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Zhang W, Zeng Y, Jiao M, Ye C, Li Y, Liu C, Wang J. Integration of high-throughput omics technologies in medicinal plant research: The new era of natural drug discovery. FRONTIERS IN PLANT SCIENCE 2023; 14:1073848. [PMID: 36743502 PMCID: PMC9891177 DOI: 10.3389/fpls.2023.1073848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Medicinal plants are natural sources to unravel novel bioactive compounds to satisfy human pharmacological potentials. The world's demand for herbal medicines is increasing year by year; however, large-scale production of medicinal plants and their derivatives is still limited. The rapid development of modern technology has stimulated multi-omics research in medicinal plants, leading to a series of breakthroughs on key genes, metabolites, enzymes involved in biosynthesis and regulation of active compounds. Here, we summarize the latest research progress on the molecular intricacy of medicinal plants, including the comparison of genomics to demonstrate variation and evolution among species, the application of transcriptomics, proteomics and metabolomics to explore dynamic changes of molecular compounds, and the utilization of potential resources for natural drug discovery. These multi-omics research provide the theoretical basis for environmental adaptation of medicinal plants and allow us to understand the chemical diversity and composition of bioactive compounds. Many medicinal herbs' phytochemical constituents and their potential health benefits are not fully explored. Given their large diversity and global distribution as well as the impacts of growth duration and environmental factors on bioactive phytochemicals in medicinal plants, it is crucial to emphasize the research needs of using multi-omics technologies to address basic and applied problems in medicinal plants to aid in developing new and improved medicinal plant resources and discovering novel medicinal ingredients.
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Affiliation(s)
- Wenting Zhang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
| | - Yuan Zeng
- School of Plant and Environmental Sciences, Virginia Tech, VA, Blacksburg, United States
- Southern Piedmont Agricultural Research and Extension Center, Virginia Tech, VA, Blackstone, United States
| | - Meng Jiao
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chanjuan Ye
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Yanrong Li
- College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Chuanguang Liu
- Rice Research Institute, Guangdong Rice Engineering Laboratory, Guangdong Key Laboratory of New Technology in Rice Breeding, Guangdong Academy of Agricultural Sciences, Guangzhou, China
| | - Jihua Wang
- Guangdong Provincial Key Laboratory of Crops Genetics & Improvement, Crops Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China
- Guangdong Provincial Engineering & Technology Research Center for Conservation and Utilization of the Genuine Southern Medicinal Resources, Guangzhou, China
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Park SY, Jung WJ, Bang G, Hwang H, Kim JY. Transcriptome and Proteome Co-Profiling Offers an Understanding of Pre-Harvest Sprouting (PHS) Molecular Mechanisms in Wheat ( Triticum aestivum). PLANTS (BASEL, SWITZERLAND) 2022; 11:2807. [PMID: 36365261 PMCID: PMC9657071 DOI: 10.3390/plants11212807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
While wheat (Triticum aestivum L.) is a widely grown and enjoyed crop, the diverse and complex global situation and climate are exacerbating the instability of its supply. In particular, pre-harvest sprouting (PHS) is one of the major abiotic stresses that frequently occurs due to irregular climate conditions, causing serious damage to wheat and its quality. In this study, transcriptomic analysis with RNA-seq and proteomic analysis with LC-MS/MS were performed in PHS-treated spikes from two wheat cultivars presenting PHS sensitivity and tolerance, respectively. A total of 13,154 differentially expressed genes (DEGs) and 706 differentially expressed proteins (DEPs) were identified in four comparison groups between the susceptible/tolerant cultivars. Gene function and correlation analysis were performed to determine the co-profiled genes and proteins affected by PHS treatment. In the functional annotation of each comparative group, similar functions were confirmed in each cultivar under PHS treatment; however, in Keumgang PHS+7 (K7) vs. Woori PHS+7 (W7), functional annotations presented clear differences in the "spliceosome" and "proteasome" pathways. In addition, our results indicate that alternative splicing and ubiquitin-proteasome support the regulation of germination and seed dormancy. This study provides an advanced understanding of the functions involved in transcription and translation related to PHS mechanisms, thus enabling specific proposals for the further analysis of germination and seed dormancy mechanisms and pathways in wheat.
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Affiliation(s)
- Sang Yong Park
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea
| | - Woo Joo Jung
- Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Korea
| | - Geul Bang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Korea
| | - Heeyoun Hwang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Korea
| | - Jae Yoon Kim
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea
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Wang Z, Wu J, Sun Z, Jiang W, Liu Y, Tang J, Meng X, Su X, Wu L, Wang L, Guo X, Peng D, Xing S. ICP-MS based metallomics and GC-MS based metabolomics reveals the physiological and metabolic responses of Dendrobium huoshanense plants exposed to Fe 3O 4 nanoparticles. Front Nutr 2022; 9:1013756. [PMID: 36245500 PMCID: PMC9558897 DOI: 10.3389/fnut.2022.1013756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Accepted: 08/30/2022] [Indexed: 11/23/2022] Open
Abstract
It is found that the growth of Dendrobium huoshanense was dependent on Fe3O4, while the bioavailability of plants to ordinary Fe3O4 was low on the earth. In order to improve the growth, quality and yield of D. huoshanense, we used Fe3O4 NPs (100 or 200 mg/L) that was easily absorbed by plants as nano-fertilizer to hydroponically treat seedlings of D. huoshanense for 3 weeks. Fe3O4 NPs induced not only earlier flowering and increased sugar content and photosynthesis, but also stressed to plants, increased MDA content and related antioxidant enzymes activities. Inductively Coupled Plasma Mass Spectrometry (ICP-MS) revealed that Fe3O4 NPs caused a significant accumulation of Fe and some other nutrient elements (Mn, Co, B, Mo) in stems of D. huoshanense. Metabolomics revealed that the metabolites were reprogrammed in D. huoshanense when under Fe3O4 NPs exposure. Fe3O4 NPs inhibited antioxidant defense-related pathways, demonstrating that Fe3O4 NPs have antioxidant capacity to protect D. huoshanense from damage. As the first study associating Fe3O4 NPs with the quality of D. huoshanense, it provided vital insights into the molecular mechanisms of how D. huoshanense responds to Fe3O4 NPs, ensuring the reasonable use of Fe3O4 NPs as nano-fertilizer.
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Affiliation(s)
- Zhaojian Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Jing Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Zongping Sun
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, China
| | - Weimin Jiang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal University, Hengyang, China
| | - Yingying Liu
- College of Humanities and International Education Exchange, Anhui University of Chinese Medicine, Hefei, China
| | - Jun Tang
- Anhui Province Key Laboratory of Environmental Hormone and Reproduction, Anhui Province Key Laboratory of Embryo Development and Reproductive Regulation, Fuyang Normal University, Fuyang, China
| | - Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, Saint Paul, MN, United States
| | - Xinglong Su
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Liping Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Longhai Wang
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Xiaohu Guo
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Daiyin Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- Anhui Province Key Laboratory of Research & Development of Chinese Medicine, Hefei, China
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Yi S, Lu H, Tian C, Xu T, Song C, Wang W, Wei P, Gu F, Liu D, Cai Y, Han B. Selection of Suitable Reference Genes for Gene Expression Normalization Studies in Dendrobium huoshanense. Genes (Basel) 2022; 13:genes13081486. [PMID: 36011396 PMCID: PMC9408602 DOI: 10.3390/genes13081486] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/16/2022] Open
Abstract
Dendrobium huoshanense is a kind of precious herb with important medicinal and edible value in China, which is widely used in traditional Chinese medicine for various diseases. Recent studies have paid close attention to the genetic expression of the biosynthetic pathway of the main active components (polysaccharides, alkaloids, and flavonoids), and real-time polymerase chain reaction (qPCR) is one of the most widely used methods for doing so. However, so far, no reference gene selections have been reported in D. huoshanense. In this study, 15 reference gene candidates (GAPDH, eIF, EF-1α, PP2A, UBCE, RPL5, TBP, APT1, MDH, PTBP3, PEPC, CYP71, NCBP2, TIP41, and F-box) were selected and evaluated for their expression stability in D. huoshanense under various experimental conditions, including in different tissues (root, stem, and leaf), abiotic stresses (oxidative, drought, cold, and UV), and hormone treatment (methyl jasmonate) using three statistical programs (geNorm, NormFinder, and BestKeeper). Then, the RefFinder program was employed to comprehensively validate the stability of the selected reference genes. Finally, the expression profiles of the CESA and GMPP genes were further analyzed, and these results indicated that TBP, NCBP2, and CYP71 were the top three most stable reference genes after comprehensive comparison, which could be used as stable reference genes for normalizing the genes expression in D. huoshanense. This study described here provides the first data regarding on reference gene selection in D. huoshanense, which will be extremely beneficial for future research on the gene expression normalization in D. huoshanense.
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Affiliation(s)
- Shanyong Yi
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Haibo Lu
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Chuanjun Tian
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
| | - Tao Xu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Cheng Song
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Wei Wang
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Peipei Wei
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Fangli Gu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Dong Liu
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
| | - Yongping Cai
- College of Life Sciences, Anhui Agricultural University, Hefei 230036, China
- Correspondence: (Y.C.); (B.H.); Tel.: +86-564-3307060 (B.H.)
| | - Bangxing Han
- Department of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an 237012, China
- Anhui Engineering Laboratory for Conservation and Sustainable Utilization of Traditional Chinese Medicine Resources, West Anhui University, Lu’an 237061, China
- Correspondence: (Y.C.); (B.H.); Tel.: +86-564-3307060 (B.H.)
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Gao L, Wang F, Hou T, Geng C, Xu T, Han B, Liu D. Dendrobium huoshanense C.Z.Tang et S.J.Cheng: A Review of Its Traditional Uses, Phytochemistry, and Pharmacology. Front Pharmacol 2022; 13:920823. [PMID: 35903345 PMCID: PMC9315951 DOI: 10.3389/fphar.2022.920823] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 05/30/2022] [Indexed: 01/29/2023] Open
Abstract
Dendrobium huoshanense, a traditional medicinal and food homologous plant, belongs to the family Orchidaceae and has a long history of medicinal use. It is reported that the stem of D. huoshanense has a variety of bioactive ingredients such as polysaccharides, flavonoids, sesquiterpenes, phenols, etc. These bioactive ingredients make D. huoshanense remarkable for its pharmacological effects on anti-tumor, immunomodulation, hepatoprotective, antioxidant, and anticataract activities. In recent years, its rich pharmacological activities have attracted extensive attention. However, there is no systematic review focusing on the chemical compositions and pharmacological effects of D. huoshanense. Therefore, the present review aims to summarize current research on the chemical compositions and pharmacological activities of D. huoshanense. This study provides valuable references and promising ideas for further investigations of D. huoshanense.
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Affiliation(s)
- Leilei Gao
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, Lu’an, China
- *Correspondence: Leilei Gao, ; Bangxing Han, ; Dong Liu,
| | - Fang Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, Lu’an, China
| | - Tingting Hou
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Chunye Geng
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- School of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Tao Xu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, Lu’an, China
| | - Bangxing Han
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, Lu’an, China
- *Correspondence: Leilei Gao, ; Bangxing Han, ; Dong Liu,
| | - Dong Liu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
- Anhui Province Traditional Chinese Medicine Resource Protection and Sustainable Utilization Engineering Laboratory, Lu’an, China
- *Correspondence: Leilei Gao, ; Bangxing Han, ; Dong Liu,
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Wu L, Meng X, Huang H, Liu Y, Jiang W, Su X, Wang Z, Meng F, Wang L, Peng D, Xing S. Comparative Proteome and Phosphoproteome Analyses Reveal Different Molecular Mechanism Between Stone Planting Under the Forest and Greenhouse Planting of Dendrobium huoshanense. FRONTIERS IN PLANT SCIENCE 2022; 13:937392. [PMID: 35873990 PMCID: PMC9301318 DOI: 10.3389/fpls.2022.937392] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
The highly esteemed Chinese herb, Dendrobium huoshanense, whose major metabolites are polysaccharides and alkaloids, is on the verge of extinction. The stone planting under the forest (SPUF) and greenhouse planting (GP) of D. huoshanense are two different cultivation methods of pharmaceutical Dendrobium with significantly differences in morphology, metabolites content and composition, and medication efficacy. Here, we conducted proteomics and phosphoproteomics analyses to reveal differences in molecular mechanisms between SPUF and GP. We identified 237 differentially expressed proteins (DEPs) between the two proteomes, and 291 modification sites belonging to 215 phosphoproteins with a phosphorylation level significantly changed (PLSC) were observed. GO, KEGG pathway, protein domain, and cluster analyses revealed that these DEPs were mainly localized in the chloroplast; involved in processes such as posttranslational modification, carbohydrate transport and metabolism, and secondary metabolite biosynthesis; and enriched in pathways mainly including linoleic acid metabolism, plant-pathogen interactions, and phenylpropanoid, cutin, suberin, and wax biosynthesis. PLSC phosphoproteins were mainly located in the chloroplast, and highly enriched in responses to different stresses and signal transduction mechanisms through protein kinase and phosphotransferase activities. Significant differences between SPUF and GP were observed by mapping the DEPs and phosphorylated proteins to photosynthesis and polysaccharide and alkaloid biosynthesis pathways. Phosphorylation characteristics and kinase categories in D. huoshanense were also clarified in this study. We analyzed different molecular mechanisms between SPUF and GP at proteomic and phosphoproteomic levels, providing valuable information for the development and utilization of D. huoshanense.
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Affiliation(s)
- Liping Wu
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Xiaoxi Meng
- Department of Horticultural Science, University of Minnesota, St. Paul, MN, United States
| | - Huizhen Huang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal University, Hengyang, China
| | - Yingying Liu
- College of Humanities and International Education Exchange, Anhui University of Chinese Medicine, Hefei, China
| | - Weimin Jiang
- Hunan Key Laboratory for Conservation and Utilization of Biological Resources in the Nanyue Mountainous Region, College of Life Sciences and Environment, Hengyang Normal University, Hengyang, China
| | - Xinglong Su
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Zhaojian Wang
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Fei Meng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
| | - Longhai Wang
- School of Integrated Chinese and Western Medicine, Anhui University of Chinese Medicine, Hefei, China
| | - Daiyin Peng
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- MOE-Anhui Joint Collaborative Innovation Center for Quality Improvement of Anhui Genuine Chinese Medicinal Materials, Hefei, China
| | - Shihai Xing
- College of Pharmacy, Anhui University of Chinese Medicine, Hefei, China
- Institute of Traditional Chinese Medicine Resources Protection and Development, Anhui Academy of Chinese Medicine, Hefei, China
- Anhui Province Key Laboratory of Research and Development of Chinese Medicine, Hefei, China
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