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Lv J, Yang S, Zhou W, Liu Z, Tan J, Wei M. Microbial regulation of plant secondary metabolites: Impact, mechanisms and prospects. Microbiol Res 2024; 283:127688. [PMID: 38479233 DOI: 10.1016/j.micres.2024.127688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/06/2024] [Accepted: 03/07/2024] [Indexed: 04/17/2024]
Abstract
Plant secondary metabolites possess a wide range of pharmacological activities and play crucial biological roles. They serve as both a defense response during pathogen attack and a valuable drug resource. The role of microorganisms in the regulation of plant secondary metabolism has been widely recognized. The addition of specific microorganisms can increase the synthesis of secondary metabolites, and their beneficial effects depend on environmental factors and plant-related microorganisms. This article summarizes the impact and regulatory mechanisms of different microorganisms on the main secondary metabolic products of plants. We emphasize the mechanisms by which microorganisms regulate hormone levels, nutrient absorption, the supply of precursor substances, and enzyme and gene expression to promote the accumulation of plant secondary metabolites. In addition, the possible negative feedback regulation of microorganisms is discussed. The identification of additional unknown microbes and other driving factors affecting plant secondary metabolism is essential. The prospects for further analysis of medicinal plant genomes and the establishment of a genetic operation system for plant secondary metabolism research are proposed. This study provides new ideas for the use of microbial resources for biological synthesis research and the improvement of crop anti-inverse traits for the use of microbial resources.
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Affiliation(s)
- Jiayan Lv
- School of Agriculture, Shenzhen Campus, Sun Yat-sen University, Guangdong, Shenzhen 518107, China
| | - Shuangyu Yang
- School of Agriculture, Shenzhen Campus, Sun Yat-sen University, Guangdong, Shenzhen 518107, China
| | - Wei Zhou
- School of Agriculture, Shenzhen Campus, Sun Yat-sen University, Guangdong, Shenzhen 518107, China
| | - Zhongwang Liu
- School of Agriculture, Shenzhen Campus, Sun Yat-sen University, Guangdong, Shenzhen 518107, China
| | - Jinfang Tan
- School of Agriculture, Shenzhen Campus, Sun Yat-sen University, Guangdong, Shenzhen 518107, China
| | - Mi Wei
- School of Agriculture, Shenzhen Campus, Sun Yat-sen University, Guangdong, Shenzhen 518107, China; Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan 432000, China.
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Jighly A. Boosting genome-wide association power and genomic prediction accuracy for date palm fruit traits with advanced statistics. Plant Sci 2024:112110. [PMID: 38704095 DOI: 10.1016/j.plantsci.2024.112110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 03/05/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024]
Abstract
The date palm is economically vital in the Middle East and North Africa, providing essential fibres, vitamins, and carbohydrates. Understanding the genetic architecture of its traits remains complex due to the tree's perennial nature and long generation times. This study aims to address these complexities by employing advanced genome-wide association (GWAS) and genomic prediction models using previously published data involving fruit acid content, sugar content, dimension, and colour traits. The multivariate GWAS model identified seven QTL, including five novel associations, that shed light on the genetic control of these traits. Furthermore, the research evaluates different genomic prediction models that considered genotype by environment and genotype by trait interactions. While colour- traits demonstrate strong predictive power, other traits display moderate accuracies across different models and scenarios aligned with the expectations when using small reference populations. When designing the cross-validation to predict new individuals, the accuracy of the best multi-trait model was significantly higher than all single-trait models for dimension traits, but not for the remaining traits, which showed similar performances. However, the cross-validation strategy that masked random phenotypic records (i.e., mimicking the unbalanced phenotypic records) showed significantly higher accuracy for all traits except acid contents. The findings underscore the importance of understanding genetic architecture for informed breeding strategies. The research emphasises the need for larger population sizes and multivariate models to enhance gene tagging power and predictive accuracy to advance date palm breeding programs. These findings support more targeted breeding in date palm, improving productivity and resilience to various environments.
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Bai W, Li C, Li W, Wang H, Han X, Wang P, Wang L. Machine learning assists prediction of genes responsible for plant specialized metabolite biosynthesis by integrating multi-omics data. BMC Genomics 2024; 25:418. [PMID: 38679745 PMCID: PMC11057162 DOI: 10.1186/s12864-024-10258-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 03/26/2024] [Indexed: 05/01/2024] Open
Abstract
BACKGROUND Plant specialized (or secondary) metabolites (PSM), also known as phytochemicals, natural products, or plant constituents, play essential roles in interactions between plants and environment. Although many research efforts have focused on discovering novel metabolites and their biosynthetic genes, the resolution of metabolic pathways and identified biosynthetic genes was limited by rudimentary analysis approaches and enormous number of candidate genes. RESULTS Here we integrated state-of-the-art automated machine learning (ML) frame AutoGluon-Tabular and multi-omics data from Arabidopsis to predict genes encoding enzymes involved in biosynthesis of plant specialized metabolite (PSM), focusing on the three main PSM categories: terpenoids, alkaloids, and phenolics. We found that the related features of genomics and proteomics were the top two crucial categories of features contributing to the model performance. Using only these key features, we built a new model in Arabidopsis, which performed better than models built with more features including those related with transcriptomics and epigenomics. Finally, the built models were validated in maize and tomato, and models tested for maize and trained with data from two other species exhibited either equivalent or superior performance to intraspecies predictions. CONCLUSIONS Our external validation results in grape and poppy on the one hand implied the applicability of our model to the other species, and on the other hand showed enormous potential to improve the prediction of enzymes synthesizing PSM with the inclusion of valid data from a wider range of species.
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Affiliation(s)
- Wenhui Bai
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, 030024, China
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, China, 518000, Shenzhen
| | - Cheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, China, 518000, Shenzhen
| | - Wei Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, China, 518000, Shenzhen
| | - Hai Wang
- National Maize Improvement Center, Key Laboratory of Crop Heterosis and Utilization, Joint Laboratory for International Cooperation in Crop Molecular Breeding, China Agricultural University, Beijing, 100193, China
| | - Xiaohong Han
- College of Computer Science and Technology (College of Data Science), Taiyuan University of Technology, Taiyuan, 030024, China.
| | - Peipei Wang
- Kunpeng Institute of Modern Agriculture at Foshan, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China.
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, China, 518000, Shenzhen.
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Yang J, Chen R, Wang C, Li C, Ye W, Zhang Z, Wang S. A widely targeted metabolite modificomics strategy for modified metabolites identification in tomato. J Integr Plant Biol 2024; 66:810-823. [PMID: 38375781 DOI: 10.1111/jipb.13629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 02/04/2024] [Indexed: 02/21/2024]
Abstract
The structural and functional diversity of plant metabolites is largely created via chemical modification of a basic backbone. However, metabolite modifications in plants have still not been thoroughly investigated by metabolomics approaches. In this study, a widely targeted metabolite modificomics (WTMM) strategy was developed based on ultra-high performance liquid chromatography-quadrupole-linear ion trap (UHPLC-Q-Trap) and UHPLC-Q-Exactive-Orbitrap (UHPLC-QE-Orbitrap), which greatly improved the detection sensitivity and the efficiency of identification of modified metabolites. A metabolite modificomics study was carried out using tomato as a model, and over 34,000 signals with MS2 information were obtained from approximately 232 neutral loss transitions. Unbiased metabolite profiling was also performed by utilizing high-resolution mass spectrometry data to annotate a total of 2,118 metabolites with 125 modification types; of these, 165 modified metabolites were identified in this study. Next, the WTMM database was used to assess diseased tomato tissues and 29 biomarkers were analyzed. In summary, the WTMM strategy is not only capable of large-scale detection and quantitative analysis of plant-modified metabolites in plants, but also can be used for plant biomarker development.
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Affiliation(s)
- Jun Yang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
| | - Ridong Chen
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
| | - Chao Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
| | - Chun Li
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
| | - Weizhen Ye
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
| | - Zhonghui Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
| | - Shouchuang Wang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, 572025, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, 572208, China
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Horn PJ, Chapman KD. Imaging plant metabolism in situ. J Exp Bot 2024; 75:1654-1670. [PMID: 37889862 PMCID: PMC10938046 DOI: 10.1093/jxb/erad423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 10/25/2023] [Indexed: 10/29/2023]
Abstract
Mass spectrometry imaging (MSI) has emerged as an invaluable analytical technique for investigating the spatial distribution of molecules within biological systems. In the realm of plant science, MSI is increasingly employed to explore metabolic processes across a wide array of plant tissues, including those in leaves, fruits, stems, roots, and seeds, spanning various plant systems such as model species, staple and energy crops, and medicinal plants. By generating spatial maps of metabolites, MSI has elucidated the distribution patterns of diverse metabolites and phytochemicals, encompassing lipids, carbohydrates, amino acids, organic acids, phenolics, terpenes, alkaloids, vitamins, pigments, and others, thereby providing insights into their metabolic pathways and functional roles. In this review, we present recent MSI studies that demonstrate the advances made in visualizing the plant spatial metabolome. Moreover, we emphasize the technical progress that enhances the identification and interpretation of spatial metabolite maps. Within a mere decade since the inception of plant MSI studies, this robust technology is poised to continue as a vital tool for tackling complex challenges in plant metabolism.
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Affiliation(s)
- Patrick J Horn
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton TX 76203, USA
| | - Kent D Chapman
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton TX 76203, USA
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Fabian MCP, Astorga RMN, Atis AAG, Pilapil LAE, Hernandez CC. Anti-diabetic and anti-inflammatory bioactive hits from Coriaria intermedia Matsum. stem and Dracontomelon dao (Blanco) Merr. & Rolfe bark through bioassay-guided fractionation and liquid chromatography-tandem mass spectrometry. Front Pharmacol 2024; 15:1349725. [PMID: 38523640 PMCID: PMC10957545 DOI: 10.3389/fphar.2024.1349725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 02/07/2024] [Indexed: 03/26/2024] Open
Abstract
Women have been found to be at a higher risk of morbidity and mortality from type 2 diabetes mellitus (T2DM) and asthma. α-Glucosidase inhibitors have been used to treat T2DM, and arachidonic acid 15-lipoxygenase (ALOX15) inhibitors have been suggested to be used as treatments for asthma and T2DM. Compounds that inhibit both enzymes may be studied as potential treatments for people with both T2DM and asthma. This study aimed to determine potential anti-diabetic and anti-inflammatory bioactive hits from Coriaria intermedia Matsum. stem and Dracontomelon dao (Blanco) Merr. & Rolfe bark. A bioassay-guided fractionation framework was used to generate bioactive fractions from C. intermedia stem and D. dao bark. Subsequently, dereplication through ultra-high performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) and database searching was performed to putatively identify the components of one bioactive fraction from each plant. Seven compounds were putatively identified from the C. intermedia stem active fraction, and six of these compounds were putatively identified from this plant for the first time. Nine compounds were putatively identified from the D. dao bark active fraction, and seven of these compounds were putatively identified from this plant for the first time. One putative compound from the C. intermedia stem active fraction (corilagin) has been previously reported to have inhibitory activity against both α-glucosidase and 15-lipoxygenase-1. It is suggested that further studies on the potential of corilagin as an anti-diabetic and anti-inflammatory treatment should be pursued based on its several beneficial pharmacological activities and its low reported toxicity.
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Affiliation(s)
| | | | | | | | - Christine Chichioco Hernandez
- Bioorganic and Natural Products Laboratory, Institute of Chemistry, University of the Philippines Diliman, Quezon City, Philippines
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Yang X, Yan S, Li G, Li Y, Li J, Cui Z, Sun S, Huo J, Sun Y. Rice-Magnaporthe oryzae interactions in resistant and susceptible rice cultivars under panicle blast infection based on defense-related enzyme activities and metabolomics. PLoS One 2024; 19:e0299999. [PMID: 38451992 PMCID: PMC10919634 DOI: 10.1371/journal.pone.0299999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Accepted: 02/19/2024] [Indexed: 03/09/2024] Open
Abstract
Rice blast, caused by rice blast fungus (Magnaporthe oryzae), is a global threat to food security, with up to 50% yield losses. Panicle blast is a severe form of rice blast, and disease responses vary between cultivars with different genotypes. Reactive oxygen species (ROS)-mediated signaling reactions and the phenylpropanoid pathway are important defense mechanisms involved in recognizing and resisting against fungal infection. To understand rice-M. oryzae interactions in resistant and susceptible cultivars, we determined dynamic changes in the activities of five defense-related enzymes in resistant cultivar jingsui 18 and susceptible cultivar jinyuan 899 infected with M. oryzae from 4 to 25 days after infection. We then performed untargeted metabolomics analyses to profile the metabolomes of the cultivars under infected and non-infected conditions. Dynamic changes in the activities of five defense-related enzymes were closely related to panicle blast resistance in rice. Metabolome data analysis identified 634 differentially accumulated metabolites (DAMs) between resistant and susceptible cultivars following infection, potentially explaining differences in disease response between varieties. The most enriched DAMs were associated with lipids and lipid-like molecules, phenylpropanoids and polyketides, organoheterocyclic compounds, organic acids and derivatives, and lignans, neolignans, and related compounds. Multiple metabolic pathways are involved in resistance to panicle blast in rice, including biosynthesis of other secondary metabolites, amino acid metabolism, lipid metabolism, phenylpropanoid biosynthesis, arachidonic acid metabolism, arginine biosynthesis, tyrosine metabolism, tryptophan metabolism, tyrosine and tryptophan biosynthesis, lysine biosynthesis, and oxidative phosphorylation.
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Affiliation(s)
- Xiurong Yang
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.China
| | - Shuangyong Yan
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.China
| | - Guangsheng Li
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.China
| | - Yuejiao Li
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.China
| | - Junling Li
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.China
| | - Zhongqiu Cui
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.China
| | - Shuqin Sun
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.China
| | - Jianfei Huo
- Institute of Plant Protection, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.China
| | - Yue Sun
- Institute of Crop Research, Tianjin Academy of Agricultural Sciences, Tianjin, P.R.China
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Tian Z, Jia J, Yin B, Chen W. Constructing the metabolic network of wheat kernels based on structure-guided chemical modification and multi-omics data. J Genet Genomics 2024:S1673-8527(24)00037-7. [PMID: 38458562 DOI: 10.1016/j.jgg.2024.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 02/27/2024] [Accepted: 02/27/2024] [Indexed: 03/10/2024]
Abstract
Metabolic network construction plays a pivotal role in unraveling the regulatory mechanism of biological activities, although it often proves to be challenging and labor-intensive, particularly with non-model organisms. In this study, we develop a computational approach that employs reaction models based on structure-guided chemical modification and related compounds to construct a metabolic network in wheat. This construction results in a comprehensive structure-guided network, including 625 identified metabolites and additional 333 putative reactions compared with the Kyoto Encyclopedia of Genes and Genomes database. Using a combination of gene annotation, reaction classification, structure similarity, and transcriptome and metabolome analysis correlations, a total of 229 potential genes related to these reactions are identified within this network. To validate the network, the functionality of a hydroxycinnamoyltransferase (TraesCS3D01G314900) for the synthesis of polyphenols and a rhamnosyltransferase (TraesCS2D01G078700) for the modification of flavonoids are verified through in vitro enzymatic studies and wheat mutant tests, respectively. Our research thus supports the utility of structure-guided chemical modification as an effective tool in identifying causal candidate genes for constructing metabolic networks and further in metabolomic genetic studies.
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Affiliation(s)
- Zhitao Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Jingqi Jia
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Bo Yin
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, Hubei 430070, China; Hubei Hongshan Laboratory, Wuhan, Hubei 430070, China.
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Zhao Y, Chen Y, Gao M, Wang Y. Alcohol dehydrogenases regulated by a MYB44 transcription factor underlie Lauraceae citral biosynthesis. Plant Physiol 2024; 194:1674-1691. [PMID: 37831423 DOI: 10.1093/plphys/kiad553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/18/2023] [Accepted: 09/23/2023] [Indexed: 10/14/2023]
Abstract
Lineage-specific terpenoids have arisen throughout the evolution of land plants and are believed to play a role in interactions between plants and the environment. Species-specific gene clusters in plants have provided insight on the evolution of secondary metabolism. Lauraceae is an ecologically important plant family whose members are also of considerable economic value given their monoterpene contents. However, the gene cluster responsible for the biosynthesis of monoterpenes remains yet to be elucidated. Here, a Lauraceae-specific citral biosynthetic gene cluster (CGC) was identified and investigated using a multifaceted approach that combined phylogenetic, collinearity, and biochemical analyses. The CGC comprises MYB44 as a regulator and 2 alcohol dehydrogenases (ADHs) as modifying enzymes, which derived from species-specific tandem and proximal duplication events. Activity and substrate divergence of the ADHs has resulted in the fruit of mountain pepper (Litsea cubeba), a core Lauraceae species, consisting of more than 80% citral. In addition, MYB44 negatively regulates citral biosynthesis by directly binding to the promoters of the ADH-encoding genes. The aggregation of citral biosynthetic pathways suggests that they may form the basis of important characteristics that enhance adaptability. The findings of this study provide insights into the evolution of and the regulatory mechanisms involved in plant terpene biosynthesis.
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Affiliation(s)
- Yunxiao Zhao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Ming Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
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Li X, Lin Y, Qin Y, Han G, Wang H, Yan Z. Beneficial endophytic fungi improve the yield and quality of Salvia miltiorrhiza by performing different ecological functions. PeerJ 2024; 12:e16959. [PMID: 38406278 PMCID: PMC10894594 DOI: 10.7717/peerj.16959] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/25/2024] [Indexed: 02/27/2024] Open
Abstract
Background Endophytic fungi can enhance the growth and synthesis of secondary metabolites in medicinal plants. Salvia miltiorrhiza Bunge is frequently employed for treating cardiovascular and cerebrovascular ailments, with the primary bioactive components being salvianolic acid and tanshinone. However, their levels in cultivated S. miltiorrhiza are inferior to that of the wild herbs, so the production of high-quality medicinal herbs is sharply declining. Consequently, the utilization of beneficial endophytic fungi to improve the yield and quality of S. miltiorrhiza holds great significance for the cultivation of medicinal plants. Methods In this study, nine non-pathogenic, endophytic fungal strains were introduced into sterile S. miltiorrhiza seedlings and cultivated both in vitro and in situ (the greenhouse). The effects of these strains on the growth indices, C and N metabolism, antioxidant activity, photosynthesis, and content of bioactive ingredients in S. miltiorrhiza were then evaluated. Results The results showed that the different genera, species, or strains of endophytic fungi regulated the growth and metabolism of S. miltiorrhiza in unique ways. These endophytic fungi primarily exerted their growth-promoting effects by increasing the net photosynthetic rate, intercellular CO2 concentration, and the activities of sucrose synthase, sucrose phosphate synthase, nitrate reductase, and glutamine synthetase. They also enhanced the adaptability and resistance to environmental stresses by improving the synthesis of osmoregulatory compounds and the activity of antioxidant enzymes. However, their regulatory effects on the growth and development of S. miltiorrhiza were affected by environmental changes. Moreover, the strains that significantly promoted the synthesis and accumulation of phenolic acids inhibited the accumulation of tanshinones components, and vice versa. The endophytic fungal strains Penicillium meloforme DS8, Berkeleyomyces basicola DS10, and Acremonium sclerotigenum DS12 enhanced the bioaccumulation of tanshinones. Fusarium solani DS16 elevated the rosmarinic acid content and yields in S. miltiorrhiza. The strain Penicillium javanicum DS5 improved the contents of dihydrotanshinone, salvianolic acid B, and rosmarinic acid. The strains P. meloforme DS8 and B. basicola DS10 improved resistance. Conclusion Various endophytic fungi affected the quality and yield of S. miltiorrhiza by regulating different physiological and metabolic pathways. This study also provides a novel and effective method to maximize the effects of beneficial endophytic fungi by selecting specific strains to design microbial communities based on the different ecological functions of endophytic fungi under varying environments and for specific production goals.
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Affiliation(s)
- Xiaoyu Li
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yali Lin
- Patent Examination Cooperation Sichuan Center of the Patent Office, CNIPA, Chengdu, Sichaun, China
| | - Yong Qin
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Guiqi Han
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Hai Wang
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Zhuyun Yan
- State Key Laboratory of Characteristic Chinese Medicine Resources in Southwest China, School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- School of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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Gao XM, Wang X, Ma WS, Yang Y, Tang LP, Yang B. Comparative metabolome profiling of Paris polyphylla var. yunnanensis cultivars and Paris luquanensis and their biological activity in zebrafish model. J Ethnopharmacol 2024; 319:117272. [PMID: 37820995 DOI: 10.1016/j.jep.2023.117272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 08/18/2023] [Accepted: 10/02/2023] [Indexed: 10/13/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Paris polyphylla var. Yunnanensis (Franch.) Hand.-Mazz., a perennial medicinal herb commonly known as "Chonglou" in Chinese, is mainly effective against innominate toxin swelling, insect sting, snake bite, traumatic injuries and various inflammatory. It is also recorded with mild toxicity. The rare species Paris luquanensis H. Li has been also used as folk medicine in Yunnan province for the same effects. Compared with P. polyphylla var. Yunnanensis (35-100 cm in height), this species has variegated leaves, and grows slower and is therefore shorter (6-23 cm in height). There are a number of different cultivars based on the shape of the petal and the height of Paris plant. However, currently, investigations into the differences of the chemical profiling of these cultivars are lacking. AIM OF THE STUDY This study aims to: (1) examine metabolites variations in Paris polyphylla var. Yunnanensis cultivars and Paris luquanensis; (2) investigate the different metabolite accumulation patterns between rhizomes and leaves and provide more useful information for the application of P. polyphylla var. Yunnanensis leaves; (3) compare in vivo effects on the recruitment of reactive oxygen species (ROS) and Neutrophils and toxic effects in zebrafish model between leaves and rhizomes of P. polyphylla var. Yunnanensis and P. luquanensis. MATERIALS AND METHODS The change patterns of metabolites in the leaves and rhizomes of four P. polyphylla var. Yunnanensis cultivars and one P. luquanensis cultivar were analyzed using an UPLC-ESI-MS/MS system. The total phenolic acid, total flavonoid, total saponin components and in vitro antioxidant activities were determined by spectrophotometric methods. The in vivo toxicity and their effects on the recruitment of ROS and neutrophils in zebrafish model were performed. RESULTS The widely targeted metabolomics method detected 695 metabolites in tested samples and classified as 15 known classes according to structures of the metabolites. By overall-comparing the SDMs discerned between leaves and rhizomes of each samples, 161 metabolites were substantially altered in all the cultivars. There are 62 and 64 SDMs showing constitutive differential accumulation between leaves and rhizomes of P. polyphylla var. Yunnanensis (samples A-D) and P. luquanensis (sample E), respectively. The levels of TSC, TPC and TFC decreased significantly in leaves as compared to rhizomes for all cultivars, with the exception of TPC in cultivar A, which is almost the same in leave and rhizome. The DPPH scavenging property and FRAP values of rhizomes are higher than those of leaves for all cultivars. However, there is no distinct different between leaves and rhizomes of different sample extracts for in vivo effects on the recruitment of ROS and neutrophils in zebrafish model. BL extracts showed high toxicity to the developing embryos. CONCLUSION As far as we are concerned, this study analyzes the P. polyphylla var. Yunnanensis and P. luquanensis variegation from the perspective of the metabolites pattern for the first time. The results give a valuable insight into the specie metabolic profiling and in vivo anti-oxidant, anti-inflammatory and toxic effects of these Paris plants.
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Affiliation(s)
- Xue Mei Gao
- The Academician Workstation, Jiangxi University of Chinese Medicine, Nanchang, 330004, Jiangxi, PR China.
| | - Xin Wang
- The Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, Yunnan, PR China
| | - Wei Si Ma
- The Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, Yunnan, PR China
| | - Yan Yang
- The Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, Yunnan, PR China
| | - Li Ping Tang
- The Academician Workstation, Jiangxi University of Chinese Medicine, Nanchang, 330004, Jiangxi, PR China
| | - Bin Yang
- The Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205, Yunnan, PR China.
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12
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Zhao J, Xu Y, Li H, An W, Yin Y, Wang B, Wang L, Wang B, Duan L, Ren X, Liang X, Wang Y, Wan R, Huang T, Zhang B, Li Y, Luo J, Cao Y. Metabolite-based genome-wide association studies enable the dissection of the genetic bases of flavonoids, betaine and spermidine in wolfberry (Lycium). Plant Biotechnol J 2024. [PMID: 38194521 DOI: 10.1111/pbi.14278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 10/28/2023] [Accepted: 12/14/2023] [Indexed: 01/11/2024]
Abstract
Wolfberry is a plant with medicinal and food values. However, its bioactive ingredients and the corresponding genetic bases have not been determined. Here, we de novo generated a chromosome-level genome assembly for wolfberry, yielding a genome sequence of ~1.77 Gb with contig N50 of 50.55 Mb and 39 224 predicted gene models. A variation map, using 307 re-sequenced accessions, was called based on this genome assembly. Furthermore, the fruit metabolome of these accessions was profiled using 563 annotated metabolites, which separated Lycium barbarum L. and non-L. barbarum L. The flavonoids, coumarins, alkaloids and nicotinic acid contents were higher in the former than in the latter. A metabolite-based genome-wide association study mapped 156 164 significant single nucleotide polymorphisms corresponding to 340 metabolites. This included 19 219 unique lead single nucleotide polymorphisms in 1517 significant association loci, of which three metabolites, flavonoids, betaine and spermidine, were highlighted. Two candidate genes, LbUGT (evm.TU.chr07.2692) and LbCHS (evm.TU.chr07.2738), with non-synonymous mutations, were associated with the flavonoids content. LbCHS is a structural gene that interacts with a nearby MYB transcription factor (evm.TU.chr07.2726) both in L. barbarum and L. ruthenicum. Thus, these three genes might be involved in the biosynthesis/metabolism of flavonoids. LbSSADH (evm.TU.chr09.627) was identified as possibly participating in betaine biosynthesis/metabolism. Four lycibarbarspermidines (E-G and O) were identified, and only the lycibarbarspermidines O content was higher in L. barbarum varieties than in non-L. barbarum varieties. The evm.TU.chr07.2680 gene associated with lycibarbarspermidines O was annotated as an acetyl-CoA-benzylalcohol acetyltransferase, suggesting that it is a candidate gene for spermidine biosynthesis. These results provide novel insights into the specific metabolite profile of non-L. barbarum L. and the genetic bases of flavonoids, betaine and spermidine biosynthesis/metabolism.
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Affiliation(s)
- Jianhua Zhao
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumchi, China
| | - Haoxia Li
- Desertification Control Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Wei An
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yue Yin
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Bin Wang
- Wuhan Matware Biotechnology Co., Ltd., Wuhan, China
| | - Liping Wang
- School of breeding and multiplcation (Sanya Institute of Breeding and Multiplication), Hainan, University, Sanya, China
| | - Bi Wang
- School of breeding and multiplcation (Sanya Institute of Breeding and Multiplication), Hainan, University, Sanya, China
| | - Linyuan Duan
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Xiaoyue Ren
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Xiaojie Liang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yajun Wang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Ru Wan
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Ting Huang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Bo Zhang
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Yanlong Li
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Jie Luo
- School of breeding and multiplcation (Sanya Institute of Breeding and Multiplication), Hainan, University, Sanya, China
| | - Youlong Cao
- National Wolfberry Engineering Research Center/Wolfberry Science Research Institute, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
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13
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Tian Z, Hu X, Xu Y, Liu M, Liu H, Li D, Hu L, Wei G, Chen W. PMhub 1.0: a comprehensive plant metabolome database. Nucleic Acids Res 2024; 52:D1579-D1587. [PMID: 37819039 PMCID: PMC10767808 DOI: 10.1093/nar/gkad811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/12/2023] [Accepted: 09/20/2023] [Indexed: 10/13/2023] Open
Abstract
The Plant Metabolome Hub (PMhub), available at https://pmhub.org.cn, is a valuable resource designed to provide scientists with comprehensive information on plant metabolites. It offers extensive details about their reference spectra, genetic foundations, chemical reactions, metabolic pathways and biological functions. The PMhub contains chemical data for 188 837 plant metabolites gathered from various sources, with 1 467 041 standard/in-silico high-resolution tandem mass-spectrometry (HRMS/MS) spectra corresponding to these metabolites. Beyond its extensive literature-derived data, PMhub also boasts a sizable collection of experimental metabolites; it contains 144 366 detected features in 10 typical plant species, with 16 423 successfully annotated by using standard/in-silico HRMS/MS data, this collection is further supplemented with thousands of features gathered from reference metabolites. For each metabolite, the PMhub enables the reconstructed of a simulated network based on structural similarities and existing metabolic pathways. Unlike previous plant-specific metabolome databases, PMhub not only contains a vast amount of metabolic data but also assembles the corresponding genomic and/or transcriptomic information, incorporating multiple methods for the comprehensive genetic analysis of metabolites. To validate the practicality, we verified a synthetic pathway for N-p-coumaroyltyramine by in vitro enzymatic activity experiments. In summary, the robust functionality provided by the PMhub will make it an indispensable tool for studying plant metabolomics.
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Affiliation(s)
- Zhitao Tian
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xin Hu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yingying Xu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Mengmeng Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Hongbo Liu
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Dongqin Li
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
| | - Lisong Hu
- Spice and Beverage Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wanning, Hainan 571533, China
| | - Guozhu Wei
- BioBioPha Co., Ltd., Kunming 650201, China
| | - Wei Chen
- National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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14
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Ahn G, Ban YJ, Shin GI, Jeong SY, Park KH, Kim WY, Cha JY. Ethylene enhances transcriptions of asparagine biosynthetic genes in soybean ( Glycine max L. Merr) leaves. Plant Signal Behav 2023; 18:2287883. [PMID: 38019725 PMCID: PMC10761183 DOI: 10.1080/15592324.2023.2287883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/19/2023] [Indexed: 12/01/2023]
Abstract
Soybean, a vital protein-rich crop, offers bioactivity that can mitigate various chronic human diseases. Nonetheless, soybean breeding poses a challenge due to the negative correlation between enhanced protein levels and overall productivity. Our previous studies demonstrated that applying gaseous phytohormone, ethylene, to soybean leaves significantly boosts the accumulation of free amino acids, particularly asparagine (Asn). Current studies also revealed that ethylene application to soybeans significantly enhanced both essential and non-essential amino acid contents in leaves and stems. Asn plays a crucial role in ammonia detoxification and reducing fatigue. However, the molecular evidence supporting this phenomenon remains elusive. This study explores the molecular mechanisms behind enhanced Asn accumulation in ethylene-treated soybean leaves. Transcriptional analysis revealed that ethylene treatments to soybean leaves enhance the transcriptional levels of key genes involved in Asn biosynthesis, such as aspartate aminotransferase (AspAT) and Asn synthetase (ASN), which aligns with our previous observations of elevated Asn levels. These findings shed light on the role of ethylene in upregulating Asn biosynthetic genes, subsequently enhancing Asn concentrations. This molecular insight into amino acid metabolism regulation provides valuable knowledge for the metabolic farming of crops, especially in elevating nutraceutical ingredients with non-genetic modification (GM) approach for improved protein content.
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Affiliation(s)
- Gyeongik Ahn
- Division of Applied Life Science (BK21four), IALS, RILS, and PBRRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Yeong Jun Ban
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Republic of Korea
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21four), IALS, RILS, and PBRRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Song Yi Jeong
- Division of Applied Life Science (BK21four), IALS, RILS, and PBRRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Ki Hun Park
- Division of Applied Life Science (BK21four), IALS, RILS, and PBRRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21four), IALS, RILS, and PBRRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Joon-Yung Cha
- Division of Applied Life Science (BK21four), IALS, RILS, and PBRRC, Gyeongsang National University, Jinju, Republic of Korea
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15
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Raclariu-Manolică AC, Socaciu C. In Search of Authenticity Biomarkers in Food Supplements Containing Sea Buckthorn: A Metabolomics Approach. Foods 2023; 12:4493. [PMID: 38137297 PMCID: PMC10742966 DOI: 10.3390/foods12244493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 12/24/2023] Open
Abstract
Sea buckthorn (Hippophae rhamnoides L.) (SB) is increasingly consumed worldwide as a food and food supplement. The remarkable richness in biologically active phytochemicals (polyphenols, carotenoids, sterols, vitamins) is responsible for its purported nutritional and health-promoting effects. Despite the considerable interest and high market demand for SB-based supplements, a limited number of studies report on the authentication of such commercially available products. Herein, untargeted metabolomics based on ultra-high-performance liquid chromatography coupled with quadrupole-time of flight mass spectrometry (UHPLC-QTOF-ESI+MS) were able to compare the phytochemical fingerprint of leaves, berries, and various categories of SB-berry herbal supplements (teas, capsules, tablets, liquids). By untargeted metabolomics, a multivariate discrimination analysis and a univariate approach (t-test and ANOVA) showed some putative authentication biomarkers for berries, e.g., xylitol, violaxanthin, tryptophan, quinic acid, quercetin-3-rutinoside. Significant dominant molecules were found for leaves: luteolin-5-glucoside, arginine, isorhamnetin 3-rutinoside, serotonin, and tocopherol. The univariate analysis showed discriminations between the different classes of food supplements using similar algorithms. Finally, eight molecules were selected and considered significant putative authentication biomarkers. Further studies will be focused on quantitative evaluation.
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Affiliation(s)
- Ancuța Cristina Raclariu-Manolică
- Stejarul Research Centre for Biological Sciences, National Institute of Research and Development for Biological Sciences, 610004 Piatra Neamț, Romania;
| | - Carmen Socaciu
- Faculty of Food Science and Technology, University of Agricultural Sciences and Veterinary Medicine Cluj Napoca, 400372 Cluj-Napoca, Romania
- BIODIATECH—Research Center for Applied Biotechnology in Diagnosis and Molecular Therapy, 400478 Cluj-Napoca, Romania
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16
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Zhao Y, Chen Y, Gao M, Wu L, Wang Y. LcMYB106 suppresses monoterpene biosynthesis by negatively regulating LcTPS32 expression in Litsea cubeba. Tree Physiol 2023; 43:2150-2161. [PMID: 37682081 DOI: 10.1093/treephys/tpad111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 05/15/2023] [Accepted: 09/05/2023] [Indexed: 09/09/2023]
Abstract
Litsea cubeba, the core species of the Lauraceae family, is valuable for the production of essential oils due to its high concentration of monoterpenes (90%). The key monoterpene synthase and metabolic regulatory network of monoterpene biosynthesis have provided new insights for improving essential oil content. However, there are few studies on the regulation mechanism of monoterpenes in L. cubeba. In this study, we investigated LcTPS32, a member of the TPS-b subfamily, and identified its function as an enzyme for the synthesis of monoterpenes, including geraniol, α-pinene, β-pinene, β-myrcene, linalool and eucalyptol. The quantitative real-time PCR analysis showed that LcTPS32 was highly expressed in the fruits of L. cubeba and contributed to the characteristic flavor of its essential oil. Overexpression of LcTPS32 resulted in a significant increase in the production of monoterpenes in L. cubeba by activating both the MVA and MEP pathways. Additionally, the study revealed that LcMYB106 played a negative regulatory role in monoterpenes biosynthesis by directly binding to the promoter of LcTPS32. Our study indicates that LcMYB106 could serve as a crucial target for metabolic engineering endeavors, aiming at enhancing the monoterpene biosynthesis in L. cubeba.
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Affiliation(s)
- Yunxiao Zhao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Rd, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Daqiao Rd, Hangzhou, Zhejiang 311400, China
| | - Yicun Chen
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Rd, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Daqiao Rd, Hangzhou, Zhejiang 311400, China
| | - Ming Gao
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Rd, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Daqiao Rd, Hangzhou, Zhejiang 311400, China
| | - Liwen Wu
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Rd, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Daqiao Rd, Hangzhou, Zhejiang 311400, China
| | - Yangdong Wang
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Xiangshan Rd, Beijing 100091, China
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Daqiao Rd, Hangzhou, Zhejiang 311400, China
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Li K, Cheng Y, Fang C. OsDWARF10, transcriptionally repressed by OsSPL3, regulates the nutritional metabolism of polished rice. Front Plant Sci 2023; 14:1322463. [PMID: 38130489 PMCID: PMC10733476 DOI: 10.3389/fpls.2023.1322463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 11/21/2023] [Indexed: 12/23/2023]
Abstract
Strigolactone (SL) plays essential roles in plant development and the metabolism of rice leaves. However, the impact of SL on the accumulation of nutritional metabolites in polished rice, as well as the transcription factors directly involved in SL synthesis, remains elusive. In this study, we performed a metabolome analysis on polished rice samples from mutants of an SL biosynthetic gene, OsDWARF10 (OsD10). Compared with those in the wild type plants, primary and secondary metabolites exhibited a series of alterations in the d10 mutants. Notably, the d10 mutants showed a substantial increase in the amino acids and vitamins content. Through a yeast one-hybridization screening assay, we identified OsSPL3 as a transcription factor that binds to the OsD10 promoter, thereby inhibiting OsD10 transcription in vivo and in vitro. Furthermore, we conducted a metabolic profiling analysis in polished rice from plants that overexpressed OsSPL3 and observed enhanced levels of amino acids and vitamins. This study identified a novel transcriptional repressor of the SL biosynthetic gene and elucidated the regulatory roles of OsSPL3 and OsD10 on the accumulation of nutritional metabolites in polished rice.
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Affiliation(s)
- Kang Li
- Hainan Yazhou Bay Seed Laboratory, Scool of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Yan Cheng
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
| | - Chuanying Fang
- Hainan Yazhou Bay Seed Laboratory, Scool of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Sanya, China
- School of Tropical Agriculture and Forestry, Hainan University, Haikou, China
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18
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Tan J, Shen M, Chai N, Liu Q, Liu YG, Zhu Q. Genome editing for plant synthetic metabolic engineering and developmental regulation. J Plant Physiol 2023; 291:154141. [PMID: 38016350 DOI: 10.1016/j.jplph.2023.154141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/31/2023] [Accepted: 11/17/2023] [Indexed: 11/30/2023]
Abstract
Plant metabolism and development are a reflection of the orderly expression of genetic information intertwined with the environment interactions. Genome editing is the cornerstone for scientists to modify endogenous genes or introduce exogenous functional genes and metabolic pathways, holding immense potential applications in molecular breeding and biosynthesis. Over the course of nearly a decade of development, genome editing has advanced significantly beyond the simple cutting of double-stranded DNA, now enabling precise base and fragment replacements, regulation of gene expression and translation, as well as epigenetic modifications. However, the utilization of genome editing in plant synthetic metabolic engineering and developmental regulation remains exploratory. Here, we provide an introduction and a comprehensive overview of the editing attributes associated with various CRISPR/Cas tools, along with diverse strategies for the meticulous control of plant metabolic pathways and developments. Furthermore, we discuss the limitations of current approaches and future prospects for genome editing-driven plant breeding.
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Affiliation(s)
- Jiantao Tan
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China.
| | - Mengyuan Shen
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Nan Chai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qi Liu
- Rice Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Genetics and Breeding of High-Quality Rice in Southern China (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Rice Engineering Laboratory, Guangzhou, 510640, China
| | - Yao-Guang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qinlong Zhu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Laboratory for Lingnan Modern Agriculture, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
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Laoué J, Havaux M, Ksas B, Tuccio B, Lecareux C, Fernandez C, Ormeño E. Long-term rain exclusion in a Mediterranean forest: response of physiological and physico-chemical traits of Quercus pubescens across seasons. Plant J 2023; 116:1293-1308. [PMID: 37596909 DOI: 10.1111/tpj.16424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/21/2023] [Accepted: 08/04/2023] [Indexed: 08/21/2023]
Abstract
With climate change, an aggravation in summer drought is expected in the Mediterranean region. To assess the impact of such a future scenario, we compared the response of Quercus pubescens, a drought-resistant deciduous oak species, to long-term amplified drought (AD) (partial rain exclusion in natura for 10 years) and natural drought (ND). We studied leaf physiological and physico-chemical trait responses to ND and AD over the seasonal cycle, with a focus on chemical traits including major groups of central (photosynthetic pigments and plastoquinones) and specialized (tocochromanols, phenolic compounds, and cuticular waxes) metabolites. Seasonality was the main driver of all leaf traits, including cuticular triterpenoids, which were highly concentrated in summer, suggesting their importance to cope with drought and thermal stress periods. Under AD, trees not only reduced CO2 assimilation (-42%) in summer and leaf concentrations of some phenolic compounds and photosynthetic pigments (carotenoids from the xanthophyll cycle) but also enhanced the levels of other photosynthetic pigments (chlorophylls, lutein, and neoxanthin) and plastochromanol-8, an antioxidant located in chloroplasts. Overall, the metabolomic adjustments across seasons and drought conditions reinforce the idea that Q. pubescens is highly resistant to drought although significant losses of antioxidant defenses and photoprotection were identified under AD.
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Affiliation(s)
- Justine Laoué
- Aix Marseille Univ., Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | - Michel Havaux
- Aix Marseille Univ., CEA, CNRS UMR 7265 BIAM, CEA/Cadarache, Saint-Paul-lès-Durance, France
| | - Brigitte Ksas
- Aix Marseille Univ., CEA, CNRS UMR 7265 BIAM, CEA/Cadarache, Saint-Paul-lès-Durance, France
| | | | - Caroline Lecareux
- Aix Marseille Univ., Univ Avignon, CNRS, IRD, IMBE, Marseille, France
| | | | - Elena Ormeño
- Aix Marseille Univ., Univ Avignon, CNRS, IRD, IMBE, Marseille, France
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Jue DW, Sang XL, Li ZX, Zhang WL, Liao QH, Tang J. Determination of the effects of pre-harvest bagging treatment on kiwifruit appearance and quality via transcriptome and metabolome analyses. Food Res Int 2023; 173:113276. [PMID: 37803588 DOI: 10.1016/j.foodres.2023.113276] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/08/2023] [Accepted: 07/11/2023] [Indexed: 10/08/2023]
Abstract
Bagging is an effective cultivation strategy to produce attractive and pollution-free kiwifruit. However, the effect and metabolic regulatory mechanism of bagging treatment on kiwifruit quality remain unclear. In this study, transcriptome and metabolome analyses were conducted to determine the regulatory network of the differential metabolites and genes after bagging. Using outer and inner yellow single-layer fruit bags, we found that bagging treatment improved the appearance of kiwifruit, increased the soluble solid content (SSC) and carotenoid and anthocyanin levels, and decreased the chlorophyll levels. We also identified 41 differentially expressed metabolites and 897 differentially expressed genes (DEGs) between the bagged and control 'Hongyang' fruit. Transcriptome and metabolome analyses revealed that the increase in SSC after bagging treatment was mainly due to the increase in D-glucosamine metabolite levels and eight DEGs involved in amino sugar and nucleotide sugar metabolic pathways. A decrease in glutamyl-tRNA reductase may be the main reason for the decrease in chlorophyll. Downregulation of lycopene epsilon cyclase and 9-cis-epoxycarotenoid dioxygenase increased carotenoid levels. Additionally, an increase in the levels of the taxifolin-3'-O-glucoside metabolite, flavonoid 3'-monooxygenase, and some transcription factors led to the increase in anthocyanin levels. This study provides novel insights into the effects of bagging on the appearance and internal quality of kiwifruit and enriches our theoretical knowledge on the regulation of color pigment synthesis in kiwifruit.
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Affiliation(s)
- Deng-Wei Jue
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan 402160, China; Southwest University, College of Horticulture and Landscape, Chongqing 400715, China
| | - Xue-Lian Sang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan 402160, China.
| | - Zhe-Xin Li
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan 402160, China
| | - Wen-Lin Zhang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan 402160, China
| | - Qin-Hong Liao
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan 402160, China
| | - Jianmin Tang
- Chongqing Key Laboratory of Economic Plant Biotechnology, Collaborative Innovation Center of Special Plant Industry in Chongqing, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, Yongchuan 402160, China.
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21
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Shen S, Wang S, Yang C, Wang C, Zhou Q, Zhou S, Zhang R, Li Y, Wang Z, Dai L, Peng W, Hao Y, Guo H, Cao G, Liu X, Yao F, Xu Q, Fernie AR, Luo J. Elucidation of the melitidin biosynthesis pathway in pummelo. J Integr Plant Biol 2023; 65:2505-2518. [PMID: 37675654 DOI: 10.1111/jipb.13564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 09/06/2023] [Indexed: 09/08/2023]
Abstract
Specialized plant metabolism is a rich resource of compounds for drug discovery. The acylated flavonoid glycoside melitidin is being developed as an anti-cholesterol statin drug candidate, but its biosynthetic route in plants has not yet been fully characterized. Here, we describe the gene discovery and functional characterization of a new flavonoid gene cluster (UDP-glucuronosyltransferases (CgUGTs), 1,2 rhamnosyltransferase (Cg1,2RhaT), acyltransferases (CgATs)) that is responsible for melitidin biosynthesis in pummelo (Citrus grandis (L.) Osbeck). Population variation analysis indicated that the tailoring of acyltransferases, specific for bitter substrates, mainly determine the natural abundance of melitidin. Moreover, 3-hydroxy-3-methylglutaryl-CoA reductase enzyme inhibition assays showed that the product from this metabolic gene cluster, melitidin, may be an effective anti-cholesterol statin drug candidate. Co-expression of these clustered genes in Nicotiana benthamiana resulted in the formation of melitidin, demonstrating the potential for metabolic engineering of melitidin in a heterologous plant system. This study establishes a biosynthetic pathway for melitidin, which provides genetic resources for the breeding and genetic improvement of pummelo aimed at fortifying the content of biologically active metabolites.
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Affiliation(s)
- Shuangqian Shen
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Shouchuang Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Chenkun Yang
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Chao Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Qianqian Zhou
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shen Zhou
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Ran Zhang
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Yufei Li
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Zixuan Wang
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Liupan Dai
- Hubei Hongshan Laboratory, College of Life Science and Technology, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenjv Peng
- National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, China
| | - Yingchen Hao
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Hao Guo
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Guangping Cao
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Xianqing Liu
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
| | - Fan Yao
- Hubei Hongshan Laboratory, College of Life Science and Technology, College of Biomedicine and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology of Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, 14476, Germany
- Centre of Plant Systems Biology and Biotechnology, Plovdiv, 4000, Bulgaria
| | - Jie Luo
- Sanya Nanfan Research Institute of Hainan University, Hainan University, Sanya, 572025, China
- Yazhouwan National Laboratory, Sanya, 572025, China
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22
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Colombié S, Prigent S, Cassan C, Hilbert-Masson G, Renaud C, Dell'Aversana E, Carillo P, Moing A, Beaumont C, Beauvoit B, McCubbin T, Nielsen LK, Gibon Y. Comparative constraint-based modelling of fruit development across species highlights nitrogen metabolism in the growth-defence trade-off. Plant J 2023; 116:786-803. [PMID: 37531405 DOI: 10.1111/tpj.16409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 08/04/2023]
Abstract
Although primary metabolism is well conserved across species, it is useful to explore the specificity of its network to assess the extent to which some pathways may contribute to particular outcomes. Constraint-based metabolic modelling is an established framework for predicting metabolic fluxes and phenotypes and helps to explore how the plant metabolic network delivers specific outcomes from temporal series. After describing the main physiological traits during fruit development, we confirmed the correlations between fruit relative growth rate (RGR), protein content and time to maturity. Then a constraint-based method is applied to a panel of eight fruit species with a knowledge-based metabolic model of heterotrophic cells describing a generic metabolic network of primary metabolism. The metabolic fluxes are estimated by constraining the model using a large set of metabolites and compounds quantified throughout fruit development. Multivariate analyses showed a clear common pattern of flux distribution during fruit development with differences between fast- and slow-growing fruits. Only the latter fruits mobilise the tricarboxylic acid cycle in addition to glycolysis, leading to a higher rate of respiration. More surprisingly, to balance nitrogen, the model suggests, on the one hand, nitrogen uptake by nitrate reductase to support a high RGR at early stages of cucumber and, on the other hand, the accumulation of alkaloids during ripening of pepper and eggplant. Finally, building virtual fruits by combining 12 biomass compounds shows that the growth-defence trade-off is supported mainly by cell wall synthesis for fast-growing fruits and by total polyphenols accumulation for slow-growing fruits.
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Affiliation(s)
- Sophie Colombié
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Sylvain Prigent
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Cédric Cassan
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Ghislaine Hilbert-Masson
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, 33882, Villenave d'Ornon, France
| | - Christel Renaud
- EGFV, Université de Bordeaux, Bordeaux Sciences Agro, INRAE, ISVV, 33882, Villenave d'Ornon, France
| | - Emilia Dell'Aversana
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100, Caserta, Italy
| | - Petronia Carillo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania "Luigi Vanvitelli", Via Vivaldi 43, 81100, Caserta, Italy
| | - Annick Moing
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
| | - Chloé Beaumont
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
| | - Bertrand Beauvoit
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
| | - Tim McCubbin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Building 75), Brisbane, QLD, 4072, Australia
| | - Lars Keld Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper Roads (Building 75), Brisbane, QLD, 4072, Australia
| | - Yves Gibon
- Univ. Bordeaux, INRAE, UMR1332 BFP, 33882, Villenave d'Ornon, France
- Bordeaux Metabolome, MetaboHUB, PHENOME-EMPHASIS, 33140, Villenave d'Ornon, France
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23
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Wen H, Yang T, Yang W, Yang M, Wang Y, Zhang J. Comparison of Metabolites and Species Classification of Thirteen Zingiberaceae Spices Based on GC-MS and Multi-Spectral Fusion Technology. Foods 2023; 12:3714. [PMID: 37893607 PMCID: PMC10606731 DOI: 10.3390/foods12203714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2023] [Revised: 09/28/2023] [Accepted: 09/30/2023] [Indexed: 10/29/2023] Open
Abstract
Due to a similar plant morphology in the majority of Zingiberaceae spices, substitution and adulteration frequently take place during the sales process. Therefore, it is important to analyze the metabolites and species classification of different Zingiberaceae spices. This study preliminarily explored the differences in the metabolites in thirteen Zingiberaceae spices through untargeted gas chromatography-mass spectrometry (GC-MS) and combined spectroscopy, establishing models for classifying different Zingiberaceae spices. On one hand, a total of 81 metabolites were successfully identified by GC-MS. Thirty-seven differential metabolites were screened using variable important in projection (VIP ≥ 1). However, the orthogonal partial least squares discriminant analysis (OPLS-DA) model established using GC-MS data only explained about 30% of the variation. On the other hand, the partial least squares discriminant analysis (PLS-DA) models with three spectral data fusion strategies were compared, and their classification accuracy reached 100%. Among them, the mid-level data fusion model based on latent variables had the best performance. This study provides a powerful tool for distinguishing different Zingiberaceae spices and assists in reducing the occurrence of substitution and adulteration phenomena.
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Affiliation(s)
- Hui Wen
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China; (H.W.); (T.Y.); (W.Y.); (M.Y.); (Y.W.)
- School of Agriculture, Yunnan University, Kunming 650504, China
| | - Tianmei Yang
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China; (H.W.); (T.Y.); (W.Y.); (M.Y.); (Y.W.)
| | - Weize Yang
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China; (H.W.); (T.Y.); (W.Y.); (M.Y.); (Y.W.)
| | - Meiquan Yang
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China; (H.W.); (T.Y.); (W.Y.); (M.Y.); (Y.W.)
| | - Yuanzhong Wang
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China; (H.W.); (T.Y.); (W.Y.); (M.Y.); (Y.W.)
| | - Jinyu Zhang
- Medicinal Plants Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650200, China; (H.W.); (T.Y.); (W.Y.); (M.Y.); (Y.W.)
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24
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Segarra-Medina C, Alseekh S, Fernie AR, Rambla JL, Pérez-Clemente RM, Gómez-Cádenas A, Zandalinas SI. Abscisic acid promotes plant acclimation to the combination of salinity and high light stress. Plant Physiol Biochem 2023; 203:108008. [PMID: 37690143 DOI: 10.1016/j.plaphy.2023.108008] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/24/2023] [Accepted: 09/05/2023] [Indexed: 09/12/2023]
Abstract
Plants encounter combinations of different abiotic stresses such as salinity (S) and high light (HL). These environmental conditions have a detrimental effect on plant growth and development, posing a threat to agricultural production. Metabolic changes play a crucial role in enabling plants to adapt to fluctuations in their environment. Furthermore, hormones such as abscisic acid (ABA), jasmonic acid (JA) and salicylic acid (SA) have been previously identified as regulators of plant responses to different abiotic stresses. Here we studied the response of Arabidopsis wild type (Col and Ler) plants and mutants impaired in hormone biosynthesis (aba2-11 and aba1-1 in ABA, aos in JA and sid2 in SA) to the combination of S and HL (S + HL). Our findings showed that aba2-11 plants displayed reduced growth, impaired photosystem II (PSII) function, increased leaf damage, and decreased survival compared to Col when subjected to stress combination. However, aos and sid2 mutants did not display significant changes in response to S + HL compared to Col, indicating a key role for ABA in promoting plant tolerance to S + HL and suggesting a marginal role for JA and SA in this process. In addition, we revealed differences in the metabolic response of plants to S + HL compared to S or HL. The analysis of altered metabolic pathways under S + HL suggested that the accumulation of flavonoids is ABA-dependent, whereas the accumulation of branched-chain amino acids (BCAAs) and proline is ABA-independent. Therefore, our study uncovered a key function for ABA in regulating the accumulation of different flavonoids in plants during S + HL.
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Affiliation(s)
- Clara Segarra-Medina
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, 12071, Castellón, Spain
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany; Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany; Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - José L Rambla
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, 12071, Castellón, Spain
| | - Rosa M Pérez-Clemente
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, 12071, Castellón, Spain
| | - Aurelio Gómez-Cádenas
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, 12071, Castellón, Spain.
| | - Sara I Zandalinas
- Department of Biology, Biochemistry and Natural Sciences, Universitat Jaume I, 12071, Castellón, Spain.
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25
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Peng M, He H, Jiang M, Wang Z, Li G, Zhuang L. Morphological, physiological and metabolomic analysis to unravel the adaptive relationship between root growth of ephemeral plants and different soil habitats. Plant Physiol Biochem 2023; 202:107986. [PMID: 37651954 DOI: 10.1016/j.plaphy.2023.107986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/17/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]
Abstract
To gain insights into the adaptive characteristics of ephemeral plants and enrich their potential for resource exploitation, the adaptive changes in two highly dominant species (Malcolmia scorpioides and Isatis violascens) to soil habitats (aeolian soil, AS; grey desert soil, GS) were investigated from the aspects of root morphology, physiology, and metabolism in this study. The results revealed that changes in root morphology and enzyme activity were affected by soil habitat. Total root length (TRL), root volume (RV) and root surface area (RSA) were higher in GS than in AS. The levels of proline (Pro), glutathione (GSH), soluble sugar (SS), and lysine (Lys) were higher in GS than in AS. Untargeted LC-MS metabolomics indicates that root metabolites of both species differed among the two soil habitats. Root responses to different soil habitats mainly affected some metabolic pathways. A total of 780 metabolites were identified, common differential metabolites (DMs) in both species included amino acids, fatty acids, organic acids, carbohydrates, benzene and derivatives, and flavonoids, which were mainly involved in carbohydrate metabolism, amino acid metabolism, flavonoid biosynthesis and fatty acid metabolism, and their abundance varied among different habitats and species. Some key DMs were significantly related to root morphology and enzyme activity, and indole, malonate, quercetin, uridine, tetrahydroharmine, and gluconolactone were important metabolites associated with root growth. Therefore, the response changes in root growth and metabolite of ephemeral plants in response to soil habitats reflect their ecological adaptation, and lay a foundation for the exploitation of plant resources in various habitats.
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Affiliation(s)
- Mengwen Peng
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Hao He
- Key Laboratory of Oasis Eco-agriculture, Xinjiang Production and Construction Corps, College of Agriculture, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Meng Jiang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Zhongke Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Guifang Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, PR China
| | - Li Zhuang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, 832003, PR China.
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26
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Zemaitis KJ, Lin VS, Ahkami AH, Winkler TE, Anderton CR, Veličković D. Expanded Coverage of Phytocompounds by Mass Spectrometry Imaging Using On-Tissue Chemical Derivatization by 4-APEBA. Anal Chem 2023; 95:12701-12709. [PMID: 37594382 DOI: 10.1021/acs.analchem.3c01345] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/19/2023]
Abstract
Probing the entirety of any species metabolome is an analytical grand challenge, especially on a cellular scale. Matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) is a common spatial metabolomics assay, but this technique has limited molecular coverage for several reasons. To expand the application space of spatial metabolomics, we developed an on-tissue chemical derivatization (OTCD) workflow using 4-APEBA for the confident identification of several dozen elusive phytocompounds. Overall, this new OTCD method enabled the annotation of roughly 280 metabolites, with only a 10% overlap in metabolic coverage when compared to analog negative ion mode MALDI-MSI on serial sections. We demonstrate that 4-APEBA outperforms other derivatization agents by providing: (1) broad specificity toward carbonyls, (2) low background, and (3) introduction of bromine isotopes. Notably, the latter two attributes also facilitate more confidence in our bioinformatics for data processing. The workflow detailed here trailblazes a path toward spatial hormonomics within plant samples, enhancing the detection of carboxylates, aldehydes, and plausibly other carbonyls. As such, several phytohormones, which have various roles within stress responses and cellular communication, can now be spatially profiled, as demonstrated in poplar root and soybean root nodule.
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Affiliation(s)
- Kevin J Zemaitis
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Vivian S Lin
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Amir H Ahkami
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Tanya E Winkler
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Christopher R Anderton
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Dušan Veličković
- Earth and Biological Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
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27
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Segarra-Medina C, Pascual LS, Alseekh S, Fernie AR, Rambla JL, Gómez-Cadenas A, Zandalinas SI. Comparison of metabolomic reconfiguration between Columbia and Landsberg ecotypes subjected to the combination of high salinity and increased irradiance. BMC Plant Biol 2023; 23:406. [PMID: 37620776 PMCID: PMC10463500 DOI: 10.1186/s12870-023-04404-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 08/07/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Plants growing in the field are subjected to combinations of abiotic stresses. These conditions pose a devastating threat to crops, decreasing their yield and causing a negative economic impact on agricultural production. Metabolic responses play a key role in plant acclimation to stress and natural variation for these metabolic changes could be key for plant adaptation to fluctuating environmental conditions. RESULTS Here we studied the metabolomic response of two Arabidopsis ecotypes (Columbia-0 [Col] and Landsberg erecta-0 [Ler]), widely used as genetic background for Arabidopsis mutant collections, subjected to the combination of high salinity and increased irradiance. Our findings demonstrate that this stress combination results in a specific metabolic response, different than that of the individual stresses. Although both ecotypes displayed reduced growth and quantum yield of photosystem II, as well as increased foliar damage and malondialdehyde accumulation, different mechanisms to tolerate the stress combination were observed. These included a relocation of amino acids and sugars to act as potential osmoprotectants, and the accumulation of different stress-protective compounds such as polyamines or secondary metabolites. CONCLUSIONS Our findings reflect an initial identification of metabolic pathways that differentially change under stress combination that could be considered in studies of stress combination of Arabidopsis mutants that include Col or Ler as genetic backgrounds.
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Affiliation(s)
- Clara Segarra-Medina
- Departamento de Biología, Bioquímica Y Ciencias Naturales, Universitat Jaume I, 12071, Castelló de La Plana, Spain
| | - Lidia S Pascual
- Departamento de Biología, Bioquímica Y Ciencias Naturales, Universitat Jaume I, 12071, Castelló de La Plana, Spain
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - José L Rambla
- Departamento de Biología, Bioquímica Y Ciencias Naturales, Universitat Jaume I, 12071, Castelló de La Plana, Spain
| | - Aurelio Gómez-Cadenas
- Departamento de Biología, Bioquímica Y Ciencias Naturales, Universitat Jaume I, 12071, Castelló de La Plana, Spain.
| | - Sara I Zandalinas
- Departamento de Biología, Bioquímica Y Ciencias Naturales, Universitat Jaume I, 12071, Castelló de La Plana, Spain.
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28
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Guo H, Cao P, Wang C, Lai J, Deng Y, Li C, Hao Y, Wu Z, Chen R, Qiang Q, Fernie AR, Yang J, Wang S. Population analysis reveals the roles of DNA methylation in tomato domestication and metabolic diversity. Sci China Life Sci 2023; 66:1888-1902. [PMID: 36971992 DOI: 10.1007/s11427-022-2299-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/17/2023] [Indexed: 03/29/2023]
Abstract
DNA methylation is an important epigenetic marker, yet its diversity and consequences in tomato breeding at the population level are largely unknown. We performed whole-genome bisulfite sequencing (WGBS), RNA sequencing, and metabolic profiling on a population comprising wild tomatoes, landraces, and cultivars. A total of 8,375 differentially methylated regions (DMRs) were identified, with methylation levels progressively decreasing from domestication to improvement. We found that over 20% of DMRs overlapped with selective sweeps. Moreover, more than 80% of DMRs in tomato were not significantly associated with single-nucleotide polymorphisms (SNPs), and DMRs had strong linkages with adjacent SNPs. We additionally profiled 339 metabolites from 364 diverse accessions and further performed a metabolic association study based on SNPs and DMRs. We detected 971 and 711 large-effect loci via SNP and DMR markers, respectively. Combined with multi-omics, we identified 13 candidate genes and updated the polyphenol biosynthetic pathway. Our results showed that DNA methylation variants could complement SNP profiling of metabolite diversity. Our study thus provides a DNA methylome map across diverse accessions and suggests that DNA methylation variation can be the genetic basis of metabolic diversity in plants.
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Affiliation(s)
- Hao Guo
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Peng Cao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Chao Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Jun Lai
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Yuan Deng
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Chun Li
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Yingchen Hao
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Zeyong Wu
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Ridong Chen
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Qi Qiang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, 144776, Germany
| | - Jun Yang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China
- College of Tropical Crops, Hainan University, Haikou, 572208, China
| | - Shouchuang Wang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya, 572025, China.
- College of Tropical Crops, Hainan University, Haikou, 572208, China.
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Murthy HN, Joseph KS, Hahn JE, Lee HS, Paek KY, Park SY. Suspension culture of somatic embryos for the production of high-value secondary metabolites. Physiol Mol Biol Plants 2023; 29:1153-1177. [PMID: 37829704 PMCID: PMC10564700 DOI: 10.1007/s12298-023-01365-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 09/13/2023] [Accepted: 09/20/2023] [Indexed: 10/14/2023]
Abstract
Secondary metabolites from plants are ubiquitous and have applications in medicines, food additives, scents, colorants, and natural pesticides. Biotechnological production of secondary metabolites that have economic benefits is an attractive alternative to conventional methods. Cell, adventitious, and hairy root suspension cultures are typically used to produce secondary metabolites. According to recent studies, somatic embryos in suspension culture are useful tools for the generation of secondary metabolites. Somatic embryogenesis is a mode of regeneration in several plant species. This review provides an update on the use of somatic embryogenesis in the production of valuable secondary metabolites. The factors influencing the generation of secondary metabolites using somatic embryos in suspension cultures, elicitation methods, and prospective applications are also discussed in this review. Graphical abstract
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Affiliation(s)
- Hosakatte Niranjana Murthy
- Department of Botany, Karnatak University, Dharwad, 580003 India
- Department of Horticultural Science, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | | | - Jong-Eun Hahn
- Department of Horticultural Science, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | - Han-Sol Lee
- Department of Horticultural Science, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | - Kee Yoeup Paek
- Department of Horticultural Science, Chungbuk National University, Cheongju, 28644 Republic of Korea
| | - So Young Park
- Department of Horticultural Science, Chungbuk National University, Cheongju, 28644 Republic of Korea
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30
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Lacchini E, Venegas-Molina J, Goossens A. Structural and functional diversity in plant specialized metabolism signals and products: The case of oxylipins and triterpenes. Curr Opin Plant Biol 2023; 74:102371. [PMID: 37148672 DOI: 10.1016/j.pbi.2023.102371] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 04/03/2023] [Accepted: 04/03/2023] [Indexed: 05/08/2023]
Abstract
Metabolic enzymes tend to evolve towards catalytic efficacy, precision and speed. This seems particularly true for ancient and conserved enzymes involved in fundamental cellular processes that are present virtually in every cell and organism and converting and producing relatively limited metabolite numbers. Nevertheless, sessile organisms like plants have an astonishing repertoire of specific (specialized) metabolites that, by numbers and chemical complexity, by far exceed primary metabolites. Most theories agree that early gene duplication, subsequent positive selection and diversifying evolution have allowed relaxed selection of duplicated metabolic genes, thus facilitating the accumulation of mutations that could broaden substrate/product specificity and lower activation barriers and kinetics. Here, we use oxylipins, oxygenated fatty acids of plastidial origin to which the phytohormone jasmonate belongs, and triterpenes, a large group of specialized metabolites whose biosynthesis is often elicited by jasmonates, to showcase the structural and functional diversity of chemical signals and products in plant metabolism.
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Affiliation(s)
- Elia Lacchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Jhon Venegas-Molina
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium
| | - Alain Goossens
- Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052, Ghent, Belgium; VIB Center for Plant Systems Biology, B-9052, Ghent, Belgium.
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31
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Claude SJ, Raman G, Park SJ. Comparative Analysis and Identification of Terpene Synthase Genes in Convallaria keiskei Leaf, Flower and Root Using RNA-Sequencing Profiling. Plants (Basel) 2023; 12:2797. [PMID: 37570951 PMCID: PMC10421360 DOI: 10.3390/plants12152797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Revised: 07/13/2023] [Accepted: 07/13/2023] [Indexed: 08/13/2023]
Abstract
The 'Lilly of the Valley' species, Convallaria, is renowned for its fragrant white flowers and distinctive fresh and green floral scent, attributed to a rich composition of volatile organic compounds (VOCs). However, the molecular mechanisms underlying the biosynthesis of this floral scent remain poorly understood due to a lack of transcriptomic data. In this study, we conducted the first comparative transcriptome analysis of C. keiskei, encompassing the leaf, flower, and root tissues. Our aim was to investigate the terpene synthase (TPS) genes and differential gene expression (DEG) patterns associated with essential oil biosynthesis. Through de novo assembly, we generated a substantial number of unigenes, with the highest count in the root (146,550), followed by the flower (116,434) and the leaf (72,044). Among the identified unigenes, we focused on fifteen putative ckTPS genes, which are involved in the synthesis of mono- and sesquiterpenes, the key aromatic compounds responsible for the essential oil biosynthesis in C. keiskei. The expression of these genes was validated using quantitative PCR analysis. Both DEG and qPCR analyses revealed the presence of ckTPS genes in the flower transcriptome, responsible for the synthesis of various compounds such as geraniol, germacrene, kaurene, linalool, nerolidol, trans-ocimene and valencene. The leaf transcriptome exhibited genes related to the biosynthesis of kaurene and trans-ocimene. In the root, the identified unigenes were associated with synthesizing kaurene, trans-ocimene and valencene. Both analyses indicated that the genes involved in mono- and sesquiterpene biosynthesis are more highly expressed in the flower compared to the leaf and root. This comprehensive study provides valuable resources for future investigations aiming to unravel the essential oil-biosynthesis-related genes in the Convallaria genus.
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Affiliation(s)
| | | | - Seon-Joo Park
- Department of Life Sciences, Yeungnam University, Gyeongsan 38541, Gyeongbuk, Republic of Korea;
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32
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Dussarrat T, Schweiger R, Ziaja D, Nguyen TTN, Krause L, Jakobs R, Eilers EJ, Müller C. Influences of chemotype and parental genotype on metabolic fingerprints of tansy plants uncovered by predictive metabolomics. Sci Rep 2023; 13:11645. [PMID: 37468576 DOI: 10.1038/s41598-023-38790-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/14/2023] [Indexed: 07/21/2023] Open
Abstract
Intraspecific plant chemodiversity shapes plant-environment interactions. Within species, chemotypes can be defined according to variation in dominant specialised metabolites belonging to certain classes. Different ecological functions could be assigned to these distinct chemotypes. However, the roles of other metabolic variation and the parental origin (or genotype) of the chemotypes remain poorly explored. Here, we first compared the capacity of terpenoid profiles and metabolic fingerprints to distinguish five chemotypes of common tansy (Tanacetum vulgare) and depict metabolic differences. Metabolic fingerprints captured higher variation in metabolites while preserving the ability to define chemotypes. These differences might influence plant performance and interactions with the environment. Next, to characterise the influence of the maternal origin on chemodiversity, we performed variation partitioning and generalised linear modelling. Our findings revealed that maternal origin was a higher source of chemical variation than chemotype. Predictive metabolomics unveiled 184 markers predicting maternal origin with 89% accuracy. These markers included, among others, phenolics, whose functions in plant-environment interactions are well established. Hence, these findings place parental genotype at the forefront of intraspecific chemodiversity. We recommend considering this factor when comparing the ecology of various chemotypes. Additionally, the combined inclusion of inherited variation in main terpenoids and other metabolites in computational models may help connect chemodiversity and evolutionary principles.
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Affiliation(s)
- Thomas Dussarrat
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
| | - Rabea Schweiger
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Dominik Ziaja
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Thuan T N Nguyen
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Liv Krause
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Ruth Jakobs
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
| | - Elisabeth J Eilers
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany
- CTL GmbH Bielefeld, Krackser Straße 12, 33659, Bielefeld, Germany
| | - Caroline Müller
- Department of Chemical Ecology, Bielefeld University, Universitätsstr. 25, 33615, Bielefeld, Germany.
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Abstract
Environmental factors such as light, water, minerals, temperature, and other organisms affect plant growth and development. Unlike animals, plants can't escape from unfavorable biotic and abiotic stresses. Thus, they evolved the ability to biosynthesize specific chemicals referred to as plant specialized metabolites in order to facilitate successful interactions with the surrounding environment, as well as with other organisms including plants, insects, microorganisms, and animals. While the exact number of plant specialized metabolites, historically called secondary metabolites, is currently unknown, it has been estimated to range from 200,000 to 1,000,000 compounds. In contrast to the species-, organ- and tissue-specific nature of plant specialized metabolites, primary metabolites are shared by all living organisms, are vital for growth, development and reproduction, and comprise only about 8,000 compounds. The biosynthesis and storage of plant specialized metabolites are developmentally and temporally regulated and depend on biotic and abiotic factors. Specific cell types, subcellular organelles, microcompartments, and/or anatomical structures are often devoted to producing and storing these compounds. The functions of many specialized metabolites are still not fully understood but are generally considered to be essential for the fitness and survival of plants, partially by interacting with other organisms in both mutualistic (for example, attraction of pollinators) and antagonistic (such as defense against herbivores and pathogens) ways. In this primer, we will focus on specialized-metabolite functions in plant defense interactions and on the genetic, molecular, and biochemical mechanisms leading to the structural diversity of specialized metabolites. Though less understood, we will also touch on the mode of action of specialized metabolites in plant defense.
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Affiliation(s)
- Xing-Qi Huang
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA; Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; Purdue Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA.
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34
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Borisjuk L, Horn P, Chapman K, Jakob PM, Gündel A, Rolletschek H. Seeing plants as never before. New Phytol 2023; 238:1775-1794. [PMID: 36895109 DOI: 10.1111/nph.18871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 02/06/2023] [Indexed: 05/04/2023]
Abstract
Imaging has long supported our ability to understand the inner life of plants, their development, and response to a dynamic environment. While optical microscopy remains the core tool for imaging, a suite of novel technologies is now beginning to make a significant contribution to visualize plant metabolism. The purpose of this review was to provide the scientific community with an overview of current imaging methods, which rely variously on either nuclear magnetic resonance (NMR), mass spectrometry (MS) or infrared (IR) spectroscopy, and to present some examples of their application in order to illustrate their utility. In addition to providing a description of the basic principles underlying these technologies, the review discusses their various advantages and limitations, reveals the current state of the art, and suggests their potential application to experimental practice. Finally, a view is presented as to how the technologies will likely develop, how these developments may encourage the formulation of novel experimental strategies, and how the enormous potential of these technologies can contribute to progress in plant science.
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Affiliation(s)
- Ljudmilla Borisjuk
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
| | - Patrick Horn
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | - Kent Chapman
- Department of Biological Sciences, BioDiscovery Institute, University of North Texas, Denton, TX, 76203, USA
| | - Peter M Jakob
- Institute of Experimental Physics 5, University of Würzburg, Am Hubland, 97074, Würzburg, Germany
| | - Andre Gündel
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
| | - Hardy Rolletschek
- Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466, Seeland-Gatersleben, Germany
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35
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Alseekh S, Fernie AR. Expanding our coverage: Strategies to detect a greater range of metabolites. Curr Opin Plant Biol 2023; 73:102335. [PMID: 36689903 DOI: 10.1016/j.pbi.2022.102335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/17/2022] [Accepted: 12/26/2022] [Indexed: 06/10/2023]
Abstract
Whilst the study of metabolites can arguably be traced back several hundred years it began in earnest in the 20th century with studies based on single metabolites or simple metabolic pathways. The advent of metabolomics and in particular the adoption of high-resolution mass spectrometry now means we can faithfully annotate and quantify in excess of 1000 plant metabolites. Whilst this is an impressive leap it falls well short of the estimated number of metabolites in the plant kingdom. This, whilst considerable and important insights have been achieved using commonly utilized approaches, there is a need to improve the coverage of the metabolome. Here, we review three largely complementary strategies (i) methods based on using chemical libraries (ii) methods based on molecular networking and (iii) approaches that link metabolomics and genetic variance. It is our contention that using all three approaches in tandem represents the best approach to tackle this challenge.
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Affiliation(s)
- Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center for Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Center for Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
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Zhang D, He J, Cheng P, Zhang Y, Khan A, Wang S, Li Z, Zhao S, Zhan X, Ma F, Li X, Guan Q. 4-methylumbelliferone (4-MU) enhances drought tolerance of apple by regulating rhizosphere microbial diversity and root architecture. Hortic Res 2023; 10:uhad099. [PMID: 37427035 PMCID: PMC10327542 DOI: 10.1093/hr/uhad099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/04/2023] [Indexed: 07/11/2023]
Abstract
The dwarfing rootstocks-mediated high-density apple orchard is becoming the main practice management. Currently, dwarfing rootstocks are widely used worldwide, but their shallow root system and drought sensitivity necessitate high irrigation requirements. Here, the root transcriptome and metabolome of dwarfing (M9-T337, a drought-sensitive rootstock) and vigorous rootstocks (Malus sieversii, a drought-tolerant species, is commonly used as a rootstock) showed that a coumarin derivative, 4-Methylumbelliferon (4-MU), was found to accumulate significantly in the roots of vigorous rootstock under drought condition. When exogenous 4-MU was applied to the roots of dwarfing rootstock under drought treatment, the plants displayed increased root biomass, higher root-to-shoot ratio, greater photosynthesis, and elevated water use efficiency. In addition, diversity and structure analysis of the rhizosphere soil microbial community demonstrated that 4-MU treatment increased the relative abundance of putatively beneficial bacteria and fungi. Of these, Pseudomonas, Bacillus, Streptomyces, and Chryseolinea bacterial strains and Acremonium, Trichoderma, and Phoma fungal strains known for root growth, or systemic resistance against drought stress, were significantly accumulated in the roots of dwarfing rootstock after 4-MU treatment under drought stress condition. Taken together, we identified a promising compound-4-MU, as a useful tool, to strengthen the drought tolerance of apple dwarfing rootstock.
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Affiliation(s)
- Dehui Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
- College of Life Science, Northwest A&F University, Yangling 712100, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Pengda Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Yutian Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Abid Khan
- Department of Horticulture, The University of Haripur, Haripur 22620, Pakistan
| | - Shicong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Shuang Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Xiangqiang Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling 712100, China
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37
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Mehta N, Meng Y, Zare R, Kamenetsky-Goldstein R, Sattely E. A developmental gradient reveals biosynthetic pathways to eukaryotic toxins in monocot geophytes. bioRxiv 2023:2023.05.12.540595. [PMID: 37214939 PMCID: PMC10197729 DOI: 10.1101/2023.05.12.540595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Numerous eukaryotic toxins that accumulate in geophytic plants are valuable in the clinic, yet their biosynthetic pathways have remained elusive. A lead example is the >150 Amaryllidaceae alkaloids (AmAs) including galantamine, an FDA-approved treatment for Alzheimer's disease. We show that while AmAs accumulate to high levels in many tissues in daffodils, biosynthesis is localized to nascent, growing tissue at the base of leaves. A similar trend is found for the production of steroidal alkaloids (e.g. cyclopamine) in corn lily. This model of active biosynthesis enabled elucidation of a complete set of biosynthetic genes for the production of AmAs. Taken together, our work sheds light on the developmental and enzymatic logic of diverse alkaloid biosynthesis in daffodil. More broadly, it suggests a paradigm for biosynthesis regulation in monocot geophytes where plants are protected from herbivory through active charging of newly formed cells with eukaryotic toxins that persist as aboveground tissue develops.
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Affiliation(s)
- Niraj Mehta
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Yifan Meng
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | - Richard Zare
- Department of Chemistry, Stanford University, Stanford, CA, 94305, USA
| | | | - Elizabeth Sattely
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
- HHMI, Stanford University, Stanford, CA 94305
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38
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Nahar L, Aycan M, Lopes Hornai EM, Baslam M, Mitsui T. Tolerance with High Yield Potential Is Provided by Lower Na + Ion Accumulation and Higher Photosynthetic Activity in Tolerant YNU31-2-4 Rice Genotype under Salinity and Multiple Heat and Salinity Stress. Plants (Basel) 2023; 12:plants12091910. [PMID: 37176968 PMCID: PMC10180928 DOI: 10.3390/plants12091910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 04/18/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023]
Abstract
The yield-reduction effect of abiotic stressors such as salinity and heat stresses with the growing world population threatens food security. Although adverse effects of salinity and heat stress on plant growth and production parameters have been documented, in nature, abiotic stresses occur sequentially or simultaneously. In this study, the stress tolerance and yield capacity of Yukinkomai, YNU31-2-4, and YNU SL rice genotypes tested under control (26 °C, 0 mM NaCl), salinity (26 °C, 75 mM NaCl), heat (31 °C, 0 mM NaCl), and heat and salinity (31 °C, 75 mM NaCl) stress combinations at vegetative and reproductive stages with six different scenarios. The results show that salinity and the heat and salinity combination stresses highly reduce plant growth performance and yield capacity. Heat stress during reproduction does not affect the yield but reduces the grain quality. The YNU31-2-4 genotype performs better under heavy salt and heat and salinity stress then the Yukinkomai and YNU SL genotypes. YNU31-2-4 genotypes accumulate less Na+ and more K+ under salt and multiple stresses. In the YNU31-2-4 genotype, low Na+ ion accumulation increases photosynthetic activity and pigment deposition, boosting the yield. Stress lowers the glucose accumulation in dry seeds, but the YNU31-2-4 genotype has a higher glucose accumulation.
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Affiliation(s)
- Lutfun Nahar
- Department of Life and Food Science, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
- Department of Agricultural Botany, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
| | - Murat Aycan
- JSPS International Research Fellow, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
| | - Ermelinda Maria Lopes Hornai
- Department of Life and Food Science, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
- National Division of Research and Statistics, Timor-Leste Ministry of Agriculture and Fisheries, Dili 626, Timor-Leste
| | - Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
- Centre d'Agrobiotechnologie et Bioinge' Nierie, Unite' deRecherche labellise' e CNRST (Centre AgroBio-tech-URL-CNRST-05), Universite' Cadi Ayyad, Marrakech 40000, Morocco
- Laboratory of Agro-Food, Biotechnologies, and Valorization of PlantBioresources (AGROBIOVAL), Department of Biology, Faculty of Science Semlalia, Cadi Ayyad University (UCA), Marrakesh 40000, Morocco
| | - Toshiaki Mitsui
- Department of Life and Food Science, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan
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39
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Wang G, Shen X, Bai C, Zhuang Z, Jiang H, Yang M, Wei X, Wu Z. Metabolomic study on the quality differences and physiological characteristics between rice cultivated in drought and flood conditions. Food Chem 2023; 425:135946. [PMID: 37300996 DOI: 10.1016/j.foodchem.2023.135946] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/05/2023] [Accepted: 03/11/2023] [Indexed: 06/12/2023]
Abstract
The differences between dry- and flood-cultivated rice and the reason behind low-quality dry-cultivated rice were clarified. The physiological traits, starch synthase activity, and grain metabolomics of 'Longdao 18' were measured and analyzed at four growth stages. The brown, milled, and whole-milled rice rates and AGPase, SSS, and SBE activity were lower after drought treatment than during flood cultivation, while the chalkiness, chalky grain rate, amylose (16.57-20.999%), protein (7.99-12.09%), and GBSS activity were higher. Related enzymatic gene expression showed significant differences. Metabolic results showed pyruvate, glycine, and methionine upregulation at 8DAF and higher citric, pyruvic, and α-ketoglutaric acid content at 15DAF. Therefore, 8DAF-15DAF represented the crucial quality formation period for dry-cultivated rice. At 8DAF, the respiratory pathways used amino acids as signaling molecules and alternative substrates to adapt to energy shortages, arid environments and rapid protein accumulation and synthesis. Excessive amylose synthesis at 15DAF accelerated reproductive growth, promoting rapid premature aging.
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Affiliation(s)
- Guan Wang
- Faculty of Agronomy Jilin Agricultural University/National Crop Variety Approval and Characterization Station, Chang Chun 130118, China
| | - Xinru Shen
- Faculty of Agronomy Jilin Agricultural University/National Crop Variety Approval and Characterization Station, Chang Chun 130118, China
| | - Chenyang Bai
- Faculty of Agronomy Jilin Agricultural University/National Crop Variety Approval and Characterization Station, Chang Chun 130118, China
| | - Zixin Zhuang
- Faculty of Agronomy Jilin Agricultural University/National Crop Variety Approval and Characterization Station, Chang Chun 130118, China
| | - Hao Jiang
- Faculty of Agronomy Jilin Agricultural University/National Crop Variety Approval and Characterization Station, Chang Chun 130118, China
| | - Meiying Yang
- College of Life Science, Jilin Agricultural University Changchun, 130118, China
| | - Xiaoshuang Wei
- Faculty of Agronomy Jilin Agricultural University/National Crop Variety Approval and Characterization Station, Chang Chun 130118, China
| | - Zhihai Wu
- Faculty of Agronomy Jilin Agricultural University/National Crop Variety Approval and Characterization Station, Chang Chun 130118, China.
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40
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Nastasi JR, Daygon VD, Kontogiorgos V, Fitzgerald MA. Qualitative Analysis of Polyphenols in Glycerol Plant Extracts Using Untargeted Metabolomics. Metabolites 2023; 13:metabo13040566. [PMID: 37110224 PMCID: PMC10146371 DOI: 10.3390/metabo13040566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Glycerol is a reliable solvent for extracting polyphenols from food and waste products. There has been an increase in the application of glycerol over benchmark alcoholic solvents such as ethanol and methanol for natural product generation because of its non-toxic nature and high extraction efficiency. However, plant extracts containing a high glycerol concentration are unsuitable for mass spectrometry-based investigation utilising electrospray ionization, inhibiting the ability to analyse compounds of interest. In this investigation, a solid phase extraction protocol is outlined for removing glycerol from plant extracts containing a high concentration of glycerol and their subsequent analysis of polyphenols using ultra-performance liquid chromatography coupled with quadrupole time of flight tandem mass spectrometry. Using this method, glycerol-based extracts of Queen Garnet Plum (Prunus salicina) were investigated and compared to ethanolic extracts. Anthocyanins and flavonoids in high abundance were found in both glycerol and ethanol extracts. The polyphenol metabolome of Queen Garnet Plum was 53% polyphenol glycoside derivatives and 47% polyphenols in their aglycone forms. Furthermore, 56% of the flavonoid derivates were found to be flavonoid glycosides, and 44% were flavonoid aglycones. In addition, two flavonoid glycosides not previously found in Queen Garnet Plum were putatively identified: Quercetin-3-O-xyloside and Quercetin-3-O-rhamnoside.
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Affiliation(s)
- Joseph Robert Nastasi
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Venea Dara Daygon
- Queensland Metabolomics and Proteomics Facility, Metabolomics Australia, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Vassilis Kontogiorgos
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Melissa A Fitzgerald
- School of Agriculture and Food Sciences, The University of Queensland, Brisbane, QLD 4072, Australia
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41
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Liu Z, Lan Y, Zhang H, Hao W, He S, Liu L, Feng X, Qie Q, Chai M, Wang Y. Responses of Aroma Related Metabolic Attributes of Opisthopappus longilobus Flowers to Environmental Changes. Plants (Basel) 2023; 12:1592. [PMID: 37111816 PMCID: PMC10140910 DOI: 10.3390/plants12081592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2023] [Revised: 03/31/2023] [Accepted: 04/02/2023] [Indexed: 06/19/2023]
Abstract
Opisthopappus longilobus (Opisthopappus) and its descendant species, Opisthopappus taihangensis, commonly thrive on the Taihang Mountains of China. Being typical cliff plants, both O. longilobus and O. taihangensis release unique aromatics. To determine the potential differentiation and environmental response patterns, comparative metabolic analysis was performed on O. longilobus wild flower (CLW), O. longilobus transplant flower (CLT), and O. taihangensis wild flower (TH) groups. Significant differences in the metabolic profiles were found, not within O. longilobus, but between O. longilobus and O. taihangensis flowers. Within these metabolites, twenty-eight substances related to the scents were obtained (one alkene, two aldehydes, three esters, eight phenols, three acids, three ketones, three alcohols, and five flavonoids), of which eugenol and chlorogenic were the primary aromatic molecules and enriched in the phenylpropane pathway. Network analysis showed that close relationships occurred among identified aromatic substances. The variation coefficient (CV) of aromatic metabolites in O. longilobus was lower than O. taihangensis. The aromatic related compounds were significantly correlated with the lowest temperatures in October and in December of the sampled sites. The results indicated that phenylpropane, particularly eugenol and chlorogenic, played important roles in the responses of O. longilobus species to environmental changes.
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42
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Kisiel A, Krzemińska A, Cembrowska-Lech D, Miller T. Data Science and Plant Metabolomics. Metabolites 2023; 13:metabo13030454. [PMID: 36984894 PMCID: PMC10054611 DOI: 10.3390/metabo13030454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/16/2023] [Accepted: 03/17/2023] [Indexed: 03/30/2023] Open
Abstract
The study of plant metabolism is one of the most complex tasks, mainly due to the huge amount and structural diversity of metabolites, as well as the fact that they react to changes in the environment and ultimately influence each other. Metabolic profiling is most often carried out using tools that include mass spectrometry (MS), which is one of the most powerful analytical methods. All this means that even when analyzing a single sample, we can obtain thousands of data. Data science has the potential to revolutionize our understanding of plant metabolism. This review demonstrates that machine learning, network analysis, and statistical modeling are some techniques being used to analyze large quantities of complex data that provide insights into plant development, growth, and how they interact with their environment. These findings could be key to improving crop yields, developing new forms of plant biotechnology, and understanding the relationship between plants and microbes. It is also necessary to consider the constraints that come with data science such as quality and availability of data, model complexity, and the need for deep knowledge of the subject in order to achieve reliable outcomes.
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Affiliation(s)
- Anna Kisiel
- Institute of Marine and Environmental Sciences, University of Szczecin, Wąska 13, 71-415 Szczecin, Poland
- Polish Society of Bioinformatics and Data Science BIODATA, Popiełuszki 4c, 71-214 Szczecin, Poland
| | - Adrianna Krzemińska
- Polish Society of Bioinformatics and Data Science BIODATA, Popiełuszki 4c, 71-214 Szczecin, Poland
| | - Danuta Cembrowska-Lech
- Polish Society of Bioinformatics and Data Science BIODATA, Popiełuszki 4c, 71-214 Szczecin, Poland
- Department of Physiology and Biochemistry, Institute of Biology, University of Szczecin, Felczaka 3c, 71-412 Szczecin, Poland
| | - Tymoteusz Miller
- Institute of Marine and Environmental Sciences, University of Szczecin, Wąska 13, 71-415 Szczecin, Poland
- Polish Society of Bioinformatics and Data Science BIODATA, Popiełuszki 4c, 71-214 Szczecin, Poland
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43
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Schlossarek D, Zhang Y, Sokolowska EM, Fernie AR, Luzarowski M, Skirycz A. Don't let go: co-fractionation mass spectrometry for untargeted mapping of protein-metabolite interactomes. Plant J 2023; 113:904-914. [PMID: 36575913 DOI: 10.1111/tpj.16084] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/20/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
The chemical complexity of metabolomes goes hand in hand with their functional diversity. Small molecules have many essential roles, many of which are executed by binding and modulating the function of a protein partner. The complex and dynamic protein-metabolite interaction (PMI) network underlies most if not all biological processes, but remains under-characterized. Herein, we highlight how co-fractionation mass spectrometry (CF-MS), a well-established approach to map protein assemblies, can be used for proteome and metabolome identification of the PMIs. We will review recent CF-MS studies, discuss the main advantages and limitations, summarize the available CF-MS guidelines, and outline future challenges and opportunities.
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Affiliation(s)
- Dennis Schlossarek
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Youjun Zhang
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Ewelina M Sokolowska
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Alisdair R Fernie
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
| | - Marcin Luzarowski
- Center for Molecular Biology Heidelberg, Heidelberg University, Heidelberg, Germany
| | - Aleksandra Skirycz
- Depeartment One, Max-Planck-Institute of Molecular Plant Physiology, 14476, Potsdam, Germany
- Boyce Thompson Institute, Ithaca, NY, 14850, USA
- School of Integrative Plant Science, Cornell University, Ithaca, NY, 14850, USA
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44
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Zhu F, Wen W, Cheng Y, Alseekh S, Fernie AR. Integrating multiomics data accelerates elucidation of plant primary and secondary metabolic pathways. aBIOTECH 2023; 4:47-56. [PMID: 37220537 PMCID: PMC10199974 DOI: 10.1007/s42994-022-00091-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/24/2022] [Indexed: 05/25/2023]
Abstract
Plants are the most important sources of food for humans, as well as supplying many ingredients that are of great importance for human health. Developing an understanding of the functional components of plant metabolism has attracted considerable attention. The rapid development of liquid chromatography and gas chromatography, coupled with mass spectrometry, has allowed the detection and characterization of many thousands of metabolites of plant origin. Nowadays, elucidating the detailed biosynthesis and degradation pathways of these metabolites represents a major bottleneck in our understanding. Recently, the decreased cost of genome and transcriptome sequencing rendered it possible to identify the genes involving in metabolic pathways. Here, we review the recent research which integrates metabolomic with different omics methods, to comprehensively identify structural and regulatory genes of the primary and secondary metabolic pathways. Finally, we discuss other novel methods that can accelerate the process of identification of metabolic pathways and, ultimately, identify metabolite function(s).
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Affiliation(s)
- Feng Zhu
- National R&D Center for Citrus Preservation, Hubei Hongshan Laboratory, National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476 Germany
| | - Weiwei Wen
- National R&D Center for Citrus Preservation, Hubei Hongshan Laboratory, National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China
| | - Yunjiang Cheng
- National R&D Center for Citrus Preservation, Hubei Hongshan Laboratory, National Key Laboratory for Germplasm Innovation and Utilization for Fruit and Vegetable Horticultural Crops, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070 China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476 Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000 Bulgaria
| | - Alisdair R. Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, Potsdam-Golm, 14476 Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, 4000 Bulgaria
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45
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Hayashi K, Alseekh S, Fernie AR. Genetic and epigenetic control of the plant metabolome. Proteomics 2023:e2200104. [PMID: 36781168 DOI: 10.1002/pmic.202200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023]
Abstract
Plant metabolites are mainly produced through chemical reactions catalysed by enzymes encoded in the genome. Mutations in enzyme-encoding or transcription factor-encoding genes can alter the metabolome by changing the enzyme's catalytic activity or abundance, respectively. Insertion of transposable elements into non-coding regions has also been reported to affect transcription and ultimately metabolite content. In addition to genetic mutations, transgenerational epigenetic variations have also been found to affect metabolic content by controlling the transcription of metabolism-related genes. However, the majority of cases reported so far, in which epigenetic mechanisms are associated with metabolism, are non-transgenerational, and are triggered by developmental signals or environmental stress. Although, accumulating research has provided evidence of strong genetic control of the metabolome, epigenetic control has been largely untouched. Here, we provide a review of the genetic and epigenetic control of metabolism with a focus on epigenetics. We discuss both transgenerational and non-transgenerational epigenetic marks regulating metabolism as well as prospects of the field of metabolic control where intricate interactions between genetics and epigenetics are involved.
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Affiliation(s)
- Koki Hayashi
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center for Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center for Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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46
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Yin Z, Huang W, Fernie AR, Yan S. Mass spectrometry imaging techniques: a versatile toolbox for plant metabolomics. Trends Plant Sci 2023; 28:250-251. [PMID: 36411181 DOI: 10.1016/j.tplants.2022.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Zhibin Yin
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
| | - Wenjie Huang
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany.
| | - Shijuan Yan
- Guangdong Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, Guangdong, China.
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47
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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) 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] [What about the content of this article? (0)] [Affiliation(s)] [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.
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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
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48
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Wei W, Li S, Li P, Yu K, Fan G, Wang Y, Zhao F, Zhang X, Feng X, Shi G, Zhang W, Song G, Dan W, Wang F, Zhang Y, Li X, Wang D, Zhang W, Pei J, Wang X, Zhao Z. QTL analysis of important agronomic traits and metabolites in foxtail millet ( Setaria italica) by RIL population and widely targeted metabolome. Front Plant Sci 2023; 13:1035906. [PMID: 36704173 PMCID: PMC9872001 DOI: 10.3389/fpls.2022.1035906] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
As a bridge between genome and phenotype, metabolome is closely related to plant growth and development. However, the research on the combination of genome, metabolome and multiple agronomic traits in foxtail millet (Setaria italica) is insufficient. Here, based on the linkage analysis of 3,452 metabolites via with high-quality genetic linkage maps, we detected a total of 1,049 metabolic quantitative trait loci (mQTLs) distributed in 11 hotspots, and 28 metabolite-related candidate genes were mined from 14 mQTLs. In addition, 136 single-environment phenotypic QTL (pQTLs) related to 63 phenotypes were identified by linkage analysis, and there were 12 hotspots on these pQTLs. We futher dissected 39 candidate genes related to agronomic traits through metabolite-phenotype correlation and gene function analysis, including Sd1 semidwarf gene, which can affect plant height by regulating GA synthesis. Combined correlation network and QTL analysis, we found that flavonoid-lignin pathway maybe closely related to plant architecture and yield in foxtail millet. For example, the correlation coefficient between apigenin 7-rutinoside and stem diameter reached 0.98, and they were co-located at 41.33-44.15 Mb of chromosome 5, further gene function analysis revealed that 5 flavonoid pathway genes, as well as Sd1, were located in this interval . Therefore, the correlation and co-localization between flavonoid-lignins and plant architecture may be due to the close linkage of their regulatory genes in millet. Besides, we also found that a combination of genomic and metabolomic for BLUP analysis can better predict plant agronomic traits than genomic or metabolomic data, independently. In conclusion, the combined analysis of mQTL and pQTL in millet have linked genetic, metabolic and agronomic traits, and is of great significance for metabolite-related molecular assisted breeding.
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Affiliation(s)
- Wei Wei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Shuangdong Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Peiyu Li
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Kuohai Yu
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Guangyu Fan
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Yixiang Wang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Fang Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xiaolei Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xiaolei Feng
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Gaolei Shi
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Weiqin Zhang
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Guoliang Song
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Wenhan Dan
- Wuhan Metware Biotechnology Co., Ltd., Wuhan, China
| | - Feng Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Yali Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xinru Li
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Dequan Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Wenying Zhang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Jingjing Pei
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Xiaoming Wang
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
| | - Zhihai Zhao
- Institute of Millet, Zhangjiakou Academy of Agricultural Science, Zhangjiakou, China
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49
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Eckardt NA, Ainsworth EA, Bahuguna RN, Broadley MR, Busch W, Carpita NC, Castrillo G, Chory J, DeHaan LR, Duarte CM, Henry A, Jagadish SVK, Langdale JA, Leakey ADB, Liao JC, Lu KJ, McCann MC, McKay JK, Odeny DA, Jorge de Oliveira E, Platten JD, Rabbi I, Rim EY, Ronald PC, Salt DE, Shigenaga AM, Wang E, Wolfe M, Zhang X. Climate change challenges, plant science solutions. Plant Cell 2023; 35:24-66. [PMID: 36222573 PMCID: PMC9806663 DOI: 10.1093/plcell/koac303] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Climate change is a defining challenge of the 21st century, and this decade is a critical time for action to mitigate the worst effects on human populations and ecosystems. Plant science can play an important role in developing crops with enhanced resilience to harsh conditions (e.g. heat, drought, salt stress, flooding, disease outbreaks) and engineering efficient carbon-capturing and carbon-sequestering plants. Here, we present examples of research being conducted in these areas and discuss challenges and open questions as a call to action for the plant science community.
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Affiliation(s)
| | - Elizabeth A Ainsworth
- USDA ARS Global Change and Photosynthesis Research Unit, Urbana, Illinois 61801, USA
| | - Rajeev N Bahuguna
- Centre for Advanced Studies on Climate Change, Dr Rajendra Prasad Central Agricultural University, Samastipur 848125, Bihar, India
| | - Martin R Broadley
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Wolfgang Busch
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | - Nicholas C Carpita
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - Gabriel Castrillo
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Joanne Chory
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, California 92037, USA
- Howard Hughes Medical Institute, Salk Institute for Biological Studies, La Jolla, California 92037, USA
| | | | - Carlos M Duarte
- Red Sea Research Center (RSRC) and Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Amelia Henry
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - S V Krishna Jagadish
- Department of Plant and Soil Science, Texas Tech University, Lubbock, Texas 79410, USA
| | - Jane A Langdale
- Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Andrew D B Leakey
- Department of Plant Biology, Department of Crop Sciences, and Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Illinois 61801, USA
| | - James C Liao
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Kuan-Jen Lu
- Institute of Biological Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Maureen C McCann
- Biosciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, USA
| | - John K McKay
- Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado 80523, USA
| | - Damaris A Odeny
- The International Crops Research Institute for the Semi-Arid Tropics–Eastern and Southern Africa, Gigiri 39063-00623, Nairobi, Kenya
| | | | - J Damien Platten
- International Rice Research Institute, Rice Breeding Innovations Platform, Los Baños, Laguna 4031, Philippines
| | - Ismail Rabbi
- International Institute of Tropical Agriculture (IITA), PMB 5320 Ibadan, Oyo, Nigeria
| | - Ellen Youngsoo Rim
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Pamela C Ronald
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
- Innovative Genomics Institute, Berkeley, California 94704, USA
| | - David E Salt
- School of Biosciences, University of Nottingham, Nottingham, NG7 2RD, UK
- Future Food Beacon of Excellence, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Alexandra M Shigenaga
- Department of Plant Pathology and the Genome Center, University of California, Davis, California 95616, USA
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Marnin Wolfe
- Auburn University, Dept. of Crop Soil and Environmental Sciences, College of Agriculture, Auburn, Alabama 36849, USA
| | - Xiaowei Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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50
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Shen S, Zhan C, Yang C, Fernie AR, Luo J. Metabolomics-centered mining of plant metabolic diversity and function: Past decade and future perspectives. Mol Plant 2023; 16:43-63. [PMID: 36114669 DOI: 10.1016/j.molp.2022.09.007] [Citation(s) in RCA: 33] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 09/06/2022] [Accepted: 09/11/2022] [Indexed: 06/15/2023]
Abstract
Plants are natural experts in organic synthesis, being able to generate large numbers of specific metabolites with widely varying structures that help them adapt to variable survival challenges. Metabolomics is a research discipline that integrates the capabilities of several types of research including analytical chemistry, statistics, and biochemistry. Its ongoing development provides strategies for gaining a systematic understanding of quantitative changes in the levels of metabolites. Metabolomics is usually performed by targeting either a specific cell, a specific tissue, or the entire organism. Considerable advances in science and technology over the last three decades have propelled us into the era of multi-omics, in which metabolomics, despite at an earlier developmental stage than genomics, transcriptomics, and proteomics, offers the distinct advantage of studying the cellular entities that have the greatest influence on end phenotype. Here, we summarize the state of the art of metabolite detection and identification, and illustrate these techniques with four case study applications: (i) comparing metabolite composition within and between species, (ii) assessing spatio-temporal metabolic changes during plant development, (iii) mining characteristic metabolites of plants in different ecological environments and upon exposure to various stresses, and (iv) assessing the performance of metabolomics as a means of functional gene identification , metabolic pathway elucidation, and metabolomics-assisted breeding through analyzing plant populations with diverse genetic variations. In addition, we highlight the prominent contributions of joint analyses of plant metabolomics and other omics datasets, including those from genomics, transcriptomics, proteomics, epigenomics, phenomics, microbiomes, and ion-omics studies. Finally, we discuss future directions and challenges exploiting metabolomics-centered approaches in understanding plant metabolic diversity.
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Affiliation(s)
- Shuangqian Shen
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Chuansong Zhan
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Chenkun Yang
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany
| | - Jie Luo
- Sanya Nanfan Research Institute of Hainan University, Hainan Yazhou Bay Seed Laboratory, Sanya 572025, China; College of Tropical Crops, Hainan University, Haikou 570228, China.
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