species have been studied for two decades. In many cases, metabolons are associated with the ER membrane, with ER-bound cytochromes P450 hypothesized to serve as nuclei for metabolon formation. Indeed, cytochromes P450 have been found to be components of flavonoid metabolons in rice, snapdragon, torenia, and soybean. Recent studies illustrate the importance of specific interactions for the efficient production and temporal/spatial distribution of flavonoids. For example, in diverse plant species, catalytically inactive type-IV chalcone isomerase-like protein serves as an enhancer of flavonoid production via its involvement in flavonoid metabolons. In soybean roots, a specific isozyme of chalcone reductase (CHR) interacts with 2-hydroxyisoflavanone synthase, to which chalcone synthase (CHS) can also bind, providing a mechanism to prevent the loss of the unstable CHR substrate during its transfer from CHS to CHR. Thus, diversification in chemical structures and temporal/spatial distribution patterns of flavonoids in plants is likely to be mediated by the formation of specific flavonoid metabolons via specific protein-protein interactions.
Collapse
|
47
|
Anguraj Vadivel AK, Renaud J, Kagale S, Dhaubhadel S. GmMYB176 Regulates Multiple Steps in Isoflavonoid Biosynthesis in Soybean. FRONTIERS IN PLANT SCIENCE 2019; 10:562. [PMID: 31130975 PMCID: PMC6509752 DOI: 10.3389/fpls.2019.00562] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 04/12/2019] [Indexed: 05/08/2023]
Abstract
Isoflavonoids are a group of plant natural compounds synthesized almost exclusively by legumes, and are abundant in soybean seeds and roots. They play important roles in plant-microbial interactions and the induction of nod gene expression in Rhizobia that form nitrogen-fixing nodules on soybean roots. Isoflavonoids also contribute to the positive health effects associated with soybean consumption by humans and animals. An R1 MYB transcription factor GmMYB176 regulates isoflavonoid biosynthesis by activating chalcone synthase (CHS) 8 gene expression in soybean. Using a combination of transcriptomic and metabolomic analyses of GmMYB176-RNAi silenced (GmMYB176-Si), GmMYB176-overexpressed (GmMYB176-OE), and control soybean hairy roots, we identified a total of 33 differentially expressed genes (DEGs) and 995 differentially produced metabolite features (DPMF) in GmMYB176-Si hairy roots, and 5727 DEGs and 149 DPMFs in GmMYB176-OE hairy roots. By a targeted approach, 25 isoflavonoid biosynthetic genes and 6 metabolites were identified as differentially regulated in GmMYB176-OE and GmMYB176-Si soybean hairy roots. Taken together, our results demonstrate the complexity of isoflavonoid biosynthesis in soybean roots and suggest that a coordinated expression of pathway genes, substrate flux and product threshold level may contribute to the dynamic of the pathway regulation.
Collapse
Affiliation(s)
- Arun Kumaran Anguraj Vadivel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, Western University, London, ON, Canada
| | - Justin Renaud
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | | | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, Western University, London, ON, Canada
- *Correspondence: Sangeeta Dhaubhadel,
| |
Collapse
|
48
|
Bian S, Li R, Xia S, Liu Y, Jin D, Xie X, Dhaubhadel S, Zhai L, Wang J, Li X. Soybean CCA1-like MYB transcription factor GmMYB133 modulates isoflavonoid biosynthesis. Biochem Biophys Res Commun 2018; 507:324-329. [PMID: 30448057 DOI: 10.1016/j.bbrc.2018.11.033] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 11/05/2018] [Indexed: 01/08/2023]
Abstract
MYB transcription factors play important roles in the regulation of phenylpropanoid biosynthesis. However, the knowledge regarding the roles of CCA1-like MYBs in phenylpropanoid pathway is limited in plants. Previously, we identified 54 CCA1-like proteins in soybean. In the study, a CCA1-like MYB (GmMYB133) was functionally characterized as a positive regulator in isoflavonoid synthesis. GmMYB133 encodes a 330 aa protein featured with one CCA1 conserved motif. Further analysis indicated that the expression pattern of GmMYB133 was near-perfectly correlated with isoflavonoid accumulation as soybean embryos develop. GmMYB133 over-expression promoted the expression of two key isoflavonoid biosynthetic genes (GmCHS8 and GmIFS2) and increased total isoflavonoid content in hairy roots. Protein-protein interaction assays indicated that GmMYB133 might form hetero- and homodimers with an isoflavonoid regulator GmMYB176 and itself, respectively, while the subcellular localization of GmMYB133 can be altered by its interaction with 14-3-3 protein. These findings provided new insights into the functional roles of CCA1-like MYB proteins in the regulation of phenylpropanoid pathway, and will contribute to the future genetic engineering in the improvement of soybean seed quality.
Collapse
Affiliation(s)
- Shaomin Bian
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Ruihua Li
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Siqi Xia
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Yajing Liu
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Donghao Jin
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Xin Xie
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Sangeeta Dhaubhadel
- Agriculture and Agri-Food Canada, London Research and Development Centre, London, ON N5V 4T3, Canada; Department of Biology, Western University, London, ON N6A 3K7, Canada
| | - Lulu Zhai
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Jingying Wang
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China
| | - Xuyan Li
- College of Plant Science, Jilin University, Changchun, 130062, Jilin, China.
| |
Collapse
|
49
|
Anguraj Vadivel AK, Krysiak K, Tian G, Dhaubhadel S. Genome-wide identification and localization of chalcone synthase family in soybean (Glycine max [L]Merr). BMC PLANT BIOLOGY 2018; 18:325. [PMID: 30509179 PMCID: PMC6278125 DOI: 10.1186/s12870-018-1569-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 11/23/2018] [Indexed: 05/23/2023]
Abstract
BACKGROUND Soybean is a paleopolyploid that has undergone two whole genome duplication events. Gene duplication is a type of genomic change that can lead to novel functions of pre-existing genes. Chalcone synthase (CHS) is the plant-specific type III polyketide synthase that catalyzes the first committed step in (iso)flavonoid biosynthesis in plants. RESULTS Here we performed a genome-wide search of CHS genes in soybean, and identified 21 GmCHS loci containing 14 unique GmCHS (GmCHS1-GmCHS14) that included 5 newly identified GmCHSs (GmCHS10-GmCHS14). Furthermore, 3 copies of GmCHS3 and 2 copies of GmCHS4 were found in soybean. Analysis of gene structure of GmCHSs revealed the presence of a single intron in protein-coding regions except for GmCHS12 that contained 3 introns. Even though GmCHS genes are located on 8 different chromosomes, a large number of these genes are present on chromosome 8 where they form 3 distinct clusters. Expression analysis of GmCHS genes revealed tissue-specific expression pattern, and that some GmCHS isoforms localize in the cytoplasm and the nucleus while other isoforms are restricted to cytoplasm only. CONCLUSION Overall, we have identified 21 GmCHS loci with 14 unique GmCHS genes in the soybean genome. Their gene structures and genomic organization together with the spatio-temporal expression and protein localization suggest their importance in the production of downstream metabolites such as (iso)flavonoids and their derived phytoalexins.
Collapse
Affiliation(s)
- Arun Kumaran Anguraj Vadivel
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3 Canada
- Department of Biology, University of Western Ontario, London, ON Canada
| | - Kevin Krysiak
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3 Canada
| | - Gang Tian
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3 Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario N5V 4T3 Canada
- Department of Biology, University of Western Ontario, London, ON Canada
| |
Collapse
|
50
|
Deshmukh AB, Datir SS, Bhonde Y, Kelkar N, Samdani P, Tamhane VA. De novo root transcriptome of a medicinally important rare tree Oroxylum indicum for characterization of the flavonoid biosynthesis pathway. PHYTOCHEMISTRY 2018; 156:201-213. [PMID: 30317159 DOI: 10.1016/j.phytochem.2018.09.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Revised: 09/25/2018] [Accepted: 09/28/2018] [Indexed: 06/08/2023]
Abstract
Oroxylum indicum (L.) Kurz is a medicinally important and rare tree species of the family Bignoniaceae. It is rich in flavonoid content and its mature roots are extensively used in Ayurvedic formulations. O. indicum specific flavonoids like oroxylin B, prunetin and oroxindin possess antibacterial, antiproliferative, antioxidant and anticancerous properties, signifying its importance in modern medicine. In the present study, de novo transcriptome analysis of O. indicum root was performed to elucidate the genes involved in flavonoid metabolism. A total of 24,625,398 high quality reads were assembled into 121,286 transcripts with N50 value 1783. The BLASTx search of 81,002 clustered transcripts against Viridiplantae Uniprot database led to annotation of 46,517 transcripts. Furthermore, Gene ontology (GO) revealed that 34,231 transcripts mapped to 3049 GO terms and KEGG analysis demonstrated that 4570 transcripts plausibly involved in 132 biosynthetic pathways. The transcriptome data indicated that cinnamyl-alcohol dehydrogenase (OinCAD) was abundant in phenylpropanoid pathway genes while; naringenin chalcone synthase (OinCHS), flavone synthase (OinFNS) and flavonoid 3', 5'-methyltransferase (OinF35 MT) were abundant in flavonoid, isoflavonoid, flavone and flavonol biosynthesis pathways, respectively. Transcription factor analysis demonstrated the abundance of MYB, bHLH and WD40 transcription factor families, which regulate the flavonoid biosynthesis. Flavonoid pathway genes displayed differential expression in young and old roots of O. indicum. The transcriptome led to the identification of 31 diverse full length Cytochrome P450 (CYP450) genes which may be involved in biosynthesis of specialized metabolites and flavonoids like baicalein and baicalin. Thus, the information obtained in this study will be a valuable tool for identifying genes and developing system biology approaches for in vitro synthesis of specialized O. indicum metabolites.
Collapse
Affiliation(s)
- Aaditi B Deshmukh
- Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India
| | - Sagar S Datir
- Department of Biotechnology, Savitribai Phule Pune University, Pune, 411007, India
| | - Yogesh Bhonde
- Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India
| | - Natasha Kelkar
- Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India
| | - Pawan Samdani
- Eumentis Cloud, Office, 310, Amenity Building, Rose Icon, Pimple Saudagar, Pune, 411027, India
| | - Vaijayanti A Tamhane
- Institute of Bioinformatics and Biotechnology (IBB), Savitribai Phule Pune University, Ganeshkhind Road, Pune, 411007, Maharashtra, India.
| |
Collapse
|