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Zheng Y, Zhao S, Zhang M, Yang L, Wu X, Tan R, Jiang H. Progress based on a multi-omics research strategy in the biosynthesis and modernization of active ingredients of Herpetospermum pedunculosum seeds. Fitoterapia 2024; 177:106113. [PMID: 38971329 DOI: 10.1016/j.fitote.2024.106113] [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] [Received: 05/07/2024] [Revised: 07/03/2024] [Accepted: 07/03/2024] [Indexed: 07/08/2024]
Abstract
Herpetospermum pedunculosum seeds also known as Herpetospermum caudigerum Wall. is the mature seed of the Herpetospermum pedunculosum(Ser.) C. B. Clarke,Cucurbitaceae. Modern pharmacological studies have shown that H. pedunculosum has hepatoprotective, anti-inflammatory, anti-gout and antibacterial pharmacological activities. The biologically active chemical components include lignin compounds such as Herpetin, Herpetetrone, Herpetoriol and so on. The natural product displays considerable skeletal diversity and structural complexity, offering significant opportunities for novel drug discovery. Based on the multi-omics research strategy and the 'gene-protein-metabolite' research framework, the biosynthetic pathway of terpenoids and lignans in H. pedunculosum has has been elucidated at multiple levels. These approaches provide comprehensive genetic information for cloning and identification of pertinent enzyme genes. Furthermore, the application of multi-omics integrative approaches provides a scientific means to elucidate entire secondary metabolic pathways. We investigated the biosynthetic pathways of lignin and terpene components in H. pedunculosum and conducted bioinformatics analysis of the crucial enzyme genes involved in the biosynthetic process using genomic and transcriptomic data. We identified candidate genes for six key enzymes in the biosynthetic pathway. This review reports on the current literature on pharmacological investigations of H. pedunculosum, proposing its potential as an antidiabetic agent. Moreover, we conclude, for the first time, the identification of key enzyme genes potentially involved in the biosynthesis of active compounds in H. pedunculosum. This review provides a scientific foundation for the discovery of novel therapeutic agents from natural sources.
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Affiliation(s)
- Yating Zheng
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 613100, PR China
| | - Siyu Zhao
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 613100, PR China
| | - Mengyu Zhang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 613100, PR China
| | - Lijiao Yang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 613100, PR China
| | - Xiaoqing Wu
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 613100, PR China
| | - Rui Tan
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 613100, PR China.
| | - Hezhong Jiang
- School of Life Science and Engineering, Southwest Jiaotong University, Chengdu 613100, PR China.
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Surendran K, Pradeep S, Pillai PP. Comparative transcriptome and metabolite profiling reveal diverse pattern of CYP-TS gene expression during corosolic acid biosynthesis in Lagerstroemia speciosa (L.) Pers. PLANT CELL REPORTS 2024; 43:122. [PMID: 38642121 DOI: 10.1007/s00299-024-03203-0] [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: 01/09/2024] [Accepted: 03/19/2024] [Indexed: 04/22/2024]
Abstract
KEY MESSAGE Extensive leaf transcriptome profiling and differential gene expression analysis of field grown and elicited shoot cultures of L. speciosa suggest that differential synthesis of CRA is mediated primarily by CYP and TS genes, showing functional diversity. Lagerstroemia speciosa L. is a tree species with medicinal and horticultural attributes. The pentacyclic triterpene, Corosolic acid (CRA) obtained from this species is widely used for the management of diabetes mellitus in traditional medicine. The high mercantile value of the compound and limited availability of innate resources entail exploration of alternative sources for CRA production. Metabolic pathway engineering for enhanced bioproduction of plant secondary metabolites is an attractive proposition for which, candidate genes in the pathway need to be identified and characterized. Therefore, in the present investigation, we focused on the identification of cytochrome P450 (CYP450) and oxidosqualene cyclases (OSC) genes and their differential expression during biosynthesis of CRA. The pattern of differential expression of these genes in the shoot cultures of L. speciosa, elicited with different epigenetic modifiers (azacytidine (AzaC), sodium butyrate (NaBu) and anacardic acid (AA)), was studied in comparison with field grown plant. Further, in vitro cultures with varying (low to high) concentrations of CRA were systematically assessed for the expression of CYP-TS and associated genes involved in CRA biosynthesis by transcriptome sequencing. The sequenced samples were de novo assembled into 180,290 transcripts of which, 92,983 transcripts were further annotated by UniProt. The results are collectively given in co-occurrence heat maps to identify the differentially expressed genes. The combined transcript and metabolite profiles along with RT-qPCR analysis resulted in the identification of CYP-TS genes with high sequence variation. Further, instances of concordant/discordant relation between CRA biosynthesis and CYP-TS gene expression were observed, indicating functional diversity in genes.
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Affiliation(s)
- Karuna Surendran
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671320, India
| | - Siya Pradeep
- Department of Genomic Science, Central University of Kerala, Kasaragod, 671320, India
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Kang JN, Lee SM, Choi JW, Lee SS, Kim CK. First Contiguous Genome Assembly of Japanese Lady Bell ( Adenophora triphylla) and Insights into Development of Different Leaf Types. Genes (Basel) 2023; 15:58. [PMID: 38254948 PMCID: PMC10815912 DOI: 10.3390/genes15010058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 01/24/2024] Open
Abstract
Adenophora triphylla is an important medicinal and food plant found in East Asia. This plant is rich in secondary metabolites such as triterpenoid saponin, and its leaves can develop into different types, such as round and linear, depending on the origin of germination even within the same species. Despite this, few studies have comprehensively characterized the development processes of different leaf types and triterpenoid saponin pathways in this plant. Herein, we provide the first report of a high-quality genome assembly of A. triphylla based on a combination of Oxford Nanopore Technologies and Illumina sequencing methods. Its genome size was estimated to be 2.6 Gb, and the assembled genome finalized as 2.48 Gb, containing 57,729 protein-coding genes. Genome completeness was assessed as 95.6% using the Benchmarking Universal Single-Copy Orthologs score. The evolutionary divergence of A. triphylla was investigated using the genomes of five plant species, including two other species in the Campanulaceae family. The species A. triphylla diverged approximately 51-118 million years ago from the other four plants, and 579 expanded/contracted gene families were clustered in the Gene Ontology terms. The expansion of the β-amyrin synthase (bAS) gene, a key enzyme in the triterpenoid saponin pathway, was identified in the A. triphylla genome. Furthermore, transcriptome analysis of the two leaf types revealed differences in the activity of starch, sucrose, unsaturated fatty acid pathways, and oxidoreductase enzymes. The heat and endoplasmic reticulum pathways related to plant stress were active in the development of round type leaf, while an enhancement of pyrimidine metabolism related to cell development was confirmed in the development of the linear type leaf. This study provides insight into the evolution of bAS genes and the development of different leaf types in A. triphylla.
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Affiliation(s)
- Ji-Nam Kang
- Genomics Division, National Institute of Agricultural Sciences, Jeonju 54874, Republic of Korea; (J.-N.K.); (S.-M.L.)
| | - Si-Myung Lee
- Genomics Division, National Institute of Agricultural Sciences, Jeonju 54874, Republic of Korea; (J.-N.K.); (S.-M.L.)
| | - Ji-Weon Choi
- Postharvest Technology Division, National Institute of Horticultural and Herbal Science, Wanju 55365, Republic of Korea;
| | - Seung-Sik Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea;
- Department of Radiation Science, University of Science and Technology, Daejeon 34113, Republic of Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju 54874, Republic of Korea; (J.-N.K.); (S.-M.L.)
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Li Y, Wang J, Li L, Song W, Li M, Hua X, Wang Y, Yuan J, Xue Z. Natural products of pentacyclic triterpenoids: from discovery to heterologous biosynthesis. Nat Prod Rep 2023; 40:1303-1353. [PMID: 36454108 DOI: 10.1039/d2np00063f] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2023]
Abstract
Covering: up to 2022Pentacyclic triterpenoids are important natural bioactive substances that are widely present in plants and fungi. They have significant medicinal efficacy, play an important role in reducing blood glucose and protecting the liver, and have anti-inflammatory, anti-oxidation, anti-fatigue, anti-viral, and anti-cancer activities. Pentacyclic triterpenoids are derived from the isoprenoid biosynthetic pathway, which generates common precursors of triterpenes and steroids, followed by cyclization with oxidosqualene cyclases (OSCs) and decoration via cytochrome P450 monooxygenases (CYP450s) and glycosyltransferases (GTs). Many biosynthetic pathways of triterpenoid saponins have been elucidated by studying their metabolic regulation network through the use of multiomics and identifying their functional genes. Unfortunately, natural resources of pentacyclic triterpenoids are limited due to their low content in plant tissues and the long growth cycle of plants. Based on the understanding of their biosynthetic pathway and transcriptional regulation, plant bioreactors and microbial cell factories are emerging as alternative means for the synthesis of desired triterpenoid saponins. The rapid development of synthetic biology, metabolic engineering, and fermentation technology has broadened channels for the accumulation of pentacyclic triterpenoid saponins. In this review, we summarize the classification, distribution, structural characteristics, and bioactivity of pentacyclic triterpenoids. We further discuss the biosynthetic pathways of pentacyclic triterpenoids and involved transcriptional regulation. Moreover, the recent progress and characteristics of heterologous biosynthesis in plants and microbial cell factories are discussed comparatively. Finally, we propose potential strategies to improve the accumulation of triterpenoid saponins, thereby providing a guide for their future biomanufacturing.
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Affiliation(s)
- Yanlin Li
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Jing Wang
- Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing, PR China
| | - Linyong Li
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Wenhui Song
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Min Li
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Xin Hua
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
| | - Yu Wang
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
| | - Jifeng Yuan
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, 361102, Fujian, PR China.
| | - Zheyong Xue
- Ministry of Education, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Northeast Forestry University, Harbin, PR China.
- Heilongjiang Key Laboratory of Plant Bioactive Substance Biosynthesis and Utilization, Northeast Forestry University, Harbin, PR China
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Lee DJ, Choi JW, Kang JN, Lee SM, Park GH, Kim CK. Chromosome-Scale Genome Assembly and Triterpenoid Saponin Biosynthesis in Korean Bellflower (Platycodon grandiflorum). Int J Mol Sci 2023; 24:ijms24076534. [PMID: 37047506 PMCID: PMC10095269 DOI: 10.3390/ijms24076534] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/24/2023] [Accepted: 03/29/2023] [Indexed: 04/03/2023] Open
Abstract
Platycodon grandiflorum belongs to the Campanulaceae family and is an important medicinal and food plant in East Asia. However, on the whole, the genome evolution of P. grandiflorum and the molecular basis of its major biochemical pathways are poorly understood. We reported a chromosome-scale genome assembly of P. grandiflorum based on a hybrid method using Oxford Nanopore Technologies, Illumina sequences, and high-throughput chromosome conformation capture (Hi-C) analysis. The assembled genome was finalized as 574 Mb, containing 41,355 protein-coding genes, and the genome completeness was assessed as 97.6% using a Benchmarking Universal Single-Copy Orthologs analysis. The P. grandiflorum genome comprises nine pseudo-chromosomes with 56.9% repeat sequences, and the transcriptome analysis revealed an expansion of the 14 beta-amylin genes related to triterpenoid saponin biosynthesis. Our findings provide an understanding of P. grandiflorum genome evolution and enable genomic-assisted breeding for the mass production of important components such as triterpenoid saponins.
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Yang J, Busta L, Jetter R, Sun Y, Wang T, Zhang W, Ni Y, Guo Y. Diversified chemical profiles of cuticular wax on alpine meadow plants of the Qinghai-Tibet Plateau. PLANTA 2023; 257:74. [PMID: 36879182 DOI: 10.1007/s00425-023-04107-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 02/25/2023] [Indexed: 06/18/2023]
Abstract
The alpine meadow plants showed great intra- and inter-genera variations of chemical profiles of cuticular waxes. Developing an understanding of wax structure-function relationships that will help us tackle global climate change requires a detailed understanding of plant wax chemistry. The goal in this study was to provide a catalog of wax structures, abundances, and compositions on alpine meadow plants. Here, leaf waxes from 33 plant species belonging to 11 families were sampled from alpine meadows of the east side of the Qinghai-Tibet Plateau. Across these species, total wax coverage varied from 2.30 μg cm-2 to 40.70 μg cm-2, showing variation both within as well as between genera and suggesting that wax variation is subject to both environmental and genetic effects. Across all wax samples, more than 140 wax compounds belonging to 13 wax compound classes were identified, including both ubiquitous wax compounds and lineage-specific compounds. Among the ubiquitous compounds (primary alcohols, alkyl esters, aldehydes, alkanes, and fatty acids), chain length profiles across a wide range of species point to key differences in the chain length specificity of alcohol and alkane formation machinery. The lineage-specific wax compound classes (diols, secondary alcohols, lactones, iso-alkanes, alkyl resorcinols, phenylethyl esters, cinnamate esters, alkyl benzoates, and triterpenoids) nearly all consisted of isomers with varying chain lengths or functional group positions, making the diversity of specialized wax compounds immense. The comparison of species relationships between chemical data and genetic data highlighted the importance of inferring phylogenetic relationships from data sets that contain a large number of variables that do not respond to environmental stimuli.
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Affiliation(s)
- Jianfeng Yang
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao, 266109, China
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- College of Animal Science and Technology, Southwest University, Chongqing, 400716, China
| | - Lucas Busta
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, 55812, USA
| | - Reinhard Jetter
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Yingpeng Sun
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao, 266109, China
| | - Tianyu Wang
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao, 266109, China
| | - Wenlan Zhang
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yu Ni
- College of Agronomy, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yanjun Guo
- Qingdao Key Laboratory of Specialty Plant Germplasm Innovation and Utilization in Saline Soils of Coastal Beach, Qingdao Agricultural University, Qingdao, 266109, China.
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
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Maldonado-Alconada AM, Castillejo MÁ, Rey MD, Labella-Ortega M, Tienda-Parrilla M, Hernández-Lao T, Honrubia-Gómez I, Ramírez-García J, Guerrero-Sanchez VM, López-Hidalgo C, Valledor L, Navarro-Cerrillo RM, Jorrin-Novo JV. Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How. Int J Mol Sci 2022; 23:9980. [PMID: 36077370 PMCID: PMC9456323 DOI: 10.3390/ijms23179980] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/29/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, "dehesa." It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors' group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.
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Affiliation(s)
- Ana María Maldonado-Alconada
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - María Ángeles Castillejo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - María-Dolores Rey
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Mónica Labella-Ortega
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Marta Tienda-Parrilla
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Tamara Hernández-Lao
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Irene Honrubia-Gómez
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Javier Ramírez-García
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
| | - Víctor M. Guerrero-Sanchez
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
- Cardiovascular Proteomics Laboratory, Centro Nacional de Investigaciones Cardiovasculares (CNIC), 28029 Madrid, Spain
| | - Cristina López-Hidalgo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
- Plant Physiology, Department of Organisms and Systems Biology, University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, 33006 Asturias, Spain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, University Institute of Biotechnology of Asturias (IUBA), University of Oviedo, 33006 Asturias, Spain
| | - Rafael M. Navarro-Cerrillo
- Evaluation and Restoration of Agronomic and Forest Systems ERSAF, Department of Forest Engineering, University of Córdoba, 14014 Cordoba, Spain
| | - Jesús V. Jorrin-Novo
- Agroforestry and Plant Biochemistry, Proteomics and Systems Biology, Department of Biochemistry and Molecular Biology, University of Cordoba, UCO-CeiA3, 14014 Cordoba, Spain
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Lertphadungkit P, Qiao X, Ye M, Bunsupa S. Characterization of oxidosqualene cyclases from Trichosanthes cucumerina L. reveals key amino acids responsible for substrate specificity of isomultiflorenol synthase. PLANTA 2022; 256:58. [PMID: 35980476 DOI: 10.1007/s00425-022-03972-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
Two key amino acids of isomultiflorenol synthase, Y125 and M254, were first proposed. They could be associated with the production of isomultiflorenol. Oxidosqualene cyclases (OSCs) are the first committed enzymes in the triterpenoid biosynthesis by converting 2,3-oxidosqualene to specific triterpenoid backbones. Thus, these enzymes are potential targets for developing plant-active compounds through the study of triterpenoid biosynthesis. We applied transcriptome information and metabolite profiling from Trichosanthes cucumerina L. to define the diversity of triterpenoids in this plant through OSCs. Isomultiflorenol synthase and cucurbitadienol synthase were previously identified in this plant. Here, three new OSCs, TcBAS, TcLAS, and TcCAS, were cloned and functionally characterized as β-amyrin synthase, lanosterol synthase, and cycloartenol synthase activities, respectively. We also took advantage of the multiple sequence alignment and molecular docking of OSCs exhibiting in this plant and other plant OSCs to identify key residues associated with isomultiflorenol synthase specificity. Two novel key amino acids, referred to the Y125 and M254, were first discovered. These results provide information on a possible catalytic mechanism for plant OSCs that produce specific products.
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Affiliation(s)
- Pornpatsorn Lertphadungkit
- Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayutthaya Road, Bangkok, 10400, Thailand
| | - Xue Qiao
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Min Ye
- State Key Laboratory of Natural and Biomimetic Drugs, School of Pharmaceutical Sciences, Peking University, 38 Xueyuan Road, Beijing, 100191, China
| | - Somnuk Bunsupa
- Department of Pharmacognosy, Faculty of Pharmacy, Mahidol University, 447 Sri-Ayutthaya Road, Bangkok, 10400, Thailand.
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Schenck CA, Busta L. Using interdisciplinary, phylogeny-guided approaches to understand the evolution of plant metabolism. PLANT MOLECULAR BIOLOGY 2022; 109:355-367. [PMID: 34816350 DOI: 10.1007/s11103-021-01220-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/05/2021] [Indexed: 06/13/2023]
Abstract
To cope with relentless environmental pressures, plants produce an arsenal of structurally diverse chemicals, often called specialized metabolites. These lineage-specific compounds are derived from the simple building blocks made by ubiquitous core metabolic pathways. Although the structures of many specialized metabolites are known, the underlying metabolic pathways and the evolutionary events that have shaped the plant chemical diversity landscape are only beginning to be understood. However, with the advent of multi-omics data sets and the relative ease of studying pathways in previously intractable non-model species, plant specialized metabolic pathways are now being systematically identified. These large datasets also provide a foundation for comparative, phylogeny-guided studies of plant metabolism. Comparisons of metabolic traits and features like chemical abundances, enzyme activities, or gene sequences from phylogenetically diverse plants provide insights into how metabolic pathways evolved. This review highlights the power of studying evolution through the lens of comparative biochemistry, particularly how placing metabolism into a phylogenetic context can help a researcher identify the metabolic innovations enabling the evolution of structurally diverse plant metabolites.
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Affiliation(s)
- Craig A Schenck
- Department of Biochemistry, University of Missouri, Columbia, MO, USA.
| | - Lucas Busta
- Department of Chemistry and Biochemistry, University of Minnesota Duluth, Duluth, MN, USA
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Serra O, Mähönen AP, Hetherington AJ, Ragni L. The Making of Plant Armor: The Periderm. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:405-432. [PMID: 34985930 DOI: 10.1146/annurev-arplant-102720-031405] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The periderm acts as armor protecting the plant's inner tissues from biotic and abiotic stress. It forms during the radial thickening of plant organs such as stems and roots and replaces the function of primary protective tissues such as the epidermis and the endodermis. A wound periderm also forms to heal and protect injured tissues. The periderm comprises a meristematic tissue called the phellogen, or cork cambium, and its derivatives: the lignosuberized phellem and the phelloderm. Research on the periderm has mainly focused on the chemical composition of the phellem due to its relevance as a raw material for industrial processes. Today, there is increasing interest in the regulatory network underlying periderm development as a novel breeding trait to improve plant resilience and to sequester CO2. Here, we discuss our current understanding of periderm formation, focusing on aspects of periderm evolution, mechanisms of periderm ontogenesis, regulatory networks underlying phellogen initiation and cork differentiation, and future challenges of periderm research.
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Affiliation(s)
- Olga Serra
- University of Girona, Department of Biology, Girona, Spain;
| | - Ari Pekka Mähönen
- Institute of Biotechnology, HiLIFE, University of Helsinki, Helsinki, Finland;
- Organismal and Evolutionary Biology Research Program, Faculty of Biological and Environmental Sciences, and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
| | | | - Laura Ragni
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, Tübingen, Germany;
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Günther J, Erthmann PØ, Khakimov B, Bak S. Reciprocal mutations of two multifunctional β-amyrin synthases from Barbarea vulgaris shift α/β-amyrin ratios. PLANT PHYSIOLOGY 2022; 188:1483-1495. [PMID: 34865155 PMCID: PMC8896598 DOI: 10.1093/plphys/kiab545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/25/2021] [Indexed: 05/09/2023]
Abstract
In the wild cruciferous wintercress (Barbarea vulgaris), β-amyrin-derived saponins are involved in resistance against insect herbivores like the major agricultural pest diamondback moth (Plutella xylostella). Enzymes belonging to the 2,3-oxidosqualene cyclase family have been identified and characterized in B. vulgaris G-type and P-type plants that differ in their natural habitat, insect resistance and saponin content. Both G-type and P-type plants possess highly similar 2,3-oxidosqualene cyclase enzymes that mainly produce β-amyrin (Barbarea vulgaris Lupeol synthase 5 G-Type; BvLUP5-G) or α-amyrin (Barbarea vulgaris Lupeol synthase 5 P-Type; BvLUP5-P), respectively. Despite the difference in product formation, the two BvLUP5 enzymes are 98% identical at the amino acid level. This provides a unique opportunity to investigate determinants of product formation, using the B. vulgaris 2,3-oxidosqualene cyclase enzymes as a model for studying amino acid residues that determine differences in product formation. In this study, we identified two amino acid residues at position 121 and 735 that are responsible for the dominant changes in generated product ratios of β-amyrin and α-amyrin in both BvLUP5 enzymes. These amino acid residues have not previously been highlighted as directly involved in 2,3-oxidosqualene cyclase product specificity. Our results highlight the functional diversity and promiscuity of 2,3-oxidosqualene cyclase enzymes. These enzymes serve as important mediators of metabolic plasticity throughout plant evolution.
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Affiliation(s)
- Jan Günther
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, University of Copenhagen, Denmark
| | - Pernille Østerbye Erthmann
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, University of Copenhagen, Denmark
| | - Bekzod Khakimov
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, University of Copenhagen, Denmark
- Department of Food Science, University of Copenhagen, Denmark
| | - Søren Bak
- Department of Plant and Environmental Sciences and Copenhagen Plant Science Center, University of Copenhagen, Denmark
- Author for communication:
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12
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Lu Y, Luo Y, Zhou J, Hu T, Tu L, Tong Y, Su P, Liu Y, Wang J, Jiang Z, Wu X, Chen X, Huang L, Gao W. Probing the functions of friedelane-type triterpene cyclases from four celastrol-producing plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 109:555-567. [PMID: 34750899 DOI: 10.1111/tpj.15575] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 10/15/2021] [Accepted: 11/01/2021] [Indexed: 06/13/2023]
Abstract
Triterpenes are among the most diverse plant natural products, and their diversity is closely related to various triterpene skeletons catalyzed by different 2,3-oxidosqualene cyclases (OSCs). Celastrol, a friedelane-type triterpene with significant bioactivities, is specifically distributed in higher plants, such as Celastraceae species. Friedelin is an important precursor for the biosynthesis of celastrol, and it is synthesized through the cyclization of 2,3-oxidosqualene, with the highest number of rearrangements being catalyzed by friedelane-type triterpene cyclases. However, the molecular mechanisms underlying the catalysis of friedelin production by friedelane-type triterpene cyclases have not yet been fully elucidated. In this study, transcriptome data of four celastrol-producing plants from Celastraceae were used to identify a total of 21 putative OSCs. Through functional characterization, the friedelane-type triterpene cyclases were separately verified in the four plants. Analysis of the selection pressure showed that purifying selection acted on these OSCs, and the friedelane-type triterpene cyclases may undergo weaker selective restriction during evolution. Molecular docking and site-directed mutagenesis revealed that changes in some amino acids that are unique to friedelane-type triterpene cyclases may lead to variations in catalytic specificity or efficiency, thereby affecting the synthesis of friedelin. Our research explored the functional diversity of triterpene synthases from a multispecies perspective. It also provides some references for further research on the relative mechanisms of friedelin biosynthesis.
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Affiliation(s)
- Yun Lu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
| | - Yunfeng Luo
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Jiawei Zhou
- College of Biotechnology and Bioengineering, Zhejiang University of Technology, Hangzhou, China
| | - Tianyuan Hu
- College of Pharmacy, School of Medicine, Hangzhou Normal University, Hangzhou, China
| | - Lichan Tu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Yuru Tong
- School of Pharmaceutical Sciences, Capital Medical University, Beijing, China
| | - Ping Su
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL, USA
| | - Yuan Liu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Jiadian Wang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Zhouqian Jiang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Xiaoyi Wu
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Xiaochao Chen
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
| | - Luqi Huang
- State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Wei Gao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, China
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
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13
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Rapid Identification of Common Secondary Metabolites of Medicinal Herbs Using High-Performance Liquid Chromatography with Evaporative Light Scattering Detector in Extracts. Metabolites 2021; 11:metabo11080489. [PMID: 34436430 PMCID: PMC8398965 DOI: 10.3390/metabo11080489] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 07/16/2021] [Accepted: 07/19/2021] [Indexed: 01/15/2023] Open
Abstract
The discovery and identification of novel natural products of medicinal importance in the herbal medicine industry becomes a challenge. The complexity of this process can be reduced by dereplication strategies. The current study includes a method based on high-performance liquid chromatography (HPLC), using the evaporative light scattering detector (ELSD) to identify the 12 most common secondary metabolites in plant extracts. Twelve compounds including rutin, taxifolin, quercetin, apigenin, kaempferol, betulinic acid, oleanolic acid, betulin, lupeol, stigmasterol, and β-sitosterol were analyzed simultaneously. The polarity of the compounds varied greatly from highly polar (flavonoids) to non-polar (triterpenes and sterols). This method was also tested for HPLC-DAD and HPLC-ESI-MS/MS analysis. Oleanolic acid and ursolic acid could not be separated in HPLC-ELSD analysis but were differentiated using LC-ESI-MS/MS analysis due to different fragment ions. The regression values (R2 > 0.996) showed good linearity in the range of 50–1000 µg/mL for all compounds. The range of LOD and LOQ values were 7.76–38.30 µg/mL and 23.52–116.06 µg/mL, respectively. %RSD and % trueness values of inter and intraday studies were mostly <10%. This method was applied on 10 species of medicinal plants. The dereplication strategy has the potential to facilitate and shorten the identification process of common secondary metabolites in complex plant extracts.
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14
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Pitakbut T, Spiteller M, Kayser O. In Vitro Production and Exudation of 20-Hydroxymaytenin from Gymnosporia heterophylla (Eckl. and Zeyh.) Loes. Cell Culture. PLANTS (BASEL, SWITZERLAND) 2021; 10:1493. [PMID: 34451538 PMCID: PMC8398937 DOI: 10.3390/plants10081493] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 07/09/2021] [Accepted: 07/10/2021] [Indexed: 12/27/2022]
Abstract
The metabolite 20-Hydroxymaytenin (20-HM) is a member of the quinone-methide pentacyclic triterpenoids (QMTs) group. This metabolite group is present only in Celastraceae plants, and it has shown various biological activities from antioxidant to anticancer properties. However, most QMTs metabolites including 20-HM cannot be synthesized in a laboratory. Therefore, we optimized a plant tissue culture protocol and examined the potential of Gymnosporia heterophylla (synonym. Maytenus heterophylla) to produce 20-HM in an in vitro experiment. For the first time, we reported the optimum callus induction medium with a high percentage success rate of 82% from the combination of 1 mg/L indole-3-butyric acid and 5 mg/L naphthalene acetic acid. Later, our cell suspension culture cultivated in the optimum medium provided approximately 0.35 mg/g fresh weight of 20-HM. This concentration is roughly 87.5 times higher than a concentration of 20-HM presenting in Elaeodendron croceum (Celastraceae) leaves. In addition, we also found that 20-HM presented in a cultivation medium, suggesting that G. heterophylla cells secreted 20-HM as an exudate in our experiment. Noticeably, 20-HM was missing when Penicillium cf. olsonii occurred in the medium. These findings hint at an antifungal property of 20-HM.
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Affiliation(s)
- Thanet Pitakbut
- Technical Biochemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany;
| | - Michael Spiteller
- Institute of Environmental Research (INFU), Department of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany;
| | - Oliver Kayser
- Technical Biochemistry, Department of Biochemical and Chemical Engineering, TU Dortmund University, 44227 Dortmund, Germany;
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Álvarez-Lugo A, Becerra A. The Role of Gene Duplication in the Divergence of Enzyme Function: A Comparative Approach. Front Genet 2021; 12:641817. [PMID: 34335678 PMCID: PMC8318041 DOI: 10.3389/fgene.2021.641817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Gene duplication is a crucial process involved in the appearance of new genes and functions. It is thought to have played a major role in the growth of enzyme families and the expansion of metabolism at the biosphere's dawn and in recent times. Here, we analyzed paralogous enzyme content within each of the seven enzymatic classes for a representative sample of prokaryotes by a comparative approach. We found a high ratio of paralogs for three enzymatic classes: oxidoreductases, isomerases, and translocases, and within each of them, most of the paralogs belong to only a few subclasses. Our results suggest an intricate scenario for the evolution of prokaryotic enzymes, involving different fates for duplicated enzymes fixed in the genome, where around 20-40% of prokaryotic enzymes have paralogs. Intracellular organisms have a lesser ratio of duplicated enzymes, whereas free-living enzymes show the highest ratios. We also found that phylogenetically close phyla and some unrelated but with the same lifestyle share similar genomic and biochemical traits, which ultimately support the idea that gene duplication is associated with environmental adaptation.
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Affiliation(s)
- Alejandro Álvarez-Lugo
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, Mexico City, Mexico.,Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Arturo Becerra
- Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City, Mexico
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Fernández-Piñán S, Boher P, Soler M, Figueras M, Serra O. Transcriptomic analysis of cork during seasonal growth highlights regulatory and developmental processes from phellogen to phellem formation. Sci Rep 2021; 11:12053. [PMID: 34103550 PMCID: PMC8187341 DOI: 10.1038/s41598-021-90938-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 05/19/2021] [Indexed: 02/05/2023] Open
Abstract
The phellogen or cork cambium stem cells that divide periclinally and outwardly specify phellem or cork. Despite the vital importance of phellem in protecting the radially-growing plant organs and wounded tissues, practically only the suberin biosynthetic process has been studied molecularly so far. Since cork oak (Quercus suber) phellogen is seasonally activated and its proliferation and specification to phellem cells is a continuous developmental process, the differentially expressed genes during the cork seasonal growth served us to identify molecular processes embracing from phellogen to mature differentiated phellem cell. At the beginning of cork growth (April), cell cycle regulation, meristem proliferation and maintenance and processes triggering cell differentiation were upregulated, showing an enrichment of phellogenic cells from which phellem cells are specified. Instead, at maximum (June) and advanced (July) cork growth, metabolic processes paralleling the phellem cell chemical composition, such as the biosynthesis of suberin, lignin, triterpenes and soluble aromatic compounds, were upregulated. Particularly in July, polysaccharides- and lignin-related secondary cell wall processes presented a maximal expression, indicating a cell wall reinforcement in the later stages of cork formation, presumably related with the initiation of latecork development. The putative function of relevant genes identified are discussed in the context of phellem ontogeny.
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Affiliation(s)
- Sandra Fernández-Piñán
- grid.5319.e0000 0001 2179 7512Laboratori del Suro, Departament de Biologia, Universitat de Girona, Campus Montilivi, 17003 Girona, Spain
| | - Pau Boher
- grid.5319.e0000 0001 2179 7512Laboratori del Suro, Departament de Biologia, Universitat de Girona, Campus Montilivi, 17003 Girona, Spain
| | - Marçal Soler
- grid.5319.e0000 0001 2179 7512Laboratori del Suro, Departament de Biologia, Universitat de Girona, Campus Montilivi, 17003 Girona, Spain
| | - Mercè Figueras
- grid.5319.e0000 0001 2179 7512Laboratori del Suro, Departament de Biologia, Universitat de Girona, Campus Montilivi, 17003 Girona, Spain
| | - Olga Serra
- grid.5319.e0000 0001 2179 7512Laboratori del Suro, Departament de Biologia, Universitat de Girona, Campus Montilivi, 17003 Girona, Spain
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A co-opted steroid synthesis gene, maintained in sorghum but not maize, is associated with a divergence in leaf wax chemistry. Proc Natl Acad Sci U S A 2021; 118:2022982118. [PMID: 33723068 PMCID: PMC8000359 DOI: 10.1073/pnas.2022982118] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Virtually all above-ground plant surfaces, such as leaf and stem exteriors, are covered in a cuticle: a wax-infused polyester. This waxy biocomposite is the largest interface between Earth’s biosphere and atmosphere. Its chemical composition is not only highly tuned to mediate nonstomatal water loss, but it also self-assembles to produce superhydrophobic surfaces, protects against UV radiation, and contains bioactive compounds that help resist microbial attack. Developing fundamental knowledge of waxy biocomposites, particularly those on crop species, is a prerequisite for an understanding of their structure–function relationships. Here, we uncover a likely genetic basis for the presence and absence, respectively, of triterpenoids in the leaf waxes of sorghum and maize—compounds previously associated with creating heat-tolerant cuticular water barriers. Virtually all land plants are coated in a cuticle, a waxy polyester that prevents nonstomatal water loss and is important for heat and drought tolerance. Here, we describe a likely genetic basis for a divergence in cuticular wax chemistry between Sorghum bicolor, a drought tolerant crop widely cultivated in hot climates, and its close relative Zea mays (maize). Combining chemical analyses, heterologous expression, and comparative genomics, we reveal that: 1) sorghum and maize leaf waxes are similar at the juvenile stage but, after the juvenile-to-adult transition, sorghum leaf waxes are rich in triterpenoids that are absent from maize; 2) biosynthesis of the majority of sorghum leaf triterpenoids is mediated by a gene that maize and sorghum both inherited from a common ancestor but that is only functionally maintained in sorghum; and 3) sorghum leaf triterpenoids accumulate in a spatial pattern that was previously shown to strengthen the cuticle and decrease water loss at high temperatures. These findings uncover the possibility for resurrection of a cuticular triterpenoid-synthesizing gene in maize that could create a more heat-tolerant water barrier on the plant’s leaf surfaces. They also provide a fundamental understanding of sorghum leaf waxes that will inform efforts to divert surface carbon to intracellular storage for bioenergy and bioproduct innovations.
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